Chapter 26

Phylogeny and the Tree of Life

PowerPoint® Lecture
Presentations for

Biology
Eighth Edition
Neil Campbell and Jane Reece
Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 26-1
Overview: Investigating the Tree of Life

• 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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Fig. 26-2
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

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Fig. 26-3
Species:
Panthera
pardus

Genus: Panthera

Family: Felidae

Order: Carnivora

Class: Mammalia

Phylum: Chordata

Kingdom: Animalia

Bacteria Domain: Eukarya Archaea

Fig. 26-3a

Class: Mammalia

Phylum: Chordata

Kingdom: Animalia

Bacteria Domain: Eukarya Archaea

Fig. 26-3b

Species:
Panthera
pardus

Genus: Panthera

Family: Felidae

Order: Carnivora
Linking Classification and Phylogeny

• Systematists depict evolutionary relationships

in branching phylogenetic trees

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Fig. 26-4
Order Family Genus Species

Panthera
Felidae
Panthera
pardus

Taxidea
Carnivora

Taxidea

Mustelidae
taxus

Lutra
Lutra lutra

Canis
latrans
Canidae

Canis

Canis
lupus
• 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 polytomy is a branch from which more than
two groups emerge

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Fig. 26-5

Branch point
(node)
Taxon A

Taxon B
Sister
taxa
Taxon C
ANCESTRAL
LINEAGE Taxon D

Taxon E

Taxon F
Common ancestor of
taxa A–F Polytomy
What We Can and Cannot Learn from
Phylogenetic Trees
• Phylogenetic trees do show patterns of descent

• Phylogenetic trees do not indicate when

species evolved or how much genetic change
occurred in a lineage
• It shouldn’t 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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Fig. 26-6
RESULTS
Minke
(Antarctica)
Minke
(Australia)
Unknown #1a,
2, 3, 4, 5, 6, 7, 8

Minke
(North Atlantic)
Unknown #9

Humpback
(North Atlantic)
Humpback
(North Pacific)
Unknown #1b

Gray

Blue
(North Atlantic)
Blue
(North Pacific)

Unknown #10,
11, 12
Unknown #13

Fin
(Mediterranean)
Fin (Iceland)
Fig. 26-6a

RESULTS
Minke
(Antarctica)
Minke
(Australia)
Unknown #1a,
2, 3, 4, 5, 6, 7, 8

Minke
(North Atlantic)
Unknown #9
Fig. 26-6b

Humpback
(North Atlantic)
Humpback
(North Pacific)
Unknown #1b

Gray

Blue
(North Atlantic)
Blue
(North Pacific)
Fig. 26-6c

Unknown #10,
11, 12
Unknown #13

Fin
(Mediterranean)
Fin (Iceland)
• Phylogenies of anthrax bacteria helped
researchers identify the source of a particular
strain of anthrax

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Fig. 26-UN1

A B D

B D C

C C B

D A A
(a) (b) (c)
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

• 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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Fig. 26-7
• Convergent evolution occurs when similar
environmental pressures and natural selection
produce similar (analogous) adaptations in
organisms from different evolutionary lineages

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• 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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Fig. 26-8
1

Deletion
2

Insertion

4
Fig. 26-8a

Deletion
2

Insertion
Fig. 26-8b

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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Fig. 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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Fig. 26-10

A A A
B Group I B B

C C C
D D D

E E Group II E Group III

F F F

G G G
(a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group
Fig. 26-10a

A
B Group I

C
D

E
F

G
(a) Monophyletic group (clade)
• A paraphyletic grouping consists of an
ancestral species and some, but not all, of the
descendants

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Fig. 26-10b

A
B

C
D

E Group II

G
(b) Paraphyletic group
• A polyphyletic grouping consists of various
species that lack a common ancestor

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Fig. 26-10c

A
B

C
D

E Group III

G
(c) Polyphyletic group
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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Fig. 26-11

TAXA Lancelet
(outgroup)

Salamander
(outgroup)
Lancelet

Lamprey

Leopard
Lamprey

Turtle
Tuna
Vertebral column Tuna
0 1 1 1 1 1
(backbone) Vertebral
column
CHARACTERS

Hinged jaws 0 0 1 1 1 1 Salamander

Hinged jaws
Four walking legs 0 0 0 1 1 1
Turtle
Four walking legs
Amniotic (shelled) 0 0 0 0 1 1
egg Amniotic egg Leopard
Hair 0 0 0 0 0 1
Hair

(a) Character table (b) Phylogenetic tree

Fig. 26-11a
TAXA

Salamander
(outgroup)

Lamprey
Lancelet

Leopard
Turtle
Tuna
Vertebral column
0 1 1 1 1 1
(backbone)

Hinged jaws 0 0 1 1 1 1
CHARACTERS

Four walking legs 0 0 0 1 1 1

Amniotic (shelled) egg 0 0 0 0 1 1

Hair 0 0 0 0 0 1

(a) Character table

Fig. 26-11b

Lancelet
(outgroup)

Lamprey

Tuna
Vertebral
column
Salamander
Hinged jaws

Turtle
Four walking legs

Amniotic egg Leopard

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
• Systematists compare each ingroup species
with the outgroup to differentiate between
shared derived and shared ancestral
characteristics

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• Homologies 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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Fig. 26-12

Drosophila

Lancelet

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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Fig. 26-13

Drosophila

Lancelet

Zebrafish

Frog

Chicken

Human

Mouse

PALEOZOIC MESOZOIC CENOZOIC

542 251 65.5 Present
Millions of years ago
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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Fig. 26-14
Human Mushroom Tulip
Human 0 30% 40%

Mushroom 0 40%

Tulip 0

(a) Percentage differences between sequences

15% 5%
5%
15% 15%
10%
20% 25%

Tree 1: More likely Tree 2: Less likely

(b) Comparison of possible trees
Fig. 26-14a

Human Mushroom Tulip

Human 0 30% 40%

Mushroom 0 40%

Tulip 0

(a) Percentage differences between sequences

Fig. 26-14b

15% 5%

5%

15% 15%

10%

20% 25%

Tree 1: More likely Tree 2: Less likely

(b) Comparison of possible trees
• Computer programs are used to search for
trees that are parsimonious and likely

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Fig. 26-15-1

Species I Species II Species III

Three phylogenetic hypotheses:

I I III

II III II

III II I
Fig. 26-15-2

Site
1 2 3 4
1/C
Species I C T A T I I III
1/C
Species II C T T C II III II
1/C
Species III A G A C II
III I
Ancestral A G T T 1/C 1/C
sequence
Fig. 26-15-3

Site
1 2 3 4
1/C
Species I C T A T I I III
1/C
Species II C T T C II III II
1/C
Species III A G A C II
III I
Ancestral A G T T 1/C 1/C
sequence
3/A 2/T 3/A
2/T I 3/A I 4/C III

II III II
4/C 4/C 2/T
III II I
3/A 4/C 2/T 4/C 2/T 3/A
Fig. 26-15-4

Site
1 2 3 4
1/C
Species I C T A T I I III
1/C
Species II C T T C II III II
1/C
Species III A G A C II
III I
Ancestral A G T T 1/C 1/C
sequence
3/A 2/T 3/A
2/T I 3/A I 4/C III

II III II
4/C 4/C 2/T
III II I
3/A 4/C 2/T 4/C 2/T 3/A

I I III

II III II

III II I
6 events 7 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

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Fig. 26-16

Lizards
and snakes

Crocodilians

Ornithischian
dinosaurs
Common
ancestor of
crocodilians, Saurischian
dinosaurs, dinosaurs
and birds
Birds
• This has been applied to infer features of
dinosaurs from their descendents: birds and
crocodiles

Animation: The Geologic Record

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Fig. 26-17

Front limb

Hind limb

Eggs
(a) Fossil remains of Oviraptor
and eggs

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

Fig. 26-17a

Front limb

Hind limb

Eggs
(a) Fossil remains of Oviraptor
and eggs
Fig. 26-17b

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

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 tool 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
• 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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• 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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Fig. 26-18
Ancestral gene

Ancestral species

Speciation with
divergence of gene

Orthologous genes
Species A Species B
(a) Orthologous genes

Species A

Gene duplication and divergence

Paralogous genes
Species A after many generations
(b) Paralogous genes
Fig. 26-18a

Ancestral gene

Ancestral species

Speciation with
divergence of gene

Species A Orthologous genes Species B

(a) Orthologous genes
Fig. 26-18b

Species A

Gene duplication and divergence

Paralogous genes
Species A after many generations
(b) Paralogous genes
Genome Evolution

• Orthologous genes are widespread and extend

across many widely varied species
• Gene number and the complexity of an
organism are not strongly linked
• 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

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Fig. 26-19

Number of mutations

90

60

30

0
0 30 60 90 120
Divergence time (millions of years)
Neutral Theory

• Neutral theory states that much evolutionary

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

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Difficulties 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
• Comparison of HIV samples throughout the
epidemic 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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Fig. 26-20
0.20

Index of base changes between HIV sequences 0.15

Computer model
of HIV
0.10
Range

0.05

0
1900 1920 1940 1960 1980 2000
Year
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
Animation: Classification Schemes

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Fig. 26-21

EUKARYA

Land plants Dinoflagellates

Green algae Forams
Ciliates Diatoms
Red algae

Amoebas
Cellular slime molds
Euglena
Trypanosomes
Animals
Leishmania
Fungi

Sulfolobus
Green nonsulfur bacteria
Thermophiles (Mitochondrion)

Spirochetes
Halophiles Chlamydia
COMMON
ANCESTOR Green
OF ALL sulfur bacteria
LIFE
Methanobacterium BACTERIA
Cyanobacteria
ARCHAEA (Plastids, including
chloroplasts)
Fig. 26-21a

Green nonsulfur bacteria

(Mitochondrion)

Spirochetes
Chlamydia
COMMON
ANCESTOR Green
OF ALL sulfur bacteria
LIFE

BACTERIA

Cyanobacteria
(Plastids, including
chloroplasts)
Fig. 26-21b

Sulfolobus

Thermophiles

Halophiles

Methanobacterium

ARCHAEA
Fig. 26-21c

EUKARYA

Land plants Dinoflagellates

Green algae Forams
Ciliates Diatoms
Red algae

Amoebas
Cellular slime molds
Euglena
Trypanosomes
Animals
Leishmania
Fungi
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 complicates efforts to
build a tree of life

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Fig. 26-22

Bacteria

Eukarya

Archaea

4 3 2 1 0
Billions of years ago
Is the Tree of Life Really a Ring?

• Some researchers suggest that eukaryotes

arose as an endosymbiosis 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

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Fig. 26-23

Eukarya

Bacteria Archaea
Fig. 26-UN2

Node Taxon A

Taxon B
Sister taxa
Taxon C

Taxon D

Taxon E
Most recent
common Polytomy Taxon F
ancestor
Fig. 26-UN3

Monophyletic group

A A A

B B B

C C C

D D D

E E E

F F F

G G G

Paraphyletic group Polyphyletic group

Fig. 26-UN4

Salamander

Lizard

Goat

Human
Fig. 26-UN5
Fig. 26-UN6
Fig. 26-UN7
Fig. 26-UN8
Fig. 26-UN9
Fig. 26-UN10
Fig. 26-UN10a
Fig. 26-UN10b
You should now be able to:

1. Explain the justification for taxonomy based on a

PhyloCode

2. Explain the importance of distinguishing between

homology and analogy

3. Distinguish between the following terms:

monophyletic, paraphyletic, and polyphyletic
groups; shared ancestral and shared derived
characters; orthologous and paralogous genes

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4. Define horizontal gene transfer and explain
how it complicates phylogenetic trees

5. Explain molecular clocks and discuss their

limitations

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