LECTURE PRESENTATIONS

For CAMPBELL BIOLOGY, NINTH EDITION

Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson

© 2011 Pearson Education, Inc.

Lectures by

Erin Barley

Kathleen Fitzpatrick

Phylogeny and the Tree of Life

Chapter 26

Overview: Investigating the Tree of Life

• Legless lizards have evolved independently in several different groups

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Figure 26.1

• Phylogeny is the evolutionary history of a species or group of related species
• The discipline of systematics classifies organisms and determines their evolutionary relationships
• Systematists use fossil, molecular, and genetic data to infer evolutionary relationships

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Figure 26.2

Figure 26.2a

Figure 26.2b

Figure 26.2c

Concept 26.1: Phylogenies show evolutionary relationships

• Taxonomy is the ordered division and naming of organisms

​

​

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Binomial Nomenclature

• In the 18th century, Carolus Linnaeus published a system of taxonomy based on resemblances
• Two key features of his system remain useful today: two-part names for species and hierarchical classification

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• The two-part scientific name of a species is called a binomial
• The first part of the name is the genus
• The second part, called the specific epithet, is unique for each species within the genus
• The first letter of the genus is capitalized, and the entire species name is italicized
• Both parts together name the species (not the specific epithet alone)

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Hierarchical Classification

• Linnaeus introduced a system for grouping species in increasingly broad categories
• The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species
• A taxonomic unit at any level of hierarchy is called a taxon
• The broader taxa are not comparable between lineages
• For example, an order of snails has less genetic diversity than an order of mammals

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Figure 26.3

Species:

Panthera pardus

Genus:

Panthera

Family:

Felidae

Order:

Carnivora

Class:

Mammalia

Phylum:

Chordata

Domain:

Bacteria

Kingdom:

Animalia

Domain:

Archaea

Domain:

Eukarya

Linking Classification and Phylogeny

• Systematists depict evolutionary relationships in branching phylogenetic trees

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Figure 26.4

Order

Family

Panthera

pardus

(leopard)

Genus

Species

Canis

latrans

(coyote)

Taxidea

taxus

(American

badger)

Lutra lutra

(European

otter)

Canis

lupus

(gray wolf)

Felidae

Carnivora

Panthera

Taxidea

Mustelidae

Lutra

Canidae

Canis

• Linnaean classification and phylogeny can differ from each other
• Systematists have proposed the PhyloCode, which recognizes only groups that include a common ancestor and all its descendents

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• A phylogenetic tree represents a hypothesis about evolutionary relationships
• Each branch point represents the divergence of two species
• Sister taxa are groups that share an immediate common ancestor

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• A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree
• A basal taxon diverges early in the history of a group and originates near the common ancestor of the group
• A polytomy is a branch from which more than two groups emerge

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Figure 26.5

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

What We Can and Cannot Learn from Phylogenetic Trees

• Phylogenetic trees show patterns of descent, not phenotypic similarity
• Phylogenetic trees do not indicate when species evolved or how much change occurred in a lineage
• It should not be assumed that a taxon evolved from the taxon next to it

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Applying Phylogenies

• Phylogeny provides important information about similar characteristics in closely related species
• A phylogeny was used to identify the species of whale from which “whale meat” originated

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Figure 26.6

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

Concept 26.2: Phylogenies are inferred from morphological and molecular data

• To infer phylogenies, systematists gather information about morphologies, genes, and biochemistry of living organisms

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Morphological and Molecular Homologies

• Phenotypic and genetic similarities due to shared ancestry are called homologies
• Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences

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Sorting Homology from Analogy

• When constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy
• Homology is similarity due to shared ancestry
• Analogy is similarity due to convergent evolution

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• Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages

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Figure 26.7

• Bat and bird wings are homologous as forelimbs, but analogous as functional wings
• Analogous structures or molecular sequences that evolved independently are also called homoplasies
• Homology can be distinguished from analogy by comparing fossil evidence and the degree of complexity
• The more complex two similar structures are, the more likely it is that they are homologous

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Evaluating Molecular Homologies

• Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms

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Figure 26.8-1

1

2

1

Figure 26.8-2

Deletion

Insertion

1

1

2

2

2

1

Figure 26.8-3

Deletion

Insertion

1

1

1

2

2

2

2

1

3

Figure 26.8-4

Deletion

Insertion

1

1

1

1

2

2

2

2

2

1

3

4

• It is also important to distinguish homology from analogy in molecular similarities
• Mathematical tools help to identify molecular homoplasies, or coincidences
• Molecular systematics uses DNA and other molecular data to determine evolutionary relationships

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Figure 26.9

Concept 26.3: Shared characters are used to construct phylogenetic trees

• Once homologous characters have been identified, they can be used to infer a phylogeny

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Cladistics

• Cladistics groups organisms by common descent
• A clade is a group of species that includes an ancestral species and all its descendants
• Clades can be nested in larger clades, but not all groupings of organisms qualify as clades

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• A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants

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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

Figure 26.10a

(a) Monophyletic group (clade)

Group 

A

B

C

D

E

F

G

• A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants

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Figure 26.10b

(b) Paraphyletic group

Group 

A

B

C

D

E

F

G

• A polyphyletic grouping consists of various species with different ancestors

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Figure 26.10c

(c) Polyphyletic group

Group 

A

B

C

D

E

F

G

Shared Ancestral and Shared Derived Characters

• In comparison with its ancestor, an organism has both shared and different characteristics

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• A shared ancestral character is a character that originated in an ancestor of the taxon
• A shared derived character is an evolutionary novelty unique to a particular clade
• A character can be both ancestral and derived, depending on the context

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Inferring Phylogenies Using Derived Characters

• When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared

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Figure 26.11

TAXA

Lancelet

(outgroup)

Lamprey

Bass

Frog

Turtle

Leopard

Vertebral

column

(backbone)

Four walking

legs

Hinged jaws

Amnion

Hair

Vertebral

column

Hinged jaws

Four walking legs

Amnion

Hair

(a) Character table

(b) Phylogenetic tree

CHARACTERS

Lancelet

(outgroup)

Lamprey

Bass

Frog

Turtle

Leopard

0

0

0

0

0

1

0

0

0

0

1

1

0

0

0

1

1

1

0

0

1

1

1

1

0

1

1

1

1

1

Figure 26.11a

TAXA

Vertebral

column

(backbone)

Four walking

legs

Hinged jaws

Amnion

Hair

(a) Character table

CHARACTERS

Lancelet

(outgroup)

Lamprey

Bass

Frog

Turtle

Leopard

0

0

0

0

0

1

0

0

0

0

1

1

0

0

0

1

1

1

0

0

1

1

1

1

0

1

1

1

1

1

Figure 26.11b

Lancelet

(outgroup)

Lamprey

Bass

Frog

Turtle

Leopard

Vertebral

column

Hinged jaws

Four walking legs

Amnion

Hair

(b) Phylogenetic tree

• An outgroup is a species or group of species that is closely related to the ingroup, the various species being studied
• The outgroup is a group that has diverged before the ingroup
• Systematists compare each ingroup species with the outgroup to differentiate between shared derived and shared ancestral characteristics

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• Characters shared by the outgroup and ingroup are ancestral characters that predate the divergence of both groups from a common ancestor

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Phylogenetic Trees with Proportional Branch Lengths

• In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular DNA sequence in that lineage

​

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Figure 26.12

Lancelet

Drosophila

Zebrafish

Frog

Chicken

Human

Mouse

• In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record

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Figure 26.13

Mouse

Human

Chicken

Frog

Zebrafish

Lancelet

Drosophila

Present

CENOZOIC

MESOZOIC

PALEOZOIC

Millions of years ago

542

251

65.5

Maximum Parsimony and Maximum Likelihood

• Systematists can never be sure of finding the best tree in a large data set
• They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood

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• Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely
• The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events

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Figure 26.14

Human

Human

Mushroom

Mushroom

Tulip

Tulip

0

0

0

30%

40%

40%

25%

15%

10%

5%

5%

15%

15%

20%

(a) Percentage differences between sequences

(b) Comparison of possible trees

Tree 1: More likely

Tree 2: Less likely

Figure 26.14a

Human

Human

Mushroom

Mushroom

Tulip

Tulip

0

0

0

30%

40%

40%

(a) Percentage differences between sequences

Figure 26.14b

25%

15%

10%

5%

5%

15%

15%

20%

(b) Comparison of possible trees

Tree 1: More likely

Tree 2: Less likely

• Computer programs are used to search for trees that are parsimonious and likely

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Figure 26.15

Species 

Species 

Species 

Three phylogenetic hypotheses:

1

2

3

4

TECHNIQUE

RESULTS

Species 

Species 

Species 

Ancestral sequence







1

2

3

4

Site

C

C

A

A

A

A

C

C

T

G

T

T

T

T

1/C

1/C

1/C

1/C

1/C

3/A

2/T

4/C

3/A

4/C

4/C

4/C

4/C

3/A

3/A

3/A

2/T

2/T

2/T

2/T

6 events

7 events

7 events

G

T



































































Figure 26.15a

1

TECHNIQUE

Three phylogenetic hypotheses:

Species 

Species 

Species 



















Figure 26.15b

TECHNIQUE

Species 

Species 

Species 

Ancestral sequence

1

2

3

4

Site

C

C

A

A

A

A

C

C

T

G

T

T

T

T

G

T

2

Figure 26.15c

TECHNIQUE

1/C

3

4

RESULTS

1/C

1/C

1/C

1/C

4/C

4/C

4/C

4/C

4/C

3/A

3/A

3/A

3/A

2/T

2/T

2/T

2/T

2/T

3/A

7 events

6 events

7 events























































Phylogenetic Trees as Hypotheses

• The best hypotheses for phylogenetic trees fit the most data: morphological, molecular, and fossil
• Phylogenetic bracketing allows us to predict features of an ancestor from features of its descendents
• For example, phylogenetic bracketing allows us to infer characteristics of dinosaurs

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Figure 26.16

Lizards

and snakes

Crocodilians

Ornithischian

dinosaurs

Saurischian

dinosaurs

Birds

Common

ancestor of

crocodilians,

dinosaurs,

and birds

• Birds and crocodiles share several features: four-chambered hearts, song, nest building, and brooding
• These characteristics likely evolved in a common ancestor and were shared by all of its descendents, including dinosaurs
• The fossil record supports nest building and brooding in dinosaurs

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Animation: The Geologic Record

Figure 26.17

Front limb

Hind limb

Eggs

(a) Fossil remains of

Oviraptor and eggs

(b) Artist’s reconstruction of the dinosaur’s

posture based on the fossil findings

Figure 26.17a

Front limb

Hind limb

Eggs

(a) Fossil remains of

Oviraptor and eggs

Figure 26.17b

(b) Artist’s reconstruction of the dinosaur’s

posture based on the fossil findings

Concept 26.4: An organism’s evolutionary history is documented in its genome

• Comparing nucleic acids or other molecules to infer relatedness is a valuable approach for tracing organisms’ evolutionary history
• DNA that codes for rRNA changes relatively slowly and is useful for investigating branching points hundreds of millions of years ago
• mtDNA evolves rapidly and can be used to explore recent evolutionary events

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Gene Duplications and Gene Families

• Gene duplication increases the number of genes in the genome, providing more opportunities for evolutionary changes
• Repeated gene duplications result in gene families
• Like homologous genes, duplicated genes can be traced to a common ancestor

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• Orthologous genes are found in a single copy in the genome and are homologous between species
• They can diverge only after speciation occurs

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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 with

divergence of gene

Gene duplication and divergence

Orthologous genes

Paralogous genes

Species A

Species B

Species C after many generations

Figure 26.18a

Formation of orthologous genes:

a product of speciation

Ancestral gene

Ancestral species

Speciation with

divergence of gene

Orthologous genes

Species A

Species B

• Paralogous genes result from gene duplication, so are found in more than one copy in the genome
• They can diverge within the clade that carries them and often evolve new functions

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Figure 26.18b

Formation of paralogous genes:

within a species

Ancestral gene

Species C

Gene duplication and divergence

Paralogous genes

Species C after many generations

Genome Evolution

• Orthologous genes are widespread and extend across many widely varied species
• For example, humans and mice diverged about 65 million years ago, and 99% of our genes are orthologous

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• Gene number and the complexity of an organism are not strongly linked
• For example, humans have only four times as many genes as yeast, a single-celled eukaryote
• Genes in complex organisms appear to be very versatile, and each gene can perform many functions

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Concept 26.5: Molecular clocks help track evolutionary time

• To extend molecular phylogenies beyond the fossil record, we must make an assumption about how change occurs over time

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Molecular Clocks

• A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change
• In orthologous genes, nucleotide substitutions are proportional to the time since they last shared a common ancestor
• In paralogous genes, nucleotide substitutions are proportional to the time since the genes became duplicated

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• Molecular clocks are calibrated against branches whose dates are known from the fossil record
• Individual genes vary in how clocklike they are

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Figure 26.19

Divergence time (millions of years)

Number of mutations

90

60

30

30

60

90

120

0

Neutral Theory

• Neutral theory states that much evolutionary change in genes and proteins has no effect on fitness and is not influenced by natural selection
• It states that the rate of molecular change in these genes and proteins should be regular like a clock

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Problems with Molecular Clocks

• The molecular clock does not run as smoothly as neutral theory predicts
• Irregularities result from natural selection in which some DNA changes are favored over others
• Estimates of evolutionary divergences older than the fossil record have a high degree of uncertainty
• The use of multiple genes may improve estimates

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Applying a Molecular Clock: The Origin of HIV

• Phylogenetic analysis shows that HIV is descended from viruses that infect chimpanzees and other primates
• HIV spread to humans more than once
• Comparison of HIV samples shows that the virus evolved in a very clocklike way
• Application of a molecular clock to one strain of HIV suggests that that strain spread to humans during the 1930s

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Figure 26.20

Year

HIV

Range

Adjusted best-fit line

(accounts for uncertain

dates of HIV sequences)

0.20

0.15

0.10

0.05

0

1900

1920

1940

1960

1980

2000

Index of base changes between HIV gene sequences

Concept 26.6: New information continues to revise our understanding of the tree of life

• Recently, we have gained insight into the very deepest branches of the tree of life through molecular systematics

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From Two Kingdoms to Three Domains

• Early taxonomists classified all species as either plants or animals
• Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia
• More recently, the three-domain system has been adopted: Bacteria, Archaea, and Eukarya
• The three-domain system is supported by data from many sequenced genomes

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Animation: Classification Schemes

Figure 26.21

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

Figure 26.21a

Bacteria

Green

nonsulfur bacteria

(Mitochondrion)

Spirochetes

Chlamydia

Cyanobacteria

Green

sulfur bacteria

(Plastids, including

chloroplasts)

COMMON

ANCESTOR

OF ALL

LIFE

Figure 26.21b

Sulfolobus

Methanobacterium

Thermophiles

Halophiles

Archaea

Figure 26.21c

Eukarya

Land plants

Green algae

Red algae

Forams

Dinoflagellates

Ciliates

Diatoms

Cellular slime molds

Amoebas

Animals

Fungi

Trypanosomes

Euglena

Leishmania

A Simple Tree of All Life

• The tree of life suggests that eukaryotes and archaea are more closely related to each other than to bacteria
• The tree of life is based largely on rRNA genes, as these have evolved slowly

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• There have been substantial interchanges of genes between organisms in different domains
• Horizontal gene transfer is the movement of genes from one genome to another
• Horizontal gene transfer occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms
• Horizontal gene transfer complicates efforts to build a tree of life

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Figure 26.22

Bacteria

Eukarya

Archaea

Billions of years ago

4

3

2

1

0

• Some researchers suggest that eukaryotes arose as an fusion between a bacterium and archaean
• If so, early evolutionary relationships might be better depicted by a ring of life instead of a tree of life

Is the Tree of Life Really a Ring?

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Figure 26.23

Archaea

Eukarya

Bacteria

Figure 26.UN01

A

A

A

B

B

B

C

C

C

D

D

D

(a)

(b)

(c)

Figure 26.UN02

Branch point

Most recent

common

ancestor

Polytomy

Sister taxa

Basal taxon

Taxon A

Taxon B

Taxon C

Taxon D

Taxon E

Taxon F

Taxon G

Figure 26.UN03

Monophyletic group

Polyphyletic group

Paraphyletic group

A

B

C

D

E

F

G

A

B

C

D

E

F

G

A

B

C

D

E

F

G

Figure 26.UN04

Salamander

Lizard

Goat

Human

Figure 26.UN05

Figure 26.UN06

Figure 26.UN07

Figure 26.UN08

Figure 26.UN09

Figure 26.UN10

Figure 26.UN11