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Phylogenetics. Phylogenetic Trees.

1. Represent presumed pat-

terns of descent. 2. Analogous to family trees. 3. Resolve taxa, e.g., species,

into clades each of which includes an ancestral tax-on and all its descendants.

4. In the figure at the right, we

can define three non-trivial clades.1

a. A (A+C+K), P (P+Y+S)

and G (G+A+P). b. A and P are nested with-

in G.

1 I define trivial clades are those consisting of a single taxon, in the present case, C and K (nested within A) and Y and S (nested within P).

Family trees and phylog-enies. In a. your aunt, parent and grandparent may still be alive. In b. and c., species A, P and G are extinct.

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Terminology.

1. Nodes are branching or terminating points. a. Internal nodes are

points of lineage splitting.

b. Terminal nodes are

coeval taxa.

2. “Taxa” can be species or higher taxonomic groups. In the figure, they are la-beled A, B, etc.

3. A pair of taxa that have a common ancestor not

shared by any other taxon are called sister taxa, e.g., A and B.

4. F is called the outgroup.

a. Outgroup inclusion “completes the tree” by identify-

ing character states presumed ancestral and hence the characteristics of a presumptive com-mon ancestor.

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b. This is called rooting the tree.

c. Typically, one chooses a taxon that, on other grounds, is believed to be

Closely related to taxa of interest, but

Less closely related to any of them than they are to each other.

d. Example. If one were

constructing a clado-gram for birds, the outgroup could be

Dromaeosauridae (includes Velocrap-tor and Deinony-chus) if fossils in-cluded.

Crocodilians if only living species con-sidered.

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Questions. 1. The node marked with a single asterisk in the figure on

page 2 represents the most recent common ancestor of _______; the node marked with two asterisks represents the most recent common ancestor of _______.

2. Identify the non-trivial clades by circling the appropriate

nodes. 3. Among the tip taxa, identify sister taxa in addition to A

and B.

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4. Consider the mammalian cladogram below. Indicated are the following divisions: Class Mammalia, which is di-vided into Prototheria (monotremes) and Theria (mam-mals that bear their young alive), and Theria, which is divided into Metatheria (marsupials) and Eutheria (pla-cental mammals). Indicate on the diagram, appropriate outgroup(s) for Eutheria and Theria.

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Determining Relatedness.

1. Two approaches. a. Phenetic – infers relatedness from overall similari-

ty. b. Cladistic –

Distinguishes ancestral from derived characters.

Infers relatedness from the presence of shared derived characters called synapomorphies.

2. In the table below,

a. Two groups of species can be defined by presence or absence of character 2.

b. The presence of characters 1, 3, 4 in all four species

is uninformative.

Trait

Species 1 2 3 4

A + - + +

B + - + +

C + + + +

D + + + +

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Questions. (# 5-7 relate to the preceding example.)

5. Assuming that characters 1, 3 and 4 are ancestral, and bearing in mind that characters can be lost as well as gained, draw two phylogenetic trees. Indicate on each where traits are acquired and lost.

6. Draw an additional tree assuming that characters 1, 3

and 4 are not ancestral. 7. Suppose now that you have an outgroup, O, for which

characters 1-4 are present and distinguished by a fifth character not found in species A-D. Assume that trait 5 is derived. Draw two phylogenies corresponding to your answers to Question 5 above. Which is more likely? Why?

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8. Assume that none of the “trait absent” characters in the table below reflect evolutionary reversals. Draw a phylo-genetic tree. Which characters is (are) ancestral?

Trait

Species Four

Limbs Live Birth

Milk Pouch

Platypus + - + -

Echidna + - + -

Kanga-roo

+ + + +

Dog + + + -

Lemur + + + -

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Principle of Parsimony.

1. In Question 7, you encountered the Principle of Par-simony: The most the plausible phylogeny is that which necessitates a. The fewest evolutionary reversals. b. Fewest independent character acquisitions.

2. An evolutionary reversal is the re-acquisition of an ancestral trait or the loss of a derived trait.

3. Fundamental point:

a. Evolutionary history, H, uniquely deter-mines character dis-tribution, D. But …

b. D does not uniquely determine H.

c. Statistics used to determine the rela-tive likelihood of al-ternative phylogenies – especially when characters are easily reversed, e.g., nucleotide sequences.

An infinite number of evolu-tionary histories are compati-ble with a given distribution of characters.

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Homology. 1. Similarity by virtue of

common descent.

a. The synapomorphies that define clades are homologies.

b. Often used in the

context of organs that have been modified to different ends in different species.

2. Serial homology (dupli-

cation and modification of parts in different ways) was first discussed by the poet, J. W. von Goethe, with reference to flower parts which he correctly believed were modified leaves –“foliar theory” of the flower.

The modified forelimbs of humans, cats, whales and bats are homologous.

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Spirally-arranged floral organs illustrating serial homology in basal angiosperms. A: Magnolia watsoniana. B: Nymphaea caerulea; C: Nymphaea gigatea var. Perry´s Baby; D: Nymphaea odorata. Note the gradual transition between petals and stamens. Bars in-dicate scale: A-C: 1.5cm; D: 600μm. From Dornelas and Dorneias (2005).

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The nondescript flowers of wild poinsettias (Euphorbia pulcherrima) are surrounded by leaves that are partially red resembling petals and partially green re-sembling sepals.

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Homology of head appendages in Onychophora and Arthropoda.. Abbreviations as follows: at, antenna; at1, first antenna; at2, second antenna; ch, chelicera; jw, jaw; le, leg; md, mandible; mx, maxilla; pp, pedipalp; sp, slime papilla. From Mayer et al (2013).

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Homoplasy – Similarity by independent acquisition.

1. Convergent evolution:

acquisition of similar traits by distant lineages.

2. Parallel evolution: ac-quisition of similar traits by closely related line-

ages.

3. Distinguishing between homology and conver-gence requires appeal to other traits.

Despite their superficial similarity (and the fact that ichthyo-saurs gave birth to live young!), the two taxa are separable on the basis of other characters such as skull morphology. Which

of the two sets of pointing hands is spouting nonsense?

Famous example of convergent evolution.

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4. Convergent or parallel? Distinction hinges on a. What one means by “closely” vs. “distantly” related.

b. Level one is looking at:

i. At the morphological level, vertebrate and ceph-

alopod eyes are convergent.

ii. At genetic level, parallel – the same regulatory genes determine their development.

If ancestral species A1 and A2 closely related, the presence of an independently acquired character in descendant species D1 and D2 is said to be an example of “parallel” evolution; if A1 and A2 distant, “convergent”.

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5. Homologous or homoplastic? Depends on one’s point of view. Pterodactyl, bat, bird wings are

a. Homologous viewed

as forelimbs – the usual view;

b. Homoplastic viewed as wings – no winged common ancestor – an alternative, but equally valid (IMO) view.

c. See also Hall. 2007. J. Hu. Evol. 52: 473-479; Pearce. 2012. Brit. J. Phil. Sci. 63: 429–448.

Right. The wings of flying

vertebrates are traditionally

cited as an example of con-

vergent evolution.

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Homology vs. Homoplasy in Mammal Dentition.

1. Four mammalian tooth types: a. incisors, b. canines, c. premolars, d. molars.

2. In living carnivores, P4, and M1, specialized for slicing.

a. Called carnassials –

b. A synapomorphy defin-ing order Carnivora.

c. Creodonts (now extinct)

a. Independently evolved carnassials, but,

b. Carnassial pair was M1/M2 or M2/M3.

c. Convergent evolution if ref. is to which cheek teeth modified; paral-lel, if to cheek teeth.

Carnassial pair, P4 (blue) / M1 (red) in a saber tooth “tiger.” Note the extreme reduction (ob-served in all felids) of the remaining post-canine dentition that consists primitively of four pre-molars and

three molars.

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When Data Conflict – a Whale of a Tale. 1. Old theory: Whales descend-

ed from extinct carnivores.

2. New theory: Whales de-scended from artiodactyls – “even-toed” ungulates.2

3. Molecular evidence sug-gests that whales descended from artiodactyls.

4. Conflicts with morphological evidence: whales lack dou-ble pulley astragalus (DPA).

a. DPA (ankle bone) is the

synapomorphy that dis-tinguishes artiodactyls from other ungulates.

b. The term “double pulley” refers to the presence of two articular surfaces – one with the tibia (leg bone), the other with the os navicular (another foot bone).

2 Hoofed mammals.

Foot bones of an Eocene artiodactyl. Its two articu-lar surfaces (shaded red and blue) allow the astragalus to articulate with the tibia (above) and the os navicular (below). In most mammals, there is only one such surface.

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5. Deriving whales from artiodactyls necessitates an evo-lutionary reversal: DPA gained, then lost.

6. Whales from carnivores more parsimonious.

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So which is it?

1. Fossil evidence: primitive whales had a double pulley astragalus.

2. In this case, paleontology

confirms molecular biology; in other cases, e.g., putative derivation of amphibians from lungfish, not.

3. Fossils always trump anat-

omy, genetics, etc., of living organisms.

Ankle bones of fossil whales (left, right) and a living pronghorn (center). Note the double pulley astragalus in all three.

Restoration of a paddling proto-whale, Rodhocetus kasrani. Forelimbs were probably folded against the body during rapid swimming by pel-vic paddling and caudal undulation when submerged. On land, Rod-hocetus supported itself on hoofed digits II, III, and IV of the hands and the undersides of the feet. From Gingerich et al. (2001).

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Astragalus anatomy in a typical mammal (left) and cetaceans

/ artiodactyls (right)

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6. Types of Taxa. 1. Monophyletic.

a. Includes the most recent

common (MRCA) ancestor and all its descendants.

b. Monophyletic taxa called

clades.

c. E.g., Mammals, birds. 2. Paraphyletic.

a. Includes the MRCA, but

not all descendants. b. E.g., Reptiles.

3. Polyphyletic.

a. Does not include MRCA. b. E.g., Flying vertebrates – the MRCA walked.

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Question. 9. Historically, terrestrial vertebrates were divided into four

classes: Amphibia, Reptilia, Mammalia and Aves (birds). Below is a cladistic analysis that reflects the fact that birds evolved from small, carnivorous dinosaurs. The four terrestrial vertebrate clades are shown in blue and their division into more familiar groups in black at the right. a. What are Tuataras and squamates? b. Which of the famil-iar groups are “reptiles?” c. If we lump these groups to-gether, resulting class, Reptilia, is paraphyletic. Explain why. Be specific.

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Reading Evolutionary Trees.

1. Unless otherwise indi-cated, branch length is arbitrary.

2. Order of tip taxa also

arbitrary.

a. The only infor-mation contained in a cladogram is the order of branching that defines the clades

b. In particular, in-

ternal nodes can be rotated with no consequence to the clades defined.

c. It follows that evo-

lutionary relations cannot be inferred by reading across the tips. See Figure caption, p. 14.

These two cladograms look different, but contain exactly the same information. You can verify this by circling the clades in each.

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Question. 10. Three of the evolutionary trees below are equivalent.

Which is different?