CHAPTER 26Phylogeny and The Tree of Life

Learning Targets

Focus Questions

1. What is binomial nomenclature? And why is it useful?

2. What are the taxanomic groups from domain to species?

3. Why must scientists sort homologies from analogies when making phylogenetic trees?

4. What are the three domains of life and how are they related to each other?

5. What problems are there with the old 5 kingdom system of classification?

FIGURE 26.3

Species:Panthera pardus

Genus:Panthera

Family:Felidae

Order:Carnivora

Class:Mammalia

Phylum:Chordata

Domain:Bacteria

Kingdom:Animalia Domain:

ArchaeaDomain:Eukarya

5 kingdom system is no longer valid…Why?

FIGURE 26.7

Are they related? How would you know?

What would you look for?

DNA USED AS INDICATOR OF RELATEDNESS…How is this done?

FIGURE 26.8-1

1

2

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FIGURE 26.8-2

Deletion

Insertion

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2

1

FIGURE 26.8-3

Deletion

Insertion

1

1

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2

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3

FIGURE 26.8-4

Deletion

Insertion

1

1

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Alignment is

awesome!

FIGURE 26.9

Even non-homologous chromosomes share ~ 25% of the genome

FIGURE 26.11

TAXA Lancelet(outgroup)

Lamprey

Bass

Frog

Turtle

Leopard

Vertebralcolumn

(backbone)

Four walkinglegs

Hinged jaws

Amnion

Hair

Vertebralcolumn

Hinged jaws

Four walking legs

Amnion

Hair

(a) Character table (b) Phylogenetic tree

CH

AR

AC

TE

RS

La

nc

ele

t(o

utg

rou

p)

La

mp

rey

Ba

ss

Fro

g

Turt

le

Le

op

ard

0

0

0

0

0

1

0

0

0

0

1

1

0

0

0

1

1

1

0

0

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1

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1

Making a Cladogram…

FIGURE 26.UN07

FIGURE 26.21

Archaea

Bacteria

Eukarya

COMMONANCESTOR

OF ALLLIFE

Land plants

Green algae

Red algae

ForamsCiliates

Dinoflagellates

Cellular slime moldsAmoebas

Animals

Fungi

EuglenaTrypanosomes

Leishmania

Sulfolobus

Thermophiles

Halophiles

Methanobacterium

Greennonsulfur bacteria

(Mitochondrion)

Spirochetes

Chlamydia

Cyanobacteria

Greensulfur bacteria

(Plastids, includingchloroplasts)

Diatoms

Look closely…which domains are more related to each other?

A branching tree?

FIGURE 26.22

Bacteria

Eukarya

Archaea

Billions of years ago

4 3 2 1 0

Horizontal Gene transfer

mitochondrionchloroplast

FIGURE 26.23

Archaea

Eukarya

Bacteria

Focus Questions

1. What is the difference between monophyletic, polyphyletic and paraphyletic groups?

2. What is the difference between orthologous and paralogous genes, why are they important?

3. What is the difference between shared derived characteristics and shared ancestral characteristics?

4. What is a molecular clock, how is it used?

FIGURE 26.10

(a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group

Group

Group

Group

A

B

C

D

E

F

G

A

B

C

D

E

F

G

A

B

C

D

E

F

G

Which is the correct way to classify?

Branch point:where lineages diverge

ANCESTRALLINEAGE

This branch pointrepresents thecommon ancestor oftaxa A–G.

This branch point forms apolytomy: an unresolvedpattern of divergence.

Sistertaxa

Basaltaxon

Taxon A

Taxon B

Taxon C

Taxon D

Taxon E

Taxon F

Taxon G

How to Read a phylogenetic Tree

Determine shared bases

Compute possibilities and apply maximum parsimony

Sometimes the results are surprising

FIGURE 26.18

Formation of orthologous genes:a product of speciation

Formation of paralogous genes:within a species

Ancestral gene Ancestral gene

Ancestral species Species C

Speciation withdivergence of gene

Gene duplication and divergence

Orthologous genes Paralogous genes

Species A Species B Species C after many generations

Not all molecular clocks run at the same rate

Mammalian Molecular Clock