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This is a lecture presentation for my BIOL 102 General Biology II students on Chapter 26: Phylogeny and the Tree of Life (Biology 9E by Campbell et al). Rob Swatski, Assistant Professor of Biology, Harrisburg Area Community College - York Campus, York, PA. Email: rjswatsk@hacc.edu Please visit my website, BioGeekiWiki, for more biology learning resources: http://robswatskibiology.wetpaint.com Visit my Flickr photostream for anatomy model photographs! http://www.flickr.com/photos/rswatski/ Thanks for looking!
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BIOL BIOL 102: 102: General Biology IIGeneral Biology II
Rob Rob SwatskiSwatski Assoc. Prof. BiologyAssoc. Prof. Biology
HACCHACC--YorkYork
Chapter Chapter 2626 Phylogeny & Phylogeny & the Tree of Lifethe Tree of Life
1
SnakeSnake This is NOT a This is NOT a
Common ScalyCommon Scaly--Foot Legless Lizard!Foot Legless Lizard! 2
The Science The Science of of
ClassificationClassification
Phylogeny
Systematics: fossil, molecular, & genetic
Taxonomy
Binomial nomenclature
3
4
5
6
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CarolusCarolus Linnaeus Linnaeus
(1707(1707--1778) 1778)
1st “modern” taxonomy system based on
physical appearances
Two key features we still use:
1. Two-part scientific names
2. Hierarchical classification
8
SystemaSystema NaturaeNaturae
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11
Binomial Binomial NomenclatureNomenclature
The 1st part of the name is the Genus (always Capitalized)
The 2nd name is the specific epithet (unique for each
species in the Genus)
The entire species name is italicized or
underlined
Both words together make up the scientific
name of a species 12 12
“Linnea, a plant of Lapland, lowly,
insignificant, disregarded,
flowering but for a brief space”
- from Linnaeus who resembles it…
13
{“little chief nipple twister” (Greek)}
Creative Scientific NamesCreative Scientific Names
Brachyanax thelestrephones (fly)
14
{“vampire squid from Hell”}
Vampyroteuthis infernalis
15
iago {“James”}, badius {Brown”}, {“King of Funk”}
Funkotriplogynium iagobadius (mite)
16
Mackenziurus johnnyi, M. joeyi, M. deedeei, M. ceejayi
17
Metallichneumon neurospatarchus (icneumonid wasp)
18
Agathidium bushi, A. cheneyi, A. rumsfeldi
(slime mold beetles) 19
Anophthalmus hitleri (blind cave beetle)
Satan eurystomus (blind cave fish) {big-mouthed Prince of Darkness}
Darthvaderum (mite)
Han solo (trilobite)
Bangiomorpha pubescens (fossil red alga)
{1st recorded sex act}
Cuterebra emasculator (bot flies) {eat testes of rodent hosts}
More Creative Scientific Names!More Creative Scientific Names!
20
DomainDomain KingdomKingdom
PhylumPhylum
ClassClass
OrderOrder
FamilyFamily
GenusGenus
SpeciesSpecies
Hierarchical Hierarchical ClassificationClassification 21
Species:
Panthera pardus
Genus:
Panthera
Family:
Felidae
Order:
Carnivora
Class:
Mammalia
Phylum:
Chordata
Domain:
Bacteria
Kingdom:
Animalia Domain:
Archaea Domain:
Eukarya 22
Order Family
Panthera pardus (leopard)
Genus Species
Canis latrans (coyote)
Taxidea taxus (American badger)
Lutra lutra (European otter)
Canis lupus (gray wolf)
Fe
lidae
Carn
ivo
ra
Pan
the
ra
Taxid
ea
Mu
ste
lida
e
Lu
tra
Can
idae
Can
is
PhylogeneticPhylogenetic TreeTree 23
24
25
Modern Modern SystematicsSystematics
Phylogeny-based
Cladistics: PhyloCode
Recognizes only groups that include a common ancestor …
… & all its descendents
26 26
PhylogeneticPhylogenetic TreesTrees
Represents a hypothesis about evolutionary relationships
Each branch point represents the divergence of 2 species
Sister taxa: groups sharing an immediate common ancestor
Rooted tree: includes a branch representing the last common
ancestor of all related taxa
Polytomy: a branch from which more than 2 groups emerge
27 27
Branch point: where lineages diverge
ANCESTRAL LINEAGE
This branch point represents the common ancestor of taxa A–G.
This branch point forms a polytomy: an unresolved pattern of divergence.
Sister taxa
Basal taxon
Taxon A
Taxon B
Taxon C
Taxon D
Taxon E
Taxon F
Taxon G
28
What Can We What Can We Learn from Learn from
PhylogeneticPhylogenetic Trees?Trees?
Show patterns of descent
They do NOT indicate when species evolved…
… or how much genetic change occurred in a
lineage
We can’t assume that a taxon evolved from the
taxon next to it on a tree 29 29
Applications Applications of Phylogenyof Phylogeny
Practical value!
Provides valuable info about similar traits in
closely-related species
Ex: Identify species of food being sold as
“whale” meat
Ex: Identify source of a particular strain of
bacteria 30 30
Minke (Southern Hemisphere)
Unknowns #1a, 2, 3, 4, 5, 6, 7, 8
Minke (North Atlantic)
Humpback (North Atlantic)
Humpback (North Pacific)
Gray
Blue
Unknowns #10, 11, 12
Unknown #13
Unknown #1b
Unknown #9
Fin (Mediterranean)
Fin (Iceland)
RESULTS
31
A
B
A A
B
B
C
C C
D
D
D
(a) (b) (c)
Which strain of Which strain of AnthraxAnthrax is it?is it?
32
Sources of Sources of PhylogeneticPhylogenetic
DataData
Morphologies
Genes
Biochemistry
Organisms with similar morphologies
or DNA are likely to be more closely related
than those with different
morphologies or DNA 33 33
Homology Homology vs. Analogyvs. Analogy
Must distinguish between similarities
when building a phylogeny
Homology: similarity due to shared ancestry
Analogy: similarity due to convergent
evolution
Convergent evolution
34 34
Marsupial mole: develops in pouch
Eutherian mole: develops in uterus
Convergent Evolution of Convergent Evolution of BurrowersBurrowers
35
Convergent Convergent EvolutionEvolution
Occurs when similar enviro pressures & natural selection produce
analogous adaptations in organisms from different
evolutionary lineages
Ex: Bat & bird wings are homologous as forelimbs …
…. but analogous as functional wings
Analogous traits that evolved independently are
also called homoplasies 36 36
Distinguishing Distinguishing Between Between
Homology & Homology & AnalogyAnalogy
Compare fossil evidence
Compare the degree of complexity
The more complex two similar structures are …
… the more likely it is that they are homologous
37 37
38
Molecular Molecular SystematicsSystematics
Analyze comparable DNA segments from different
organisms
Use computer programs & mathematical tools
Recognizes only groups that include a common
ancestor …
Once homologous characters have been identified, they can be
used to infer a phylogeny
Deletion
Insertion
1
1
1
1
2
2
2
2
2
1
3
4
Aligning Aligning Segments Segments of DNAof DNA
39
Molecular Molecular HomoplasiesHomoplasies
Two species that are not closely related can share
25% of their bases …
… by coincidence!
Mathematical tools are used to help identify
homoplasies
40 40
41
CladisticsCladistics
Grouping organisms by common descent
Clade: a group of species that includes
an ancestral species & all its descendants
Clades can be nested into larger clades …
… but not all groupings of
organisms qualify as clades
42 42
A
B
C
D
E
F
G
Group I
43
A
B
C
D
E
F
G
Group I
Monophyletic Monophyletic CladeClade (Group)(Group)
Consists of the ancestor species & all its descendents 44
A
B
C
D
E
F
G
Group II
ParaphyleticParaphyletic CladeClade (Group)(Group)
Consists of an ancestral species & some, but not all, of its descendents 45
Group
A
B
C
D
E
F
G
Polyphyletic Polyphyletic CladeClade (Group)(Group)
Consists of various species that lack a common ancestor 46
Shared Shared CharactersCharacters
Shared ancestral character: originated in an ancestor of
the taxon
Shared derived character: an evolutionary novelty unique
to a specific clade
A character can be both ancestral & derived – it depends on the context
Infer phylogenies knowing in which clade a shared derived
character 1st appeared 47 47
OutgroupsOutgroups & & IngroupsIngroups
Outgroup: A species (or group of species) closely
related to the ingroup
Ingroup: the various species being studied
The goal is to differentiate
between shared derived & ancestral
characters
Homologies shared by both the
outgroup & ingroup are ancestral
characters 48 48
TAXATAXA
Leo
par
d
Bas
s
Vertebral column (backbone)
Hinged jaws
Four walking legs
Amniotic (shelled) egg
Hair
Character Character TTableable
0
0 0
0
0
0
0 0
0
0
0 0
0 0 0 1
1 1
1 1 1
1
1 1
1
1
1 1
1 1
Constructing a Constructing a PhylogeneticPhylogenetic TreeTree
49
Lancelet
(outgroup)
Lamprey
Bass
Frog
Turtle
Leopard
Vertebral
column
Hinged jaws
Four walking legs
Amnion
Hair
PhylogeneticPhylogenetic TTreeree 50
Drosophila
Lancelet
Zebrafish
Frog
Human
Chicken
Mouse
In some trees, the length of a branch can reflect the # of genetic changes that have occurred in a particular DNA
sequence in that lineage
51
Drosophila
Lancelet
Zebrafish
Frog
Human
Chicken
Mouse
CENOZOIC
Present 65.5
MESOZOIC
251
Millions of years ago
PALEOZOIC
542
In other trees, branch length can represent chronological time & branching points can be determined from the
fossil record
52
Assumes that the tree requiring the fewest shared derived
characters is the most likely
Maximum ParsimonyMaximum Parsimony
53
A tree can be found that reflects the most likely sequence of evolutionary events, given
certain rules about how DNA changes over time
Maximum LikelihoodMaximum Likelihood
54
Percentage Percentage differences differences between sequencesbetween sequences
Human 40%
40%
30% 0
0
0
Human Mushroom
Mushroom
Tulip
Tulip
55
15%
Tree 1: More likely Tree 2: Less likely
15% 15%
5%
5%
10%
25% 20%
Comparison of possible trees Comparison of possible trees with different likelihoodswith different likelihoods 56
PhylogeneticPhylogenetic Trees as Trees as
HypothesesHypotheses
The best hypotheses for phylogenetic trees fit the
most data
Use morphological, molecular, & fossil data
Phylogenetic bracketing: use features of
descendents to predict features of an ancestor
Infer features of dinosaurs from their descendents:
birds & crocodiles 57 57
Common ancestor of crocodilians, dinosaurs, & birds
Birds
Lizards & snakes
Crocodilians
Ornithischian dinosaurs
Saurischian dinosaurs
PhylogeneticPhylogenetic tree of birds & their close relativestree of birds & their close relatives
58
Fossil remains of Oviraptor & eggs (dinosaurs built nests & brooded their eggs)
Eggs
Front limb
Hind limb
59
Artist’s reconstruction of the dinosaur’s egg-brooding
posture
60
Molecular Molecular Evidence for Evidence for PhylogenyPhylogeny
DNA that codes for rRNA changes
relatively slowly
Useful for investigating distant branching
points
mtDNA (mitochondrial DNA):
evolves rapidly
Used to explore recent evolutionary events
61 61
Gene Gene DuplicationsDuplications
Increase the # of genes in the genome
Provides more opportunities for
evolutionary changes
Can be traced to a common ancestor
Homologous genes
62 62
OrthologousOrthologous GenesGenes
Found in a single copy in the genome
Are homologous between species
Can diverge only after speciation occurs
Widespread & extend across many diverse
species 63 63
Ancestral gene
Ancestral species
Speciation with divergence of gene
Species A Species B Orthologous genes
OrthologousOrthologous GenesGenes
64
ParalogousParalogous GenesGenes
Result from gene duplication
Found in multiple copies in the genome
Can diverge within the clade that carries them
Often evolve new functions
65 65
Ancestral gene
Species C
Gene duplication and divergence
Paralogous genes
Species C after many generations
ParalogousParalogous GenesGenes
66
Genome Genome EvolutionEvolution
Gene number & species complexity are not
strongly linked
Genes in complex organisms are very
versatile
Each gene can perform many functions
67 67
Revisions to Revisions to the Tree of Lifethe Tree of Life
Only plants & animals, at first…then 5 kingdoms
Monera, Protista, Fungi, Plantae, & Animalia
The 3-domain system has been adopted: Bacteria,
Archaea, Eukarya
Eukarya & Archaea are more closely related to
each other than to Bacteria (rRNA genes)
68 68
Archaea
Bacteria
Eukarya
COMMON ANCESTOR
OF ALL LIFE
Land plants
Green algae
Red algae
Forams Ciliates
Dinoflagellates
Cellular slime molds Amoebas
Animals
Fungi
Euglena
Trypanosomes
Leishmania
Sulfolobus
Thermophiles
Halophiles
Methanobacterium
Green nonsulfur bacteria
(Mitochondrion)
Spirochetes
Chlamydia
Cyanobacteria
Green sulfur bacteria
(Plastids, including chloroplasts)
Diatoms
The The 3 3 Domains Domains
of Lifeof Life
69
3
Archaea
Bacteria
Eukarya
Billions of years ago
4 2 1 0
70
Horizontal Gene TransferHorizontal Gene Transfer
71
EndosymbiosisEndosymbiosis & a & a Ring of Ring of Life?Life?
Archaea
Eukarya
Bacteria
A Ring of LifeA Ring of Life 72
74
CreditsCredits by Rob Swatski, 2013
http://robswatskibiology.wetpaint.com
Visit my website for more Visit my website for more Biology study Biology study resources!resources!
http://www.flickr.com/photos/rswatski
Please send your comments and feedback to: rjswatsk@hacc.edu
This work bears an Attribution-Noncommercial
Share Alike Creative Commons license.
Images used in this work bear a Creative Commons license and are attributed to their original
authors.
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