biol 102 chp 26: phylogeny and the tree of life

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

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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

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4

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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

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SystemaSystema NaturaeNaturae

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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…

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{“little chief nipple twister” (Greek)}

Creative Scientific NamesCreative Scientific Names

Brachyanax thelestrephones (fly)

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{“vampire squid from Hell”}

Vampyroteuthis infernalis

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iago {“James”}, badius {Brown”}, {“King of Funk”}

Funkotriplogynium iagobadius (mite)

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Mackenziurus johnnyi, M. joeyi, M. deedeei, M. ceejayi

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Metallichneumon neurospatarchus (icneumonid wasp)

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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!

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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

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Modern Modern SystematicsSystematics

Phylogeny-based

Cladistics: PhyloCode

Recognizes only groups that include a common ancestor …

… & all its descendents

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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

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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

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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

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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?

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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

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Marsupial mole: develops in pouch

Eutherian mole: develops in uterus

Convergent Evolution of Convergent Evolution of BurrowersBurrowers

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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

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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

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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

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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

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A

B

C

D

E

F

G

Group I

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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

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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

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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

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Assumes that the tree requiring the fewest shared derived

characters is the most likely

Maximum ParsimonyMaximum Parsimony

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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

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Percentage Percentage differences differences between sequencesbetween sequences

Human 40%

40%

30% 0

0

0

Human Mushroom

Mushroom

Tulip

Tulip

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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

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Fossil remains of Oviraptor & eggs (dinosaurs built nests & brooded their eggs)

Eggs

Front limb

Hind limb

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Artist’s reconstruction of the dinosaur’s egg-brooding

posture

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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

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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

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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

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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

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Ancestral gene

Species C

Gene duplication and divergence

Paralogous genes

Species C after many generations

ParalogousParalogous GenesGenes

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Genome Genome EvolutionEvolution

Gene number & species complexity are not

strongly linked

Genes in complex organisms are very

versatile

Each gene can perform many functions

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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)

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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

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3

Archaea

Bacteria

Eukarya

Billions of years ago

4 2 1 0

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Horizontal Gene TransferHorizontal Gene Transfer

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EndosymbiosisEndosymbiosis & a & a Ring of Ring of Life?Life?

Archaea

Eukarya

Bacteria

A Ring of LifeA Ring of Life 72

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CreditsCredits by Rob Swatski, 2013

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