Phylogeny and the Tree of Life

Chapter 26

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

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

Figure 26.2

Taxonomy is the ordered division and naming of organisms.

Concept 26.1: Phylogenies show evolutionary relationships

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
• 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)

​

Figure 26.3

Species:

Panthera pardus

Genus:

Panthera

Family:

Felidae

Order:

Carnivora

Class:

Mammalia

Phylum:

Chordata

Domain:

Bacteria

Kingdom:

Animalia

Domain:

Archaea

Domain:

Eukarya

• 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

​

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

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

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
• 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

​

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

​

Evaluating Molecular Homologies

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

Deletion

Insertion

1

1

1

1

2

2

2

2

2

1

3

4

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
• 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

​

Shared Ancestral and Shared Derived Characters

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

​

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

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

Inferring Phylogenies Using Derived Characters

Figure 26.12

Lancelet

Drosophila

Zebrafish

Frog

Chicken

Human

Mouse

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.

Figure 26.13

Mouse

Human

Chicken

Frog

Zebrafish

Lancelet

Drosophila

Present

CENOZOIC

MESOZOIC

PALEOZOIC

Millions of years ago

542

251

65.5

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

Animation: The Geologic Record

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
• A molecular clock uses constant rates of evolution in some genes to estimate the absolute time of evolutionary change
• Molecular clocks are calibrated against branches whose dates are known from the fossil record
• Individual genes vary in how clocklike they are

​

​

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

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

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
• 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

​

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

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

• 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

Figure 26.22

Bacteria

Eukarya

Archaea

Billions of years ago

4

3

2

1

0

Figure 26.UN05

Figure 26.UN06

Figure 26.UN07

Figure 26.UN08

Figure 26.UN09

Figure 26.UN10

Figure 26.UN11