An integrative approach to understanding bird origins

Authors Xing Xu Zhonghe Zhou Robert Dudley Susan Mackem Cheng-Ming Chuong Gregory M Erickson David J Varricchio

This is an Accepted Manuscript of an article published in Science on December 12 2014 It is available online httpsdxdoiorg101126science1253293

X Xu et al Science 346 1253293 (2014) DOI 101126science1253293

Made available through Montana State Universityrsquos ScholarWorks scholarworksmontanaedu

An integrative approach to understanding bird origins

Xing Xu Zhonghe Zhou Key Laboratory of Vertebrate Evolution and Human Origins Institute of Vertebrate Paleontology and Paleoanthropology Chinese Academy of Sciences Beijing 100044 PR China

Recent discoveries of spectacular dinosaur fossils overwhelmingly support the hypothesis that birds are descended from maniraptoran theropod dinosaurs and furthermore demonstrate that distinctive bird characteristics such as feathers flight endothermic physiology unique strategies for reproduction and growth and a novel pulmonary system originated among Mesozoic terrestrial dinosaurs The transition from ground-living to flight-capable theropod dinosaurs now probably represents one of the best-documented major evolutionary transitions in life history Recent studies in developmental biology and other disciplines provide additional insights into how bird characteristics originated and evolved The iconic features of extant birds for the most part evolved in a gradual and stepwise fashion throughout archosaur evolution However new data also highlight occasional bursts of morphological novelty at certain stages particularly close to the origin of birds and an unavoidable complex mosaic evolutionary distribution of major bird characteristics on the theropod tree Research into bird origins provides a premier example of how paleontological and neontological data can interact to reveal the complexity of major innovations to answer key evolutionary questions and to lead to new research directions A better understanding of bird origins requires multifaceted and integrative approaches yet fossils necessarily provide the final test of any evolutionary model

The origin of birds is one of the most enduring and dramatic evolutionary debates (1ndash3) Whether the primarily small-sized birds are nested within a theropod group including the gigantic Tyrannosaurus rex is of great interest to both the academic com-munity and general public More challenging is whether the origin of major bird characteristics can be traced among the Mesozoic terrestrial theropod dinosaurs Recent discoveries of spectacular dinosaur fossils from China and elsewhere (Fig 1) provide significant new information to address these issues and also prompt numerous studies in disciplines other than paleontology to explain how bird characteristics originated and evolved (4ndash11) Whereas these new discoveries and studies have addressed many issues on the origin of birds they also open new research directions A better understanding of the origin of birds requires a more integrative approach and this is particularly true given that understanding bird origins is more about reconstructing the evolutionary patterns of major bird characteristics than just filling the gaps between birds and their theropod ancestors In this review we present a brief introduction to recent advances on this topic discuss several issues that have interested both paleontologists and scientists in other fields and finally provide our thoughts on how to proceed using an integrative approach in evolutionary biology For the convenience of further discussion we define the vernacular term ldquobirdsrdquo (avians in many publications) to

Family tree of birds and relatives

A reliable phylogeny sets the framework for reconstructing the evolutionary sequence of major bird characters Although birds are widely accepted to form a monophyletic group (ie a group composed of an ancestor and all its descendants) within the Archosauromorpha the identity of their closest relatives has been hotly debated (1ndash3 12)

The last four decades have witnessed an un-precedented accumulation of evidence support-ing the hypothesis that birds are maniraptoran theropods (BMT hypothesis) (2 3 13) and most likely closely related to the troodontids andor dromaeosaurs (14ndash23) The BMT hypothesis is supported by numerous skeletal behavioral and physiological resemblances between nonavialan theropod dinosaurs (hereafter theropods) and birds These resemblances are derived from such birdlike theropods as the dromaeosaur Deinonychus the troodontid Saurornithoides and others (24 25) dinosaur fossils preserving gastroliths for digestion (26) highly pneumatic theropod skeletons (27ndash29) dinosaur nests preserving

(34ndash36) and bone microstructures indicating fast growth rates (37) among others Nearly all published numerical phylogenetic analyses support the BMT hypothesis (15ndash23 38) Comparatively other hypotheses on bird origin are based on a small number of similarities from certain parts of the body between birds and the proposed groups (1) One recently published numerical phylogenetic analysis places birds and other maniraptoran theropods at the base of the Archosauria rather than within the Theropoda (12) but this analysis is flawed in several aspects including a strongly biased data set used for the analysis (39)

Although birds are now widely accepted to be theropods maniraptorans and paravians there is an unresolved debate on what are the most basal birds Suggested taxa include the probably flighted Archaeopteryx and Rahonavis (40) the enigmatic scansoriop-terygids (41) the four-winged Anchiornis and its kin (21 42) and the Gondwanan unenlagiid theropods (38 43) Many recent studies suggest that Rahonavis other unenlagiids and Anchiornis and its kin are deinonychosaurs (16 17 22 44 45) Several analyses even place the iconic Archaeopteryx at the base of the Deinonychosauria(22) yet other studies suggest that the Deinonycho-sauria itself is paraphyletic with the troodontids more close-ly related to birds than the dromaeosaurs (21) or vice versa (20) A radical suggestion is that the oviraptoro-saurs are closely related to the scansoriop-terygids (38 46 47) and further that they together represent the first major branching in bird evolution (46) Despite these debates considerable consensus exists for the general branching pattern of major theropod groups (15ndash23 38) here used as a framework for further discussions on bird origins (Fig 2)

Recently discovered transitional forms toward modern birdsNumerous recently discovered fossils of theropods and early birds have filled the morphological functional and temporal gaps along the line to modern birds These discoveries have helped ad-dress several important issues repeatedly raised to challenge the BMT hypothesis (1 48 49) such as the origins of feathers and flight the ldquotem-poral paradoxrdquo in the stratigraphic distribution of theropod fossils (ie most of the diversity of coelurosaurian theropods occurs much later in the fossil record than Archaeopteryx in the Late Jurassic) and the supposed homological incon-gruities (eg the suggested homologies of three fingers in tetanuran theropods are different from those of living birds)

Numerous discoveries demonstrate that many bird characteristics have their origins among theropods or a more inclusive group (Fig 2) For example the discoveries of Mahakala and other basal members of derived theropod groups

Robert Dudley Department of Integrative Biology University of California Berkeley CA 94720 USASusan Mackem Cancer and Developmental Biology Laboratory Center for Cancer Research NCI-Frederick NIH Frederick MD 21702 USACheng-Ming Chuong Department of Pathology University of Southern California CA 90033 USA amp Cheng Kung University Laboratory for Wound Repair and Regeneration Graduated Institute of Clinical Medicine Tainan 70101 Taiwan

Gregory M Erickson Department of Biological Science Florida State University Tallahassee FL 32306-4295 USADavid J Varricchio Earth Sciences Montana State University Bozeman MT 59717 USA

correspond to Avialae a stem-based taxon defined as the most-inclusive clade containing Passer domesticus but not Dromaeosaurus albertensis or Troodon formosus

suggest that extreme miniaturization and later-ally movable arms necessary for flapping flightare ancestral for paravian theropods (43 50 51)The ceratosaur Limusaurus with a highly reducedpollex might represent a key stage in theropodhand evolution (52) the megalosaur Sciurumimus(Fig 1A) the compsognathid Sinosauropteryx(Fig 1B) and a few other dinosaursmdashincludingeven some ornithischiansmdashdocument the appear-ance of primitive feathers (53ndash57) Other discov-eries include the oviraptorosaur Caudipteryx (58)the deinonychosaur Anchiornis (Fig 1C) Micro-raptor (Fig 1D) and several other maniraptoransthat have pennaceous (vaned) feathers (45 57ndash59)The troodontid Mei (Fig 1E) preserves a birdlikeldquotuck-inrdquo sleeping posture (60) In contrast a num-ber of basal birds resemble theropods in manyfeatures For example new Archaeopteryx speci-mens indicate that this early bird has tetrara-diate palatine as in theropods and probably aspecialized second pedal digit as in deinonycho-saurs (61) Jeholornis (Fig 1F) has a dromaeosaur-like long stiff bony tail (62) and the short-tailedSapeornis (Fig 1G) has a shoulder girdle similarto those of the deinonychosaurs (63)Earlier studies demonstrate that the temporal

paradox is not a real problem for the BMT hy-pothesis which is in fact more consistent withthe stratigraphic record than any other alter-native phylogenetic hypothesis regarding theorigin of birds (64) Nonetheless recent inves-

tigations in the Jurassic have resulted in thediscoveries of well-preserved fossils of severalderived theropod groups including Tyranno-sauroidea (65) Alvarezsauroidea (23) Troodon-tidae (45) and possibly Therizinosauroidea (66)and Oviraptorosauria (38 41) These discoveriesimprove the stratigraphic fit of the theropodfossil record to the BMT hypothesis (23) andhave effectively resolved the so-called temporalparadox problem by showing that many coelur-osaurian groups occur earlier than Archaeop-teryx in the fossil record (Fig 2)Newly discovered fossils and relevant analyses

demonstrate that salient bird characteristics havea sequential and stepwise transformational pat-tern with many arising early in dinosaur evolu-tion undergoing modifications through theropodsand finally approaching the modern conditionclose to the origin of the crown group birds (Fig 2)For example the unusually crouched hindlimbfor bipedal locomotion that characterizes modernbirds was acquired in stepwise fashion throughmuch of theropod evolution (67) and both thefurcula (68) and the ldquosemilunaterdquo carpal (69) ap-peared early in theropod evolution Notably ma-jor bird characteristics often exhibit a complexmosaic evolutionary distribution throughout thetheropod tree and several evolutionary stages arecharacterized by accelerated changes (70) Forexample the early evolution of paravian theropodsfeatures cerebral expansion and elaboration of

visually associated brain regions (71) forelimbenlargement (22 67) acquisition of a crouchedknee-based hindlimb locomotor system (67) andcomplex pinnate feathers associated with in-creased melanosome diversity which implies akey physiological shift (72) Together these fea-tures may suggest the appearance of flight cap-ability at the base of the Paraves (22 67)

Transitional features in dinosaurian reproduction and growth

Living birds display a set of unique reproductivefeatures unknown in other extant vertebratesNevertheless based on the study of eggs eggshellembryos and nesting traces most paleontologistsagree that various anatomical features includingaspects of egg shape ornamentation microstruc-ture and porosity characteristic of living birdstrace their origin to the maniraptoran theropodssuch as oviraptorosaurs and troodontids Cur-rently our understanding of reproduction indromaeosaurs remains limited as only one taxonis associated with any reproductive materialnamely a Deinonychus specimen found on topof eggs (33) These features together with adult-egg associations clutch configurations and nesttraces further suggest that associated behavioraland physiological attributesmay also have evolvedbefore the origin of birds These maniraptorandinosaurs share with modern birds eggs withhard calcitic shells with narrow units relativeto overall shell thickness a second structurallayer of vertical prisms sparse and narrow poresat least some squamatic structure and calciumabsorption (ldquocrateringrdquo) of the mammillae by thedeveloping embryo (34ndash36 73) Egg size rela-tive to adult size in both oviraptorosaurs andtroodontids is large in comparison to the ratiosfor all other theropods (74) Further these eggsgreatly exceed those typical of modern reptilesof similar body mass but are less than 40 thesize expected in a bird of similar adult bodymass (74)On the basis of discoveries of within-clutch

egg pairing (31) and of specimens with two eggswithin or in close proximity to adult skeletons(75 76) maniraptorans have been inferred tohave sequential ovulation as in birds but fromtwo functional ovaries and oviducts (mono-autochronic ovulation) (31) Adult-clutch asso-ciations some preserving brooding posturesare known for four oviraptorosaurs (30 77) twotroodontids (31 32) a dromaeosaur (33) andone basal bird (74) providing clear evidence forparental care of eggs The extra-large clutchesof these dinosaurs exceed the mass of thosefor equivalent-sized extant reptiles and birds bytwo to fourfold (78) Such large clutch sizes areakin to those of modern birds showing pater-nal or maternal parental care as opposed to thoseexhibiting biparental care (79) None of theclutch-associated adults (n = 8) of nonavialanmaniraptorans has any osteo-histologic featuresassociated with egg-laying females Thus the largeclutches of oviraptorosaurs and troodontids mayfavor communal nesting and paternal (male-only)care for these groups (80 81)

Fig 1 Selected recently discovered transitional forms of theropods and early birds The basaltetanuran Sciurumimus (A) and the basal coelurosaur Sinosauropteryx (B) with filamentousfeathers The deinonychosaurs Anchiornis (C) and Microraptor (D) with numerous skeletal andintegumentary features including large vaned feathers on hindlimbs that are also present in basalbirds (E) The troodontid Mei with a birdlike tuck-in sleeping posture The basal birds Jeholornis witha dromaeosaur-like tail (F) and Sapeornis with a typical deinonychosaurian shoulder girdle (G)

The eggshell and eggs of oviraptorosaurs anddromaeosaurs where known are two-layeredmoderately porous and only weakly asymmetric(33 34 36 73) although the ornamented eggsof alvarezsaurs have a three-layered eggshell

(82) In contrast troodontids exhibit a morestrongly asymmetric egg lacking ornamenta-tion with potentially three structural shell lay-ers and low porosity (Fig 3A) and they arestructured more like modern bird eggs than

like those of other dinosaurs (83 84) In addi-tion the tighter clutch configuration greaterexposure of eggs (Fig 3B) and avialan levels ofporosity favor contact incubation in troodontids(85 86)

Fig 2 Selected species on a temporally calibrated archosauromorphanphylogeny showing the evolution of major characteristics along the bird-line The phylogeny is a combination of two recently published analyses Thebasal part of the tree is derived from (55) and the upper part from (16) Skeletalsilhouettes of several archosauromorphans show the general morpholog-ical features along the bird-line within this group and they are the basalarchosauromorphan Euparkeria the basal crocodilomorph Sphenosuchusthe basal theropod Coelophysis the basal coelurosaur Protoceratosaurusthe basal paravian Anchiornis the basal avialan Archaeopteryx the basalpygostylian Sapeornis the basal ornithuromorphan Yanornis and the crowngroup bird Columba (bottom to top) Acronyms in the figure ACVP advancedcostosternal ventilator pump AET arm elongation and thickening AFC armflapping capability AL aerial locomotion AOO active ovary and oviduct BL

bipedal locomotion BMR basal metabolic rate CASPE cervical air sacs pos-terior extension CCIASE cranial and caudal intrathoracic air ascs elaborationCE cerebral expansion ECFSC egg clutch free of sediment cover EM extrememiniaturization ER egg rotation ES egg size FF filamentous feathers FPBfusion of pelvic bones GR growth rate IA increased asymmetry ICI improvedcontact incubation IL iterative laying KBL knee-based locomotion KS kineticskull LFC laterally folding capability LP low porosity MO monoautochronicovulation PC paternal care PPO pubis posterior orientation PSP plowshare-shaped pygostyle RLP rodlike pygostyle RMILTAY rapid maturity in less thana year SAE slightly asymmetrical egg SBT short bony tail SP skeletalpneumatization TFH three-fingered hand TL third (external) layer UB uni-directional breathing US unornamented surface VABRE visually associatedbrain regions elaboration VF vaned feathers

Despite these similarities with modern birdsoviraptorosaurs troodontids and even Cretaceousenantiornithine birds differ reproductively frommodern birds in a few key features includingmore elongate egg shape and eggs largely buriedwith sediment during incubation (73 74 87 88)Relative egg size increases markedly from the-ropods to basal birds of the Mesozoic with thelatter laying eggs 50 to 70 the expected size ofthose in extant birds (74) Several specimens ofbasal birds preserve a single mass of circularobjects Although their interpretation remainsdebated (89) these may represent ovaries withmature ovarian follicles and suggest that basalbirds had only one active ovary and oviduct as inmost modern birds (90) Modern birds differ fromenantiornithines in producing relatively largereggs that are incubated in the absence of sedi-ment (74) These features highlight the gradualacquisition of ldquomodernrdquo reproductive traits fromMesozoic theropods throughMesozoic birds suchas enantiornithines and on to modern birds

Reproductive adaptations may have implica-tions for three other aspects of bird evolutionthe development of feathers metabolism andflight First elongate forelimb and tail feathersin oviraptorosaurs parallel the brooding pos-tures adopted by adults and lengthening of thefeathers may reflect selection for egg care (91)Reproduction in maniraptoran dinosaurs mayalso imply physiological similarities with birdsEgg pairs suggest a reproductive output similarto that of basal birds (74) Additionally iterativelaying together with the complex clutch config-urations and presumed synchronous hatching(83) in these theropods further implies thatboth adult body and incubation temperatureswere elevated over ambient conditions (92)Finally ground nesting the basal condition inmodern birds has been used to argue for aldquoground-uprdquo origin of flight (11) However otherfactors may have initially constrained groundnesting Through the theropod-bird transitioneggs were incubated within sediments which

suggests that they may have lacked chalazae(31 74) [chords of albumen present in birds thatallow the embryo to maintain an upright positionduring egg rotation (93)] Thus without chalazaearboreal maniraptoran dinosaurs may have beenrequired to incubate eggs within sediments inorder to prevent detrimental egg rotation (31)as occurs in modern crocodilians (94)The development growth and physiology of

theropods and basal birds have been exploredusing a variety of approaches Birds are notableamong living vertebrates in being endothermsdeveloping explosively to adult sizes in less thana year (very large forms such as ostriches areexceptions) and having exceptionally high basalmetabolic rates (95) However some osteo-histological studies show that the bone histol-ogy of enantiornithine birds is nearly avascularcomposed of slowly deposited parallel-fiberedmatrix and having growth lines (96) which areunlike the bones of most dinosaurs (ie withfast-growing and highly vascularized fibro-lamellarbone with growth lines) and these studies sug-gest that basal birds had slowed their growthcompared with their dinosaur ancestors Further-more because maximal growth rates strongly cor-relate with metabolic rates (95) they likely hadlower basal metabolic rates than dinosaursConstruction of mass-age growth curves showed

that nonavialan dinosaurs as a whole althoughprobably endothermic did not have a physiol-ogy exactly like modern birds (97) They grewfaster than living reptiles but somewhat slowerthan most precocial birds and considerably slowerthan altricial forms scaled to the same size His-tologic analysis shows that several derived the-ropods Archaeopteryx and other basal birdsinherited this dinosaurian physiology and tookover a year to reach somatic maturity (98) (Fig 3C and D) The last conclusion has been sup-ported by further growth line evidence in otherbasal birds (99) The miniaturization event onceassociated with the cladogenesis of birds actuallyoccurred in paravian theropods (50 51 98) andconsequently the nearly avascular bone in somebasal lineages of birds and small theropods issimply a scaling effect Modern bone types andpresumably the remarkable elevated metabolicrates of birdsmdashwhich allow growth to adult sizesin less than a yearmdashappear to have evolved nearthe cladogenesis of ornithurine birds during theCretaceous Period (37 98 100) although in-creased growth and metabolic rates occurredearly in theropod evolution (Fig 2) [Note Thepioneering studies that established dinosaurgrowth rates were recently criticized for insuf-ficient sample size and other issues (101) How-ever a subsequent comprehensive specimen-richanalysis (102) strongly supports both the method-ology and conclusions about dinosaur and basalbird growth rates and physiology]

Complex evolution of avialan traitsBird morphology features many unique adapta-tions and the evolution of some of these traitsis so complex that a comprehensive understand-ing is wanting How the theropod hand evolved

Body mass (kg)

AM

P

R

Rate = 1977 (mass)0733

R2 = 0975

100000

100000

10000

1000

100

10

1

0101 1 10 100 1000 10000

Max

imum

gro

wth

rat

e (g

day

)

A B

C D

Fig 3 Maniraptoran reproduction and growth (A) Eggshell of Troodon in radial thin section showingthree microstructural layers (separated by white bars) as common to many extant birds Scale bar05 mm (B) Troodon nesting trace with clutch of 24 eggs preserved under white plaster jacket Topsof the eggs were exposed within the nest structure and were incubating by an attending adult rep-resenting a transitional stage between the fully buried clutches of most nonavialan dinosaurs and thesediment-free clutches typical of modern birds Tape measure equals 1 m (C) Histological section ofan Archaeopteryx femur The section shown in polarized light microscopy shows the characteristiclong bone histology of basal-most birds composed of parallel fibered bone matrix with negligiblevascularization Growth lines are also commonplace but are not evident in this particular specimen(Munich Archaeopteryx Bayerische Staatssammlung fuumlr Palaontologie und Geologie BSPG 199950)The histology matches that of same-sized nonavialan dinosaurs but not that of modern birds (D)Maximal growth rates for Archaeopteryx compared with nonavialan dinosaurs and living vertebratesArchaeopteryx growth rates (skeleton) fall on the line at the lowermost bound of the nonavialan dinosaurregression line (blue individual species values are shown as black diamonds) R typical extant reptiliangrowth rates P typical extant precocial land bird growth rates M typical extant marsupial growth ratesA typical extant altricial land bird growth rates Graphic is from (98)

into the bird wing continues to be a hotly de-bated issue in evolutionary biology Tradition-ally paleontological analysis of theropod digitreductions indicated that the three-digit handarose by unilateral loss of digits IV and V re-sulting in a I II III digit formula (103) In con-trast the use of ldquopositionalrdquo criteria of embryologicprecursors to identify digits in modern birdsrevealed a digit 2 3 4 formula (104 105) To re-solve this paradox it has been proposed that ahomeotic transformation of digits occurred thatconverted the embryonic precursors to I II andIII in the adult (frameshift hypothesis) (103) Con-founding any reconciliation of evidence fromthese disciplines paleontological analyses typicallyrely on adult morphology to infer evolutionarylinks whereas developmental studies generallyfocus on very transient vestigial embryonic rem-nants to infer homologies with adult structuresthat have been lost entirely during evolution Incontrast to cellular fate determination morpho-logical identity of a complex structure is generallynot defined by any specific and unique geneticldquomarkersrdquo which creates difficulty in assigningunique homologiesNevertheless the analysis of expression of

spatially regulated genes in the embryonic limbwhich can be considered ldquophenotypicrdquo criteriafor digit assignment has provided support forthe frameshift hypothesis in that certain geneexpression patterns normally correlated withdigit I are retained in the first digit of the chickembryo hand In addition recent more com-prehensive genome-wide expression profilingcomparing chick embryo hand and foot digitprecursors also supports a I II III phenotypicformula in that the expression profiles of thefirst digit in both the hand and foot are re-markably similar (106) Genetic lineage trac-ing of Shh-expressing cells in the chick whichnormally contribute to digits IV and V in thepentadactyl mouse further suggests that digitIV is phenotypically absent from the chickhand (8 107) All of the phenotypic data fromchick embryos are likewise compatible with theclassic paleontological interpretation of a digitI-II-III formula if the avialan embryo ldquoposi-tionalrdquo evidence of digit precursors is discountedas being either misleading or incorrect Howeverthis requires a shift in the primary limb axisto run through digit 3 (axis shift hypothesis)both in extinct and modern tetanuran theropods(108) rather than through digit 4 as occurs inmost tetrapods except urodeles (109) becausethe primary limb axis must by definition in-clude the first digit to form in the embryo Infact a shortcoming of the positional data onvestigial digit condensations appearing in theembryonic hands of various avialan species isthat although a remnant of a positional fourthcondensation (which could be either IV or V)is clearly posterior (lateral) to the three digitsthat are retained in the adult the identificationof a vestigial anterior (medial) condensation iscontroversial and it is based on indistinctelements that could represent other structures[see review in (110)] A reevaluation of digit

condensation formation in mouse embryosalso suggests that some of the traditional ap-proaches used to visualize early digit condensa-tions may be inadequate and could miss evidencefor noncontiguous digit loss (gaps between con-densations) In mouse genetic modulation of sig-nals critical for regulating digit pattern andnumber across vertebrate species results in theinitial loss of a central rather than lateral digit(111 112) This suggests that in principle a I-II-IV formula is also possible (central loss hy-pothesis) The I-II-IV formula would explainthe persistence of digit 1 and still retain theprimary axis extending through digit 4 which isthe accepted rule in all living tetrapods excepturodeles Note that the expression profiling datain chick (106) also revealed mixed expressionfeatures for the lateral digits which could beconstrued as compatible with a I-IIIII-IV avialanhand formula (or the presence of digit IV) Takentogether these developmental studies now leave

open the possibility of I-II-III or even I-II-IV orI-III-IV formulas for the modern avialan handConversely more recent analyses of digit mor-phologies in ceratosaurian and basal tetanurantheropods (52) lend some support to a II III IVtheropod formula with secondary transformationsto produce final I II III morphologies throughmultiple partial homeotic transformations (lat-eral shift hypothesis)To reconcile the paradox of digit homolo-

gies between theropods and birds all of theproposed models (Fig 4A) require either mul-tiple events entailing the reduction and thenreappearance of a positional digit 4 to retainthe primary limb axis or require that the pri-mary axis has undergone a novel shift in itsposition from digit 4 to 3 Clearly whereas muchprogress has been made a final resolution tothis ongoing debate demands additional workfrom both paleontological and developmentalperspectives (110)

Five-fingeredtheropods

Four-fingeredtheropods

Three-fingeredtheropods

Frame-shift

Lateral-shift

Axis-shift

Central-loss

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIII

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIIIV

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIII

12345

IIIIIIIVV

12345

III

IVV

12345

III

IV

1 m

A

B

Fig 4 The evolution of theropod hand and respiratory system (A) Diagrams depicting four hypothesesfor the evolution of wing digits Color shading bordered by solid line refers to fully formed digits and bydash line to reduced digits Colored bars refer to different ldquomorphologicrdquo digits Arabic numerals refer topositional embryonic digit precursors A combination of different colors refers to a mixture of differentmorphological features pertaining to different phenotypes in one digit (B) Reconstruction of pulmonarycomponents [cervical air-sac system (green) lung (orange) and abdominal air-sac system (blue)] in thetheropod Majungatholus Graphic from (27)

A highly efficient flow-through ventilation anda high-compliance air-sac system uniquely char-acterize the avialan respiratory system (27) Per-ceived differences in the respiratory systems oftheropods and other reptiles such as crocodi-lians from those of birds have been invalidlyused as evidence against the BMT hypothesis(49) Nevertheless cervical and anterior dorsalvertebrae are clearly pneumatic in nearly alltheropods (29) and documentation of exten-sive skeletal pneumaticity in theropods such asMajungasaurus and Aerosteon (27 28) dem-onstrates that a complex air-sac system andbirdlike respiration evolved in birdsrsquo theropodancestors (Fig 4B) Furthermore recent ana-tomical and physiological studies reveal thatalligators (7 113) and even monitor lizards (114)exhibit respiratory systems and unidirectionalbreathing akin to those of birds These studiesdemonstrate that unidirectional breathing is aprimitive characteristic of archosaurs or an evenmore inclusive group with the complex air-sacsystem evolving later within Archosauria Weightsavings might have driven the evolution of post-cranial skeletal pneumatization in early theropods

(29) and in addition to large-bodied theropodssmall maniraptoran theropods such as basaloviraptorosaurs dromaeosaurs and troodontidsevolved the complex air-sac system similar tothat of birds (28 29)

Morphogenesis and early evolution of feathersFeathers were once considered to be uniqueavialan structures The presence of feathers isinferred in several theropods based on osteo-logical correlates eg quill knobs (115 116) [al-though the presence of quill knobs in the basaltetanuran Concavenator has been questioned(117)] or pygostyles (118) Short filaments havebeen identified as feathers in the alvarezsaurShuvuuia (119) Direct evidence came to lightin China in 1996 with the discovery of the fea-thered Sinosauropteryx (120) Since then nu-merous specimens of most theropod groups andeven three ornithischian groups preserving fea-thers have been recovered from the Jurassicand Cretaceous beds of northeastern China(13 21 41 45 57) and from the Jurassic andCretaceous beds of Germany Russia and Canada

(55 56 121ndash123) These feathers fall into severalmajor morphotypes (Fig 5) ranging from mono-filamentous feathers to highly complex flightfeathers (57) The phylogenetic distribution ofthese feathers largely concurs with the predic-tions from a developmental model of living birds(4) although some of these morphotypes areabsent in living birds (57 124)The findings of feathers in dinosaurs prompted

developmental studies over the last decade in-vestigating the molecular mechanisms regulat-ing feather development and regeneration inchickens (125) We can now propose the follow-ing ldquomolecular circuitsrdquo regarding tissue morpho-genesis and the evolution of modern feathersEach molecular circuit has specific features andcan be modulated to produce a diversity ofmorphology(i) Cylindrical topology and the downshift of

stem cell ring The formation of loose mesen-chyme in the bud core allows a tube configura-tion with basal layer facing inside Driven byWnt signaling feather stem cells now are posi-tioned near the base forming a ring config-uration (126 127) It can remain as a tube or the

Fig 5 The morphogenesis and evolution of feathers in dinosaurs (A)Monofilamentous feathers in Tianyulong (B) Broad monofilamentous feathers inBeipiaosaurus Radially branched feathers in Sinosauropteryx (C) Sinornitho-saurus (D) and Anchiornis (E) Bilaterally branched feathers in Dilong (F)and Sinornithosaurus (G) (H) Wing flight feathers with symmetrical vanesin Anchiornis (I) Pedal flight feathers with asymmetrical vanes in Micro-raptor (J) Rachis-dominant tail feathers in Confuciusornis (K) Proximally

ribbonlike tail feathers in Similicaudipteryx (L) Phylogenetic distribution ofmajor feather morphotypes (monofilamentous radially branched bilater-ally branched symmetrical flight and asymmetrical flight feathers) amongdinosaurs (M) Major novel morphogenetic events and molecular pathwaysduring feather evolutionThese major feather morphotypes can be explained byselective usage of the five novel ldquomolecular circuitsrdquo discussed in the text Redarrows flank a feather

subsequent caspase-dependent selective apopto-sis can open up the tube allowing feather vaneformation (128)(ii) Hierarchical branching and barbbarbule

pattern formation Ratio of local activators (nog-gin Shh and so on) and inhibitors (bone mor-phogenetic proteins) regulate the number andsize of barb versus rachidial ridges (5 129) Barbridges which depend on Wnt 3a gradient canrun parallel to each other to form radial sym-metric feathers or angle toward the rachis toform bilateral symmetric feathers (130)(iii) Follicle formation and regenerative cycling

During development matrix maetalloproteinasendashdependent tissue invagination allows epithelia totopologically fold into a follicle (131) Follicle con-figuration allows protection of feather progenitorsStem cells and dermal papilla are now clusterednear the follicle base and can undergo dickkopfWntndashdependent cyclic regeneration (132)(iv) Temporal regulation of stem cells along

the proximal-distal axis During feather forma-tion the molecular microenvironment and mor-phology can change along the distal (formedearlier) and proximal (formed later) throughmodulation of fibroblast growth factorndashsproutactivity (133)(v) Organ metamorphosis and regional spe-

cific feather types Upon regeneration modulatedby the body macroenvironments different fea-ther morphotypes (downy contour and flightfeathers) can form on different body regions andin different physiological stages for optimal per-formance (134)The aforementioned morphogenetic proces-

ses can be assembled selectively in various or-ders and independently to produce basic-tondashmore complex feather morphotypes (Fig 5) Themonofilamentous feathers seen in ornithischians(54 56 57) and some theropods (55 57) two setsof morphologically different flight feathersduring ontogeny in the oviraptorosau-rian Similicaudipteryx (124) and theextensive leg feathering (particular-ly pedal feathering) in a number oftheropods and early birds (135) implya variety of rearrangements in themorphogenetic modules The wide oc-currence of pedal feathering in the-ropods and early birds (135) and anextensive distribution of scales onthe bodies of both feathered thero-pods (eg Juravenator) and featheredornithischians (eg the ceratopsianPsittacosaurus and the ornithopodKullindadromeus) remain particularlyinteresting from both developmentaland evolutionary perspectives (56 135)and will no doubt play into further dis-cussions on feather-scale relationshipsThe diverse forms of theropod fea-

thers apparently suggest a comparablemyriad of functions Initial functionsof feathers more likely include ther-moregulation and communication rath-er than flight (57) Several differentlines of data highlight the importance

of communication in early feather evolution(41 57 117 136) particularly by color patternsinferred via preserved melanosome morpho-logies in some theropods and early birds (136 137)although several studies have questioned theidentifications of melanosomes in specimensof feathered theropods and early birds (48 138)One study shows an increased diversity of melano-some morphologies associated with the appear-ance of complex pinnate feathers during theropodevolution (72) This finding supports developmentaldata showing that unique topological arrange-ments allowing feathers to generate complex formsalso permits the generation of visibly complexpigment patterns and pattern renewal duringsexual maturation (139)

Four-winged dinosaurs and the origins of aerial behaviorSeveral flight-related anatomical features suchas hollow bones and the furcula originated inearly theropods basal paravians had many hall-mark features necessary for flight includingextremely small body size (50 70) a laterallyoriented long and robust forelimb (22 67) anenlarged forebrain and other derived neurolog-ical adaptations (71) and large flight feathers(Figs 1 and 2) Particularly surprising are therecent discoveries of large flight feathers form-ing a planar surface on the legs of some basalparaviansmdashfor example those with asymmetricalvanes on both the tibia and metatarsus of somebasal dromaeosaurs such as Microraptor (59)large feathers with symmetrical vanes on both thetibia and metatarsus of the troodontid Anchiornis(45) the basal bird Sapeornis and several otherbasal paravians (135) and large vaned feath-ers on tibiae of several basal birds includingArchaeopteryx confuciusornithids and enan-tiornithines (135) These structures clearly wouldhave been relevant to flight origins The evolu-

tion of flight nonetheless remains highly de-bated with a few recently proposed scenariosincluding factors as diverse as muscle hyperpla-sia (140) and the use of wings to assist in cur-sorial ascent of inclines based on neontologicalobservations (11) Multifactorial explanations forthe origins of flight are likely as this behaviorhas not been uniquely categorized given varia-bility in wing and tail configurations amongtheropods and early birds (45 59 135 141 142)flight probably had complex biomechanicalorigins (142 143)Fundamental to all hypotheses of wing evo-

lution however must be consideration of thosecircumstances that elicited aerial behavior inancestrally terrestrial taxa In all extant verte-brate and invertebrate gliders flight is associ-ated with gravitational acceleration downwardfrom heights and with the use in aerodynamiccontrol of diverse body structures including butnot limited to limbs once aloft (143) The dis-coveries of four-winged theropods and earlybirds (Fig 6) are consistent with the gravity-assisted hypothesis for the origin of bird flightMoreover the concurrent presence of a largeand flattened tail along with potential use ofthe feathered hind legs in aerodynamic controlsuggests substantial capacity for using these asrudders and for maneuvering even during theearliest stages of bird evolution (10 144) Aerialrighting reflexes targeting movement while aloftand controlled landings all would have been en-hanced via bilaterally asymmetric motions ofeither wing pair In other words incipient andnonequilibrium flight behaviors would poten-tially associate with a four-winged and long-tailed arrangement in theropods and early birds(Fig 6) There still remains disagreement as tothe definitional criteria used to indicate thefour-winged and long-tailed condition and as towhether large flight feathers with symmetrical

Columba

JeholornisSapeornis

Archaeopteryx

AnchiornisMicroraptor

Epidexipteryx

Fig 6 Airfoils of selectedmaniraptorans Airfoils (in blue) of the basal dromaeosaurMicroraptor the basal troodontidAnchiornis the basal birds Archaeopteryx Sapeornis and Jeholornis and a modern pigeon Feathered airfoils aregreater in number and are more distally positioned in early birds and their closest theropod relatives than inmodern birds The scansoriopterygid Epidexipteryx has stiff downlike feathers (in green) on both the forelimb andhindlimb and long ribbonlike feathers on the tail the aerodynamic functions of which remain poorly known

vanes in some basal paravians including earlybirds would create useful aerodynamic forcesduring aerial behaviors (117)Use of the hind wings and potentially the

tail to generate vertical force also results in amore posterior and stable position for the cen-ter of lift (10 144) (as can be deduced from batand pterosaur wings based on patagial connec-tions to the hindlegs) Such a hindwing config-uration contributes to static stability in glidingwhereas subsequent functional shifts to the fore-wings alone with associated reductions in tailsize and leg feathering (135) would have requiredoffsetting aerodynamic control via flapping mo-tions (145) Potential tradeoffs between increasedsize of the forewings and the intensity of theirkinematic activation (eg greater frequency andamplitude of flapping) are not well understoodalthough robotic models of early avialan mor-phologies can be informative (146) Such progres-sive anterior specialization of the flight apparatuswith enhanced forces produced by the emergingforelimb locomotor module (145) is nonethelessderived from an ancestrally four-winged plat-form (Fig 6)

Future perspectivesAlternative phylogenetic hypotheses suggest adifferent evolutionary sequence of major birdcharacteristics and imply a different ecologicalorigin of the group (22) Consequently a refinedmore robust phylogeny will be imperative tomove our studies forward Increasing characterand taxon sampling in recent theropod phylo-genetic studies has in theory helped improvethe accuracy of phylogenetic reconstructions butbetter character formulation and more accuratescorings are imperative at present pending bet-ter understanding of the morphologies of manyrecently discovered transitional formsIn terms of character evolution an integrative

approach combining paleontological neontolog-ical developmental geochronological and evenpaleoenvironmental data is particularly desir-able A recent integrative study combining de-velopmental neontological and paleontologicaldata shows that birds evolved their highly spe-cialized cranium mainly by paedomorphisis (147)another study using both neontological and pa-leontological data to reconstruct melanosomeevolution suggests that feathers have changedsignificantly in their melanosome morphologyamong pennaraptoran theropods which impliesa physiological shift before the evolution of flight(72) and that concurs in association with exten-sive postcranial skeletal pneumaticity whichsuggests the presence of birdlike endothermy(29) Similar approaches should be applied toother major structures Certain avialan structuressuch as feathers and visual system are novel inboth genetic and morphological terms There areemerging data on how the genetic code affects themorphogenesis of these structures in developmen-tal biology How the genetic code and expressionpattern evolved can be inferred by a detailedcomparison of homologous structures in thero-pods early birds and modern birds

The construction of molecular phylogenieswould enable a much better understanding ofthe genealogical relations among birds and theirtheropod relatives and the steps leading to theevolution of birds Although once the topic ofscience-fiction movies preserved organic remainshave purportedly been recovered from Tyranno-saurus and the hadrosaur Brachylophosaurus(148 149) and from even older fossils such asEarly Jurassic Lufengosaurus specimens (150)Greater examination along these lines in fossilsspanning the theropod-bird transition is a po-tentially fruitful avenue for future investigationThe increasing interest in the origins of birds

from developmental biology and other disciplineshas enriched our understanding of this impor-tant evolutionary event (8 10 11) and alternativeevolutionary models on various aspects of theorigin of birds have sometimes been providedbased on neontological data (4 11) Howeverany evolutionary model must be tested using thefossil record Consequently dense fossil samplingalong the line to birds and better understandingof the transitional forms play a key role in thediscussion on this issue

REFERENCES AND NOTES

1 A Feduccia The Origin and Evolution of Birds (Yale UnivPress New Haven CT ed 2 1999) pp 466

2 Z Zhou The origin and early evolution of birds Discoveriesdisputes and perspectives from fossil evidenceNaturwissenschaften 91 455ndash471 (2004) doi 101007s00114-004-0570-4 pmid 15365634

3 L M Witmer in Mesozoic Birds Above the Heads ofDinosaurs L M Chiappe L M Witmer Eds (Univ ofCalifornia Press Berkeley 2002) pp 3ndash30

4 R O Prum Development and evolutionary origin of feathersJ Exp Zool 285 291ndash306 (1999) doi 101002(SICI)1097-010X(19991215)2854lt291AID-JEZ1gt30CO2-9pmid 10578107

5 M Yu P Wu R B Widelitz C-M Chuong Themorphogenesis of feathers Nature 420 308ndash312 (2002)doi 101038nature01196 pmid 12442169

6 A O Vargas T Kohlsdorf J F Fallon J VandenbrooksG P Wagner The evolution of HoxD-11 expression in thebird wing Insights from Alligator mississippiensis PLOS ONE3 e3325 (2008) doi 101371journalpone0003325pmid 18833328

7 C G Farmer K Sanders Unidirectional airflow in the lungsof alligators Science 327 338ndash340 (2010) doi 101126science1180219 pmid 20075253

8 K Tamura N Nomura R Seki S Yonei-TamuraH Yokoyama Embryological evidence identifies wing digitsin birds as digits 1 2 and 3 Science 331 753ndash757 (2011)doi 101126science1198229 pmid 21311019

9 C L Organ A M Shedlock A Meade M PagelS V Edwards Origin of avian genome size and structurein non-avian dinosaurs Nature 446 180ndash184 (2007)doi 101038nature05621 pmid 17344851

10 D Evangelista et al Aerodynamic characteristics of afeathered dinosaur measured using physical modelsEffects of form on static stability and control effectivenessPLOS ONE 9 e85203 (2014) doi 101371journalpone0085203 pmid 24454820

11 K P Dial Wing-assisted incline running and the evolutionof flight Science 299 402ndash404 (2003) doi 101126science1078237 pmid 12532020

12 F C James J A Pourtless IV Cladistics and the origin ofbirds A review and two new analyses Ornithol Monogr66 1ndash78 (2009) doi 101525om20096611

13 M Norell X Xu Feathered dinosaurs Annu Rev EarthPlanet Sci 33 277ndash299 (2005) doi 101146annurevearth33092203122511

14 J Gauthier Saurischian monophyly and the origin of birdsMem Calif Acad Sci 8 1ndash55 (1986)

15 P C Sereno The evolution of dinosaurs Science 2842137ndash2147 (1999) doi 101126science28454232137pmid 10381873

16 A H Turner P J Makovicky M A Norell A review ofdromaeosaurid systematics and paravian phylogeny Bull AmMus Nat Hist 371 1ndash206 (2012) doi 1012067481

17 P Senter J I Kirkland D D DeBlieux S Madsen N TothNew dromaeosaurids (Dinosauria Theropoda) from theLower Cretaceous of Utah and the evolution of thedromaeosaurid tail PLOS ONE 7 e36790 (2012)doi 101371journalpone0036790 pmid 22615813

18 T R Holtz Jr A new phylogeny of the carnivorous dinosaursGaia 15 5ndash61 (1998)

19 O W M Rauhut The interrelationships and evolution ofbasal theropod dinosaurs Spec Pap Paleontology 69 1ndash213(2003)

20 M A Norell J M Clark P J Makovicky in New Perspectives onthe Origin and Evolution of Birds J Gauthier L F Gall Eds(Yale Univ Press New Haven CT 2001) pp 49ndash67

21 P Godefroit et al A Jurassic avialan dinosaur from Chinaresolves the early phylogenetic history of birds Nature 498359ndash362 (2013) doi 101038nature12168 pmid 23719374

22 X Xu H You K Du F Han An Archaeopteryx-like theropodfrom China and the origin of Avialae Nature 475 465ndash470(2011) doi 101038nature10288 pmid 21796204

23 J N Choiniere et al A basal alvarezsauroid theropod fromthe early Late Jurassic of Xinjiang China Science 327571ndash574 (2010) doi 101126science1182143pmid 20110503

24 J H Ostrom The osteology of Deinonychus antirrhopus anunusual theropod from the Lower Cretaceous of MontanaBull Peabody Mus Nat Hist 30 1ndash165 (1969)

25 R Barsbold Predatory dinosaurs from the Cretaceousof Mongolia Tr Sovm Sov-Mong Paleontol Eksped 191ndash117 (1983)

26 O Wings thesis The University of Bonn (2004)27 P M OrsquoConnor L P A M Claessens Basic avian pulmonary

design and flow-through ventilation in non-avian theropoddinosaurs Nature 436 253ndash256 (2005) doi 101038nature03716 pmid 16015329

28 P C Sereno et al Evidence for avian intrathoracic air sacsin a new predatory dinosaur from Argentina PLOS ONE3 e3303 (2008) doi 101371journalpone0003303pmid 18825273

29 R B J Benson R J Butler M T Carrano P M OrsquoConnorAir-filled postcranial bones in theropod dinosaursPhysiological implications and the lsquoreptilersquo-bird transitionBiol Rev Camb Philos Soc 87 168ndash193 (2012) doi 101111j1469-185X201100190x pmid 21733078

30 M A Norell J M Clark L M Chiappe D DashzevegA nesting dinosaur Nature 378 774ndash776 (1995)doi 101038378774a0

31 D J Varricchio F Jackson J J Borkowski J R HornerNest and egg clutches of the dinosaur Troodon formosusand the evolution of avian reproductive traits Nature 385247ndash250 (1997) doi 101038385247a0

32 G M Erickson K Curry Rogers D J Varricchio M A NorellX Xu Growth patterns in brooding dinosaurs reveals thetiming of sexual maturity in non-avian dinosaurs and genesisof the avian condition Biol Lett 3 558ndash561 (2007)pmid 17638674

33 G Grellet-Tinner P Makovicky A possible egg of thedromaeosaur Deinonychus antirrhopus Phylogenetic andbiological implications Can J Earth Sci 43 705ndash719 (2006)doi 101139e06-033

34 G Grellet-Tinner L M Chiappe in Feathered DragonsStudies on the Transition from Dinosaurs to Birds P J CurrieE B Koppelhus M A Shugar J L Wright Eds (IndianaUniv Press Bloomington 2004) pp 185ndash214

35 D J Varricchio F D Jackson A phylogenetic assessment ofprismatic dinosaur eggs from the Cretaceous Two MedicineFormation of Montana J Vertebr Paleontol 24 931ndash937 (2004)doi 1016710272-4634(2004)024[0931APAOPD]20CO2

36 D K Zelenitsky F Therrien Phylogenetic analysis ofreproductive traits of maniraptoran theropods and itsimplications for egg parataxonomy Paleontology 51 807ndash816(2008) doi 101111j1475-4983200800770x

37 K Padian A J de Ricqlegraves J R Horner Dinosaurian growthrates and bird origins Nature 412 405ndash408 (2001)doi 10103835086500 pmid 11473307

38 F L Agnoliacuten F E Novas Avian Ancestors A Review of thePhylogenetic Relationships of the Theropods UnenlagiidaeMicroraptoria Anchiornis and Scansoriopterygidae (SpringerDordrecht Heidelberg 2013)

39 P J Makovicky L E Zanno in Living Dinosaurs TheEvolutionary History of Modern Birds G J Dyke G KaiserEds (Wiley-Blackwell Oxford 2011) pp 9ndash29

suggest that extreme miniaturization and later-ally movable arms necessary for flapping flightare ancestral for paravian theropods (43 50 51)The ceratosaur Limusaurus with a highly reducedpollex might represent a key stage in theropodhand evolution (52) the megalosaur Sciurumimus(Fig 1A) the compsognathid Sinosauropteryx(Fig 1B) and a few other dinosaursmdashincludingeven some ornithischiansmdashdocument the appear-ance of primitive feathers (53ndash57) Other discov-eries include the oviraptorosaur Caudipteryx (58)the deinonychosaur Anchiornis (Fig 1C) Micro-raptor (Fig 1D) and several other maniraptoransthat have pennaceous (vaned) feathers (45 57ndash59)The troodontid Mei (Fig 1E) preserves a birdlikeldquotuck-inrdquo sleeping posture (60) In contrast a num-ber of basal birds resemble theropods in manyfeatures For example new Archaeopteryx speci-mens indicate that this early bird has tetrara-diate palatine as in theropods and probably aspecialized second pedal digit as in deinonycho-saurs (61) Jeholornis (Fig 1F) has a dromaeosaur-like long stiff bony tail (62) and the short-tailedSapeornis (Fig 1G) has a shoulder girdle similarto those of the deinonychosaurs (63)Earlier studies demonstrate that the temporal

paradox is not a real problem for the BMT hy-pothesis which is in fact more consistent withthe stratigraphic record than any other alter-native phylogenetic hypothesis regarding theorigin of birds (64) Nonetheless recent inves-

tigations in the Jurassic have resulted in thediscoveries of well-preserved fossils of severalderived theropod groups including Tyranno-sauroidea (65) Alvarezsauroidea (23) Troodon-tidae (45) and possibly Therizinosauroidea (66)and Oviraptorosauria (38 41) These discoveriesimprove the stratigraphic fit of the theropodfossil record to the BMT hypothesis (23) andhave effectively resolved the so-called temporalparadox problem by showing that many coelur-osaurian groups occur earlier than Archaeop-teryx in the fossil record (Fig 2)Newly discovered fossils and relevant analyses

demonstrate that salient bird characteristics havea sequential and stepwise transformational pat-tern with many arising early in dinosaur evolu-tion undergoing modifications through theropodsand finally approaching the modern conditionclose to the origin of the crown group birds (Fig 2)For example the unusually crouched hindlimbfor bipedal locomotion that characterizes modernbirds was acquired in stepwise fashion throughmuch of theropod evolution (67) and both thefurcula (68) and the ldquosemilunaterdquo carpal (69) ap-peared early in theropod evolution Notably ma-jor bird characteristics often exhibit a complexmosaic evolutionary distribution throughout thetheropod tree and several evolutionary stages arecharacterized by accelerated changes (70) Forexample the early evolution of paravian theropodsfeatures cerebral expansion and elaboration of

visually associated brain regions (71) forelimbenlargement (22 67) acquisition of a crouchedknee-based hindlimb locomotor system (67) andcomplex pinnate feathers associated with in-creased melanosome diversity which implies akey physiological shift (72) Together these fea-tures may suggest the appearance of flight cap-ability at the base of the Paraves (22 67)

Transitional features in dinosaurian reproduction and growth

Living birds display a set of unique reproductivefeatures unknown in other extant vertebratesNevertheless based on the study of eggs eggshellembryos and nesting traces most paleontologistsagree that various anatomical features includingaspects of egg shape ornamentation microstruc-ture and porosity characteristic of living birdstrace their origin to the maniraptoran theropodssuch as oviraptorosaurs and troodontids Cur-rently our understanding of reproduction indromaeosaurs remains limited as only one taxonis associated with any reproductive materialnamely a Deinonychus specimen found on topof eggs (33) These features together with adult-egg associations clutch configurations and nesttraces further suggest that associated behavioraland physiological attributesmay also have evolvedbefore the origin of birds These maniraptorandinosaurs share with modern birds eggs withhard calcitic shells with narrow units relativeto overall shell thickness a second structurallayer of vertical prisms sparse and narrow poresat least some squamatic structure and calciumabsorption (ldquocrateringrdquo) of the mammillae by thedeveloping embryo (34ndash36 73) Egg size rela-tive to adult size in both oviraptorosaurs andtroodontids is large in comparison to the ratiosfor all other theropods (74) Further these eggsgreatly exceed those typical of modern reptilesof similar body mass but are less than 40 thesize expected in a bird of similar adult bodymass (74)On the basis of discoveries of within-clutch

egg pairing (31) and of specimens with two eggswithin or in close proximity to adult skeletons(75 76) maniraptorans have been inferred tohave sequential ovulation as in birds but fromtwo functional ovaries and oviducts (mono-autochronic ovulation) (31) Adult-clutch asso-ciations some preserving brooding posturesare known for four oviraptorosaurs (30 77) twotroodontids (31 32) a dromaeosaur (33) andone basal bird (74) providing clear evidence forparental care of eggs The extra-large clutchesof these dinosaurs exceed the mass of thosefor equivalent-sized extant reptiles and birds bytwo to fourfold (78) Such large clutch sizes areakin to those of modern birds showing pater-nal or maternal parental care as opposed to thoseexhibiting biparental care (79) None of theclutch-associated adults (n = 8) of nonavialanmaniraptorans has any osteo-histologic featuresassociated with egg-laying females Thus the largeclutches of oviraptorosaurs and troodontids mayfavor communal nesting and paternal (male-only)care for these groups (80 81)

Fig 1 Selected recently discovered transitional forms of theropods and early birds The basaltetanuran Sciurumimus (A) and the basal coelurosaur Sinosauropteryx (B) with filamentousfeathers The deinonychosaurs Anchiornis (C) and Microraptor (D) with numerous skeletal andintegumentary features including large vaned feathers on hindlimbs that are also present in basalbirds (E) The troodontid Mei with a birdlike tuck-in sleeping posture The basal birds Jeholornis witha dromaeosaur-like tail (F) and Sapeornis with a typical deinonychosaurian shoulder girdle (G)

The eggshell and eggs of oviraptorosaurs anddromaeosaurs where known are two-layeredmoderately porous and only weakly asymmetric(33 34 36 73) although the ornamented eggsof alvarezsaurs have a three-layered eggshell

(82) In contrast troodontids exhibit a morestrongly asymmetric egg lacking ornamenta-tion with potentially three structural shell lay-ers and low porosity (Fig 3A) and they arestructured more like modern bird eggs than

like those of other dinosaurs (83 84) In addi-tion the tighter clutch configuration greaterexposure of eggs (Fig 3B) and avialan levels ofporosity favor contact incubation in troodontids(85 86)

Fig 2 Selected species on a temporally calibrated archosauromorphanphylogeny showing the evolution of major characteristics along the bird-line The phylogeny is a combination of two recently published analyses Thebasal part of the tree is derived from (55) and the upper part from (16) Skeletalsilhouettes of several archosauromorphans show the general morpholog-ical features along the bird-line within this group and they are the basalarchosauromorphan Euparkeria the basal crocodilomorph Sphenosuchusthe basal theropod Coelophysis the basal coelurosaur Protoceratosaurusthe basal paravian Anchiornis the basal avialan Archaeopteryx the basalpygostylian Sapeornis the basal ornithuromorphan Yanornis and the crowngroup bird Columba (bottom to top) Acronyms in the figure ACVP advancedcostosternal ventilator pump AET arm elongation and thickening AFC armflapping capability AL aerial locomotion AOO active ovary and oviduct BL

bipedal locomotion BMR basal metabolic rate CASPE cervical air sacs pos-terior extension CCIASE cranial and caudal intrathoracic air ascs elaborationCE cerebral expansion ECFSC egg clutch free of sediment cover EM extrememiniaturization ER egg rotation ES egg size FF filamentous feathers FPBfusion of pelvic bones GR growth rate IA increased asymmetry ICI improvedcontact incubation IL iterative laying KBL knee-based locomotion KS kineticskull LFC laterally folding capability LP low porosity MO monoautochronicovulation PC paternal care PPO pubis posterior orientation PSP plowshare-shaped pygostyle RLP rodlike pygostyle RMILTAY rapid maturity in less thana year SAE slightly asymmetrical egg SBT short bony tail SP skeletalpneumatization TFH three-fingered hand TL third (external) layer UB uni-directional breathing US unornamented surface VABRE visually associatedbrain regions elaboration VF vaned feathers

Despite these similarities with modern birdsoviraptorosaurs troodontids and even Cretaceousenantiornithine birds differ reproductively frommodern birds in a few key features includingmore elongate egg shape and eggs largely buriedwith sediment during incubation (73 74 87 88)Relative egg size increases markedly from the-ropods to basal birds of the Mesozoic with thelatter laying eggs 50 to 70 the expected size ofthose in extant birds (74) Several specimens ofbasal birds preserve a single mass of circularobjects Although their interpretation remainsdebated (89) these may represent ovaries withmature ovarian follicles and suggest that basalbirds had only one active ovary and oviduct as inmost modern birds (90) Modern birds differ fromenantiornithines in producing relatively largereggs that are incubated in the absence of sedi-ment (74) These features highlight the gradualacquisition of ldquomodernrdquo reproductive traits fromMesozoic theropods throughMesozoic birds suchas enantiornithines and on to modern birds

Reproductive adaptations may have implica-tions for three other aspects of bird evolutionthe development of feathers metabolism andflight First elongate forelimb and tail feathersin oviraptorosaurs parallel the brooding pos-tures adopted by adults and lengthening of thefeathers may reflect selection for egg care (91)Reproduction in maniraptoran dinosaurs mayalso imply physiological similarities with birdsEgg pairs suggest a reproductive output similarto that of basal birds (74) Additionally iterativelaying together with the complex clutch config-urations and presumed synchronous hatching(83) in these theropods further implies thatboth adult body and incubation temperatureswere elevated over ambient conditions (92)Finally ground nesting the basal condition inmodern birds has been used to argue for aldquoground-uprdquo origin of flight (11) However otherfactors may have initially constrained groundnesting Through the theropod-bird transitioneggs were incubated within sediments which

suggests that they may have lacked chalazae(31 74) [chords of albumen present in birds thatallow the embryo to maintain an upright positionduring egg rotation (93)] Thus without chalazaearboreal maniraptoran dinosaurs may have beenrequired to incubate eggs within sediments inorder to prevent detrimental egg rotation (31)as occurs in modern crocodilians (94)The development growth and physiology of

theropods and basal birds have been exploredusing a variety of approaches Birds are notableamong living vertebrates in being endothermsdeveloping explosively to adult sizes in less thana year (very large forms such as ostriches areexceptions) and having exceptionally high basalmetabolic rates (95) However some osteo-histological studies show that the bone histol-ogy of enantiornithine birds is nearly avascularcomposed of slowly deposited parallel-fiberedmatrix and having growth lines (96) which areunlike the bones of most dinosaurs (ie withfast-growing and highly vascularized fibro-lamellarbone with growth lines) and these studies sug-gest that basal birds had slowed their growthcompared with their dinosaur ancestors Further-more because maximal growth rates strongly cor-relate with metabolic rates (95) they likely hadlower basal metabolic rates than dinosaursConstruction of mass-age growth curves showed

that nonavialan dinosaurs as a whole althoughprobably endothermic did not have a physiol-ogy exactly like modern birds (97) They grewfaster than living reptiles but somewhat slowerthan most precocial birds and considerably slowerthan altricial forms scaled to the same size His-tologic analysis shows that several derived the-ropods Archaeopteryx and other basal birdsinherited this dinosaurian physiology and tookover a year to reach somatic maturity (98) (Fig 3C and D) The last conclusion has been sup-ported by further growth line evidence in otherbasal birds (99) The miniaturization event onceassociated with the cladogenesis of birds actuallyoccurred in paravian theropods (50 51 98) andconsequently the nearly avascular bone in somebasal lineages of birds and small theropods issimply a scaling effect Modern bone types andpresumably the remarkable elevated metabolicrates of birdsmdashwhich allow growth to adult sizesin less than a yearmdashappear to have evolved nearthe cladogenesis of ornithurine birds during theCretaceous Period (37 98 100) although in-creased growth and metabolic rates occurredearly in theropod evolution (Fig 2) [Note Thepioneering studies that established dinosaurgrowth rates were recently criticized for insuf-ficient sample size and other issues (101) How-ever a subsequent comprehensive specimen-richanalysis (102) strongly supports both the method-ology and conclusions about dinosaur and basalbird growth rates and physiology]

Complex evolution of avialan traitsBird morphology features many unique adapta-tions and the evolution of some of these traitsis so complex that a comprehensive understand-ing is wanting How the theropod hand evolved

Body mass (kg)

AM

P

R

Rate = 1977 (mass)0733

R2 = 0975

100000

100000

10000

1000

100

10

1

0101 1 10 100 1000 10000

Max

imum

gro

wth

rat

e (g

day

)

A B

C D

Fig 3 Maniraptoran reproduction and growth (A) Eggshell of Troodon in radial thin section showingthree microstructural layers (separated by white bars) as common to many extant birds Scale bar05 mm (B) Troodon nesting trace with clutch of 24 eggs preserved under white plaster jacket Topsof the eggs were exposed within the nest structure and were incubating by an attending adult rep-resenting a transitional stage between the fully buried clutches of most nonavialan dinosaurs and thesediment-free clutches typical of modern birds Tape measure equals 1 m (C) Histological section ofan Archaeopteryx femur The section shown in polarized light microscopy shows the characteristiclong bone histology of basal-most birds composed of parallel fibered bone matrix with negligiblevascularization Growth lines are also commonplace but are not evident in this particular specimen(Munich Archaeopteryx Bayerische Staatssammlung fuumlr Palaontologie und Geologie BSPG 199950)The histology matches that of same-sized nonavialan dinosaurs but not that of modern birds (D)Maximal growth rates for Archaeopteryx compared with nonavialan dinosaurs and living vertebratesArchaeopteryx growth rates (skeleton) fall on the line at the lowermost bound of the nonavialan dinosaurregression line (blue individual species values are shown as black diamonds) R typical extant reptiliangrowth rates P typical extant precocial land bird growth rates M typical extant marsupial growth ratesA typical extant altricial land bird growth rates Graphic is from (98)

into the bird wing continues to be a hotly de-bated issue in evolutionary biology Tradition-ally paleontological analysis of theropod digitreductions indicated that the three-digit handarose by unilateral loss of digits IV and V re-sulting in a I II III digit formula (103) In con-trast the use of ldquopositionalrdquo criteria of embryologicprecursors to identify digits in modern birdsrevealed a digit 2 3 4 formula (104 105) To re-solve this paradox it has been proposed that ahomeotic transformation of digits occurred thatconverted the embryonic precursors to I II andIII in the adult (frameshift hypothesis) (103) Con-founding any reconciliation of evidence fromthese disciplines paleontological analyses typicallyrely on adult morphology to infer evolutionarylinks whereas developmental studies generallyfocus on very transient vestigial embryonic rem-nants to infer homologies with adult structuresthat have been lost entirely during evolution Incontrast to cellular fate determination morpho-logical identity of a complex structure is generallynot defined by any specific and unique geneticldquomarkersrdquo which creates difficulty in assigningunique homologiesNevertheless the analysis of expression of

spatially regulated genes in the embryonic limbwhich can be considered ldquophenotypicrdquo criteriafor digit assignment has provided support forthe frameshift hypothesis in that certain geneexpression patterns normally correlated withdigit I are retained in the first digit of the chickembryo hand In addition recent more com-prehensive genome-wide expression profilingcomparing chick embryo hand and foot digitprecursors also supports a I II III phenotypicformula in that the expression profiles of thefirst digit in both the hand and foot are re-markably similar (106) Genetic lineage trac-ing of Shh-expressing cells in the chick whichnormally contribute to digits IV and V in thepentadactyl mouse further suggests that digitIV is phenotypically absent from the chickhand (8 107) All of the phenotypic data fromchick embryos are likewise compatible with theclassic paleontological interpretation of a digitI-II-III formula if the avialan embryo ldquoposi-tionalrdquo evidence of digit precursors is discountedas being either misleading or incorrect Howeverthis requires a shift in the primary limb axisto run through digit 3 (axis shift hypothesis)both in extinct and modern tetanuran theropods(108) rather than through digit 4 as occurs inmost tetrapods except urodeles (109) becausethe primary limb axis must by definition in-clude the first digit to form in the embryo Infact a shortcoming of the positional data onvestigial digit condensations appearing in theembryonic hands of various avialan species isthat although a remnant of a positional fourthcondensation (which could be either IV or V)is clearly posterior (lateral) to the three digitsthat are retained in the adult the identificationof a vestigial anterior (medial) condensation iscontroversial and it is based on indistinctelements that could represent other structures[see review in (110)] A reevaluation of digit

condensation formation in mouse embryosalso suggests that some of the traditional ap-proaches used to visualize early digit condensa-tions may be inadequate and could miss evidencefor noncontiguous digit loss (gaps between con-densations) In mouse genetic modulation of sig-nals critical for regulating digit pattern andnumber across vertebrate species results in theinitial loss of a central rather than lateral digit(111 112) This suggests that in principle a I-II-IV formula is also possible (central loss hy-pothesis) The I-II-IV formula would explainthe persistence of digit 1 and still retain theprimary axis extending through digit 4 which isthe accepted rule in all living tetrapods excepturodeles Note that the expression profiling datain chick (106) also revealed mixed expressionfeatures for the lateral digits which could beconstrued as compatible with a I-IIIII-IV avialanhand formula (or the presence of digit IV) Takentogether these developmental studies now leave

open the possibility of I-II-III or even I-II-IV orI-III-IV formulas for the modern avialan handConversely more recent analyses of digit mor-phologies in ceratosaurian and basal tetanurantheropods (52) lend some support to a II III IVtheropod formula with secondary transformationsto produce final I II III morphologies throughmultiple partial homeotic transformations (lat-eral shift hypothesis)To reconcile the paradox of digit homolo-

gies between theropods and birds all of theproposed models (Fig 4A) require either mul-tiple events entailing the reduction and thenreappearance of a positional digit 4 to retainthe primary limb axis or require that the pri-mary axis has undergone a novel shift in itsposition from digit 4 to 3 Clearly whereas muchprogress has been made a final resolution tothis ongoing debate demands additional workfrom both paleontological and developmentalperspectives (110)

Five-fingeredtheropods

Four-fingeredtheropods

Three-fingeredtheropods

Frame-shift

Lateral-shift

Axis-shift

Central-loss

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIII

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIIIV

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIII

12345

IIIIIIIVV

12345

III

IVV

12345

III

IV

1 m

A

B

Fig 4 The evolution of theropod hand and respiratory system (A) Diagrams depicting four hypothesesfor the evolution of wing digits Color shading bordered by solid line refers to fully formed digits and bydash line to reduced digits Colored bars refer to different ldquomorphologicrdquo digits Arabic numerals refer topositional embryonic digit precursors A combination of different colors refers to a mixture of differentmorphological features pertaining to different phenotypes in one digit (B) Reconstruction of pulmonarycomponents [cervical air-sac system (green) lung (orange) and abdominal air-sac system (blue)] in thetheropod Majungatholus Graphic from (27)

A highly efficient flow-through ventilation anda high-compliance air-sac system uniquely char-acterize the avialan respiratory system (27) Per-ceived differences in the respiratory systems oftheropods and other reptiles such as crocodi-lians from those of birds have been invalidlyused as evidence against the BMT hypothesis(49) Nevertheless cervical and anterior dorsalvertebrae are clearly pneumatic in nearly alltheropods (29) and documentation of exten-sive skeletal pneumaticity in theropods such asMajungasaurus and Aerosteon (27 28) dem-onstrates that a complex air-sac system andbirdlike respiration evolved in birdsrsquo theropodancestors (Fig 4B) Furthermore recent ana-tomical and physiological studies reveal thatalligators (7 113) and even monitor lizards (114)exhibit respiratory systems and unidirectionalbreathing akin to those of birds These studiesdemonstrate that unidirectional breathing is aprimitive characteristic of archosaurs or an evenmore inclusive group with the complex air-sacsystem evolving later within Archosauria Weightsavings might have driven the evolution of post-cranial skeletal pneumatization in early theropods

(29) and in addition to large-bodied theropodssmall maniraptoran theropods such as basaloviraptorosaurs dromaeosaurs and troodontidsevolved the complex air-sac system similar tothat of birds (28 29)

Morphogenesis and early evolution of feathersFeathers were once considered to be uniqueavialan structures The presence of feathers isinferred in several theropods based on osteo-logical correlates eg quill knobs (115 116) [al-though the presence of quill knobs in the basaltetanuran Concavenator has been questioned(117)] or pygostyles (118) Short filaments havebeen identified as feathers in the alvarezsaurShuvuuia (119) Direct evidence came to lightin China in 1996 with the discovery of the fea-thered Sinosauropteryx (120) Since then nu-merous specimens of most theropod groups andeven three ornithischian groups preserving fea-thers have been recovered from the Jurassicand Cretaceous beds of northeastern China(13 21 41 45 57) and from the Jurassic andCretaceous beds of Germany Russia and Canada

(55 56 121ndash123) These feathers fall into severalmajor morphotypes (Fig 5) ranging from mono-filamentous feathers to highly complex flightfeathers (57) The phylogenetic distribution ofthese feathers largely concurs with the predic-tions from a developmental model of living birds(4) although some of these morphotypes areabsent in living birds (57 124)The findings of feathers in dinosaurs prompted

developmental studies over the last decade in-vestigating the molecular mechanisms regulat-ing feather development and regeneration inchickens (125) We can now propose the follow-ing ldquomolecular circuitsrdquo regarding tissue morpho-genesis and the evolution of modern feathersEach molecular circuit has specific features andcan be modulated to produce a diversity ofmorphology(i) Cylindrical topology and the downshift of

stem cell ring The formation of loose mesen-chyme in the bud core allows a tube configura-tion with basal layer facing inside Driven byWnt signaling feather stem cells now are posi-tioned near the base forming a ring config-uration (126 127) It can remain as a tube or the

Fig 5 The morphogenesis and evolution of feathers in dinosaurs (A)Monofilamentous feathers in Tianyulong (B) Broad monofilamentous feathers inBeipiaosaurus Radially branched feathers in Sinosauropteryx (C) Sinornitho-saurus (D) and Anchiornis (E) Bilaterally branched feathers in Dilong (F)and Sinornithosaurus (G) (H) Wing flight feathers with symmetrical vanesin Anchiornis (I) Pedal flight feathers with asymmetrical vanes in Micro-raptor (J) Rachis-dominant tail feathers in Confuciusornis (K) Proximally

ribbonlike tail feathers in Similicaudipteryx (L) Phylogenetic distribution ofmajor feather morphotypes (monofilamentous radially branched bilater-ally branched symmetrical flight and asymmetrical flight feathers) amongdinosaurs (M) Major novel morphogenetic events and molecular pathwaysduring feather evolutionThese major feather morphotypes can be explained byselective usage of the five novel ldquomolecular circuitsrdquo discussed in the text Redarrows flank a feather

subsequent caspase-dependent selective apopto-sis can open up the tube allowing feather vaneformation (128)(ii) Hierarchical branching and barbbarbule

pattern formation Ratio of local activators (nog-gin Shh and so on) and inhibitors (bone mor-phogenetic proteins) regulate the number andsize of barb versus rachidial ridges (5 129) Barbridges which depend on Wnt 3a gradient canrun parallel to each other to form radial sym-metric feathers or angle toward the rachis toform bilateral symmetric feathers (130)(iii) Follicle formation and regenerative cycling

During development matrix maetalloproteinasendashdependent tissue invagination allows epithelia totopologically fold into a follicle (131) Follicle con-figuration allows protection of feather progenitorsStem cells and dermal papilla are now clusterednear the follicle base and can undergo dickkopfWntndashdependent cyclic regeneration (132)(iv) Temporal regulation of stem cells along

the proximal-distal axis During feather forma-tion the molecular microenvironment and mor-phology can change along the distal (formedearlier) and proximal (formed later) throughmodulation of fibroblast growth factorndashsproutactivity (133)(v) Organ metamorphosis and regional spe-

cific feather types Upon regeneration modulatedby the body macroenvironments different fea-ther morphotypes (downy contour and flightfeathers) can form on different body regions andin different physiological stages for optimal per-formance (134)The aforementioned morphogenetic proces-

ses can be assembled selectively in various or-ders and independently to produce basic-tondashmore complex feather morphotypes (Fig 5) Themonofilamentous feathers seen in ornithischians(54 56 57) and some theropods (55 57) two setsof morphologically different flight feathersduring ontogeny in the oviraptorosau-rian Similicaudipteryx (124) and theextensive leg feathering (particular-ly pedal feathering) in a number oftheropods and early birds (135) implya variety of rearrangements in themorphogenetic modules The wide oc-currence of pedal feathering in the-ropods and early birds (135) and anextensive distribution of scales onthe bodies of both feathered thero-pods (eg Juravenator) and featheredornithischians (eg the ceratopsianPsittacosaurus and the ornithopodKullindadromeus) remain particularlyinteresting from both developmentaland evolutionary perspectives (56 135)and will no doubt play into further dis-cussions on feather-scale relationshipsThe diverse forms of theropod fea-

thers apparently suggest a comparablemyriad of functions Initial functionsof feathers more likely include ther-moregulation and communication rath-er than flight (57) Several differentlines of data highlight the importance

of communication in early feather evolution(41 57 117 136) particularly by color patternsinferred via preserved melanosome morpho-logies in some theropods and early birds (136 137)although several studies have questioned theidentifications of melanosomes in specimensof feathered theropods and early birds (48 138)One study shows an increased diversity of melano-some morphologies associated with the appear-ance of complex pinnate feathers during theropodevolution (72) This finding supports developmentaldata showing that unique topological arrange-ments allowing feathers to generate complex formsalso permits the generation of visibly complexpigment patterns and pattern renewal duringsexual maturation (139)

Four-winged dinosaurs and the origins of aerial behaviorSeveral flight-related anatomical features suchas hollow bones and the furcula originated inearly theropods basal paravians had many hall-mark features necessary for flight includingextremely small body size (50 70) a laterallyoriented long and robust forelimb (22 67) anenlarged forebrain and other derived neurolog-ical adaptations (71) and large flight feathers(Figs 1 and 2) Particularly surprising are therecent discoveries of large flight feathers form-ing a planar surface on the legs of some basalparaviansmdashfor example those with asymmetricalvanes on both the tibia and metatarsus of somebasal dromaeosaurs such as Microraptor (59)large feathers with symmetrical vanes on both thetibia and metatarsus of the troodontid Anchiornis(45) the basal bird Sapeornis and several otherbasal paravians (135) and large vaned feath-ers on tibiae of several basal birds includingArchaeopteryx confuciusornithids and enan-tiornithines (135) These structures clearly wouldhave been relevant to flight origins The evolu-

tion of flight nonetheless remains highly de-bated with a few recently proposed scenariosincluding factors as diverse as muscle hyperpla-sia (140) and the use of wings to assist in cur-sorial ascent of inclines based on neontologicalobservations (11) Multifactorial explanations forthe origins of flight are likely as this behaviorhas not been uniquely categorized given varia-bility in wing and tail configurations amongtheropods and early birds (45 59 135 141 142)flight probably had complex biomechanicalorigins (142 143)Fundamental to all hypotheses of wing evo-

lution however must be consideration of thosecircumstances that elicited aerial behavior inancestrally terrestrial taxa In all extant verte-brate and invertebrate gliders flight is associ-ated with gravitational acceleration downwardfrom heights and with the use in aerodynamiccontrol of diverse body structures including butnot limited to limbs once aloft (143) The dis-coveries of four-winged theropods and earlybirds (Fig 6) are consistent with the gravity-assisted hypothesis for the origin of bird flightMoreover the concurrent presence of a largeand flattened tail along with potential use ofthe feathered hind legs in aerodynamic controlsuggests substantial capacity for using these asrudders and for maneuvering even during theearliest stages of bird evolution (10 144) Aerialrighting reflexes targeting movement while aloftand controlled landings all would have been en-hanced via bilaterally asymmetric motions ofeither wing pair In other words incipient andnonequilibrium flight behaviors would poten-tially associate with a four-winged and long-tailed arrangement in theropods and early birds(Fig 6) There still remains disagreement as tothe definitional criteria used to indicate thefour-winged and long-tailed condition and as towhether large flight feathers with symmetrical

Columba

JeholornisSapeornis

Archaeopteryx

AnchiornisMicroraptor

Epidexipteryx

Fig 6 Airfoils of selectedmaniraptorans Airfoils (in blue) of the basal dromaeosaurMicroraptor the basal troodontidAnchiornis the basal birds Archaeopteryx Sapeornis and Jeholornis and a modern pigeon Feathered airfoils aregreater in number and are more distally positioned in early birds and their closest theropod relatives than inmodern birds The scansoriopterygid Epidexipteryx has stiff downlike feathers (in green) on both the forelimb andhindlimb and long ribbonlike feathers on the tail the aerodynamic functions of which remain poorly known

vanes in some basal paravians including earlybirds would create useful aerodynamic forcesduring aerial behaviors (117)Use of the hind wings and potentially the

tail to generate vertical force also results in amore posterior and stable position for the cen-ter of lift (10 144) (as can be deduced from batand pterosaur wings based on patagial connec-tions to the hindlegs) Such a hindwing config-uration contributes to static stability in glidingwhereas subsequent functional shifts to the fore-wings alone with associated reductions in tailsize and leg feathering (135) would have requiredoffsetting aerodynamic control via flapping mo-tions (145) Potential tradeoffs between increasedsize of the forewings and the intensity of theirkinematic activation (eg greater frequency andamplitude of flapping) are not well understoodalthough robotic models of early avialan mor-phologies can be informative (146) Such progres-sive anterior specialization of the flight apparatuswith enhanced forces produced by the emergingforelimb locomotor module (145) is nonethelessderived from an ancestrally four-winged plat-form (Fig 6)

Future perspectivesAlternative phylogenetic hypotheses suggest adifferent evolutionary sequence of major birdcharacteristics and imply a different ecologicalorigin of the group (22) Consequently a refinedmore robust phylogeny will be imperative tomove our studies forward Increasing characterand taxon sampling in recent theropod phylo-genetic studies has in theory helped improvethe accuracy of phylogenetic reconstructions butbetter character formulation and more accuratescorings are imperative at present pending bet-ter understanding of the morphologies of manyrecently discovered transitional formsIn terms of character evolution an integrative

approach combining paleontological neontolog-ical developmental geochronological and evenpaleoenvironmental data is particularly desir-able A recent integrative study combining de-velopmental neontological and paleontologicaldata shows that birds evolved their highly spe-cialized cranium mainly by paedomorphisis (147)another study using both neontological and pa-leontological data to reconstruct melanosomeevolution suggests that feathers have changedsignificantly in their melanosome morphologyamong pennaraptoran theropods which impliesa physiological shift before the evolution of flight(72) and that concurs in association with exten-sive postcranial skeletal pneumaticity whichsuggests the presence of birdlike endothermy(29) Similar approaches should be applied toother major structures Certain avialan structuressuch as feathers and visual system are novel inboth genetic and morphological terms There areemerging data on how the genetic code affects themorphogenesis of these structures in developmen-tal biology How the genetic code and expressionpattern evolved can be inferred by a detailedcomparison of homologous structures in thero-pods early birds and modern birds

The construction of molecular phylogenieswould enable a much better understanding ofthe genealogical relations among birds and theirtheropod relatives and the steps leading to theevolution of birds Although once the topic ofscience-fiction movies preserved organic remainshave purportedly been recovered from Tyranno-saurus and the hadrosaur Brachylophosaurus(148 149) and from even older fossils such asEarly Jurassic Lufengosaurus specimens (150)Greater examination along these lines in fossilsspanning the theropod-bird transition is a po-tentially fruitful avenue for future investigationThe increasing interest in the origins of birds

from developmental biology and other disciplineshas enriched our understanding of this impor-tant evolutionary event (8 10 11) and alternativeevolutionary models on various aspects of theorigin of birds have sometimes been providedbased on neontological data (4 11) Howeverany evolutionary model must be tested using thefossil record Consequently dense fossil samplingalong the line to birds and better understandingof the transitional forms play a key role in thediscussion on this issue

REFERENCES AND NOTES

1 A Feduccia The Origin and Evolution of Birds (Yale UnivPress New Haven CT ed 2 1999) pp 466

2 Z Zhou The origin and early evolution of birds Discoveriesdisputes and perspectives from fossil evidenceNaturwissenschaften 91 455ndash471 (2004) doi 101007s00114-004-0570-4 pmid 15365634

3 L M Witmer in Mesozoic Birds Above the Heads ofDinosaurs L M Chiappe L M Witmer Eds (Univ ofCalifornia Press Berkeley 2002) pp 3ndash30

4 R O Prum Development and evolutionary origin of feathersJ Exp Zool 285 291ndash306 (1999) doi 101002(SICI)1097-010X(19991215)2854lt291AID-JEZ1gt30CO2-9pmid 10578107

5 M Yu P Wu R B Widelitz C-M Chuong Themorphogenesis of feathers Nature 420 308ndash312 (2002)doi 101038nature01196 pmid 12442169

6 A O Vargas T Kohlsdorf J F Fallon J VandenbrooksG P Wagner The evolution of HoxD-11 expression in thebird wing Insights from Alligator mississippiensis PLOS ONE3 e3325 (2008) doi 101371journalpone0003325pmid 18833328

7 C G Farmer K Sanders Unidirectional airflow in the lungsof alligators Science 327 338ndash340 (2010) doi 101126science1180219 pmid 20075253

8 K Tamura N Nomura R Seki S Yonei-TamuraH Yokoyama Embryological evidence identifies wing digitsin birds as digits 1 2 and 3 Science 331 753ndash757 (2011)doi 101126science1198229 pmid 21311019

9 C L Organ A M Shedlock A Meade M PagelS V Edwards Origin of avian genome size and structurein non-avian dinosaurs Nature 446 180ndash184 (2007)doi 101038nature05621 pmid 17344851

10 D Evangelista et al Aerodynamic characteristics of afeathered dinosaur measured using physical modelsEffects of form on static stability and control effectivenessPLOS ONE 9 e85203 (2014) doi 101371journalpone0085203 pmid 24454820

11 K P Dial Wing-assisted incline running and the evolutionof flight Science 299 402ndash404 (2003) doi 101126science1078237 pmid 12532020

12 F C James J A Pourtless IV Cladistics and the origin ofbirds A review and two new analyses Ornithol Monogr66 1ndash78 (2009) doi 101525om20096611

13 M Norell X Xu Feathered dinosaurs Annu Rev EarthPlanet Sci 33 277ndash299 (2005) doi 101146annurevearth33092203122511

14 J Gauthier Saurischian monophyly and the origin of birdsMem Calif Acad Sci 8 1ndash55 (1986)

15 P C Sereno The evolution of dinosaurs Science 2842137ndash2147 (1999) doi 101126science28454232137pmid 10381873

16 A H Turner P J Makovicky M A Norell A review ofdromaeosaurid systematics and paravian phylogeny Bull AmMus Nat Hist 371 1ndash206 (2012) doi 1012067481

17 P Senter J I Kirkland D D DeBlieux S Madsen N TothNew dromaeosaurids (Dinosauria Theropoda) from theLower Cretaceous of Utah and the evolution of thedromaeosaurid tail PLOS ONE 7 e36790 (2012)doi 101371journalpone0036790 pmid 22615813

18 T R Holtz Jr A new phylogeny of the carnivorous dinosaursGaia 15 5ndash61 (1998)

19 O W M Rauhut The interrelationships and evolution ofbasal theropod dinosaurs Spec Pap Paleontology 69 1ndash213(2003)

20 M A Norell J M Clark P J Makovicky in New Perspectives onthe Origin and Evolution of Birds J Gauthier L F Gall Eds(Yale Univ Press New Haven CT 2001) pp 49ndash67

21 P Godefroit et al A Jurassic avialan dinosaur from Chinaresolves the early phylogenetic history of birds Nature 498359ndash362 (2013) doi 101038nature12168 pmid 23719374

22 X Xu H You K Du F Han An Archaeopteryx-like theropodfrom China and the origin of Avialae Nature 475 465ndash470(2011) doi 101038nature10288 pmid 21796204

23 J N Choiniere et al A basal alvarezsauroid theropod fromthe early Late Jurassic of Xinjiang China Science 327571ndash574 (2010) doi 101126science1182143pmid 20110503

24 J H Ostrom The osteology of Deinonychus antirrhopus anunusual theropod from the Lower Cretaceous of MontanaBull Peabody Mus Nat Hist 30 1ndash165 (1969)

25 R Barsbold Predatory dinosaurs from the Cretaceousof Mongolia Tr Sovm Sov-Mong Paleontol Eksped 191ndash117 (1983)

26 O Wings thesis The University of Bonn (2004)27 P M OrsquoConnor L P A M Claessens Basic avian pulmonary

design and flow-through ventilation in non-avian theropoddinosaurs Nature 436 253ndash256 (2005) doi 101038nature03716 pmid 16015329

28 P C Sereno et al Evidence for avian intrathoracic air sacsin a new predatory dinosaur from Argentina PLOS ONE3 e3303 (2008) doi 101371journalpone0003303pmid 18825273

29 R B J Benson R J Butler M T Carrano P M OrsquoConnorAir-filled postcranial bones in theropod dinosaursPhysiological implications and the lsquoreptilersquo-bird transitionBiol Rev Camb Philos Soc 87 168ndash193 (2012) doi 101111j1469-185X201100190x pmid 21733078

30 M A Norell J M Clark L M Chiappe D DashzevegA nesting dinosaur Nature 378 774ndash776 (1995)doi 101038378774a0

31 D J Varricchio F Jackson J J Borkowski J R HornerNest and egg clutches of the dinosaur Troodon formosusand the evolution of avian reproductive traits Nature 385247ndash250 (1997) doi 101038385247a0

32 G M Erickson K Curry Rogers D J Varricchio M A NorellX Xu Growth patterns in brooding dinosaurs reveals thetiming of sexual maturity in non-avian dinosaurs and genesisof the avian condition Biol Lett 3 558ndash561 (2007)pmid 17638674

33 G Grellet-Tinner P Makovicky A possible egg of thedromaeosaur Deinonychus antirrhopus Phylogenetic andbiological implications Can J Earth Sci 43 705ndash719 (2006)doi 101139e06-033

34 G Grellet-Tinner L M Chiappe in Feathered DragonsStudies on the Transition from Dinosaurs to Birds P J CurrieE B Koppelhus M A Shugar J L Wright Eds (IndianaUniv Press Bloomington 2004) pp 185ndash214

35 D J Varricchio F D Jackson A phylogenetic assessment ofprismatic dinosaur eggs from the Cretaceous Two MedicineFormation of Montana J Vertebr Paleontol 24 931ndash937 (2004)doi 1016710272-4634(2004)024[0931APAOPD]20CO2

36 D K Zelenitsky F Therrien Phylogenetic analysis ofreproductive traits of maniraptoran theropods and itsimplications for egg parataxonomy Paleontology 51 807ndash816(2008) doi 101111j1475-4983200800770x

37 K Padian A J de Ricqlegraves J R Horner Dinosaurian growthrates and bird origins Nature 412 405ndash408 (2001)doi 10103835086500 pmid 11473307

38 F L Agnoliacuten F E Novas Avian Ancestors A Review of thePhylogenetic Relationships of the Theropods UnenlagiidaeMicroraptoria Anchiornis and Scansoriopterygidae (SpringerDordrecht Heidelberg 2013)

39 P J Makovicky L E Zanno in Living Dinosaurs TheEvolutionary History of Modern Birds G J Dyke G KaiserEds (Wiley-Blackwell Oxford 2011) pp 9ndash29

The eggshell and eggs of oviraptorosaurs anddromaeosaurs where known are two-layeredmoderately porous and only weakly asymmetric(33 34 36 73) although the ornamented eggsof alvarezsaurs have a three-layered eggshell

(82) In contrast troodontids exhibit a morestrongly asymmetric egg lacking ornamenta-tion with potentially three structural shell lay-ers and low porosity (Fig 3A) and they arestructured more like modern bird eggs than

like those of other dinosaurs (83 84) In addi-tion the tighter clutch configuration greaterexposure of eggs (Fig 3B) and avialan levels ofporosity favor contact incubation in troodontids(85 86)

Fig 2 Selected species on a temporally calibrated archosauromorphanphylogeny showing the evolution of major characteristics along the bird-line The phylogeny is a combination of two recently published analyses Thebasal part of the tree is derived from (55) and the upper part from (16) Skeletalsilhouettes of several archosauromorphans show the general morpholog-ical features along the bird-line within this group and they are the basalarchosauromorphan Euparkeria the basal crocodilomorph Sphenosuchusthe basal theropod Coelophysis the basal coelurosaur Protoceratosaurusthe basal paravian Anchiornis the basal avialan Archaeopteryx the basalpygostylian Sapeornis the basal ornithuromorphan Yanornis and the crowngroup bird Columba (bottom to top) Acronyms in the figure ACVP advancedcostosternal ventilator pump AET arm elongation and thickening AFC armflapping capability AL aerial locomotion AOO active ovary and oviduct BL

bipedal locomotion BMR basal metabolic rate CASPE cervical air sacs pos-terior extension CCIASE cranial and caudal intrathoracic air ascs elaborationCE cerebral expansion ECFSC egg clutch free of sediment cover EM extrememiniaturization ER egg rotation ES egg size FF filamentous feathers FPBfusion of pelvic bones GR growth rate IA increased asymmetry ICI improvedcontact incubation IL iterative laying KBL knee-based locomotion KS kineticskull LFC laterally folding capability LP low porosity MO monoautochronicovulation PC paternal care PPO pubis posterior orientation PSP plowshare-shaped pygostyle RLP rodlike pygostyle RMILTAY rapid maturity in less thana year SAE slightly asymmetrical egg SBT short bony tail SP skeletalpneumatization TFH three-fingered hand TL third (external) layer UB uni-directional breathing US unornamented surface VABRE visually associatedbrain regions elaboration VF vaned feathers

Despite these similarities with modern birdsoviraptorosaurs troodontids and even Cretaceousenantiornithine birds differ reproductively frommodern birds in a few key features includingmore elongate egg shape and eggs largely buriedwith sediment during incubation (73 74 87 88)Relative egg size increases markedly from the-ropods to basal birds of the Mesozoic with thelatter laying eggs 50 to 70 the expected size ofthose in extant birds (74) Several specimens ofbasal birds preserve a single mass of circularobjects Although their interpretation remainsdebated (89) these may represent ovaries withmature ovarian follicles and suggest that basalbirds had only one active ovary and oviduct as inmost modern birds (90) Modern birds differ fromenantiornithines in producing relatively largereggs that are incubated in the absence of sedi-ment (74) These features highlight the gradualacquisition of ldquomodernrdquo reproductive traits fromMesozoic theropods throughMesozoic birds suchas enantiornithines and on to modern birds

Reproductive adaptations may have implica-tions for three other aspects of bird evolutionthe development of feathers metabolism andflight First elongate forelimb and tail feathersin oviraptorosaurs parallel the brooding pos-tures adopted by adults and lengthening of thefeathers may reflect selection for egg care (91)Reproduction in maniraptoran dinosaurs mayalso imply physiological similarities with birdsEgg pairs suggest a reproductive output similarto that of basal birds (74) Additionally iterativelaying together with the complex clutch config-urations and presumed synchronous hatching(83) in these theropods further implies thatboth adult body and incubation temperatureswere elevated over ambient conditions (92)Finally ground nesting the basal condition inmodern birds has been used to argue for aldquoground-uprdquo origin of flight (11) However otherfactors may have initially constrained groundnesting Through the theropod-bird transitioneggs were incubated within sediments which

suggests that they may have lacked chalazae(31 74) [chords of albumen present in birds thatallow the embryo to maintain an upright positionduring egg rotation (93)] Thus without chalazaearboreal maniraptoran dinosaurs may have beenrequired to incubate eggs within sediments inorder to prevent detrimental egg rotation (31)as occurs in modern crocodilians (94)The development growth and physiology of

theropods and basal birds have been exploredusing a variety of approaches Birds are notableamong living vertebrates in being endothermsdeveloping explosively to adult sizes in less thana year (very large forms such as ostriches areexceptions) and having exceptionally high basalmetabolic rates (95) However some osteo-histological studies show that the bone histol-ogy of enantiornithine birds is nearly avascularcomposed of slowly deposited parallel-fiberedmatrix and having growth lines (96) which areunlike the bones of most dinosaurs (ie withfast-growing and highly vascularized fibro-lamellarbone with growth lines) and these studies sug-gest that basal birds had slowed their growthcompared with their dinosaur ancestors Further-more because maximal growth rates strongly cor-relate with metabolic rates (95) they likely hadlower basal metabolic rates than dinosaursConstruction of mass-age growth curves showed

that nonavialan dinosaurs as a whole althoughprobably endothermic did not have a physiol-ogy exactly like modern birds (97) They grewfaster than living reptiles but somewhat slowerthan most precocial birds and considerably slowerthan altricial forms scaled to the same size His-tologic analysis shows that several derived the-ropods Archaeopteryx and other basal birdsinherited this dinosaurian physiology and tookover a year to reach somatic maturity (98) (Fig 3C and D) The last conclusion has been sup-ported by further growth line evidence in otherbasal birds (99) The miniaturization event onceassociated with the cladogenesis of birds actuallyoccurred in paravian theropods (50 51 98) andconsequently the nearly avascular bone in somebasal lineages of birds and small theropods issimply a scaling effect Modern bone types andpresumably the remarkable elevated metabolicrates of birdsmdashwhich allow growth to adult sizesin less than a yearmdashappear to have evolved nearthe cladogenesis of ornithurine birds during theCretaceous Period (37 98 100) although in-creased growth and metabolic rates occurredearly in theropod evolution (Fig 2) [Note Thepioneering studies that established dinosaurgrowth rates were recently criticized for insuf-ficient sample size and other issues (101) How-ever a subsequent comprehensive specimen-richanalysis (102) strongly supports both the method-ology and conclusions about dinosaur and basalbird growth rates and physiology]

Complex evolution of avialan traitsBird morphology features many unique adapta-tions and the evolution of some of these traitsis so complex that a comprehensive understand-ing is wanting How the theropod hand evolved

Body mass (kg)

AM

P

R

Rate = 1977 (mass)0733

R2 = 0975

100000

100000

10000

1000

100

10

1

0101 1 10 100 1000 10000

Max

imum

gro

wth

rat

e (g

day

)

A B

C D

Fig 3 Maniraptoran reproduction and growth (A) Eggshell of Troodon in radial thin section showingthree microstructural layers (separated by white bars) as common to many extant birds Scale bar05 mm (B) Troodon nesting trace with clutch of 24 eggs preserved under white plaster jacket Topsof the eggs were exposed within the nest structure and were incubating by an attending adult rep-resenting a transitional stage between the fully buried clutches of most nonavialan dinosaurs and thesediment-free clutches typical of modern birds Tape measure equals 1 m (C) Histological section ofan Archaeopteryx femur The section shown in polarized light microscopy shows the characteristiclong bone histology of basal-most birds composed of parallel fibered bone matrix with negligiblevascularization Growth lines are also commonplace but are not evident in this particular specimen(Munich Archaeopteryx Bayerische Staatssammlung fuumlr Palaontologie und Geologie BSPG 199950)The histology matches that of same-sized nonavialan dinosaurs but not that of modern birds (D)Maximal growth rates for Archaeopteryx compared with nonavialan dinosaurs and living vertebratesArchaeopteryx growth rates (skeleton) fall on the line at the lowermost bound of the nonavialan dinosaurregression line (blue individual species values are shown as black diamonds) R typical extant reptiliangrowth rates P typical extant precocial land bird growth rates M typical extant marsupial growth ratesA typical extant altricial land bird growth rates Graphic is from (98)

into the bird wing continues to be a hotly de-bated issue in evolutionary biology Tradition-ally paleontological analysis of theropod digitreductions indicated that the three-digit handarose by unilateral loss of digits IV and V re-sulting in a I II III digit formula (103) In con-trast the use of ldquopositionalrdquo criteria of embryologicprecursors to identify digits in modern birdsrevealed a digit 2 3 4 formula (104 105) To re-solve this paradox it has been proposed that ahomeotic transformation of digits occurred thatconverted the embryonic precursors to I II andIII in the adult (frameshift hypothesis) (103) Con-founding any reconciliation of evidence fromthese disciplines paleontological analyses typicallyrely on adult morphology to infer evolutionarylinks whereas developmental studies generallyfocus on very transient vestigial embryonic rem-nants to infer homologies with adult structuresthat have been lost entirely during evolution Incontrast to cellular fate determination morpho-logical identity of a complex structure is generallynot defined by any specific and unique geneticldquomarkersrdquo which creates difficulty in assigningunique homologiesNevertheless the analysis of expression of

spatially regulated genes in the embryonic limbwhich can be considered ldquophenotypicrdquo criteriafor digit assignment has provided support forthe frameshift hypothesis in that certain geneexpression patterns normally correlated withdigit I are retained in the first digit of the chickembryo hand In addition recent more com-prehensive genome-wide expression profilingcomparing chick embryo hand and foot digitprecursors also supports a I II III phenotypicformula in that the expression profiles of thefirst digit in both the hand and foot are re-markably similar (106) Genetic lineage trac-ing of Shh-expressing cells in the chick whichnormally contribute to digits IV and V in thepentadactyl mouse further suggests that digitIV is phenotypically absent from the chickhand (8 107) All of the phenotypic data fromchick embryos are likewise compatible with theclassic paleontological interpretation of a digitI-II-III formula if the avialan embryo ldquoposi-tionalrdquo evidence of digit precursors is discountedas being either misleading or incorrect Howeverthis requires a shift in the primary limb axisto run through digit 3 (axis shift hypothesis)both in extinct and modern tetanuran theropods(108) rather than through digit 4 as occurs inmost tetrapods except urodeles (109) becausethe primary limb axis must by definition in-clude the first digit to form in the embryo Infact a shortcoming of the positional data onvestigial digit condensations appearing in theembryonic hands of various avialan species isthat although a remnant of a positional fourthcondensation (which could be either IV or V)is clearly posterior (lateral) to the three digitsthat are retained in the adult the identificationof a vestigial anterior (medial) condensation iscontroversial and it is based on indistinctelements that could represent other structures[see review in (110)] A reevaluation of digit

condensation formation in mouse embryosalso suggests that some of the traditional ap-proaches used to visualize early digit condensa-tions may be inadequate and could miss evidencefor noncontiguous digit loss (gaps between con-densations) In mouse genetic modulation of sig-nals critical for regulating digit pattern andnumber across vertebrate species results in theinitial loss of a central rather than lateral digit(111 112) This suggests that in principle a I-II-IV formula is also possible (central loss hy-pothesis) The I-II-IV formula would explainthe persistence of digit 1 and still retain theprimary axis extending through digit 4 which isthe accepted rule in all living tetrapods excepturodeles Note that the expression profiling datain chick (106) also revealed mixed expressionfeatures for the lateral digits which could beconstrued as compatible with a I-IIIII-IV avialanhand formula (or the presence of digit IV) Takentogether these developmental studies now leave

open the possibility of I-II-III or even I-II-IV orI-III-IV formulas for the modern avialan handConversely more recent analyses of digit mor-phologies in ceratosaurian and basal tetanurantheropods (52) lend some support to a II III IVtheropod formula with secondary transformationsto produce final I II III morphologies throughmultiple partial homeotic transformations (lat-eral shift hypothesis)To reconcile the paradox of digit homolo-

gies between theropods and birds all of theproposed models (Fig 4A) require either mul-tiple events entailing the reduction and thenreappearance of a positional digit 4 to retainthe primary limb axis or require that the pri-mary axis has undergone a novel shift in itsposition from digit 4 to 3 Clearly whereas muchprogress has been made a final resolution tothis ongoing debate demands additional workfrom both paleontological and developmentalperspectives (110)

Five-fingeredtheropods

Four-fingeredtheropods

Three-fingeredtheropods

Frame-shift

Lateral-shift

Axis-shift

Central-loss

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIII

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIIIV

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIII

12345

IIIIIIIVV

12345

III

IVV

12345

III

IV

1 m

A

B

Fig 4 The evolution of theropod hand and respiratory system (A) Diagrams depicting four hypothesesfor the evolution of wing digits Color shading bordered by solid line refers to fully formed digits and bydash line to reduced digits Colored bars refer to different ldquomorphologicrdquo digits Arabic numerals refer topositional embryonic digit precursors A combination of different colors refers to a mixture of differentmorphological features pertaining to different phenotypes in one digit (B) Reconstruction of pulmonarycomponents [cervical air-sac system (green) lung (orange) and abdominal air-sac system (blue)] in thetheropod Majungatholus Graphic from (27)

A highly efficient flow-through ventilation anda high-compliance air-sac system uniquely char-acterize the avialan respiratory system (27) Per-ceived differences in the respiratory systems oftheropods and other reptiles such as crocodi-lians from those of birds have been invalidlyused as evidence against the BMT hypothesis(49) Nevertheless cervical and anterior dorsalvertebrae are clearly pneumatic in nearly alltheropods (29) and documentation of exten-sive skeletal pneumaticity in theropods such asMajungasaurus and Aerosteon (27 28) dem-onstrates that a complex air-sac system andbirdlike respiration evolved in birdsrsquo theropodancestors (Fig 4B) Furthermore recent ana-tomical and physiological studies reveal thatalligators (7 113) and even monitor lizards (114)exhibit respiratory systems and unidirectionalbreathing akin to those of birds These studiesdemonstrate that unidirectional breathing is aprimitive characteristic of archosaurs or an evenmore inclusive group with the complex air-sacsystem evolving later within Archosauria Weightsavings might have driven the evolution of post-cranial skeletal pneumatization in early theropods

(29) and in addition to large-bodied theropodssmall maniraptoran theropods such as basaloviraptorosaurs dromaeosaurs and troodontidsevolved the complex air-sac system similar tothat of birds (28 29)

Morphogenesis and early evolution of feathersFeathers were once considered to be uniqueavialan structures The presence of feathers isinferred in several theropods based on osteo-logical correlates eg quill knobs (115 116) [al-though the presence of quill knobs in the basaltetanuran Concavenator has been questioned(117)] or pygostyles (118) Short filaments havebeen identified as feathers in the alvarezsaurShuvuuia (119) Direct evidence came to lightin China in 1996 with the discovery of the fea-thered Sinosauropteryx (120) Since then nu-merous specimens of most theropod groups andeven three ornithischian groups preserving fea-thers have been recovered from the Jurassicand Cretaceous beds of northeastern China(13 21 41 45 57) and from the Jurassic andCretaceous beds of Germany Russia and Canada

(55 56 121ndash123) These feathers fall into severalmajor morphotypes (Fig 5) ranging from mono-filamentous feathers to highly complex flightfeathers (57) The phylogenetic distribution ofthese feathers largely concurs with the predic-tions from a developmental model of living birds(4) although some of these morphotypes areabsent in living birds (57 124)The findings of feathers in dinosaurs prompted

developmental studies over the last decade in-vestigating the molecular mechanisms regulat-ing feather development and regeneration inchickens (125) We can now propose the follow-ing ldquomolecular circuitsrdquo regarding tissue morpho-genesis and the evolution of modern feathersEach molecular circuit has specific features andcan be modulated to produce a diversity ofmorphology(i) Cylindrical topology and the downshift of

stem cell ring The formation of loose mesen-chyme in the bud core allows a tube configura-tion with basal layer facing inside Driven byWnt signaling feather stem cells now are posi-tioned near the base forming a ring config-uration (126 127) It can remain as a tube or the

Fig 5 The morphogenesis and evolution of feathers in dinosaurs (A)Monofilamentous feathers in Tianyulong (B) Broad monofilamentous feathers inBeipiaosaurus Radially branched feathers in Sinosauropteryx (C) Sinornitho-saurus (D) and Anchiornis (E) Bilaterally branched feathers in Dilong (F)and Sinornithosaurus (G) (H) Wing flight feathers with symmetrical vanesin Anchiornis (I) Pedal flight feathers with asymmetrical vanes in Micro-raptor (J) Rachis-dominant tail feathers in Confuciusornis (K) Proximally

ribbonlike tail feathers in Similicaudipteryx (L) Phylogenetic distribution ofmajor feather morphotypes (monofilamentous radially branched bilater-ally branched symmetrical flight and asymmetrical flight feathers) amongdinosaurs (M) Major novel morphogenetic events and molecular pathwaysduring feather evolutionThese major feather morphotypes can be explained byselective usage of the five novel ldquomolecular circuitsrdquo discussed in the text Redarrows flank a feather

subsequent caspase-dependent selective apopto-sis can open up the tube allowing feather vaneformation (128)(ii) Hierarchical branching and barbbarbule

pattern formation Ratio of local activators (nog-gin Shh and so on) and inhibitors (bone mor-phogenetic proteins) regulate the number andsize of barb versus rachidial ridges (5 129) Barbridges which depend on Wnt 3a gradient canrun parallel to each other to form radial sym-metric feathers or angle toward the rachis toform bilateral symmetric feathers (130)(iii) Follicle formation and regenerative cycling

During development matrix maetalloproteinasendashdependent tissue invagination allows epithelia totopologically fold into a follicle (131) Follicle con-figuration allows protection of feather progenitorsStem cells and dermal papilla are now clusterednear the follicle base and can undergo dickkopfWntndashdependent cyclic regeneration (132)(iv) Temporal regulation of stem cells along

the proximal-distal axis During feather forma-tion the molecular microenvironment and mor-phology can change along the distal (formedearlier) and proximal (formed later) throughmodulation of fibroblast growth factorndashsproutactivity (133)(v) Organ metamorphosis and regional spe-

cific feather types Upon regeneration modulatedby the body macroenvironments different fea-ther morphotypes (downy contour and flightfeathers) can form on different body regions andin different physiological stages for optimal per-formance (134)The aforementioned morphogenetic proces-

ses can be assembled selectively in various or-ders and independently to produce basic-tondashmore complex feather morphotypes (Fig 5) Themonofilamentous feathers seen in ornithischians(54 56 57) and some theropods (55 57) two setsof morphologically different flight feathersduring ontogeny in the oviraptorosau-rian Similicaudipteryx (124) and theextensive leg feathering (particular-ly pedal feathering) in a number oftheropods and early birds (135) implya variety of rearrangements in themorphogenetic modules The wide oc-currence of pedal feathering in the-ropods and early birds (135) and anextensive distribution of scales onthe bodies of both feathered thero-pods (eg Juravenator) and featheredornithischians (eg the ceratopsianPsittacosaurus and the ornithopodKullindadromeus) remain particularlyinteresting from both developmentaland evolutionary perspectives (56 135)and will no doubt play into further dis-cussions on feather-scale relationshipsThe diverse forms of theropod fea-

thers apparently suggest a comparablemyriad of functions Initial functionsof feathers more likely include ther-moregulation and communication rath-er than flight (57) Several differentlines of data highlight the importance

of communication in early feather evolution(41 57 117 136) particularly by color patternsinferred via preserved melanosome morpho-logies in some theropods and early birds (136 137)although several studies have questioned theidentifications of melanosomes in specimensof feathered theropods and early birds (48 138)One study shows an increased diversity of melano-some morphologies associated with the appear-ance of complex pinnate feathers during theropodevolution (72) This finding supports developmentaldata showing that unique topological arrange-ments allowing feathers to generate complex formsalso permits the generation of visibly complexpigment patterns and pattern renewal duringsexual maturation (139)

Four-winged dinosaurs and the origins of aerial behaviorSeveral flight-related anatomical features suchas hollow bones and the furcula originated inearly theropods basal paravians had many hall-mark features necessary for flight includingextremely small body size (50 70) a laterallyoriented long and robust forelimb (22 67) anenlarged forebrain and other derived neurolog-ical adaptations (71) and large flight feathers(Figs 1 and 2) Particularly surprising are therecent discoveries of large flight feathers form-ing a planar surface on the legs of some basalparaviansmdashfor example those with asymmetricalvanes on both the tibia and metatarsus of somebasal dromaeosaurs such as Microraptor (59)large feathers with symmetrical vanes on both thetibia and metatarsus of the troodontid Anchiornis(45) the basal bird Sapeornis and several otherbasal paravians (135) and large vaned feath-ers on tibiae of several basal birds includingArchaeopteryx confuciusornithids and enan-tiornithines (135) These structures clearly wouldhave been relevant to flight origins The evolu-

tion of flight nonetheless remains highly de-bated with a few recently proposed scenariosincluding factors as diverse as muscle hyperpla-sia (140) and the use of wings to assist in cur-sorial ascent of inclines based on neontologicalobservations (11) Multifactorial explanations forthe origins of flight are likely as this behaviorhas not been uniquely categorized given varia-bility in wing and tail configurations amongtheropods and early birds (45 59 135 141 142)flight probably had complex biomechanicalorigins (142 143)Fundamental to all hypotheses of wing evo-

lution however must be consideration of thosecircumstances that elicited aerial behavior inancestrally terrestrial taxa In all extant verte-brate and invertebrate gliders flight is associ-ated with gravitational acceleration downwardfrom heights and with the use in aerodynamiccontrol of diverse body structures including butnot limited to limbs once aloft (143) The dis-coveries of four-winged theropods and earlybirds (Fig 6) are consistent with the gravity-assisted hypothesis for the origin of bird flightMoreover the concurrent presence of a largeand flattened tail along with potential use ofthe feathered hind legs in aerodynamic controlsuggests substantial capacity for using these asrudders and for maneuvering even during theearliest stages of bird evolution (10 144) Aerialrighting reflexes targeting movement while aloftand controlled landings all would have been en-hanced via bilaterally asymmetric motions ofeither wing pair In other words incipient andnonequilibrium flight behaviors would poten-tially associate with a four-winged and long-tailed arrangement in theropods and early birds(Fig 6) There still remains disagreement as tothe definitional criteria used to indicate thefour-winged and long-tailed condition and as towhether large flight feathers with symmetrical

Columba

JeholornisSapeornis

Archaeopteryx

AnchiornisMicroraptor

Epidexipteryx

Fig 6 Airfoils of selectedmaniraptorans Airfoils (in blue) of the basal dromaeosaurMicroraptor the basal troodontidAnchiornis the basal birds Archaeopteryx Sapeornis and Jeholornis and a modern pigeon Feathered airfoils aregreater in number and are more distally positioned in early birds and their closest theropod relatives than inmodern birds The scansoriopterygid Epidexipteryx has stiff downlike feathers (in green) on both the forelimb andhindlimb and long ribbonlike feathers on the tail the aerodynamic functions of which remain poorly known

vanes in some basal paravians including earlybirds would create useful aerodynamic forcesduring aerial behaviors (117)Use of the hind wings and potentially the

tail to generate vertical force also results in amore posterior and stable position for the cen-ter of lift (10 144) (as can be deduced from batand pterosaur wings based on patagial connec-tions to the hindlegs) Such a hindwing config-uration contributes to static stability in glidingwhereas subsequent functional shifts to the fore-wings alone with associated reductions in tailsize and leg feathering (135) would have requiredoffsetting aerodynamic control via flapping mo-tions (145) Potential tradeoffs between increasedsize of the forewings and the intensity of theirkinematic activation (eg greater frequency andamplitude of flapping) are not well understoodalthough robotic models of early avialan mor-phologies can be informative (146) Such progres-sive anterior specialization of the flight apparatuswith enhanced forces produced by the emergingforelimb locomotor module (145) is nonethelessderived from an ancestrally four-winged plat-form (Fig 6)

Future perspectivesAlternative phylogenetic hypotheses suggest adifferent evolutionary sequence of major birdcharacteristics and imply a different ecologicalorigin of the group (22) Consequently a refinedmore robust phylogeny will be imperative tomove our studies forward Increasing characterand taxon sampling in recent theropod phylo-genetic studies has in theory helped improvethe accuracy of phylogenetic reconstructions butbetter character formulation and more accuratescorings are imperative at present pending bet-ter understanding of the morphologies of manyrecently discovered transitional formsIn terms of character evolution an integrative

approach combining paleontological neontolog-ical developmental geochronological and evenpaleoenvironmental data is particularly desir-able A recent integrative study combining de-velopmental neontological and paleontologicaldata shows that birds evolved their highly spe-cialized cranium mainly by paedomorphisis (147)another study using both neontological and pa-leontological data to reconstruct melanosomeevolution suggests that feathers have changedsignificantly in their melanosome morphologyamong pennaraptoran theropods which impliesa physiological shift before the evolution of flight(72) and that concurs in association with exten-sive postcranial skeletal pneumaticity whichsuggests the presence of birdlike endothermy(29) Similar approaches should be applied toother major structures Certain avialan structuressuch as feathers and visual system are novel inboth genetic and morphological terms There areemerging data on how the genetic code affects themorphogenesis of these structures in developmen-tal biology How the genetic code and expressionpattern evolved can be inferred by a detailedcomparison of homologous structures in thero-pods early birds and modern birds

The construction of molecular phylogenieswould enable a much better understanding ofthe genealogical relations among birds and theirtheropod relatives and the steps leading to theevolution of birds Although once the topic ofscience-fiction movies preserved organic remainshave purportedly been recovered from Tyranno-saurus and the hadrosaur Brachylophosaurus(148 149) and from even older fossils such asEarly Jurassic Lufengosaurus specimens (150)Greater examination along these lines in fossilsspanning the theropod-bird transition is a po-tentially fruitful avenue for future investigationThe increasing interest in the origins of birds

from developmental biology and other disciplineshas enriched our understanding of this impor-tant evolutionary event (8 10 11) and alternativeevolutionary models on various aspects of theorigin of birds have sometimes been providedbased on neontological data (4 11) Howeverany evolutionary model must be tested using thefossil record Consequently dense fossil samplingalong the line to birds and better understandingof the transitional forms play a key role in thediscussion on this issue

REFERENCES AND NOTES

1 A Feduccia The Origin and Evolution of Birds (Yale UnivPress New Haven CT ed 2 1999) pp 466

2 Z Zhou The origin and early evolution of birds Discoveriesdisputes and perspectives from fossil evidenceNaturwissenschaften 91 455ndash471 (2004) doi 101007s00114-004-0570-4 pmid 15365634

3 L M Witmer in Mesozoic Birds Above the Heads ofDinosaurs L M Chiappe L M Witmer Eds (Univ ofCalifornia Press Berkeley 2002) pp 3ndash30

4 R O Prum Development and evolutionary origin of feathersJ Exp Zool 285 291ndash306 (1999) doi 101002(SICI)1097-010X(19991215)2854lt291AID-JEZ1gt30CO2-9pmid 10578107

5 M Yu P Wu R B Widelitz C-M Chuong Themorphogenesis of feathers Nature 420 308ndash312 (2002)doi 101038nature01196 pmid 12442169

6 A O Vargas T Kohlsdorf J F Fallon J VandenbrooksG P Wagner The evolution of HoxD-11 expression in thebird wing Insights from Alligator mississippiensis PLOS ONE3 e3325 (2008) doi 101371journalpone0003325pmid 18833328

7 C G Farmer K Sanders Unidirectional airflow in the lungsof alligators Science 327 338ndash340 (2010) doi 101126science1180219 pmid 20075253

8 K Tamura N Nomura R Seki S Yonei-TamuraH Yokoyama Embryological evidence identifies wing digitsin birds as digits 1 2 and 3 Science 331 753ndash757 (2011)doi 101126science1198229 pmid 21311019

9 C L Organ A M Shedlock A Meade M PagelS V Edwards Origin of avian genome size and structurein non-avian dinosaurs Nature 446 180ndash184 (2007)doi 101038nature05621 pmid 17344851

10 D Evangelista et al Aerodynamic characteristics of afeathered dinosaur measured using physical modelsEffects of form on static stability and control effectivenessPLOS ONE 9 e85203 (2014) doi 101371journalpone0085203 pmid 24454820

11 K P Dial Wing-assisted incline running and the evolutionof flight Science 299 402ndash404 (2003) doi 101126science1078237 pmid 12532020

12 F C James J A Pourtless IV Cladistics and the origin ofbirds A review and two new analyses Ornithol Monogr66 1ndash78 (2009) doi 101525om20096611

13 M Norell X Xu Feathered dinosaurs Annu Rev EarthPlanet Sci 33 277ndash299 (2005) doi 101146annurevearth33092203122511

14 J Gauthier Saurischian monophyly and the origin of birdsMem Calif Acad Sci 8 1ndash55 (1986)

15 P C Sereno The evolution of dinosaurs Science 2842137ndash2147 (1999) doi 101126science28454232137pmid 10381873

16 A H Turner P J Makovicky M A Norell A review ofdromaeosaurid systematics and paravian phylogeny Bull AmMus Nat Hist 371 1ndash206 (2012) doi 1012067481

17 P Senter J I Kirkland D D DeBlieux S Madsen N TothNew dromaeosaurids (Dinosauria Theropoda) from theLower Cretaceous of Utah and the evolution of thedromaeosaurid tail PLOS ONE 7 e36790 (2012)doi 101371journalpone0036790 pmid 22615813

18 T R Holtz Jr A new phylogeny of the carnivorous dinosaursGaia 15 5ndash61 (1998)

19 O W M Rauhut The interrelationships and evolution ofbasal theropod dinosaurs Spec Pap Paleontology 69 1ndash213(2003)

20 M A Norell J M Clark P J Makovicky in New Perspectives onthe Origin and Evolution of Birds J Gauthier L F Gall Eds(Yale Univ Press New Haven CT 2001) pp 49ndash67

21 P Godefroit et al A Jurassic avialan dinosaur from Chinaresolves the early phylogenetic history of birds Nature 498359ndash362 (2013) doi 101038nature12168 pmid 23719374

22 X Xu H You K Du F Han An Archaeopteryx-like theropodfrom China and the origin of Avialae Nature 475 465ndash470(2011) doi 101038nature10288 pmid 21796204

23 J N Choiniere et al A basal alvarezsauroid theropod fromthe early Late Jurassic of Xinjiang China Science 327571ndash574 (2010) doi 101126science1182143pmid 20110503

24 J H Ostrom The osteology of Deinonychus antirrhopus anunusual theropod from the Lower Cretaceous of MontanaBull Peabody Mus Nat Hist 30 1ndash165 (1969)

25 R Barsbold Predatory dinosaurs from the Cretaceousof Mongolia Tr Sovm Sov-Mong Paleontol Eksped 191ndash117 (1983)

26 O Wings thesis The University of Bonn (2004)27 P M OrsquoConnor L P A M Claessens Basic avian pulmonary

design and flow-through ventilation in non-avian theropoddinosaurs Nature 436 253ndash256 (2005) doi 101038nature03716 pmid 16015329

28 P C Sereno et al Evidence for avian intrathoracic air sacsin a new predatory dinosaur from Argentina PLOS ONE3 e3303 (2008) doi 101371journalpone0003303pmid 18825273

29 R B J Benson R J Butler M T Carrano P M OrsquoConnorAir-filled postcranial bones in theropod dinosaursPhysiological implications and the lsquoreptilersquo-bird transitionBiol Rev Camb Philos Soc 87 168ndash193 (2012) doi 101111j1469-185X201100190x pmid 21733078

30 M A Norell J M Clark L M Chiappe D DashzevegA nesting dinosaur Nature 378 774ndash776 (1995)doi 101038378774a0

31 D J Varricchio F Jackson J J Borkowski J R HornerNest and egg clutches of the dinosaur Troodon formosusand the evolution of avian reproductive traits Nature 385247ndash250 (1997) doi 101038385247a0

32 G M Erickson K Curry Rogers D J Varricchio M A NorellX Xu Growth patterns in brooding dinosaurs reveals thetiming of sexual maturity in non-avian dinosaurs and genesisof the avian condition Biol Lett 3 558ndash561 (2007)pmid 17638674

33 G Grellet-Tinner P Makovicky A possible egg of thedromaeosaur Deinonychus antirrhopus Phylogenetic andbiological implications Can J Earth Sci 43 705ndash719 (2006)doi 101139e06-033

34 G Grellet-Tinner L M Chiappe in Feathered DragonsStudies on the Transition from Dinosaurs to Birds P J CurrieE B Koppelhus M A Shugar J L Wright Eds (IndianaUniv Press Bloomington 2004) pp 185ndash214

35 D J Varricchio F D Jackson A phylogenetic assessment ofprismatic dinosaur eggs from the Cretaceous Two MedicineFormation of Montana J Vertebr Paleontol 24 931ndash937 (2004)doi 1016710272-4634(2004)024[0931APAOPD]20CO2

36 D K Zelenitsky F Therrien Phylogenetic analysis ofreproductive traits of maniraptoran theropods and itsimplications for egg parataxonomy Paleontology 51 807ndash816(2008) doi 101111j1475-4983200800770x

37 K Padian A J de Ricqlegraves J R Horner Dinosaurian growthrates and bird origins Nature 412 405ndash408 (2001)doi 10103835086500 pmid 11473307

38 F L Agnoliacuten F E Novas Avian Ancestors A Review of thePhylogenetic Relationships of the Theropods UnenlagiidaeMicroraptoria Anchiornis and Scansoriopterygidae (SpringerDordrecht Heidelberg 2013)

39 P J Makovicky L E Zanno in Living Dinosaurs TheEvolutionary History of Modern Birds G J Dyke G KaiserEds (Wiley-Blackwell Oxford 2011) pp 9ndash29

Despite these similarities with modern birdsoviraptorosaurs troodontids and even Cretaceousenantiornithine birds differ reproductively frommodern birds in a few key features includingmore elongate egg shape and eggs largely buriedwith sediment during incubation (73 74 87 88)Relative egg size increases markedly from the-ropods to basal birds of the Mesozoic with thelatter laying eggs 50 to 70 the expected size ofthose in extant birds (74) Several specimens ofbasal birds preserve a single mass of circularobjects Although their interpretation remainsdebated (89) these may represent ovaries withmature ovarian follicles and suggest that basalbirds had only one active ovary and oviduct as inmost modern birds (90) Modern birds differ fromenantiornithines in producing relatively largereggs that are incubated in the absence of sedi-ment (74) These features highlight the gradualacquisition of ldquomodernrdquo reproductive traits fromMesozoic theropods throughMesozoic birds suchas enantiornithines and on to modern birds

Reproductive adaptations may have implica-tions for three other aspects of bird evolutionthe development of feathers metabolism andflight First elongate forelimb and tail feathersin oviraptorosaurs parallel the brooding pos-tures adopted by adults and lengthening of thefeathers may reflect selection for egg care (91)Reproduction in maniraptoran dinosaurs mayalso imply physiological similarities with birdsEgg pairs suggest a reproductive output similarto that of basal birds (74) Additionally iterativelaying together with the complex clutch config-urations and presumed synchronous hatching(83) in these theropods further implies thatboth adult body and incubation temperatureswere elevated over ambient conditions (92)Finally ground nesting the basal condition inmodern birds has been used to argue for aldquoground-uprdquo origin of flight (11) However otherfactors may have initially constrained groundnesting Through the theropod-bird transitioneggs were incubated within sediments which

suggests that they may have lacked chalazae(31 74) [chords of albumen present in birds thatallow the embryo to maintain an upright positionduring egg rotation (93)] Thus without chalazaearboreal maniraptoran dinosaurs may have beenrequired to incubate eggs within sediments inorder to prevent detrimental egg rotation (31)as occurs in modern crocodilians (94)The development growth and physiology of

theropods and basal birds have been exploredusing a variety of approaches Birds are notableamong living vertebrates in being endothermsdeveloping explosively to adult sizes in less thana year (very large forms such as ostriches areexceptions) and having exceptionally high basalmetabolic rates (95) However some osteo-histological studies show that the bone histol-ogy of enantiornithine birds is nearly avascularcomposed of slowly deposited parallel-fiberedmatrix and having growth lines (96) which areunlike the bones of most dinosaurs (ie withfast-growing and highly vascularized fibro-lamellarbone with growth lines) and these studies sug-gest that basal birds had slowed their growthcompared with their dinosaur ancestors Further-more because maximal growth rates strongly cor-relate with metabolic rates (95) they likely hadlower basal metabolic rates than dinosaursConstruction of mass-age growth curves showed

that nonavialan dinosaurs as a whole althoughprobably endothermic did not have a physiol-ogy exactly like modern birds (97) They grewfaster than living reptiles but somewhat slowerthan most precocial birds and considerably slowerthan altricial forms scaled to the same size His-tologic analysis shows that several derived the-ropods Archaeopteryx and other basal birdsinherited this dinosaurian physiology and tookover a year to reach somatic maturity (98) (Fig 3C and D) The last conclusion has been sup-ported by further growth line evidence in otherbasal birds (99) The miniaturization event onceassociated with the cladogenesis of birds actuallyoccurred in paravian theropods (50 51 98) andconsequently the nearly avascular bone in somebasal lineages of birds and small theropods issimply a scaling effect Modern bone types andpresumably the remarkable elevated metabolicrates of birdsmdashwhich allow growth to adult sizesin less than a yearmdashappear to have evolved nearthe cladogenesis of ornithurine birds during theCretaceous Period (37 98 100) although in-creased growth and metabolic rates occurredearly in theropod evolution (Fig 2) [Note Thepioneering studies that established dinosaurgrowth rates were recently criticized for insuf-ficient sample size and other issues (101) How-ever a subsequent comprehensive specimen-richanalysis (102) strongly supports both the method-ology and conclusions about dinosaur and basalbird growth rates and physiology]

Complex evolution of avialan traitsBird morphology features many unique adapta-tions and the evolution of some of these traitsis so complex that a comprehensive understand-ing is wanting How the theropod hand evolved

Body mass (kg)

AM

P

R

Rate = 1977 (mass)0733

R2 = 0975

100000

100000

10000

1000

100

10

1

0101 1 10 100 1000 10000

Max

imum

gro

wth

rat

e (g

day

)

A B

C D

Fig 3 Maniraptoran reproduction and growth (A) Eggshell of Troodon in radial thin section showingthree microstructural layers (separated by white bars) as common to many extant birds Scale bar05 mm (B) Troodon nesting trace with clutch of 24 eggs preserved under white plaster jacket Topsof the eggs were exposed within the nest structure and were incubating by an attending adult rep-resenting a transitional stage between the fully buried clutches of most nonavialan dinosaurs and thesediment-free clutches typical of modern birds Tape measure equals 1 m (C) Histological section ofan Archaeopteryx femur The section shown in polarized light microscopy shows the characteristiclong bone histology of basal-most birds composed of parallel fibered bone matrix with negligiblevascularization Growth lines are also commonplace but are not evident in this particular specimen(Munich Archaeopteryx Bayerische Staatssammlung fuumlr Palaontologie und Geologie BSPG 199950)The histology matches that of same-sized nonavialan dinosaurs but not that of modern birds (D)Maximal growth rates for Archaeopteryx compared with nonavialan dinosaurs and living vertebratesArchaeopteryx growth rates (skeleton) fall on the line at the lowermost bound of the nonavialan dinosaurregression line (blue individual species values are shown as black diamonds) R typical extant reptiliangrowth rates P typical extant precocial land bird growth rates M typical extant marsupial growth ratesA typical extant altricial land bird growth rates Graphic is from (98)

into the bird wing continues to be a hotly de-bated issue in evolutionary biology Tradition-ally paleontological analysis of theropod digitreductions indicated that the three-digit handarose by unilateral loss of digits IV and V re-sulting in a I II III digit formula (103) In con-trast the use of ldquopositionalrdquo criteria of embryologicprecursors to identify digits in modern birdsrevealed a digit 2 3 4 formula (104 105) To re-solve this paradox it has been proposed that ahomeotic transformation of digits occurred thatconverted the embryonic precursors to I II andIII in the adult (frameshift hypothesis) (103) Con-founding any reconciliation of evidence fromthese disciplines paleontological analyses typicallyrely on adult morphology to infer evolutionarylinks whereas developmental studies generallyfocus on very transient vestigial embryonic rem-nants to infer homologies with adult structuresthat have been lost entirely during evolution Incontrast to cellular fate determination morpho-logical identity of a complex structure is generallynot defined by any specific and unique geneticldquomarkersrdquo which creates difficulty in assigningunique homologiesNevertheless the analysis of expression of

spatially regulated genes in the embryonic limbwhich can be considered ldquophenotypicrdquo criteriafor digit assignment has provided support forthe frameshift hypothesis in that certain geneexpression patterns normally correlated withdigit I are retained in the first digit of the chickembryo hand In addition recent more com-prehensive genome-wide expression profilingcomparing chick embryo hand and foot digitprecursors also supports a I II III phenotypicformula in that the expression profiles of thefirst digit in both the hand and foot are re-markably similar (106) Genetic lineage trac-ing of Shh-expressing cells in the chick whichnormally contribute to digits IV and V in thepentadactyl mouse further suggests that digitIV is phenotypically absent from the chickhand (8 107) All of the phenotypic data fromchick embryos are likewise compatible with theclassic paleontological interpretation of a digitI-II-III formula if the avialan embryo ldquoposi-tionalrdquo evidence of digit precursors is discountedas being either misleading or incorrect Howeverthis requires a shift in the primary limb axisto run through digit 3 (axis shift hypothesis)both in extinct and modern tetanuran theropods(108) rather than through digit 4 as occurs inmost tetrapods except urodeles (109) becausethe primary limb axis must by definition in-clude the first digit to form in the embryo Infact a shortcoming of the positional data onvestigial digit condensations appearing in theembryonic hands of various avialan species isthat although a remnant of a positional fourthcondensation (which could be either IV or V)is clearly posterior (lateral) to the three digitsthat are retained in the adult the identificationof a vestigial anterior (medial) condensation iscontroversial and it is based on indistinctelements that could represent other structures[see review in (110)] A reevaluation of digit

condensation formation in mouse embryosalso suggests that some of the traditional ap-proaches used to visualize early digit condensa-tions may be inadequate and could miss evidencefor noncontiguous digit loss (gaps between con-densations) In mouse genetic modulation of sig-nals critical for regulating digit pattern andnumber across vertebrate species results in theinitial loss of a central rather than lateral digit(111 112) This suggests that in principle a I-II-IV formula is also possible (central loss hy-pothesis) The I-II-IV formula would explainthe persistence of digit 1 and still retain theprimary axis extending through digit 4 which isthe accepted rule in all living tetrapods excepturodeles Note that the expression profiling datain chick (106) also revealed mixed expressionfeatures for the lateral digits which could beconstrued as compatible with a I-IIIII-IV avialanhand formula (or the presence of digit IV) Takentogether these developmental studies now leave

open the possibility of I-II-III or even I-II-IV orI-III-IV formulas for the modern avialan handConversely more recent analyses of digit mor-phologies in ceratosaurian and basal tetanurantheropods (52) lend some support to a II III IVtheropod formula with secondary transformationsto produce final I II III morphologies throughmultiple partial homeotic transformations (lat-eral shift hypothesis)To reconcile the paradox of digit homolo-

gies between theropods and birds all of theproposed models (Fig 4A) require either mul-tiple events entailing the reduction and thenreappearance of a positional digit 4 to retainthe primary limb axis or require that the pri-mary axis has undergone a novel shift in itsposition from digit 4 to 3 Clearly whereas muchprogress has been made a final resolution tothis ongoing debate demands additional workfrom both paleontological and developmentalperspectives (110)

Five-fingeredtheropods

Four-fingeredtheropods

Three-fingeredtheropods

Frame-shift

Lateral-shift

Axis-shift

Central-loss

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIII

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIIIV

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIII

12345

IIIIIIIVV

12345

III

IVV

12345

III

IV

1 m

A

B

Fig 4 The evolution of theropod hand and respiratory system (A) Diagrams depicting four hypothesesfor the evolution of wing digits Color shading bordered by solid line refers to fully formed digits and bydash line to reduced digits Colored bars refer to different ldquomorphologicrdquo digits Arabic numerals refer topositional embryonic digit precursors A combination of different colors refers to a mixture of differentmorphological features pertaining to different phenotypes in one digit (B) Reconstruction of pulmonarycomponents [cervical air-sac system (green) lung (orange) and abdominal air-sac system (blue)] in thetheropod Majungatholus Graphic from (27)

A highly efficient flow-through ventilation anda high-compliance air-sac system uniquely char-acterize the avialan respiratory system (27) Per-ceived differences in the respiratory systems oftheropods and other reptiles such as crocodi-lians from those of birds have been invalidlyused as evidence against the BMT hypothesis(49) Nevertheless cervical and anterior dorsalvertebrae are clearly pneumatic in nearly alltheropods (29) and documentation of exten-sive skeletal pneumaticity in theropods such asMajungasaurus and Aerosteon (27 28) dem-onstrates that a complex air-sac system andbirdlike respiration evolved in birdsrsquo theropodancestors (Fig 4B) Furthermore recent ana-tomical and physiological studies reveal thatalligators (7 113) and even monitor lizards (114)exhibit respiratory systems and unidirectionalbreathing akin to those of birds These studiesdemonstrate that unidirectional breathing is aprimitive characteristic of archosaurs or an evenmore inclusive group with the complex air-sacsystem evolving later within Archosauria Weightsavings might have driven the evolution of post-cranial skeletal pneumatization in early theropods

(29) and in addition to large-bodied theropodssmall maniraptoran theropods such as basaloviraptorosaurs dromaeosaurs and troodontidsevolved the complex air-sac system similar tothat of birds (28 29)

Morphogenesis and early evolution of feathersFeathers were once considered to be uniqueavialan structures The presence of feathers isinferred in several theropods based on osteo-logical correlates eg quill knobs (115 116) [al-though the presence of quill knobs in the basaltetanuran Concavenator has been questioned(117)] or pygostyles (118) Short filaments havebeen identified as feathers in the alvarezsaurShuvuuia (119) Direct evidence came to lightin China in 1996 with the discovery of the fea-thered Sinosauropteryx (120) Since then nu-merous specimens of most theropod groups andeven three ornithischian groups preserving fea-thers have been recovered from the Jurassicand Cretaceous beds of northeastern China(13 21 41 45 57) and from the Jurassic andCretaceous beds of Germany Russia and Canada

(55 56 121ndash123) These feathers fall into severalmajor morphotypes (Fig 5) ranging from mono-filamentous feathers to highly complex flightfeathers (57) The phylogenetic distribution ofthese feathers largely concurs with the predic-tions from a developmental model of living birds(4) although some of these morphotypes areabsent in living birds (57 124)The findings of feathers in dinosaurs prompted

developmental studies over the last decade in-vestigating the molecular mechanisms regulat-ing feather development and regeneration inchickens (125) We can now propose the follow-ing ldquomolecular circuitsrdquo regarding tissue morpho-genesis and the evolution of modern feathersEach molecular circuit has specific features andcan be modulated to produce a diversity ofmorphology(i) Cylindrical topology and the downshift of

stem cell ring The formation of loose mesen-chyme in the bud core allows a tube configura-tion with basal layer facing inside Driven byWnt signaling feather stem cells now are posi-tioned near the base forming a ring config-uration (126 127) It can remain as a tube or the

Fig 5 The morphogenesis and evolution of feathers in dinosaurs (A)Monofilamentous feathers in Tianyulong (B) Broad monofilamentous feathers inBeipiaosaurus Radially branched feathers in Sinosauropteryx (C) Sinornitho-saurus (D) and Anchiornis (E) Bilaterally branched feathers in Dilong (F)and Sinornithosaurus (G) (H) Wing flight feathers with symmetrical vanesin Anchiornis (I) Pedal flight feathers with asymmetrical vanes in Micro-raptor (J) Rachis-dominant tail feathers in Confuciusornis (K) Proximally

ribbonlike tail feathers in Similicaudipteryx (L) Phylogenetic distribution ofmajor feather morphotypes (monofilamentous radially branched bilater-ally branched symmetrical flight and asymmetrical flight feathers) amongdinosaurs (M) Major novel morphogenetic events and molecular pathwaysduring feather evolutionThese major feather morphotypes can be explained byselective usage of the five novel ldquomolecular circuitsrdquo discussed in the text Redarrows flank a feather

subsequent caspase-dependent selective apopto-sis can open up the tube allowing feather vaneformation (128)(ii) Hierarchical branching and barbbarbule

pattern formation Ratio of local activators (nog-gin Shh and so on) and inhibitors (bone mor-phogenetic proteins) regulate the number andsize of barb versus rachidial ridges (5 129) Barbridges which depend on Wnt 3a gradient canrun parallel to each other to form radial sym-metric feathers or angle toward the rachis toform bilateral symmetric feathers (130)(iii) Follicle formation and regenerative cycling

During development matrix maetalloproteinasendashdependent tissue invagination allows epithelia totopologically fold into a follicle (131) Follicle con-figuration allows protection of feather progenitorsStem cells and dermal papilla are now clusterednear the follicle base and can undergo dickkopfWntndashdependent cyclic regeneration (132)(iv) Temporal regulation of stem cells along

the proximal-distal axis During feather forma-tion the molecular microenvironment and mor-phology can change along the distal (formedearlier) and proximal (formed later) throughmodulation of fibroblast growth factorndashsproutactivity (133)(v) Organ metamorphosis and regional spe-

cific feather types Upon regeneration modulatedby the body macroenvironments different fea-ther morphotypes (downy contour and flightfeathers) can form on different body regions andin different physiological stages for optimal per-formance (134)The aforementioned morphogenetic proces-

ses can be assembled selectively in various or-ders and independently to produce basic-tondashmore complex feather morphotypes (Fig 5) Themonofilamentous feathers seen in ornithischians(54 56 57) and some theropods (55 57) two setsof morphologically different flight feathersduring ontogeny in the oviraptorosau-rian Similicaudipteryx (124) and theextensive leg feathering (particular-ly pedal feathering) in a number oftheropods and early birds (135) implya variety of rearrangements in themorphogenetic modules The wide oc-currence of pedal feathering in the-ropods and early birds (135) and anextensive distribution of scales onthe bodies of both feathered thero-pods (eg Juravenator) and featheredornithischians (eg the ceratopsianPsittacosaurus and the ornithopodKullindadromeus) remain particularlyinteresting from both developmentaland evolutionary perspectives (56 135)and will no doubt play into further dis-cussions on feather-scale relationshipsThe diverse forms of theropod fea-

thers apparently suggest a comparablemyriad of functions Initial functionsof feathers more likely include ther-moregulation and communication rath-er than flight (57) Several differentlines of data highlight the importance

of communication in early feather evolution(41 57 117 136) particularly by color patternsinferred via preserved melanosome morpho-logies in some theropods and early birds (136 137)although several studies have questioned theidentifications of melanosomes in specimensof feathered theropods and early birds (48 138)One study shows an increased diversity of melano-some morphologies associated with the appear-ance of complex pinnate feathers during theropodevolution (72) This finding supports developmentaldata showing that unique topological arrange-ments allowing feathers to generate complex formsalso permits the generation of visibly complexpigment patterns and pattern renewal duringsexual maturation (139)

Four-winged dinosaurs and the origins of aerial behaviorSeveral flight-related anatomical features suchas hollow bones and the furcula originated inearly theropods basal paravians had many hall-mark features necessary for flight includingextremely small body size (50 70) a laterallyoriented long and robust forelimb (22 67) anenlarged forebrain and other derived neurolog-ical adaptations (71) and large flight feathers(Figs 1 and 2) Particularly surprising are therecent discoveries of large flight feathers form-ing a planar surface on the legs of some basalparaviansmdashfor example those with asymmetricalvanes on both the tibia and metatarsus of somebasal dromaeosaurs such as Microraptor (59)large feathers with symmetrical vanes on both thetibia and metatarsus of the troodontid Anchiornis(45) the basal bird Sapeornis and several otherbasal paravians (135) and large vaned feath-ers on tibiae of several basal birds includingArchaeopteryx confuciusornithids and enan-tiornithines (135) These structures clearly wouldhave been relevant to flight origins The evolu-

tion of flight nonetheless remains highly de-bated with a few recently proposed scenariosincluding factors as diverse as muscle hyperpla-sia (140) and the use of wings to assist in cur-sorial ascent of inclines based on neontologicalobservations (11) Multifactorial explanations forthe origins of flight are likely as this behaviorhas not been uniquely categorized given varia-bility in wing and tail configurations amongtheropods and early birds (45 59 135 141 142)flight probably had complex biomechanicalorigins (142 143)Fundamental to all hypotheses of wing evo-

lution however must be consideration of thosecircumstances that elicited aerial behavior inancestrally terrestrial taxa In all extant verte-brate and invertebrate gliders flight is associ-ated with gravitational acceleration downwardfrom heights and with the use in aerodynamiccontrol of diverse body structures including butnot limited to limbs once aloft (143) The dis-coveries of four-winged theropods and earlybirds (Fig 6) are consistent with the gravity-assisted hypothesis for the origin of bird flightMoreover the concurrent presence of a largeand flattened tail along with potential use ofthe feathered hind legs in aerodynamic controlsuggests substantial capacity for using these asrudders and for maneuvering even during theearliest stages of bird evolution (10 144) Aerialrighting reflexes targeting movement while aloftand controlled landings all would have been en-hanced via bilaterally asymmetric motions ofeither wing pair In other words incipient andnonequilibrium flight behaviors would poten-tially associate with a four-winged and long-tailed arrangement in theropods and early birds(Fig 6) There still remains disagreement as tothe definitional criteria used to indicate thefour-winged and long-tailed condition and as towhether large flight feathers with symmetrical

Columba

JeholornisSapeornis

Archaeopteryx

AnchiornisMicroraptor

Epidexipteryx

Fig 6 Airfoils of selectedmaniraptorans Airfoils (in blue) of the basal dromaeosaurMicroraptor the basal troodontidAnchiornis the basal birds Archaeopteryx Sapeornis and Jeholornis and a modern pigeon Feathered airfoils aregreater in number and are more distally positioned in early birds and their closest theropod relatives than inmodern birds The scansoriopterygid Epidexipteryx has stiff downlike feathers (in green) on both the forelimb andhindlimb and long ribbonlike feathers on the tail the aerodynamic functions of which remain poorly known

vanes in some basal paravians including earlybirds would create useful aerodynamic forcesduring aerial behaviors (117)Use of the hind wings and potentially the

tail to generate vertical force also results in amore posterior and stable position for the cen-ter of lift (10 144) (as can be deduced from batand pterosaur wings based on patagial connec-tions to the hindlegs) Such a hindwing config-uration contributes to static stability in glidingwhereas subsequent functional shifts to the fore-wings alone with associated reductions in tailsize and leg feathering (135) would have requiredoffsetting aerodynamic control via flapping mo-tions (145) Potential tradeoffs between increasedsize of the forewings and the intensity of theirkinematic activation (eg greater frequency andamplitude of flapping) are not well understoodalthough robotic models of early avialan mor-phologies can be informative (146) Such progres-sive anterior specialization of the flight apparatuswith enhanced forces produced by the emergingforelimb locomotor module (145) is nonethelessderived from an ancestrally four-winged plat-form (Fig 6)

Future perspectivesAlternative phylogenetic hypotheses suggest adifferent evolutionary sequence of major birdcharacteristics and imply a different ecologicalorigin of the group (22) Consequently a refinedmore robust phylogeny will be imperative tomove our studies forward Increasing characterand taxon sampling in recent theropod phylo-genetic studies has in theory helped improvethe accuracy of phylogenetic reconstructions butbetter character formulation and more accuratescorings are imperative at present pending bet-ter understanding of the morphologies of manyrecently discovered transitional formsIn terms of character evolution an integrative

approach combining paleontological neontolog-ical developmental geochronological and evenpaleoenvironmental data is particularly desir-able A recent integrative study combining de-velopmental neontological and paleontologicaldata shows that birds evolved their highly spe-cialized cranium mainly by paedomorphisis (147)another study using both neontological and pa-leontological data to reconstruct melanosomeevolution suggests that feathers have changedsignificantly in their melanosome morphologyamong pennaraptoran theropods which impliesa physiological shift before the evolution of flight(72) and that concurs in association with exten-sive postcranial skeletal pneumaticity whichsuggests the presence of birdlike endothermy(29) Similar approaches should be applied toother major structures Certain avialan structuressuch as feathers and visual system are novel inboth genetic and morphological terms There areemerging data on how the genetic code affects themorphogenesis of these structures in developmen-tal biology How the genetic code and expressionpattern evolved can be inferred by a detailedcomparison of homologous structures in thero-pods early birds and modern birds

The construction of molecular phylogenieswould enable a much better understanding ofthe genealogical relations among birds and theirtheropod relatives and the steps leading to theevolution of birds Although once the topic ofscience-fiction movies preserved organic remainshave purportedly been recovered from Tyranno-saurus and the hadrosaur Brachylophosaurus(148 149) and from even older fossils such asEarly Jurassic Lufengosaurus specimens (150)Greater examination along these lines in fossilsspanning the theropod-bird transition is a po-tentially fruitful avenue for future investigationThe increasing interest in the origins of birds

from developmental biology and other disciplineshas enriched our understanding of this impor-tant evolutionary event (8 10 11) and alternativeevolutionary models on various aspects of theorigin of birds have sometimes been providedbased on neontological data (4 11) Howeverany evolutionary model must be tested using thefossil record Consequently dense fossil samplingalong the line to birds and better understandingof the transitional forms play a key role in thediscussion on this issue

REFERENCES AND NOTES

1 A Feduccia The Origin and Evolution of Birds (Yale UnivPress New Haven CT ed 2 1999) pp 466

2 Z Zhou The origin and early evolution of birds Discoveriesdisputes and perspectives from fossil evidenceNaturwissenschaften 91 455ndash471 (2004) doi 101007s00114-004-0570-4 pmid 15365634

3 L M Witmer in Mesozoic Birds Above the Heads ofDinosaurs L M Chiappe L M Witmer Eds (Univ ofCalifornia Press Berkeley 2002) pp 3ndash30

4 R O Prum Development and evolutionary origin of feathersJ Exp Zool 285 291ndash306 (1999) doi 101002(SICI)1097-010X(19991215)2854lt291AID-JEZ1gt30CO2-9pmid 10578107

5 M Yu P Wu R B Widelitz C-M Chuong Themorphogenesis of feathers Nature 420 308ndash312 (2002)doi 101038nature01196 pmid 12442169

6 A O Vargas T Kohlsdorf J F Fallon J VandenbrooksG P Wagner The evolution of HoxD-11 expression in thebird wing Insights from Alligator mississippiensis PLOS ONE3 e3325 (2008) doi 101371journalpone0003325pmid 18833328

7 C G Farmer K Sanders Unidirectional airflow in the lungsof alligators Science 327 338ndash340 (2010) doi 101126science1180219 pmid 20075253

8 K Tamura N Nomura R Seki S Yonei-TamuraH Yokoyama Embryological evidence identifies wing digitsin birds as digits 1 2 and 3 Science 331 753ndash757 (2011)doi 101126science1198229 pmid 21311019

9 C L Organ A M Shedlock A Meade M PagelS V Edwards Origin of avian genome size and structurein non-avian dinosaurs Nature 446 180ndash184 (2007)doi 101038nature05621 pmid 17344851

10 D Evangelista et al Aerodynamic characteristics of afeathered dinosaur measured using physical modelsEffects of form on static stability and control effectivenessPLOS ONE 9 e85203 (2014) doi 101371journalpone0085203 pmid 24454820

11 K P Dial Wing-assisted incline running and the evolutionof flight Science 299 402ndash404 (2003) doi 101126science1078237 pmid 12532020

12 F C James J A Pourtless IV Cladistics and the origin ofbirds A review and two new analyses Ornithol Monogr66 1ndash78 (2009) doi 101525om20096611

13 M Norell X Xu Feathered dinosaurs Annu Rev EarthPlanet Sci 33 277ndash299 (2005) doi 101146annurevearth33092203122511

14 J Gauthier Saurischian monophyly and the origin of birdsMem Calif Acad Sci 8 1ndash55 (1986)

15 P C Sereno The evolution of dinosaurs Science 2842137ndash2147 (1999) doi 101126science28454232137pmid 10381873

16 A H Turner P J Makovicky M A Norell A review ofdromaeosaurid systematics and paravian phylogeny Bull AmMus Nat Hist 371 1ndash206 (2012) doi 1012067481

17 P Senter J I Kirkland D D DeBlieux S Madsen N TothNew dromaeosaurids (Dinosauria Theropoda) from theLower Cretaceous of Utah and the evolution of thedromaeosaurid tail PLOS ONE 7 e36790 (2012)doi 101371journalpone0036790 pmid 22615813

18 T R Holtz Jr A new phylogeny of the carnivorous dinosaursGaia 15 5ndash61 (1998)

19 O W M Rauhut The interrelationships and evolution ofbasal theropod dinosaurs Spec Pap Paleontology 69 1ndash213(2003)

20 M A Norell J M Clark P J Makovicky in New Perspectives onthe Origin and Evolution of Birds J Gauthier L F Gall Eds(Yale Univ Press New Haven CT 2001) pp 49ndash67

21 P Godefroit et al A Jurassic avialan dinosaur from Chinaresolves the early phylogenetic history of birds Nature 498359ndash362 (2013) doi 101038nature12168 pmid 23719374

22 X Xu H You K Du F Han An Archaeopteryx-like theropodfrom China and the origin of Avialae Nature 475 465ndash470(2011) doi 101038nature10288 pmid 21796204

23 J N Choiniere et al A basal alvarezsauroid theropod fromthe early Late Jurassic of Xinjiang China Science 327571ndash574 (2010) doi 101126science1182143pmid 20110503

24 J H Ostrom The osteology of Deinonychus antirrhopus anunusual theropod from the Lower Cretaceous of MontanaBull Peabody Mus Nat Hist 30 1ndash165 (1969)

25 R Barsbold Predatory dinosaurs from the Cretaceousof Mongolia Tr Sovm Sov-Mong Paleontol Eksped 191ndash117 (1983)

26 O Wings thesis The University of Bonn (2004)27 P M OrsquoConnor L P A M Claessens Basic avian pulmonary

design and flow-through ventilation in non-avian theropoddinosaurs Nature 436 253ndash256 (2005) doi 101038nature03716 pmid 16015329

28 P C Sereno et al Evidence for avian intrathoracic air sacsin a new predatory dinosaur from Argentina PLOS ONE3 e3303 (2008) doi 101371journalpone0003303pmid 18825273

29 R B J Benson R J Butler M T Carrano P M OrsquoConnorAir-filled postcranial bones in theropod dinosaursPhysiological implications and the lsquoreptilersquo-bird transitionBiol Rev Camb Philos Soc 87 168ndash193 (2012) doi 101111j1469-185X201100190x pmid 21733078

30 M A Norell J M Clark L M Chiappe D DashzevegA nesting dinosaur Nature 378 774ndash776 (1995)doi 101038378774a0

31 D J Varricchio F Jackson J J Borkowski J R HornerNest and egg clutches of the dinosaur Troodon formosusand the evolution of avian reproductive traits Nature 385247ndash250 (1997) doi 101038385247a0

32 G M Erickson K Curry Rogers D J Varricchio M A NorellX Xu Growth patterns in brooding dinosaurs reveals thetiming of sexual maturity in non-avian dinosaurs and genesisof the avian condition Biol Lett 3 558ndash561 (2007)pmid 17638674

33 G Grellet-Tinner P Makovicky A possible egg of thedromaeosaur Deinonychus antirrhopus Phylogenetic andbiological implications Can J Earth Sci 43 705ndash719 (2006)doi 101139e06-033

34 G Grellet-Tinner L M Chiappe in Feathered DragonsStudies on the Transition from Dinosaurs to Birds P J CurrieE B Koppelhus M A Shugar J L Wright Eds (IndianaUniv Press Bloomington 2004) pp 185ndash214

35 D J Varricchio F D Jackson A phylogenetic assessment ofprismatic dinosaur eggs from the Cretaceous Two MedicineFormation of Montana J Vertebr Paleontol 24 931ndash937 (2004)doi 1016710272-4634(2004)024[0931APAOPD]20CO2

36 D K Zelenitsky F Therrien Phylogenetic analysis ofreproductive traits of maniraptoran theropods and itsimplications for egg parataxonomy Paleontology 51 807ndash816(2008) doi 101111j1475-4983200800770x

37 K Padian A J de Ricqlegraves J R Horner Dinosaurian growthrates and bird origins Nature 412 405ndash408 (2001)doi 10103835086500 pmid 11473307

38 F L Agnoliacuten F E Novas Avian Ancestors A Review of thePhylogenetic Relationships of the Theropods UnenlagiidaeMicroraptoria Anchiornis and Scansoriopterygidae (SpringerDordrecht Heidelberg 2013)

39 P J Makovicky L E Zanno in Living Dinosaurs TheEvolutionary History of Modern Birds G J Dyke G KaiserEds (Wiley-Blackwell Oxford 2011) pp 9ndash29

into the bird wing continues to be a hotly de-bated issue in evolutionary biology Tradition-ally paleontological analysis of theropod digitreductions indicated that the three-digit handarose by unilateral loss of digits IV and V re-sulting in a I II III digit formula (103) In con-trast the use of ldquopositionalrdquo criteria of embryologicprecursors to identify digits in modern birdsrevealed a digit 2 3 4 formula (104 105) To re-solve this paradox it has been proposed that ahomeotic transformation of digits occurred thatconverted the embryonic precursors to I II andIII in the adult (frameshift hypothesis) (103) Con-founding any reconciliation of evidence fromthese disciplines paleontological analyses typicallyrely on adult morphology to infer evolutionarylinks whereas developmental studies generallyfocus on very transient vestigial embryonic rem-nants to infer homologies with adult structuresthat have been lost entirely during evolution Incontrast to cellular fate determination morpho-logical identity of a complex structure is generallynot defined by any specific and unique geneticldquomarkersrdquo which creates difficulty in assigningunique homologiesNevertheless the analysis of expression of

spatially regulated genes in the embryonic limbwhich can be considered ldquophenotypicrdquo criteriafor digit assignment has provided support forthe frameshift hypothesis in that certain geneexpression patterns normally correlated withdigit I are retained in the first digit of the chickembryo hand In addition recent more com-prehensive genome-wide expression profilingcomparing chick embryo hand and foot digitprecursors also supports a I II III phenotypicformula in that the expression profiles of thefirst digit in both the hand and foot are re-markably similar (106) Genetic lineage trac-ing of Shh-expressing cells in the chick whichnormally contribute to digits IV and V in thepentadactyl mouse further suggests that digitIV is phenotypically absent from the chickhand (8 107) All of the phenotypic data fromchick embryos are likewise compatible with theclassic paleontological interpretation of a digitI-II-III formula if the avialan embryo ldquoposi-tionalrdquo evidence of digit precursors is discountedas being either misleading or incorrect Howeverthis requires a shift in the primary limb axisto run through digit 3 (axis shift hypothesis)both in extinct and modern tetanuran theropods(108) rather than through digit 4 as occurs inmost tetrapods except urodeles (109) becausethe primary limb axis must by definition in-clude the first digit to form in the embryo Infact a shortcoming of the positional data onvestigial digit condensations appearing in theembryonic hands of various avialan species isthat although a remnant of a positional fourthcondensation (which could be either IV or V)is clearly posterior (lateral) to the three digitsthat are retained in the adult the identificationof a vestigial anterior (medial) condensation iscontroversial and it is based on indistinctelements that could represent other structures[see review in (110)] A reevaluation of digit

condensation formation in mouse embryosalso suggests that some of the traditional ap-proaches used to visualize early digit condensa-tions may be inadequate and could miss evidencefor noncontiguous digit loss (gaps between con-densations) In mouse genetic modulation of sig-nals critical for regulating digit pattern andnumber across vertebrate species results in theinitial loss of a central rather than lateral digit(111 112) This suggests that in principle a I-II-IV formula is also possible (central loss hy-pothesis) The I-II-IV formula would explainthe persistence of digit 1 and still retain theprimary axis extending through digit 4 which isthe accepted rule in all living tetrapods excepturodeles Note that the expression profiling datain chick (106) also revealed mixed expressionfeatures for the lateral digits which could beconstrued as compatible with a I-IIIII-IV avialanhand formula (or the presence of digit IV) Takentogether these developmental studies now leave

open the possibility of I-II-III or even I-II-IV orI-III-IV formulas for the modern avialan handConversely more recent analyses of digit mor-phologies in ceratosaurian and basal tetanurantheropods (52) lend some support to a II III IVtheropod formula with secondary transformationsto produce final I II III morphologies throughmultiple partial homeotic transformations (lat-eral shift hypothesis)To reconcile the paradox of digit homolo-

gies between theropods and birds all of theproposed models (Fig 4A) require either mul-tiple events entailing the reduction and thenreappearance of a positional digit 4 to retainthe primary limb axis or require that the pri-mary axis has undergone a novel shift in itsposition from digit 4 to 3 Clearly whereas muchprogress has been made a final resolution tothis ongoing debate demands additional workfrom both paleontological and developmentalperspectives (110)

Five-fingeredtheropods

Four-fingeredtheropods

Three-fingeredtheropods

Frame-shift

Lateral-shift

Axis-shift

Central-loss

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIII

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIIIV

12345

IIIIIIIVV

12345

IIIIIIIV

12345

IIIIII

12345

IIIIIIIVV

12345

III

IVV

12345

III

IV

1 m

A

B

Fig 4 The evolution of theropod hand and respiratory system (A) Diagrams depicting four hypothesesfor the evolution of wing digits Color shading bordered by solid line refers to fully formed digits and bydash line to reduced digits Colored bars refer to different ldquomorphologicrdquo digits Arabic numerals refer topositional embryonic digit precursors A combination of different colors refers to a mixture of differentmorphological features pertaining to different phenotypes in one digit (B) Reconstruction of pulmonarycomponents [cervical air-sac system (green) lung (orange) and abdominal air-sac system (blue)] in thetheropod Majungatholus Graphic from (27)

A highly efficient flow-through ventilation anda high-compliance air-sac system uniquely char-acterize the avialan respiratory system (27) Per-ceived differences in the respiratory systems oftheropods and other reptiles such as crocodi-lians from those of birds have been invalidlyused as evidence against the BMT hypothesis(49) Nevertheless cervical and anterior dorsalvertebrae are clearly pneumatic in nearly alltheropods (29) and documentation of exten-sive skeletal pneumaticity in theropods such asMajungasaurus and Aerosteon (27 28) dem-onstrates that a complex air-sac system andbirdlike respiration evolved in birdsrsquo theropodancestors (Fig 4B) Furthermore recent ana-tomical and physiological studies reveal thatalligators (7 113) and even monitor lizards (114)exhibit respiratory systems and unidirectionalbreathing akin to those of birds These studiesdemonstrate that unidirectional breathing is aprimitive characteristic of archosaurs or an evenmore inclusive group with the complex air-sacsystem evolving later within Archosauria Weightsavings might have driven the evolution of post-cranial skeletal pneumatization in early theropods

(29) and in addition to large-bodied theropodssmall maniraptoran theropods such as basaloviraptorosaurs dromaeosaurs and troodontidsevolved the complex air-sac system similar tothat of birds (28 29)

Morphogenesis and early evolution of feathersFeathers were once considered to be uniqueavialan structures The presence of feathers isinferred in several theropods based on osteo-logical correlates eg quill knobs (115 116) [al-though the presence of quill knobs in the basaltetanuran Concavenator has been questioned(117)] or pygostyles (118) Short filaments havebeen identified as feathers in the alvarezsaurShuvuuia (119) Direct evidence came to lightin China in 1996 with the discovery of the fea-thered Sinosauropteryx (120) Since then nu-merous specimens of most theropod groups andeven three ornithischian groups preserving fea-thers have been recovered from the Jurassicand Cretaceous beds of northeastern China(13 21 41 45 57) and from the Jurassic andCretaceous beds of Germany Russia and Canada

(55 56 121ndash123) These feathers fall into severalmajor morphotypes (Fig 5) ranging from mono-filamentous feathers to highly complex flightfeathers (57) The phylogenetic distribution ofthese feathers largely concurs with the predic-tions from a developmental model of living birds(4) although some of these morphotypes areabsent in living birds (57 124)The findings of feathers in dinosaurs prompted

developmental studies over the last decade in-vestigating the molecular mechanisms regulat-ing feather development and regeneration inchickens (125) We can now propose the follow-ing ldquomolecular circuitsrdquo regarding tissue morpho-genesis and the evolution of modern feathersEach molecular circuit has specific features andcan be modulated to produce a diversity ofmorphology(i) Cylindrical topology and the downshift of

stem cell ring The formation of loose mesen-chyme in the bud core allows a tube configura-tion with basal layer facing inside Driven byWnt signaling feather stem cells now are posi-tioned near the base forming a ring config-uration (126 127) It can remain as a tube or the

Fig 5 The morphogenesis and evolution of feathers in dinosaurs (A)Monofilamentous feathers in Tianyulong (B) Broad monofilamentous feathers inBeipiaosaurus Radially branched feathers in Sinosauropteryx (C) Sinornitho-saurus (D) and Anchiornis (E) Bilaterally branched feathers in Dilong (F)and Sinornithosaurus (G) (H) Wing flight feathers with symmetrical vanesin Anchiornis (I) Pedal flight feathers with asymmetrical vanes in Micro-raptor (J) Rachis-dominant tail feathers in Confuciusornis (K) Proximally

ribbonlike tail feathers in Similicaudipteryx (L) Phylogenetic distribution ofmajor feather morphotypes (monofilamentous radially branched bilater-ally branched symmetrical flight and asymmetrical flight feathers) amongdinosaurs (M) Major novel morphogenetic events and molecular pathwaysduring feather evolutionThese major feather morphotypes can be explained byselective usage of the five novel ldquomolecular circuitsrdquo discussed in the text Redarrows flank a feather

subsequent caspase-dependent selective apopto-sis can open up the tube allowing feather vaneformation (128)(ii) Hierarchical branching and barbbarbule

pattern formation Ratio of local activators (nog-gin Shh and so on) and inhibitors (bone mor-phogenetic proteins) regulate the number andsize of barb versus rachidial ridges (5 129) Barbridges which depend on Wnt 3a gradient canrun parallel to each other to form radial sym-metric feathers or angle toward the rachis toform bilateral symmetric feathers (130)(iii) Follicle formation and regenerative cycling

During development matrix maetalloproteinasendashdependent tissue invagination allows epithelia totopologically fold into a follicle (131) Follicle con-figuration allows protection of feather progenitorsStem cells and dermal papilla are now clusterednear the follicle base and can undergo dickkopfWntndashdependent cyclic regeneration (132)(iv) Temporal regulation of stem cells along

the proximal-distal axis During feather forma-tion the molecular microenvironment and mor-phology can change along the distal (formedearlier) and proximal (formed later) throughmodulation of fibroblast growth factorndashsproutactivity (133)(v) Organ metamorphosis and regional spe-

cific feather types Upon regeneration modulatedby the body macroenvironments different fea-ther morphotypes (downy contour and flightfeathers) can form on different body regions andin different physiological stages for optimal per-formance (134)The aforementioned morphogenetic proces-

ses can be assembled selectively in various or-ders and independently to produce basic-tondashmore complex feather morphotypes (Fig 5) Themonofilamentous feathers seen in ornithischians(54 56 57) and some theropods (55 57) two setsof morphologically different flight feathersduring ontogeny in the oviraptorosau-rian Similicaudipteryx (124) and theextensive leg feathering (particular-ly pedal feathering) in a number oftheropods and early birds (135) implya variety of rearrangements in themorphogenetic modules The wide oc-currence of pedal feathering in the-ropods and early birds (135) and anextensive distribution of scales onthe bodies of both feathered thero-pods (eg Juravenator) and featheredornithischians (eg the ceratopsianPsittacosaurus and the ornithopodKullindadromeus) remain particularlyinteresting from both developmentaland evolutionary perspectives (56 135)and will no doubt play into further dis-cussions on feather-scale relationshipsThe diverse forms of theropod fea-

thers apparently suggest a comparablemyriad of functions Initial functionsof feathers more likely include ther-moregulation and communication rath-er than flight (57) Several differentlines of data highlight the importance

of communication in early feather evolution(41 57 117 136) particularly by color patternsinferred via preserved melanosome morpho-logies in some theropods and early birds (136 137)although several studies have questioned theidentifications of melanosomes in specimensof feathered theropods and early birds (48 138)One study shows an increased diversity of melano-some morphologies associated with the appear-ance of complex pinnate feathers during theropodevolution (72) This finding supports developmentaldata showing that unique topological arrange-ments allowing feathers to generate complex formsalso permits the generation of visibly complexpigment patterns and pattern renewal duringsexual maturation (139)

Four-winged dinosaurs and the origins of aerial behaviorSeveral flight-related anatomical features suchas hollow bones and the furcula originated inearly theropods basal paravians had many hall-mark features necessary for flight includingextremely small body size (50 70) a laterallyoriented long and robust forelimb (22 67) anenlarged forebrain and other derived neurolog-ical adaptations (71) and large flight feathers(Figs 1 and 2) Particularly surprising are therecent discoveries of large flight feathers form-ing a planar surface on the legs of some basalparaviansmdashfor example those with asymmetricalvanes on both the tibia and metatarsus of somebasal dromaeosaurs such as Microraptor (59)large feathers with symmetrical vanes on both thetibia and metatarsus of the troodontid Anchiornis(45) the basal bird Sapeornis and several otherbasal paravians (135) and large vaned feath-ers on tibiae of several basal birds includingArchaeopteryx confuciusornithids and enan-tiornithines (135) These structures clearly wouldhave been relevant to flight origins The evolu-

tion of flight nonetheless remains highly de-bated with a few recently proposed scenariosincluding factors as diverse as muscle hyperpla-sia (140) and the use of wings to assist in cur-sorial ascent of inclines based on neontologicalobservations (11) Multifactorial explanations forthe origins of flight are likely as this behaviorhas not been uniquely categorized given varia-bility in wing and tail configurations amongtheropods and early birds (45 59 135 141 142)flight probably had complex biomechanicalorigins (142 143)Fundamental to all hypotheses of wing evo-

lution however must be consideration of thosecircumstances that elicited aerial behavior inancestrally terrestrial taxa In all extant verte-brate and invertebrate gliders flight is associ-ated with gravitational acceleration downwardfrom heights and with the use in aerodynamiccontrol of diverse body structures including butnot limited to limbs once aloft (143) The dis-coveries of four-winged theropods and earlybirds (Fig 6) are consistent with the gravity-assisted hypothesis for the origin of bird flightMoreover the concurrent presence of a largeand flattened tail along with potential use ofthe feathered hind legs in aerodynamic controlsuggests substantial capacity for using these asrudders and for maneuvering even during theearliest stages of bird evolution (10 144) Aerialrighting reflexes targeting movement while aloftand controlled landings all would have been en-hanced via bilaterally asymmetric motions ofeither wing pair In other words incipient andnonequilibrium flight behaviors would poten-tially associate with a four-winged and long-tailed arrangement in theropods and early birds(Fig 6) There still remains disagreement as tothe definitional criteria used to indicate thefour-winged and long-tailed condition and as towhether large flight feathers with symmetrical

Columba

JeholornisSapeornis

Archaeopteryx

AnchiornisMicroraptor

Epidexipteryx

Fig 6 Airfoils of selectedmaniraptorans Airfoils (in blue) of the basal dromaeosaurMicroraptor the basal troodontidAnchiornis the basal birds Archaeopteryx Sapeornis and Jeholornis and a modern pigeon Feathered airfoils aregreater in number and are more distally positioned in early birds and their closest theropod relatives than inmodern birds The scansoriopterygid Epidexipteryx has stiff downlike feathers (in green) on both the forelimb andhindlimb and long ribbonlike feathers on the tail the aerodynamic functions of which remain poorly known

vanes in some basal paravians including earlybirds would create useful aerodynamic forcesduring aerial behaviors (117)Use of the hind wings and potentially the

tail to generate vertical force also results in amore posterior and stable position for the cen-ter of lift (10 144) (as can be deduced from batand pterosaur wings based on patagial connec-tions to the hindlegs) Such a hindwing config-uration contributes to static stability in glidingwhereas subsequent functional shifts to the fore-wings alone with associated reductions in tailsize and leg feathering (135) would have requiredoffsetting aerodynamic control via flapping mo-tions (145) Potential tradeoffs between increasedsize of the forewings and the intensity of theirkinematic activation (eg greater frequency andamplitude of flapping) are not well understoodalthough robotic models of early avialan mor-phologies can be informative (146) Such progres-sive anterior specialization of the flight apparatuswith enhanced forces produced by the emergingforelimb locomotor module (145) is nonethelessderived from an ancestrally four-winged plat-form (Fig 6)

Future perspectivesAlternative phylogenetic hypotheses suggest adifferent evolutionary sequence of major birdcharacteristics and imply a different ecologicalorigin of the group (22) Consequently a refinedmore robust phylogeny will be imperative tomove our studies forward Increasing characterand taxon sampling in recent theropod phylo-genetic studies has in theory helped improvethe accuracy of phylogenetic reconstructions butbetter character formulation and more accuratescorings are imperative at present pending bet-ter understanding of the morphologies of manyrecently discovered transitional formsIn terms of character evolution an integrative

approach combining paleontological neontolog-ical developmental geochronological and evenpaleoenvironmental data is particularly desir-able A recent integrative study combining de-velopmental neontological and paleontologicaldata shows that birds evolved their highly spe-cialized cranium mainly by paedomorphisis (147)another study using both neontological and pa-leontological data to reconstruct melanosomeevolution suggests that feathers have changedsignificantly in their melanosome morphologyamong pennaraptoran theropods which impliesa physiological shift before the evolution of flight(72) and that concurs in association with exten-sive postcranial skeletal pneumaticity whichsuggests the presence of birdlike endothermy(29) Similar approaches should be applied toother major structures Certain avialan structuressuch as feathers and visual system are novel inboth genetic and morphological terms There areemerging data on how the genetic code affects themorphogenesis of these structures in developmen-tal biology How the genetic code and expressionpattern evolved can be inferred by a detailedcomparison of homologous structures in thero-pods early birds and modern birds

The construction of molecular phylogenieswould enable a much better understanding ofthe genealogical relations among birds and theirtheropod relatives and the steps leading to theevolution of birds Although once the topic ofscience-fiction movies preserved organic remainshave purportedly been recovered from Tyranno-saurus and the hadrosaur Brachylophosaurus(148 149) and from even older fossils such asEarly Jurassic Lufengosaurus specimens (150)Greater examination along these lines in fossilsspanning the theropod-bird transition is a po-tentially fruitful avenue for future investigationThe increasing interest in the origins of birds

from developmental biology and other disciplineshas enriched our understanding of this impor-tant evolutionary event (8 10 11) and alternativeevolutionary models on various aspects of theorigin of birds have sometimes been providedbased on neontological data (4 11) Howeverany evolutionary model must be tested using thefossil record Consequently dense fossil samplingalong the line to birds and better understandingof the transitional forms play a key role in thediscussion on this issue

REFERENCES AND NOTES

1 A Feduccia The Origin and Evolution of Birds (Yale UnivPress New Haven CT ed 2 1999) pp 466

2 Z Zhou The origin and early evolution of birds Discoveriesdisputes and perspectives from fossil evidenceNaturwissenschaften 91 455ndash471 (2004) doi 101007s00114-004-0570-4 pmid 15365634

3 L M Witmer in Mesozoic Birds Above the Heads ofDinosaurs L M Chiappe L M Witmer Eds (Univ ofCalifornia Press Berkeley 2002) pp 3ndash30

4 R O Prum Development and evolutionary origin of feathersJ Exp Zool 285 291ndash306 (1999) doi 101002(SICI)1097-010X(19991215)2854lt291AID-JEZ1gt30CO2-9pmid 10578107

5 M Yu P Wu R B Widelitz C-M Chuong Themorphogenesis of feathers Nature 420 308ndash312 (2002)doi 101038nature01196 pmid 12442169

6 A O Vargas T Kohlsdorf J F Fallon J VandenbrooksG P Wagner The evolution of HoxD-11 expression in thebird wing Insights from Alligator mississippiensis PLOS ONE3 e3325 (2008) doi 101371journalpone0003325pmid 18833328

7 C G Farmer K Sanders Unidirectional airflow in the lungsof alligators Science 327 338ndash340 (2010) doi 101126science1180219 pmid 20075253

8 K Tamura N Nomura R Seki S Yonei-TamuraH Yokoyama Embryological evidence identifies wing digitsin birds as digits 1 2 and 3 Science 331 753ndash757 (2011)doi 101126science1198229 pmid 21311019

9 C L Organ A M Shedlock A Meade M PagelS V Edwards Origin of avian genome size and structurein non-avian dinosaurs Nature 446 180ndash184 (2007)doi 101038nature05621 pmid 17344851

10 D Evangelista et al Aerodynamic characteristics of afeathered dinosaur measured using physical modelsEffects of form on static stability and control effectivenessPLOS ONE 9 e85203 (2014) doi 101371journalpone0085203 pmid 24454820

11 K P Dial Wing-assisted incline running and the evolutionof flight Science 299 402ndash404 (2003) doi 101126science1078237 pmid 12532020

12 F C James J A Pourtless IV Cladistics and the origin ofbirds A review and two new analyses Ornithol Monogr66 1ndash78 (2009) doi 101525om20096611

13 M Norell X Xu Feathered dinosaurs Annu Rev EarthPlanet Sci 33 277ndash299 (2005) doi 101146annurevearth33092203122511

14 J Gauthier Saurischian monophyly and the origin of birdsMem Calif Acad Sci 8 1ndash55 (1986)

15 P C Sereno The evolution of dinosaurs Science 2842137ndash2147 (1999) doi 101126science28454232137pmid 10381873

16 A H Turner P J Makovicky M A Norell A review ofdromaeosaurid systematics and paravian phylogeny Bull AmMus Nat Hist 371 1ndash206 (2012) doi 1012067481

17 P Senter J I Kirkland D D DeBlieux S Madsen N TothNew dromaeosaurids (Dinosauria Theropoda) from theLower Cretaceous of Utah and the evolution of thedromaeosaurid tail PLOS ONE 7 e36790 (2012)doi 101371journalpone0036790 pmid 22615813

18 T R Holtz Jr A new phylogeny of the carnivorous dinosaursGaia 15 5ndash61 (1998)

19 O W M Rauhut The interrelationships and evolution ofbasal theropod dinosaurs Spec Pap Paleontology 69 1ndash213(2003)

20 M A Norell J M Clark P J Makovicky in New Perspectives onthe Origin and Evolution of Birds J Gauthier L F Gall Eds(Yale Univ Press New Haven CT 2001) pp 49ndash67

21 P Godefroit et al A Jurassic avialan dinosaur from Chinaresolves the early phylogenetic history of birds Nature 498359ndash362 (2013) doi 101038nature12168 pmid 23719374

22 X Xu H You K Du F Han An Archaeopteryx-like theropodfrom China and the origin of Avialae Nature 475 465ndash470(2011) doi 101038nature10288 pmid 21796204

23 J N Choiniere et al A basal alvarezsauroid theropod fromthe early Late Jurassic of Xinjiang China Science 327571ndash574 (2010) doi 101126science1182143pmid 20110503

24 J H Ostrom The osteology of Deinonychus antirrhopus anunusual theropod from the Lower Cretaceous of MontanaBull Peabody Mus Nat Hist 30 1ndash165 (1969)

25 R Barsbold Predatory dinosaurs from the Cretaceousof Mongolia Tr Sovm Sov-Mong Paleontol Eksped 191ndash117 (1983)

26 O Wings thesis The University of Bonn (2004)27 P M OrsquoConnor L P A M Claessens Basic avian pulmonary

design and flow-through ventilation in non-avian theropoddinosaurs Nature 436 253ndash256 (2005) doi 101038nature03716 pmid 16015329

28 P C Sereno et al Evidence for avian intrathoracic air sacsin a new predatory dinosaur from Argentina PLOS ONE3 e3303 (2008) doi 101371journalpone0003303pmid 18825273

29 R B J Benson R J Butler M T Carrano P M OrsquoConnorAir-filled postcranial bones in theropod dinosaursPhysiological implications and the lsquoreptilersquo-bird transitionBiol Rev Camb Philos Soc 87 168ndash193 (2012) doi 101111j1469-185X201100190x pmid 21733078

30 M A Norell J M Clark L M Chiappe D DashzevegA nesting dinosaur Nature 378 774ndash776 (1995)doi 101038378774a0

31 D J Varricchio F Jackson J J Borkowski J R HornerNest and egg clutches of the dinosaur Troodon formosusand the evolution of avian reproductive traits Nature 385247ndash250 (1997) doi 101038385247a0

32 G M Erickson K Curry Rogers D J Varricchio M A NorellX Xu Growth patterns in brooding dinosaurs reveals thetiming of sexual maturity in non-avian dinosaurs and genesisof the avian condition Biol Lett 3 558ndash561 (2007)pmid 17638674

33 G Grellet-Tinner P Makovicky A possible egg of thedromaeosaur Deinonychus antirrhopus Phylogenetic andbiological implications Can J Earth Sci 43 705ndash719 (2006)doi 101139e06-033

34 G Grellet-Tinner L M Chiappe in Feathered DragonsStudies on the Transition from Dinosaurs to Birds P J CurrieE B Koppelhus M A Shugar J L Wright Eds (IndianaUniv Press Bloomington 2004) pp 185ndash214

35 D J Varricchio F D Jackson A phylogenetic assessment ofprismatic dinosaur eggs from the Cretaceous Two MedicineFormation of Montana J Vertebr Paleontol 24 931ndash937 (2004)doi 1016710272-4634(2004)024[0931APAOPD]20CO2

36 D K Zelenitsky F Therrien Phylogenetic analysis ofreproductive traits of maniraptoran theropods and itsimplications for egg parataxonomy Paleontology 51 807ndash816(2008) doi 101111j1475-4983200800770x

37 K Padian A J de Ricqlegraves J R Horner Dinosaurian growthrates and bird origins Nature 412 405ndash408 (2001)doi 10103835086500 pmid 11473307

38 F L Agnoliacuten F E Novas Avian Ancestors A Review of thePhylogenetic Relationships of the Theropods UnenlagiidaeMicroraptoria Anchiornis and Scansoriopterygidae (SpringerDordrecht Heidelberg 2013)

39 P J Makovicky L E Zanno in Living Dinosaurs TheEvolutionary History of Modern Birds G J Dyke G KaiserEds (Wiley-Blackwell Oxford 2011) pp 9ndash29

A highly efficient flow-through ventilation anda high-compliance air-sac system uniquely char-acterize the avialan respiratory system (27) Per-ceived differences in the respiratory systems oftheropods and other reptiles such as crocodi-lians from those of birds have been invalidlyused as evidence against the BMT hypothesis(49) Nevertheless cervical and anterior dorsalvertebrae are clearly pneumatic in nearly alltheropods (29) and documentation of exten-sive skeletal pneumaticity in theropods such asMajungasaurus and Aerosteon (27 28) dem-onstrates that a complex air-sac system andbirdlike respiration evolved in birdsrsquo theropodancestors (Fig 4B) Furthermore recent ana-tomical and physiological studies reveal thatalligators (7 113) and even monitor lizards (114)exhibit respiratory systems and unidirectionalbreathing akin to those of birds These studiesdemonstrate that unidirectional breathing is aprimitive characteristic of archosaurs or an evenmore inclusive group with the complex air-sacsystem evolving later within Archosauria Weightsavings might have driven the evolution of post-cranial skeletal pneumatization in early theropods

(29) and in addition to large-bodied theropodssmall maniraptoran theropods such as basaloviraptorosaurs dromaeosaurs and troodontidsevolved the complex air-sac system similar tothat of birds (28 29)

Morphogenesis and early evolution of feathersFeathers were once considered to be uniqueavialan structures The presence of feathers isinferred in several theropods based on osteo-logical correlates eg quill knobs (115 116) [al-though the presence of quill knobs in the basaltetanuran Concavenator has been questioned(117)] or pygostyles (118) Short filaments havebeen identified as feathers in the alvarezsaurShuvuuia (119) Direct evidence came to lightin China in 1996 with the discovery of the fea-thered Sinosauropteryx (120) Since then nu-merous specimens of most theropod groups andeven three ornithischian groups preserving fea-thers have been recovered from the Jurassicand Cretaceous beds of northeastern China(13 21 41 45 57) and from the Jurassic andCretaceous beds of Germany Russia and Canada

(55 56 121ndash123) These feathers fall into severalmajor morphotypes (Fig 5) ranging from mono-filamentous feathers to highly complex flightfeathers (57) The phylogenetic distribution ofthese feathers largely concurs with the predic-tions from a developmental model of living birds(4) although some of these morphotypes areabsent in living birds (57 124)The findings of feathers in dinosaurs prompted

developmental studies over the last decade in-vestigating the molecular mechanisms regulat-ing feather development and regeneration inchickens (125) We can now propose the follow-ing ldquomolecular circuitsrdquo regarding tissue morpho-genesis and the evolution of modern feathersEach molecular circuit has specific features andcan be modulated to produce a diversity ofmorphology(i) Cylindrical topology and the downshift of

stem cell ring The formation of loose mesen-chyme in the bud core allows a tube configura-tion with basal layer facing inside Driven byWnt signaling feather stem cells now are posi-tioned near the base forming a ring config-uration (126 127) It can remain as a tube or the

Fig 5 The morphogenesis and evolution of feathers in dinosaurs (A)Monofilamentous feathers in Tianyulong (B) Broad monofilamentous feathers inBeipiaosaurus Radially branched feathers in Sinosauropteryx (C) Sinornitho-saurus (D) and Anchiornis (E) Bilaterally branched feathers in Dilong (F)and Sinornithosaurus (G) (H) Wing flight feathers with symmetrical vanesin Anchiornis (I) Pedal flight feathers with asymmetrical vanes in Micro-raptor (J) Rachis-dominant tail feathers in Confuciusornis (K) Proximally

ribbonlike tail feathers in Similicaudipteryx (L) Phylogenetic distribution ofmajor feather morphotypes (monofilamentous radially branched bilater-ally branched symmetrical flight and asymmetrical flight feathers) amongdinosaurs (M) Major novel morphogenetic events and molecular pathwaysduring feather evolutionThese major feather morphotypes can be explained byselective usage of the five novel ldquomolecular circuitsrdquo discussed in the text Redarrows flank a feather

subsequent caspase-dependent selective apopto-sis can open up the tube allowing feather vaneformation (128)(ii) Hierarchical branching and barbbarbule

pattern formation Ratio of local activators (nog-gin Shh and so on) and inhibitors (bone mor-phogenetic proteins) regulate the number andsize of barb versus rachidial ridges (5 129) Barbridges which depend on Wnt 3a gradient canrun parallel to each other to form radial sym-metric feathers or angle toward the rachis toform bilateral symmetric feathers (130)(iii) Follicle formation and regenerative cycling

During development matrix maetalloproteinasendashdependent tissue invagination allows epithelia totopologically fold into a follicle (131) Follicle con-figuration allows protection of feather progenitorsStem cells and dermal papilla are now clusterednear the follicle base and can undergo dickkopfWntndashdependent cyclic regeneration (132)(iv) Temporal regulation of stem cells along

the proximal-distal axis During feather forma-tion the molecular microenvironment and mor-phology can change along the distal (formedearlier) and proximal (formed later) throughmodulation of fibroblast growth factorndashsproutactivity (133)(v) Organ metamorphosis and regional spe-

cific feather types Upon regeneration modulatedby the body macroenvironments different fea-ther morphotypes (downy contour and flightfeathers) can form on different body regions andin different physiological stages for optimal per-formance (134)The aforementioned morphogenetic proces-

ses can be assembled selectively in various or-ders and independently to produce basic-tondashmore complex feather morphotypes (Fig 5) Themonofilamentous feathers seen in ornithischians(54 56 57) and some theropods (55 57) two setsof morphologically different flight feathersduring ontogeny in the oviraptorosau-rian Similicaudipteryx (124) and theextensive leg feathering (particular-ly pedal feathering) in a number oftheropods and early birds (135) implya variety of rearrangements in themorphogenetic modules The wide oc-currence of pedal feathering in the-ropods and early birds (135) and anextensive distribution of scales onthe bodies of both feathered thero-pods (eg Juravenator) and featheredornithischians (eg the ceratopsianPsittacosaurus and the ornithopodKullindadromeus) remain particularlyinteresting from both developmentaland evolutionary perspectives (56 135)and will no doubt play into further dis-cussions on feather-scale relationshipsThe diverse forms of theropod fea-

thers apparently suggest a comparablemyriad of functions Initial functionsof feathers more likely include ther-moregulation and communication rath-er than flight (57) Several differentlines of data highlight the importance

of communication in early feather evolution(41 57 117 136) particularly by color patternsinferred via preserved melanosome morpho-logies in some theropods and early birds (136 137)although several studies have questioned theidentifications of melanosomes in specimensof feathered theropods and early birds (48 138)One study shows an increased diversity of melano-some morphologies associated with the appear-ance of complex pinnate feathers during theropodevolution (72) This finding supports developmentaldata showing that unique topological arrange-ments allowing feathers to generate complex formsalso permits the generation of visibly complexpigment patterns and pattern renewal duringsexual maturation (139)

Four-winged dinosaurs and the origins of aerial behaviorSeveral flight-related anatomical features suchas hollow bones and the furcula originated inearly theropods basal paravians had many hall-mark features necessary for flight includingextremely small body size (50 70) a laterallyoriented long and robust forelimb (22 67) anenlarged forebrain and other derived neurolog-ical adaptations (71) and large flight feathers(Figs 1 and 2) Particularly surprising are therecent discoveries of large flight feathers form-ing a planar surface on the legs of some basalparaviansmdashfor example those with asymmetricalvanes on both the tibia and metatarsus of somebasal dromaeosaurs such as Microraptor (59)large feathers with symmetrical vanes on both thetibia and metatarsus of the troodontid Anchiornis(45) the basal bird Sapeornis and several otherbasal paravians (135) and large vaned feath-ers on tibiae of several basal birds includingArchaeopteryx confuciusornithids and enan-tiornithines (135) These structures clearly wouldhave been relevant to flight origins The evolu-

tion of flight nonetheless remains highly de-bated with a few recently proposed scenariosincluding factors as diverse as muscle hyperpla-sia (140) and the use of wings to assist in cur-sorial ascent of inclines based on neontologicalobservations (11) Multifactorial explanations forthe origins of flight are likely as this behaviorhas not been uniquely categorized given varia-bility in wing and tail configurations amongtheropods and early birds (45 59 135 141 142)flight probably had complex biomechanicalorigins (142 143)Fundamental to all hypotheses of wing evo-

lution however must be consideration of thosecircumstances that elicited aerial behavior inancestrally terrestrial taxa In all extant verte-brate and invertebrate gliders flight is associ-ated with gravitational acceleration downwardfrom heights and with the use in aerodynamiccontrol of diverse body structures including butnot limited to limbs once aloft (143) The dis-coveries of four-winged theropods and earlybirds (Fig 6) are consistent with the gravity-assisted hypothesis for the origin of bird flightMoreover the concurrent presence of a largeand flattened tail along with potential use ofthe feathered hind legs in aerodynamic controlsuggests substantial capacity for using these asrudders and for maneuvering even during theearliest stages of bird evolution (10 144) Aerialrighting reflexes targeting movement while aloftand controlled landings all would have been en-hanced via bilaterally asymmetric motions ofeither wing pair In other words incipient andnonequilibrium flight behaviors would poten-tially associate with a four-winged and long-tailed arrangement in theropods and early birds(Fig 6) There still remains disagreement as tothe definitional criteria used to indicate thefour-winged and long-tailed condition and as towhether large flight feathers with symmetrical

Columba

JeholornisSapeornis

Archaeopteryx

AnchiornisMicroraptor

Epidexipteryx

Fig 6 Airfoils of selectedmaniraptorans Airfoils (in blue) of the basal dromaeosaurMicroraptor the basal troodontidAnchiornis the basal birds Archaeopteryx Sapeornis and Jeholornis and a modern pigeon Feathered airfoils aregreater in number and are more distally positioned in early birds and their closest theropod relatives than inmodern birds The scansoriopterygid Epidexipteryx has stiff downlike feathers (in green) on both the forelimb andhindlimb and long ribbonlike feathers on the tail the aerodynamic functions of which remain poorly known

vanes in some basal paravians including earlybirds would create useful aerodynamic forcesduring aerial behaviors (117)Use of the hind wings and potentially the

tail to generate vertical force also results in amore posterior and stable position for the cen-ter of lift (10 144) (as can be deduced from batand pterosaur wings based on patagial connec-tions to the hindlegs) Such a hindwing config-uration contributes to static stability in glidingwhereas subsequent functional shifts to the fore-wings alone with associated reductions in tailsize and leg feathering (135) would have requiredoffsetting aerodynamic control via flapping mo-tions (145) Potential tradeoffs between increasedsize of the forewings and the intensity of theirkinematic activation (eg greater frequency andamplitude of flapping) are not well understoodalthough robotic models of early avialan mor-phologies can be informative (146) Such progres-sive anterior specialization of the flight apparatuswith enhanced forces produced by the emergingforelimb locomotor module (145) is nonethelessderived from an ancestrally four-winged plat-form (Fig 6)

Future perspectivesAlternative phylogenetic hypotheses suggest adifferent evolutionary sequence of major birdcharacteristics and imply a different ecologicalorigin of the group (22) Consequently a refinedmore robust phylogeny will be imperative tomove our studies forward Increasing characterand taxon sampling in recent theropod phylo-genetic studies has in theory helped improvethe accuracy of phylogenetic reconstructions butbetter character formulation and more accuratescorings are imperative at present pending bet-ter understanding of the morphologies of manyrecently discovered transitional formsIn terms of character evolution an integrative

approach combining paleontological neontolog-ical developmental geochronological and evenpaleoenvironmental data is particularly desir-able A recent integrative study combining de-velopmental neontological and paleontologicaldata shows that birds evolved their highly spe-cialized cranium mainly by paedomorphisis (147)another study using both neontological and pa-leontological data to reconstruct melanosomeevolution suggests that feathers have changedsignificantly in their melanosome morphologyamong pennaraptoran theropods which impliesa physiological shift before the evolution of flight(72) and that concurs in association with exten-sive postcranial skeletal pneumaticity whichsuggests the presence of birdlike endothermy(29) Similar approaches should be applied toother major structures Certain avialan structuressuch as feathers and visual system are novel inboth genetic and morphological terms There areemerging data on how the genetic code affects themorphogenesis of these structures in developmen-tal biology How the genetic code and expressionpattern evolved can be inferred by a detailedcomparison of homologous structures in thero-pods early birds and modern birds

The construction of molecular phylogenieswould enable a much better understanding ofthe genealogical relations among birds and theirtheropod relatives and the steps leading to theevolution of birds Although once the topic ofscience-fiction movies preserved organic remainshave purportedly been recovered from Tyranno-saurus and the hadrosaur Brachylophosaurus(148 149) and from even older fossils such asEarly Jurassic Lufengosaurus specimens (150)Greater examination along these lines in fossilsspanning the theropod-bird transition is a po-tentially fruitful avenue for future investigationThe increasing interest in the origins of birds

from developmental biology and other disciplineshas enriched our understanding of this impor-tant evolutionary event (8 10 11) and alternativeevolutionary models on various aspects of theorigin of birds have sometimes been providedbased on neontological data (4 11) Howeverany evolutionary model must be tested using thefossil record Consequently dense fossil samplingalong the line to birds and better understandingof the transitional forms play a key role in thediscussion on this issue

REFERENCES AND NOTES

1 A Feduccia The Origin and Evolution of Birds (Yale UnivPress New Haven CT ed 2 1999) pp 466

2 Z Zhou The origin and early evolution of birds Discoveriesdisputes and perspectives from fossil evidenceNaturwissenschaften 91 455ndash471 (2004) doi 101007s00114-004-0570-4 pmid 15365634

3 L M Witmer in Mesozoic Birds Above the Heads ofDinosaurs L M Chiappe L M Witmer Eds (Univ ofCalifornia Press Berkeley 2002) pp 3ndash30

4 R O Prum Development and evolutionary origin of feathersJ Exp Zool 285 291ndash306 (1999) doi 101002(SICI)1097-010X(19991215)2854lt291AID-JEZ1gt30CO2-9pmid 10578107

5 M Yu P Wu R B Widelitz C-M Chuong Themorphogenesis of feathers Nature 420 308ndash312 (2002)doi 101038nature01196 pmid 12442169

6 A O Vargas T Kohlsdorf J F Fallon J VandenbrooksG P Wagner The evolution of HoxD-11 expression in thebird wing Insights from Alligator mississippiensis PLOS ONE3 e3325 (2008) doi 101371journalpone0003325pmid 18833328

7 C G Farmer K Sanders Unidirectional airflow in the lungsof alligators Science 327 338ndash340 (2010) doi 101126science1180219 pmid 20075253

8 K Tamura N Nomura R Seki S Yonei-TamuraH Yokoyama Embryological evidence identifies wing digitsin birds as digits 1 2 and 3 Science 331 753ndash757 (2011)doi 101126science1198229 pmid 21311019

9 C L Organ A M Shedlock A Meade M PagelS V Edwards Origin of avian genome size and structurein non-avian dinosaurs Nature 446 180ndash184 (2007)doi 101038nature05621 pmid 17344851

10 D Evangelista et al Aerodynamic characteristics of afeathered dinosaur measured using physical modelsEffects of form on static stability and control effectivenessPLOS ONE 9 e85203 (2014) doi 101371journalpone0085203 pmid 24454820

11 K P Dial Wing-assisted incline running and the evolutionof flight Science 299 402ndash404 (2003) doi 101126science1078237 pmid 12532020

12 F C James J A Pourtless IV Cladistics and the origin ofbirds A review and two new analyses Ornithol Monogr66 1ndash78 (2009) doi 101525om20096611

13 M Norell X Xu Feathered dinosaurs Annu Rev EarthPlanet Sci 33 277ndash299 (2005) doi 101146annurevearth33092203122511

14 J Gauthier Saurischian monophyly and the origin of birdsMem Calif Acad Sci 8 1ndash55 (1986)

15 P C Sereno The evolution of dinosaurs Science 2842137ndash2147 (1999) doi 101126science28454232137pmid 10381873

16 A H Turner P J Makovicky M A Norell A review ofdromaeosaurid systematics and paravian phylogeny Bull AmMus Nat Hist 371 1ndash206 (2012) doi 1012067481

17 P Senter J I Kirkland D D DeBlieux S Madsen N TothNew dromaeosaurids (Dinosauria Theropoda) from theLower Cretaceous of Utah and the evolution of thedromaeosaurid tail PLOS ONE 7 e36790 (2012)doi 101371journalpone0036790 pmid 22615813

18 T R Holtz Jr A new phylogeny of the carnivorous dinosaursGaia 15 5ndash61 (1998)

19 O W M Rauhut The interrelationships and evolution ofbasal theropod dinosaurs Spec Pap Paleontology 69 1ndash213(2003)

20 M A Norell J M Clark P J Makovicky in New Perspectives onthe Origin and Evolution of Birds J Gauthier L F Gall Eds(Yale Univ Press New Haven CT 2001) pp 49ndash67

21 P Godefroit et al A Jurassic avialan dinosaur from Chinaresolves the early phylogenetic history of birds Nature 498359ndash362 (2013) doi 101038nature12168 pmid 23719374

22 X Xu H You K Du F Han An Archaeopteryx-like theropodfrom China and the origin of Avialae Nature 475 465ndash470(2011) doi 101038nature10288 pmid 21796204

23 J N Choiniere et al A basal alvarezsauroid theropod fromthe early Late Jurassic of Xinjiang China Science 327571ndash574 (2010) doi 101126science1182143pmid 20110503

24 J H Ostrom The osteology of Deinonychus antirrhopus anunusual theropod from the Lower Cretaceous of MontanaBull Peabody Mus Nat Hist 30 1ndash165 (1969)

25 R Barsbold Predatory dinosaurs from the Cretaceousof Mongolia Tr Sovm Sov-Mong Paleontol Eksped 191ndash117 (1983)

26 O Wings thesis The University of Bonn (2004)27 P M OrsquoConnor L P A M Claessens Basic avian pulmonary

design and flow-through ventilation in non-avian theropoddinosaurs Nature 436 253ndash256 (2005) doi 101038nature03716 pmid 16015329

28 P C Sereno et al Evidence for avian intrathoracic air sacsin a new predatory dinosaur from Argentina PLOS ONE3 e3303 (2008) doi 101371journalpone0003303pmid 18825273

29 R B J Benson R J Butler M T Carrano P M OrsquoConnorAir-filled postcranial bones in theropod dinosaursPhysiological implications and the lsquoreptilersquo-bird transitionBiol Rev Camb Philos Soc 87 168ndash193 (2012) doi 101111j1469-185X201100190x pmid 21733078

30 M A Norell J M Clark L M Chiappe D DashzevegA nesting dinosaur Nature 378 774ndash776 (1995)doi 101038378774a0

31 D J Varricchio F Jackson J J Borkowski J R HornerNest and egg clutches of the dinosaur Troodon formosusand the evolution of avian reproductive traits Nature 385247ndash250 (1997) doi 101038385247a0

32 G M Erickson K Curry Rogers D J Varricchio M A NorellX Xu Growth patterns in brooding dinosaurs reveals thetiming of sexual maturity in non-avian dinosaurs and genesisof the avian condition Biol Lett 3 558ndash561 (2007)pmid 17638674

33 G Grellet-Tinner P Makovicky A possible egg of thedromaeosaur Deinonychus antirrhopus Phylogenetic andbiological implications Can J Earth Sci 43 705ndash719 (2006)doi 101139e06-033

34 G Grellet-Tinner L M Chiappe in Feathered DragonsStudies on the Transition from Dinosaurs to Birds P J CurrieE B Koppelhus M A Shugar J L Wright Eds (IndianaUniv Press Bloomington 2004) pp 185ndash214

35 D J Varricchio F D Jackson A phylogenetic assessment ofprismatic dinosaur eggs from the Cretaceous Two MedicineFormation of Montana J Vertebr Paleontol 24 931ndash937 (2004)doi 1016710272-4634(2004)024[0931APAOPD]20CO2

36 D K Zelenitsky F Therrien Phylogenetic analysis ofreproductive traits of maniraptoran theropods and itsimplications for egg parataxonomy Paleontology 51 807ndash816(2008) doi 101111j1475-4983200800770x

37 K Padian A J de Ricqlegraves J R Horner Dinosaurian growthrates and bird origins Nature 412 405ndash408 (2001)doi 10103835086500 pmid 11473307

38 F L Agnoliacuten F E Novas Avian Ancestors A Review of thePhylogenetic Relationships of the Theropods UnenlagiidaeMicroraptoria Anchiornis and Scansoriopterygidae (SpringerDordrecht Heidelberg 2013)

39 P J Makovicky L E Zanno in Living Dinosaurs TheEvolutionary History of Modern Birds G J Dyke G KaiserEds (Wiley-Blackwell Oxford 2011) pp 9ndash29

subsequent caspase-dependent selective apopto-sis can open up the tube allowing feather vaneformation (128)(ii) Hierarchical branching and barbbarbule

pattern formation Ratio of local activators (nog-gin Shh and so on) and inhibitors (bone mor-phogenetic proteins) regulate the number andsize of barb versus rachidial ridges (5 129) Barbridges which depend on Wnt 3a gradient canrun parallel to each other to form radial sym-metric feathers or angle toward the rachis toform bilateral symmetric feathers (130)(iii) Follicle formation and regenerative cycling

During development matrix maetalloproteinasendashdependent tissue invagination allows epithelia totopologically fold into a follicle (131) Follicle con-figuration allows protection of feather progenitorsStem cells and dermal papilla are now clusterednear the follicle base and can undergo dickkopfWntndashdependent cyclic regeneration (132)(iv) Temporal regulation of stem cells along

the proximal-distal axis During feather forma-tion the molecular microenvironment and mor-phology can change along the distal (formedearlier) and proximal (formed later) throughmodulation of fibroblast growth factorndashsproutactivity (133)(v) Organ metamorphosis and regional spe-

cific feather types Upon regeneration modulatedby the body macroenvironments different fea-ther morphotypes (downy contour and flightfeathers) can form on different body regions andin different physiological stages for optimal per-formance (134)The aforementioned morphogenetic proces-

ses can be assembled selectively in various or-ders and independently to produce basic-tondashmore complex feather morphotypes (Fig 5) Themonofilamentous feathers seen in ornithischians(54 56 57) and some theropods (55 57) two setsof morphologically different flight feathersduring ontogeny in the oviraptorosau-rian Similicaudipteryx (124) and theextensive leg feathering (particular-ly pedal feathering) in a number oftheropods and early birds (135) implya variety of rearrangements in themorphogenetic modules The wide oc-currence of pedal feathering in the-ropods and early birds (135) and anextensive distribution of scales onthe bodies of both feathered thero-pods (eg Juravenator) and featheredornithischians (eg the ceratopsianPsittacosaurus and the ornithopodKullindadromeus) remain particularlyinteresting from both developmentaland evolutionary perspectives (56 135)and will no doubt play into further dis-cussions on feather-scale relationshipsThe diverse forms of theropod fea-

thers apparently suggest a comparablemyriad of functions Initial functionsof feathers more likely include ther-moregulation and communication rath-er than flight (57) Several differentlines of data highlight the importance

of communication in early feather evolution(41 57 117 136) particularly by color patternsinferred via preserved melanosome morpho-logies in some theropods and early birds (136 137)although several studies have questioned theidentifications of melanosomes in specimensof feathered theropods and early birds (48 138)One study shows an increased diversity of melano-some morphologies associated with the appear-ance of complex pinnate feathers during theropodevolution (72) This finding supports developmentaldata showing that unique topological arrange-ments allowing feathers to generate complex formsalso permits the generation of visibly complexpigment patterns and pattern renewal duringsexual maturation (139)

Four-winged dinosaurs and the origins of aerial behaviorSeveral flight-related anatomical features suchas hollow bones and the furcula originated inearly theropods basal paravians had many hall-mark features necessary for flight includingextremely small body size (50 70) a laterallyoriented long and robust forelimb (22 67) anenlarged forebrain and other derived neurolog-ical adaptations (71) and large flight feathers(Figs 1 and 2) Particularly surprising are therecent discoveries of large flight feathers form-ing a planar surface on the legs of some basalparaviansmdashfor example those with asymmetricalvanes on both the tibia and metatarsus of somebasal dromaeosaurs such as Microraptor (59)large feathers with symmetrical vanes on both thetibia and metatarsus of the troodontid Anchiornis(45) the basal bird Sapeornis and several otherbasal paravians (135) and large vaned feath-ers on tibiae of several basal birds includingArchaeopteryx confuciusornithids and enan-tiornithines (135) These structures clearly wouldhave been relevant to flight origins The evolu-

tion of flight nonetheless remains highly de-bated with a few recently proposed scenariosincluding factors as diverse as muscle hyperpla-sia (140) and the use of wings to assist in cur-sorial ascent of inclines based on neontologicalobservations (11) Multifactorial explanations forthe origins of flight are likely as this behaviorhas not been uniquely categorized given varia-bility in wing and tail configurations amongtheropods and early birds (45 59 135 141 142)flight probably had complex biomechanicalorigins (142 143)Fundamental to all hypotheses of wing evo-

lution however must be consideration of thosecircumstances that elicited aerial behavior inancestrally terrestrial taxa In all extant verte-brate and invertebrate gliders flight is associ-ated with gravitational acceleration downwardfrom heights and with the use in aerodynamiccontrol of diverse body structures including butnot limited to limbs once aloft (143) The dis-coveries of four-winged theropods and earlybirds (Fig 6) are consistent with the gravity-assisted hypothesis for the origin of bird flightMoreover the concurrent presence of a largeand flattened tail along with potential use ofthe feathered hind legs in aerodynamic controlsuggests substantial capacity for using these asrudders and for maneuvering even during theearliest stages of bird evolution (10 144) Aerialrighting reflexes targeting movement while aloftand controlled landings all would have been en-hanced via bilaterally asymmetric motions ofeither wing pair In other words incipient andnonequilibrium flight behaviors would poten-tially associate with a four-winged and long-tailed arrangement in theropods and early birds(Fig 6) There still remains disagreement as tothe definitional criteria used to indicate thefour-winged and long-tailed condition and as towhether large flight feathers with symmetrical

Columba

JeholornisSapeornis

Archaeopteryx

AnchiornisMicroraptor

Epidexipteryx

Fig 6 Airfoils of selectedmaniraptorans Airfoils (in blue) of the basal dromaeosaurMicroraptor the basal troodontidAnchiornis the basal birds Archaeopteryx Sapeornis and Jeholornis and a modern pigeon Feathered airfoils aregreater in number and are more distally positioned in early birds and their closest theropod relatives than inmodern birds The scansoriopterygid Epidexipteryx has stiff downlike feathers (in green) on both the forelimb andhindlimb and long ribbonlike feathers on the tail the aerodynamic functions of which remain poorly known

vanes in some basal paravians including earlybirds would create useful aerodynamic forcesduring aerial behaviors (117)Use of the hind wings and potentially the

tail to generate vertical force also results in amore posterior and stable position for the cen-ter of lift (10 144) (as can be deduced from batand pterosaur wings based on patagial connec-tions to the hindlegs) Such a hindwing config-uration contributes to static stability in glidingwhereas subsequent functional shifts to the fore-wings alone with associated reductions in tailsize and leg feathering (135) would have requiredoffsetting aerodynamic control via flapping mo-tions (145) Potential tradeoffs between increasedsize of the forewings and the intensity of theirkinematic activation (eg greater frequency andamplitude of flapping) are not well understoodalthough robotic models of early avialan mor-phologies can be informative (146) Such progres-sive anterior specialization of the flight apparatuswith enhanced forces produced by the emergingforelimb locomotor module (145) is nonethelessderived from an ancestrally four-winged plat-form (Fig 6)

Future perspectivesAlternative phylogenetic hypotheses suggest adifferent evolutionary sequence of major birdcharacteristics and imply a different ecologicalorigin of the group (22) Consequently a refinedmore robust phylogeny will be imperative tomove our studies forward Increasing characterand taxon sampling in recent theropod phylo-genetic studies has in theory helped improvethe accuracy of phylogenetic reconstructions butbetter character formulation and more accuratescorings are imperative at present pending bet-ter understanding of the morphologies of manyrecently discovered transitional formsIn terms of character evolution an integrative

approach combining paleontological neontolog-ical developmental geochronological and evenpaleoenvironmental data is particularly desir-able A recent integrative study combining de-velopmental neontological and paleontologicaldata shows that birds evolved their highly spe-cialized cranium mainly by paedomorphisis (147)another study using both neontological and pa-leontological data to reconstruct melanosomeevolution suggests that feathers have changedsignificantly in their melanosome morphologyamong pennaraptoran theropods which impliesa physiological shift before the evolution of flight(72) and that concurs in association with exten-sive postcranial skeletal pneumaticity whichsuggests the presence of birdlike endothermy(29) Similar approaches should be applied toother major structures Certain avialan structuressuch as feathers and visual system are novel inboth genetic and morphological terms There areemerging data on how the genetic code affects themorphogenesis of these structures in developmen-tal biology How the genetic code and expressionpattern evolved can be inferred by a detailedcomparison of homologous structures in thero-pods early birds and modern birds

The construction of molecular phylogenieswould enable a much better understanding ofthe genealogical relations among birds and theirtheropod relatives and the steps leading to theevolution of birds Although once the topic ofscience-fiction movies preserved organic remainshave purportedly been recovered from Tyranno-saurus and the hadrosaur Brachylophosaurus(148 149) and from even older fossils such asEarly Jurassic Lufengosaurus specimens (150)Greater examination along these lines in fossilsspanning the theropod-bird transition is a po-tentially fruitful avenue for future investigationThe increasing interest in the origins of birds

from developmental biology and other disciplineshas enriched our understanding of this impor-tant evolutionary event (8 10 11) and alternativeevolutionary models on various aspects of theorigin of birds have sometimes been providedbased on neontological data (4 11) Howeverany evolutionary model must be tested using thefossil record Consequently dense fossil samplingalong the line to birds and better understandingof the transitional forms play a key role in thediscussion on this issue

REFERENCES AND NOTES

1 A Feduccia The Origin and Evolution of Birds (Yale UnivPress New Haven CT ed 2 1999) pp 466

2 Z Zhou The origin and early evolution of birds Discoveriesdisputes and perspectives from fossil evidenceNaturwissenschaften 91 455ndash471 (2004) doi 101007s00114-004-0570-4 pmid 15365634

3 L M Witmer in Mesozoic Birds Above the Heads ofDinosaurs L M Chiappe L M Witmer Eds (Univ ofCalifornia Press Berkeley 2002) pp 3ndash30

4 R O Prum Development and evolutionary origin of feathersJ Exp Zool 285 291ndash306 (1999) doi 101002(SICI)1097-010X(19991215)2854lt291AID-JEZ1gt30CO2-9pmid 10578107

5 M Yu P Wu R B Widelitz C-M Chuong Themorphogenesis of feathers Nature 420 308ndash312 (2002)doi 101038nature01196 pmid 12442169

6 A O Vargas T Kohlsdorf J F Fallon J VandenbrooksG P Wagner The evolution of HoxD-11 expression in thebird wing Insights from Alligator mississippiensis PLOS ONE3 e3325 (2008) doi 101371journalpone0003325pmid 18833328

7 C G Farmer K Sanders Unidirectional airflow in the lungsof alligators Science 327 338ndash340 (2010) doi 101126science1180219 pmid 20075253

8 K Tamura N Nomura R Seki S Yonei-TamuraH Yokoyama Embryological evidence identifies wing digitsin birds as digits 1 2 and 3 Science 331 753ndash757 (2011)doi 101126science1198229 pmid 21311019

9 C L Organ A M Shedlock A Meade M PagelS V Edwards Origin of avian genome size and structurein non-avian dinosaurs Nature 446 180ndash184 (2007)doi 101038nature05621 pmid 17344851

10 D Evangelista et al Aerodynamic characteristics of afeathered dinosaur measured using physical modelsEffects of form on static stability and control effectivenessPLOS ONE 9 e85203 (2014) doi 101371journalpone0085203 pmid 24454820

11 K P Dial Wing-assisted incline running and the evolutionof flight Science 299 402ndash404 (2003) doi 101126science1078237 pmid 12532020

12 F C James J A Pourtless IV Cladistics and the origin ofbirds A review and two new analyses Ornithol Monogr66 1ndash78 (2009) doi 101525om20096611

13 M Norell X Xu Feathered dinosaurs Annu Rev EarthPlanet Sci 33 277ndash299 (2005) doi 101146annurevearth33092203122511

14 J Gauthier Saurischian monophyly and the origin of birdsMem Calif Acad Sci 8 1ndash55 (1986)

15 P C Sereno The evolution of dinosaurs Science 2842137ndash2147 (1999) doi 101126science28454232137pmid 10381873

16 A H Turner P J Makovicky M A Norell A review ofdromaeosaurid systematics and paravian phylogeny Bull AmMus Nat Hist 371 1ndash206 (2012) doi 1012067481

17 P Senter J I Kirkland D D DeBlieux S Madsen N TothNew dromaeosaurids (Dinosauria Theropoda) from theLower Cretaceous of Utah and the evolution of thedromaeosaurid tail PLOS ONE 7 e36790 (2012)doi 101371journalpone0036790 pmid 22615813

18 T R Holtz Jr A new phylogeny of the carnivorous dinosaursGaia 15 5ndash61 (1998)

19 O W M Rauhut The interrelationships and evolution ofbasal theropod dinosaurs Spec Pap Paleontology 69 1ndash213(2003)

20 M A Norell J M Clark P J Makovicky in New Perspectives onthe Origin and Evolution of Birds J Gauthier L F Gall Eds(Yale Univ Press New Haven CT 2001) pp 49ndash67

21 P Godefroit et al A Jurassic avialan dinosaur from Chinaresolves the early phylogenetic history of birds Nature 498359ndash362 (2013) doi 101038nature12168 pmid 23719374

22 X Xu H You K Du F Han An Archaeopteryx-like theropodfrom China and the origin of Avialae Nature 475 465ndash470(2011) doi 101038nature10288 pmid 21796204

23 J N Choiniere et al A basal alvarezsauroid theropod fromthe early Late Jurassic of Xinjiang China Science 327571ndash574 (2010) doi 101126science1182143pmid 20110503

24 J H Ostrom The osteology of Deinonychus antirrhopus anunusual theropod from the Lower Cretaceous of MontanaBull Peabody Mus Nat Hist 30 1ndash165 (1969)

25 R Barsbold Predatory dinosaurs from the Cretaceousof Mongolia Tr Sovm Sov-Mong Paleontol Eksped 191ndash117 (1983)

26 O Wings thesis The University of Bonn (2004)27 P M OrsquoConnor L P A M Claessens Basic avian pulmonary

design and flow-through ventilation in non-avian theropoddinosaurs Nature 436 253ndash256 (2005) doi 101038nature03716 pmid 16015329

28 P C Sereno et al Evidence for avian intrathoracic air sacsin a new predatory dinosaur from Argentina PLOS ONE3 e3303 (2008) doi 101371journalpone0003303pmid 18825273

29 R B J Benson R J Butler M T Carrano P M OrsquoConnorAir-filled postcranial bones in theropod dinosaursPhysiological implications and the lsquoreptilersquo-bird transitionBiol Rev Camb Philos Soc 87 168ndash193 (2012) doi 101111j1469-185X201100190x pmid 21733078

30 M A Norell J M Clark L M Chiappe D DashzevegA nesting dinosaur Nature 378 774ndash776 (1995)doi 101038378774a0

31 D J Varricchio F Jackson J J Borkowski J R HornerNest and egg clutches of the dinosaur Troodon formosusand the evolution of avian reproductive traits Nature 385247ndash250 (1997) doi 101038385247a0

32 G M Erickson K Curry Rogers D J Varricchio M A NorellX Xu Growth patterns in brooding dinosaurs reveals thetiming of sexual maturity in non-avian dinosaurs and genesisof the avian condition Biol Lett 3 558ndash561 (2007)pmid 17638674

33 G Grellet-Tinner P Makovicky A possible egg of thedromaeosaur Deinonychus antirrhopus Phylogenetic andbiological implications Can J Earth Sci 43 705ndash719 (2006)doi 101139e06-033

34 G Grellet-Tinner L M Chiappe in Feathered DragonsStudies on the Transition from Dinosaurs to Birds P J CurrieE B Koppelhus M A Shugar J L Wright Eds (IndianaUniv Press Bloomington 2004) pp 185ndash214

35 D J Varricchio F D Jackson A phylogenetic assessment ofprismatic dinosaur eggs from the Cretaceous Two MedicineFormation of Montana J Vertebr Paleontol 24 931ndash937 (2004)doi 1016710272-4634(2004)024[0931APAOPD]20CO2

36 D K Zelenitsky F Therrien Phylogenetic analysis ofreproductive traits of maniraptoran theropods and itsimplications for egg parataxonomy Paleontology 51 807ndash816(2008) doi 101111j1475-4983200800770x

37 K Padian A J de Ricqlegraves J R Horner Dinosaurian growthrates and bird origins Nature 412 405ndash408 (2001)doi 10103835086500 pmid 11473307

38 F L Agnoliacuten F E Novas Avian Ancestors A Review of thePhylogenetic Relationships of the Theropods UnenlagiidaeMicroraptoria Anchiornis and Scansoriopterygidae (SpringerDordrecht Heidelberg 2013)

39 P J Makovicky L E Zanno in Living Dinosaurs TheEvolutionary History of Modern Birds G J Dyke G KaiserEds (Wiley-Blackwell Oxford 2011) pp 9ndash29

vanes in some basal paravians including earlybirds would create useful aerodynamic forcesduring aerial behaviors (117)Use of the hind wings and potentially the

tail to generate vertical force also results in amore posterior and stable position for the cen-ter of lift (10 144) (as can be deduced from batand pterosaur wings based on patagial connec-tions to the hindlegs) Such a hindwing config-uration contributes to static stability in glidingwhereas subsequent functional shifts to the fore-wings alone with associated reductions in tailsize and leg feathering (135) would have requiredoffsetting aerodynamic control via flapping mo-tions (145) Potential tradeoffs between increasedsize of the forewings and the intensity of theirkinematic activation (eg greater frequency andamplitude of flapping) are not well understoodalthough robotic models of early avialan mor-phologies can be informative (146) Such progres-sive anterior specialization of the flight apparatuswith enhanced forces produced by the emergingforelimb locomotor module (145) is nonethelessderived from an ancestrally four-winged plat-form (Fig 6)

Future perspectivesAlternative phylogenetic hypotheses suggest adifferent evolutionary sequence of major birdcharacteristics and imply a different ecologicalorigin of the group (22) Consequently a refinedmore robust phylogeny will be imperative tomove our studies forward Increasing characterand taxon sampling in recent theropod phylo-genetic studies has in theory helped improvethe accuracy of phylogenetic reconstructions butbetter character formulation and more accuratescorings are imperative at present pending bet-ter understanding of the morphologies of manyrecently discovered transitional formsIn terms of character evolution an integrative

approach combining paleontological neontolog-ical developmental geochronological and evenpaleoenvironmental data is particularly desir-able A recent integrative study combining de-velopmental neontological and paleontologicaldata shows that birds evolved their highly spe-cialized cranium mainly by paedomorphisis (147)another study using both neontological and pa-leontological data to reconstruct melanosomeevolution suggests that feathers have changedsignificantly in their melanosome morphologyamong pennaraptoran theropods which impliesa physiological shift before the evolution of flight(72) and that concurs in association with exten-sive postcranial skeletal pneumaticity whichsuggests the presence of birdlike endothermy(29) Similar approaches should be applied toother major structures Certain avialan structuressuch as feathers and visual system are novel inboth genetic and morphological terms There areemerging data on how the genetic code affects themorphogenesis of these structures in developmen-tal biology How the genetic code and expressionpattern evolved can be inferred by a detailedcomparison of homologous structures in thero-pods early birds and modern birds

The construction of molecular phylogenieswould enable a much better understanding ofthe genealogical relations among birds and theirtheropod relatives and the steps leading to theevolution of birds Although once the topic ofscience-fiction movies preserved organic remainshave purportedly been recovered from Tyranno-saurus and the hadrosaur Brachylophosaurus(148 149) and from even older fossils such asEarly Jurassic Lufengosaurus specimens (150)Greater examination along these lines in fossilsspanning the theropod-bird transition is a po-tentially fruitful avenue for future investigationThe increasing interest in the origins of birds

from developmental biology and other disciplineshas enriched our understanding of this impor-tant evolutionary event (8 10 11) and alternativeevolutionary models on various aspects of theorigin of birds have sometimes been providedbased on neontological data (4 11) Howeverany evolutionary model must be tested using thefossil record Consequently dense fossil samplingalong the line to birds and better understandingof the transitional forms play a key role in thediscussion on this issue

REFERENCES AND NOTES

1 A Feduccia The Origin and Evolution of Birds (Yale UnivPress New Haven CT ed 2 1999) pp 466

2 Z Zhou The origin and early evolution of birds Discoveriesdisputes and perspectives from fossil evidenceNaturwissenschaften 91 455ndash471 (2004) doi 101007s00114-004-0570-4 pmid 15365634

3 L M Witmer in Mesozoic Birds Above the Heads ofDinosaurs L M Chiappe L M Witmer Eds (Univ ofCalifornia Press Berkeley 2002) pp 3ndash30

4 R O Prum Development and evolutionary origin of feathersJ Exp Zool 285 291ndash306 (1999) doi 101002(SICI)1097-010X(19991215)2854lt291AID-JEZ1gt30CO2-9pmid 10578107

5 M Yu P Wu R B Widelitz C-M Chuong Themorphogenesis of feathers Nature 420 308ndash312 (2002)doi 101038nature01196 pmid 12442169

6 A O Vargas T Kohlsdorf J F Fallon J VandenbrooksG P Wagner The evolution of HoxD-11 expression in thebird wing Insights from Alligator mississippiensis PLOS ONE3 e3325 (2008) doi 101371journalpone0003325pmid 18833328

7 C G Farmer K Sanders Unidirectional airflow in the lungsof alligators Science 327 338ndash340 (2010) doi 101126science1180219 pmid 20075253

8 K Tamura N Nomura R Seki S Yonei-TamuraH Yokoyama Embryological evidence identifies wing digitsin birds as digits 1 2 and 3 Science 331 753ndash757 (2011)doi 101126science1198229 pmid 21311019

9 C L Organ A M Shedlock A Meade M PagelS V Edwards Origin of avian genome size and structurein non-avian dinosaurs Nature 446 180ndash184 (2007)doi 101038nature05621 pmid 17344851

10 D Evangelista et al Aerodynamic characteristics of afeathered dinosaur measured using physical modelsEffects of form on static stability and control effectivenessPLOS ONE 9 e85203 (2014) doi 101371journalpone0085203 pmid 24454820

11 K P Dial Wing-assisted incline running and the evolutionof flight Science 299 402ndash404 (2003) doi 101126science1078237 pmid 12532020

12 F C James J A Pourtless IV Cladistics and the origin ofbirds A review and two new analyses Ornithol Monogr66 1ndash78 (2009) doi 101525om20096611

13 M Norell X Xu Feathered dinosaurs Annu Rev EarthPlanet Sci 33 277ndash299 (2005) doi 101146annurevearth33092203122511

14 J Gauthier Saurischian monophyly and the origin of birdsMem Calif Acad Sci 8 1ndash55 (1986)

15 P C Sereno The evolution of dinosaurs Science 2842137ndash2147 (1999) doi 101126science28454232137pmid 10381873

16 A H Turner P J Makovicky M A Norell A review ofdromaeosaurid systematics and paravian phylogeny Bull AmMus Nat Hist 371 1ndash206 (2012) doi 1012067481

17 P Senter J I Kirkland D D DeBlieux S Madsen N TothNew dromaeosaurids (Dinosauria Theropoda) from theLower Cretaceous of Utah and the evolution of thedromaeosaurid tail PLOS ONE 7 e36790 (2012)doi 101371journalpone0036790 pmid 22615813

18 T R Holtz Jr A new phylogeny of the carnivorous dinosaursGaia 15 5ndash61 (1998)

19 O W M Rauhut The interrelationships and evolution ofbasal theropod dinosaurs Spec Pap Paleontology 69 1ndash213(2003)

20 M A Norell J M Clark P J Makovicky in New Perspectives onthe Origin and Evolution of Birds J Gauthier L F Gall Eds(Yale Univ Press New Haven CT 2001) pp 49ndash67

21 P Godefroit et al A Jurassic avialan dinosaur from Chinaresolves the early phylogenetic history of birds Nature 498359ndash362 (2013) doi 101038nature12168 pmid 23719374

22 X Xu H You K Du F Han An Archaeopteryx-like theropodfrom China and the origin of Avialae Nature 475 465ndash470(2011) doi 101038nature10288 pmid 21796204

23 J N Choiniere et al A basal alvarezsauroid theropod fromthe early Late Jurassic of Xinjiang China Science 327571ndash574 (2010) doi 101126science1182143pmid 20110503

24 J H Ostrom The osteology of Deinonychus antirrhopus anunusual theropod from the Lower Cretaceous of MontanaBull Peabody Mus Nat Hist 30 1ndash165 (1969)

25 R Barsbold Predatory dinosaurs from the Cretaceousof Mongolia Tr Sovm Sov-Mong Paleontol Eksped 191ndash117 (1983)

26 O Wings thesis The University of Bonn (2004)27 P M OrsquoConnor L P A M Claessens Basic avian pulmonary

design and flow-through ventilation in non-avian theropoddinosaurs Nature 436 253ndash256 (2005) doi 101038nature03716 pmid 16015329

28 P C Sereno et al Evidence for avian intrathoracic air sacsin a new predatory dinosaur from Argentina PLOS ONE3 e3303 (2008) doi 101371journalpone0003303pmid 18825273

29 R B J Benson R J Butler M T Carrano P M OrsquoConnorAir-filled postcranial bones in theropod dinosaursPhysiological implications and the lsquoreptilersquo-bird transitionBiol Rev Camb Philos Soc 87 168ndash193 (2012) doi 101111j1469-185X201100190x pmid 21733078

30 M A Norell J M Clark L M Chiappe D DashzevegA nesting dinosaur Nature 378 774ndash776 (1995)doi 101038378774a0

31 D J Varricchio F Jackson J J Borkowski J R HornerNest and egg clutches of the dinosaur Troodon formosusand the evolution of avian reproductive traits Nature 385247ndash250 (1997) doi 101038385247a0

32 G M Erickson K Curry Rogers D J Varricchio M A NorellX Xu Growth patterns in brooding dinosaurs reveals thetiming of sexual maturity in non-avian dinosaurs and genesisof the avian condition Biol Lett 3 558ndash561 (2007)pmid 17638674

33 G Grellet-Tinner P Makovicky A possible egg of thedromaeosaur Deinonychus antirrhopus Phylogenetic andbiological implications Can J Earth Sci 43 705ndash719 (2006)doi 101139e06-033

34 G Grellet-Tinner L M Chiappe in Feathered DragonsStudies on the Transition from Dinosaurs to Birds P J CurrieE B Koppelhus M A Shugar J L Wright Eds (IndianaUniv Press Bloomington 2004) pp 185ndash214

35 D J Varricchio F D Jackson A phylogenetic assessment ofprismatic dinosaur eggs from the Cretaceous Two MedicineFormation of Montana J Vertebr Paleontol 24 931ndash937 (2004)doi 1016710272-4634(2004)024[0931APAOPD]20CO2

36 D K Zelenitsky F Therrien Phylogenetic analysis ofreproductive traits of maniraptoran theropods and itsimplications for egg parataxonomy Paleontology 51 807ndash816(2008) doi 101111j1475-4983200800770x

37 K Padian A J de Ricqlegraves J R Horner Dinosaurian growthrates and bird origins Nature 412 405ndash408 (2001)doi 10103835086500 pmid 11473307

38 F L Agnoliacuten F E Novas Avian Ancestors A Review of thePhylogenetic Relationships of the Theropods UnenlagiidaeMicroraptoria Anchiornis and Scansoriopterygidae (SpringerDordrecht Heidelberg 2013)

39 P J Makovicky L E Zanno in Living Dinosaurs TheEvolutionary History of Modern Birds G J Dyke G KaiserEds (Wiley-Blackwell Oxford 2011) pp 9ndash29

40 C A Forster S D Sampson L M Chiappe D W KrauseThe theropod ancestry of birds New evidence from theLate Cretaceous of Madagascar Science 279 1915ndash1919(1998) doi 101126science27953581915 pmid 9506938

41 F Zhang Z Zhou X Xu X Wang C Sullivan A bizarreJurassic maniraptoran from China with elongate ribbon-likefeathers Nature 455 1105ndash1108 (2008) doi 101038nature07447 pmid 18948955

42 X Xu et al A new feathered maniraptoran dinosaur fossilthat fills a morphological gap in avian origin Chin Sci Bull54 430ndash435 (2009) doi 101007s11434-009-0009-6

43 F E Novas P F Puertat New evidence concerning avianorigins from the Late Cretaceous of Patagonia Nature 387390ndash392 (1997) doi 101038387390a0

44 P J Makovicky S Apesteguiacutea F L Agnoliacuten The earliestdromaeosaurid theropod from South America Nature 4371007ndash1011 (2005) doi 101038nature03996 pmid 16222297

45 D Hu L Hou L Zhang X Xu A pre-Archaeopteryxtroodontid theropod from China with long feathers on themetatarsus Nature 461 640ndash643 (2009) doi 101038nature08322 pmid 19794491

46 X Xu Q-Y Ma D-Y Hu Pre-Archaeopteryx coelurosauriandinosaurs and their implications for understanding avianorigins Chin Sci Bull 55 3971ndash3977 (2010) doi 101007s11434-010-4150-z

47 J OConnor C Sullivan Vertebr PalAsiat 52 3 (2014)48 A Feduccia Bird origins anew Auk 130 1ndash12 (2013)

doi 101525auk20131301149 J A Ruben et al Pulmonary function and metabolic

physiology of theropod dinosaurs Science 283 514ndash516(1999) doi 101126science2835401514 pmid 9915693

50 A H Turner D Pol J A Clarke G M Erickson M A NorellA basal dromaeosaurid and size evolution preceding avianflight Science 317 1378ndash1381 (2007)pmid 17823350

51 X Xu M A Norell X L Wang P J Makovicky X C WuA basal troodontid from the Early Cretaceous of China Nature415 780ndash784 (2002) doi 101038415780a pmid 11845206

52 X Xu et al A Jurassic ceratosaur from China helps clarifyavian digital homologies Nature 459 940ndash944 (2009)doi 101038nature08124 pmid 19536256

53 P Chen Z Dong S Zhen An exceptionally well-preservedtheropod dinosaur from the Yixian Formation of ChinaNature 391 147ndash152 (1998) doi 10103834356

54 X T Zheng H L You X Xu Z M Dong An Early Cretaceousheterodontosaurid dinosaur with filamentous integumentarystructures Nature 458 333ndash336 (2009) doi 101038nature07856 pmid 19295609

55 O W M Rauhut C Foth H Tischlinger M A NorellExceptionally preserved juvenile megalosauroid theropoddinosaur with filamentous integument from the Late Jurassicof Germany Proc Natl Acad Sci USA 109 11746ndash11751(2012) doi 101073pnas1203238109 pmid 22753486

56 P Godefroit et al A Jurassic ornithischian dinosaur fromSiberia with both feathers and scales Science 345 451ndash455(2014) doi 101126science1253351 pmid 25061209

57 X Xu Y Guo Vertebr PalAsiat 47 311 (2009)58 Q Ji P J Currie M A Norell S A Ji Two feathered

dinosaurs from northeastern China Nature 393 753 (1998)doi 10103831635

59 X Xu et al Four-winged dinosaurs from China Nature 421335ndash340 (2003) doi 101038nature01342 pmid 12540892

60 X Xu M A Norell A new troodontid dinosaur from Chinawith avian-like sleeping posture Nature 431 838ndash841(2004) doi 101038nature02898 pmid 15483610

61 G Mayr B Pohl S Hartman D S Peters The tenth skeletalspecimen of Archaeopteryx Zool J Linn Soc 149 97ndash116(2007) doi 101111j1096-3642200600245x

62 Z Zhou F Zhang A long-tailed seed-eating bird from theEarly Cretaceous of China Nature 418 405ndash409 (2002)doi 101038nature00930 pmid 12140555

63 Z H Zhou F C Zhang Anatomy of the primitive birdSapeornis chaoyangensis from the Early Cretaceous ofLiaoning China Can J Earth Sci 40 731ndash747 (2003)doi 101139e03-011

64 C A Brochu M A Norell in New Perspectives on the Originand Early Evolution of Birds J A Gauthier L F Gall Eds(Peabody Museum of Natural History Yale Univ New HavenCT 2001) pp 511ndash536

65 X Xu et al A basal tyrannosauroid dinosaur from the LateJurassic of China Nature 439 715ndash718 (2006) doi 101038nature04511 pmid 16467836

66 J M Clark T Maryanska R Barsbold in The DinosauriaD B Weishampel P Dodson H Osmolska Eds (Univ ofCalifornia Press Berkeley ed 2 2004) pp 151ndash164

67 V Allen K T Bates Z Li J R Hutchinson Linking theevolution of body shape and locomotor biomechanics inbird-line archosaurs Nature 497 104ndash107 (2013)doi 101038nature12059 pmid 23615616

68 C Lipkin P C Sereno J R Horner The furcula inSuchomimus tenerensis and Tyrannosaurus rex (DinosauriaTheropoda Tetanurae) J Paleontol 81 1523ndash1527 (2007)doi 10166606-0241

69 X Xu F Han Q Zhao Homologies and homeotictransformation of the theropod lsquosemilunatersquo carpal Sci Rep4 6042 (2014)pmid 25116378

70 M S Y Lee A Cau D Naish G J Dyke Sustainedminiaturization and anatomical innovation in the dinosaurianancestors of birds Science 345 562ndash566 (2014)doi 101126science1252243 pmid 25082702

71 A M Balanoff G S Bever T B Rowe M A NorellEvolutionary origins of the avian brain Nature 501 93ndash96(2013) doi 101038nature12424 pmid 23903660

72 Q Li et al Melanosome evolution indicates a keyphysiological shift within feathered dinosaurs Nature 507350ndash353 (2014) doi 101038nature12973 pmid 24522537

73 K E Mikhailov Fossil and recent eggshell in amnioticvertebrates fine structure comparative morphology andclassification Spec Pap Palaeontol 56 1ndash80 (1997)

74 D J Varricchio D E Barta Revisiting Sabaths Wlarger avianeggsW from the Gobi Cretaceous Acta Palaeontol Pol104202app000852014 (2014)

75 T Sato Y-N Cheng X-C Wu D K Zelenitsky Y-F HsiaoA pair of shelled eggs inside a female dinosaur Science 308375 (2005) doi 101126science1110578 pmid 15831749

76 T He D J Varricchio F Jackson X Jin A W PoustJ Vertebr Paleontol 3 (abstr) 108 (2012)

77 F Fanti P J Currie D Badamgarav New specimens ofNemegtomaia from the Baruungoyot and Nemegt formations(Late Cretaceous) of Mongolia PLOS ONE 7 e31330 (2012)doi 101371journalpone0031330 pmid 22347465

78 D J Varricchio F D Jackson Origins of avian reproductionAnswers and questions from dinosaurs Palaeovertebrata32 149 (2003)

79 G F Birchard M Ruta D C Deeming Evolution of parentalincubation behaviour in dinosaurs cannot be inferredfrom clutch mass in birds Biol Lett 9 20130036 (2013)doi 101098rsbl20130036

80 S L Vehrencamp Evolutionary routes to joint-female nestingin birds Behav Ecol 11 334ndash344 (2000) doi 101093beheco113334

81 D J Varricchio et al Avian paternal care had dinosaurorigin Science 322 1826ndash1828 (2008) doi 101126science1163245 pmid 19095938

82 F L Agnolin J E Powell F E Novas M Kundraacutet Newalvarezsaurid (Dinosauria Theropoda) from uppermostCretaceous of north-western Patagonia with associatedeggs Cretac Res 35 33ndash56 (2012) doi 101016jcretres201111014

83 D J Varricchio J R Horner F D Jackson Embryos andeggs for the Cretaceous theropod dinosaur Troodonformosus J Vertebr Paleontol 22 564ndash576 (2002)doi 1016710272-4634(2002)022[0564EAEFTC]20CO2

84 F D Jackson J R Horner D J Varricchio A study of aTroodon egg containing embryonic remains usingepifluorescence microscopy and other techniques CretacRes 31 255ndash262 (2010) doi 101016jcretres200911006

85 D J Varricchio F Jackson C N Trueman A nesting tracewith eggs for the Cretaceous theropod dinosaur Troodonformosus J Vertebr Paleontol 19 91ndash100 (1999)doi 10108002724634199910011125

86 D J Varricchio F D Jackson R A Jackson D K ZelenitskyPorosity and water vapor conductance of two Troodonformosus eggs An assessment of incubation strategy in amaniraptoran dinosaur Paleobiology 39 278ndash296 (2013)doi 10166611042

87 K Sabath Acta Palaeontol Pol 36 151 (1991)88 N Loacutepez-Martiacutenez E Vicens A new peculiar dinosaur egg

Sankofa pyrenaica oogen nov oosp nov from the UpperCretaceous coastal deposits of the Aren Formationsouth-central Pyrenees Lleida Catalonia Spain Paleontology55 325ndash339 (2012) doi 101111j1475-4983201101114x

89 G Mayr A Manegold Can ovarian follicles fossilize Nature499 E1 (2013) doi 101038nature12367 pmid 23846661

90 X Zheng et al Preservation of ovarian follicles reveals earlyevolution of avian reproductive behaviour Nature 495 507ndash511(2013) doi 101038nature11985 pmid 23503663

91 T P Hopp M J Orsen in Feathered Dragons Studieson the Transition from Dinosaurs to Birds P J Currie

E B Koppelhus M A Shugar J L Wright Eds (IndianaUniv Press 2004) pp 234ndash250

92 D J Varricchio F D Jackson in Feathered DragonsStudies on the Transition from Dinosaurs to Birds P J CurrieE B Koppelhus M A Shugar J L Wright Eds (IndianaUniv Press Bloomington 2004) pp 215ndash233

93 J K Terres The Audubon Society Encyclopedia of NorthAmerican Birds (Wings Books New York 1995)

94 D C Deeming in Egg Incubation D C DeemingM W J Ferguson Eds (Cambridge Univ PressCambridge 1991) pp 307ndash323

95 I W A Calder Size Function and Life History (Harvard UnivPress Cambridge 1984) pp 431

96 A Chinsamy L Chiappe P Dodson Growth rings in Mesozoicbirds Nature 368 196ndash197 (1994) doi 101038368196a0

97 G M Erickson K C Rogers S A Yerby Dinosaurian growthpatterns and rapid avian growth rates Nature 412429ndash433 (2001) doi 10103835086558 pmid 11473315

98 G M Erickson et al Was dinosaurian physiology inheritedby birds Reconciling slow growth in ArchaeopteryxPLOS ONE 4 e7390 (2009) doi 101371journalpone0007390 pmid 19816582

99 A Chinsamy L M Chiappe J Marugaacuten-Loboacuten G ChunlingZ Fengjiao Gender identification of the Mesozoic birdConfuciusornis sanctus Nat Commun 4 1381 (2013)doi 101038ncomms2377 pmid 23340421

100 A Chinsamy in Mesozoic Birds Above the Heads ofDinosaurs L M Chiappe L M Witmer Eds (Univ ofCalifornia Press Berkeley 2002) pp 421ndash431

101 N P Myhrvold Revisiting the estimation of dinosaur growthrates PLOS ONE 8 e81917 (2013) doi 101371journalpone0081917 pmid 24358133

102 J M Grady B J Enquist E Dettweiler-RobinsonN A Wright F A Smith Evidence for mesothermy indinosaurs Science 344 1268ndash1272 (2014) doi 101126science1253143 pmid 24926017

103 G P Wagner J A Gauthier 123 = 234 A solutionto the problem of the homology of the digits in the avianhand Proc Natl Acad Sci USA 96 5111ndash5116 (1999)doi 101073pnas9695111 pmid 10220427

104 M A G de Bakker et al Digit loss in archosaur evolutionand the interplay between selection and constraintsNature 500 445ndash448 (2013) doi 101038nature12336pmid 23831646

105 A C Burke A Feduccia Developmental patterns and theidentification of homologies in the avian hand Science 278666ndash668 (1997) doi 101126science2785338666

106 Z Wang R L Young H Xue G P Wagner Transcriptomicanalysis of avian digits reveals conserved and deriveddigit identities in birds Nature 477 583ndash586 (2011)doi 101038nature10391 pmid 21892187

107 M Towers J Signolet A Sherman H Sang C TickleInsights into bird wing evolution and digit specificationfrom polarizing region fate maps Nat Commun 2 426(2011) doi 101038ncomms1437 pmid 21829188

108 S Chatterjee Counting the fingers of birds and dinosaursScience 280 355 (1998) doi 101126science2805362355a

109 N H Shubin P Alberch Evol Biol 20 319 (1986)110 X Xu S Mackem Tracing the evolution of avian wing digits

Curr Biol 23 R538 (2013) doi 101016jcub201304071111 P J Scherz E McGlinn S Nissim C J Tabin Extended

exposure to Sonic hedgehog is required for patterning theposterior digits of the vertebrate limb Dev Biol 308343ndash354 (2007) doi 101016jydbio200705030pmid 17610861

112 J Zhu et al Uncoupling Sonic hedgehog control of patternand expansion of the developing limb bud Dev Cell 14624ndash632 (2008) doi 101016jdevcel200801008pmid 18410737

113 E R Schachner J R Hutchinson C Farmer Pulmonaryanatomy in the Nile crocodile and the evolution ofunidirectional airflow in Archosauria PeerJ 1 e60 (2013)doi 107717peerj60 pmid 23638399

114 E R Schachner R L Cieri J P Butler C G FarmerUnidirectional pulmonary airflow patterns in the savannahmonitor lizard Nature 506 367ndash370 (2014) doi 101038nature12871 pmid 24336209

115 A H Turner P J Makovicky M A Norell Feather quill knobsin the dinosaur Velociraptor Science 317 1721 (2007)doi 101126science1145076 pmid 17885130

116 F Ortega F Escaso J L Sanz A bizarre humpedCarcharodontosauria (Theropoda) from the lower cretaceousof Spain Nature 467 203ndash206 (2010) doi 101038nature09181 pmid 20829793

117 C Foth H Tischlinger O W M Rauhut New specimen ofArchaeopteryx provides insights into the evolution ofpennaceous feathers Nature 511 79ndash82 (2014)doi 101038nature13467 pmid 24990749

118 R Barsbold H Osmolska M Watabe P J CurrieK Tsogtbaatar A new oviraptorosaur (DinosauriaTheropoda) from Mongolia The first dinosaur with apygostyle Acta Palaeontol Pol 45 97ndash106 (2000)

119 M H Schweitzer et al Beta-keratin specific immunologicalreactivity in feather-like structures of the cretaceousalvarezsaurid Shuvuuia deserti J Exp Zool 285 146ndash157(1999) doi 101002(SICI)1097-010X(19990815)2852lt146AID-JEZ7gt30CO2-A pmid 10440726

120 Q Ji S A Ji On the discovery of the earliest fossil bird inChina (Sinosauropteryx gen nov) and the origin of birdsChinese Geol 233 30ndash33 (1996)

121 U B Goumlhlich L M Chiappe A new carnivorous dinosaurfrom the Late Jurassic Solnhofen archipelago Nature 440329ndash332 (2006) doi 101038nature04579 pmid 16541071

122 D K Zelenitsky et al Feathered non-avian dinosaursfrom North America provide insight into wing origins Science338 510ndash514 (2012) doi 101126science1225376pmid 23112330

123 R C McKellar B D E Chatterton A P Wolfe P J CurrieA diverse assemblage of Late Cretaceous dinosaur and birdfeathers from Canadian amber Science 333 1619ndash1622(2011) doi 101126science1203344 pmid 21921196

124 X Xu X Zheng H You Exceptional dinosaur fossilsshow ontogenetic development of early feathers Nature464 1338ndash1341 (2010) doi 101038nature08965pmid 20428169

125 CF Chen et al Development regeneration and evolution offeathers Annu Rev Anim Biosci (2014) pmid 25387232

126 Z Yue T X Jiang R B Widelitz C M Chuong Mappingstem cell activities in the feather follicle Nature 4381026ndash1029 (2005) doi 101038nature04222pmid 16355227

127 R Chodankar et al Shift of localized growth zonescontributes to skin appendage morphogenesis Role of theWntb-catenin pathway J Invest Dermatol 120 20ndash26(2003) doi 101046j1523-1747200312008x

128 C H Chang et al Sculpting skin appendages out ofepidermal layers via temporally and spatially regulatedapoptotic events J Invest Dermatol 122 1348ndash1355 (2004)doi 101111j0022-202X200422611x pmid 15175023

129 M P Harris J F Fallon R O Prum Shh-Bmp2 signalingmodule and the evolutionary origin and diversification offeathers J Exp Zool 294 160ndash176 (2002) doi 101002jez10157 pmid 12210117

130 Z Yue T X Jiang R B Widelitz C M Chuong Wnt3agradient converts radial to bilateral feather symmetry viatopological arrangement of epithelia Proc Natl Acad Sci USA103 951ndash955 (2006) doi 101073pnas0506894103pmid 16418297

131 T X Jiang T L Tuan P Wu R B Widelitz C M ChuongFrom buds to follicles Matrix metalloproteinases indevelopmental tissue remodeling during feathermorphogenesis Differentiation 81 307ndash314 (2011)doi 101016jdiff201103004 pmid 21497985

132 Q Chu et al Dkk2Frzb in the dermal papillae regulatesfeather regeneration Dev Biol 387 167ndash178 (2014)doi 101016jydbio201401010 pmid 24463139

133 Z Yue T X Jiang P Wu R B Widelitz C M ChuongSproutyFGF signaling regulates the proximal-distal feathermorphology and the size of dermal papillae Dev Biol 37245ndash54 (2012) doi 101016jydbio201209004 pmid 23000358

134 C M Chuong V A Randall R B Widelitz P WuT X Jiang Physiological regeneration of skin appendages andimplications for regenerative medicine Physiology (Bethesda)27 61ndash72 (2012) doi 101152physiol000282011pmid 22505663

135 X Zheng et al Hind wings in basal birds and the evolution ofleg feathers Science 339 1309ndash1312 (2013) doi 101126science1228753 pmid 23493711

136 Q Li et al Reconstruction of Microraptor and the evolutionof iridescent plumage Science 335 1215ndash1219 (2012)doi 101126science1213780 pmid 22403389

137 F Zhang et al Fossilized melanosomes and the colour ofCretaceous dinosaurs and birds Nature 463 1075ndash1078(2010) doi 101038nature08740 pmid 20107440

138 A E Moyer et al Melanosomes or microbes Testing analternative hypothesis for the origin of microbodies in fossilfeathers Sci Rep 4 4233 (2014) doi 101038srep04233pmid 24595214

139 S J Lin et al Topology of feather melanocyte progenitorniche allows complex pigment patterns to emerge Science340 1442ndash1445 (2013) doi 101126science1230374 pmid23618762

140 S A Newman Thermogenesis muscle hyperplasia and theorigin of birds BioEssays 33 653ndash656 (2011) doi 101002bies201100061 pmid 21695679

141 J OrsquoConnor et al Unique caudal plumage of Jeholornisand complex tail evolution in early birds Proc Natl AcadSci USA 110 17404ndash17408 (2013) doi 101073pnas1316979110 pmid 24101506

142 N R Longrich J Vinther Q Meng Q Li A P RussellPrimitive wing feather arrangement in Archaeopteryxlithographica and Anchiornis huxleyi Curr Biol 22

2262ndash2267 (2012) doi 101016jcub201209052pmid 23177480

143 R Dudley et al Gliding and the functional origins offlight Biomechanical novelty or necessity Annu RevEcol Evol Syst 38 179ndash201 (2007) doi 101146annurevecolsys37091305110014

144 G Dyke et al Aerodynamic performance of the feathereddinosaur Microraptor and the evolution of feathered flightNat Commun 4 2489 (2013) doi 101038ncomms3489pmid 24048346

145 S M Gatesy K P Dial Locomotor modules and theevolution of avian flight Evolution 50 331 (1996)doi 1023072410804

146 K Peterson P Birkmeyer R Dudley R S FearingA wing-assisted running robot and implications for avianflight evolution Bioinspir Biomim 6 046008 (2011)doi 1010881748-318264046008 pmid 22004831

147 B A S Bhullar et al Birds have paedomorphic dinosaurskulls Nature 487 223ndash226 (2012) doi 101038nature11146 pmid 22722850

148 J M Asara M H Schweitzer L M Freimark M PhillipsL C Cantley Protein sequences from mastodon andTyrannosaurus rex revealed by mass spectrometryScience 316 280ndash285 (2007) doi 101126science1137614pmid 17431180

149 M H Schweitzer et al Biomolecular characterization andprotein sequences of the Campanian hadrosaur B canadensisScience 324 626ndash631 (2009) doi 101126science1165069pmid 19407199

150 R R Reisz et al Embryology of Early Jurassic dinosaurfrom China with evidence of preserved organic remainsNature 496 210ndash214 (2013) doi 101038nature11978pmid 23579680

ACKNOWLEDGMENTS

We thank Y Liu L Xing R Li X Ding P M OrsquoConnor M EllisonH Zang and K Womble for illustrations XX and ZHZ thankX Zheng (Shandong Tianyu Museum of Nature) and H Li(Jizantang Museum) for access to specimens in their care DJVthanks the Fukui Prefecture Dinosaur Museum for researchsupport XX and ZHZ are supported by the National NaturalScience Foundation of China (41120124002) and 973 program(2012CB821900) CMC by US National Institute of Arthritisand Musculoskeletal Diseases NIH grant AR 60306 and 47364GME by NSF grants DBI 0446224 and EAR 044186549 andDJV by NSF grant EAR 0847777

101126science1253293

1253293-10 12 DECEMBER 2014 bull VOL 346 ISSUE 6215 sciencemagorg SCIENCE