NOTES: Chapter 26

Phylogeny and the Tree of Life

Phylogeny: the evolutionary history of a

species or group of species

● Systematics: discipline focused on classifying organisms and determining their evolutionary relationships

● The fossil record: the ordered array of fossils, within layers, or strata, of sedimentary rock

● Paleontologists: collect and interpret fossils

a “family tree”…

Linnaeus

convinced us to

use a hierarchical

classification

system

Darwin provided us

with the mechanism by

which evolution results

in descent with

modification

● Taxonomy – naming & classifying organisms

● Systematics – naming & classifying

organisms according to

their evolutionary relationships

● Phylogenetics – reconstructing the

evolutionary relationships

among organisms

Systematics

Phylogenetics

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

Aptenodytes forsteri

● The two-part scientific name of a species is called a binomial

● The first part of the name is the genus

● The second part 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

Binomial Nomenclature

Chelonia mydas

Hierarchical Classification

● 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

Species:

Panthera pardus

Genus:

Panthera

Family:

Felidae

Order:

Carnivora

Class:

Mammalia

Phylum:

Chordata

Domain:

Bacteria

Kingdom:

Animalia Domain:

ArchaeaDomain:

Eukarya

5 Kingdom classification system in

use through the late 1900s

5 Kingdom classification system in

use through the late 1900s

gave way to Woese’s 3 Domains

5 Kingdom classification system in

use through the late 1900s

gave way to Woese’s 3 Domains

and multiple Kingdoms

“Did King Philip

Come Over From

Great Spain?”

The Major Lineages of Life: the 5 Kingdom System

Living organisms (now PLUS 3 domains!)

Prokaryotic Eukaryotic

Simple/unicells Multicellular

Autotrophic Heterotrophic

Absorptive Ingestive

nutrition nutrition

(Animalia)(Fungi)

(Plantae)

(Protista)

(Monera)

Linking Classification and

Phylogeny

● Systematists

depict evolutionary

relationships in

branching

phylogenetic

trees

Order Family

Pantherapardus(leopard)

Genus Species

Canislatrans(coyote)

Taxideataxus(Americanbadger)

Lutra lutra(Europeanotter)

Canislupus(gray wolf)

Felid

ae

Ca

rniv

ora

Pa

nth

eraT

ax

idea

Mu

stelida

e

Lu

tra

Ca

nid

ae

Can

is

Macroevolution & Phylogeny

–

hypothesized genealogy

traced back to the last

common ancestor (i.e., the

most recent) through

hierarchical, dichotomous

branching

● Phylogenetic tree -

● 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

Phylogenetic Trees

● 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

Phylogenetic Trees

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

Macroevolution & Phylogeny

Phylogenetic tree, phylogeny, or cladogram

● Node – branch point,

speciation event

Constructing Phylogenetic

Trees● Sorting homology vs. analogy...

● Homology: likenesses attributed to common or shared ancestry

● Analogy: likenesses attributed to similar ecological roles and natural selection

● Convergent evolution: species from different evolutionary branches that resemble one another due to similar ecological roles

Phylogenies – HOMOLOGY

HOMOLOGIES: Similar characters (e.g.,

morphological, behavioral, molecular, etc. traits or

features) suggest relatedness…

Wasps

[Hymenoptera]

● Homologous characters share common ancestry

**Lack of similarity among taxa results from

DIVERGENCE

Phylogenies – HOMOLOGY

● As a general rule, the more homologous

characters shared by two species, the

more closely they are related

● Sequences of DNA & RNA (nucleotides) and

proteins (amino acids) are used as characters; as a

general rule, the more recently two species shared a

common ancestor, the more similar their sequences

Phylogenies – HOMOLOGY

Phylogenies - ANALOGY

But, not all similarity derives from common ancestry!

CONVERGENT EVOLUTION: can produce superficially

similar traits that lack homology with one another

● Analogous characters do not share common

ancestry

**Similarity among taxa results from CONVERGENCE

Phylogenies - ANALOGY

Evaluating Molecular

Homologies:

● Systematists use computer programs and

mathematical tools when analyzing comparable

DNA segments from different organisms

● Molecular systematics uses DNA and other

molecular data (i.e. amino acid sequences) to

determine evolutionary relationships

Deletion

Insertion

1

1

1

1

2

2

2

2

2

1

3

4

Cladistic Analysis

Each nucleotide can be treated as a character

Character changes (mutations) from the ancestral

to the derived state include:

Substitutions

Insertions

Deletions

…AGCTCTAGG…

…AGCTATAGG…

…AGCTCTAGG…

…AGCTGATCTAGG…

…AGCTCTAGG…

…AGCTCTAGG…

Mutations

Shared characters are used to

construct phylogenetic trees

● Once homologous characters have been

identified, they can be used to infer a phylogeny

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

● A valid clade is monophyletic, signifying

that it consists of the ancestor species and

all its descendants

(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

CLADISTICS:

(b) Paraphyletic group

Group

A

B

C

D

E

F

G

● A polyphyletic grouping consists of various

species with different ancestors

CLADISTICS:

(c) Polyphyletic group

Group

A

B

C

D

E

F

G

(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

Macroevolution & Phylogeny

A clade is a monophyletic group, i.e., an

ancestral species and all of its descendents

Phylogenetic tree, phylogeny, or cladogram

Macroevolution & Phylogeny

Taxonomic groups often reflect true 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 (“new”) to a particular clade

● A character can be both ancestral and derived,

depending on the context

Ancestral vs. Derived Characters

Inferring Phylogenies Using

Derived Characters

● When inferring evolutionary relationships, it is

useful to know in which clade a shared derived

character first appeared

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

CH

AR

AC

TE

RS

Lan

cele

t

(ou

tgro

up

)

Lam

pre

y

Bass

Fro

g

Tu

rtle

Leo

pard

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

TAXA

Vertebral

column

(backbone)

Four walking

legs

Hinged jaws

Amnion

Hair

(a) Character table

CH

AR

AC

TE

RS

Lan

cele

t

(ou

tgro

up

)

Lam

pre

y

Bass

Fro

g

Tu

rtle

Leo

pard

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

Lancelet

(outgroup)

Lamprey

Bass

Frog

Turtle

Leopard

Vertebral

column

Hinged jaws

Four walking legs

Amnion

Hair

(b) Phylogenetic tree

Cladistic Analysis

All

similar

characters

Analogies

Homologies

Shared

Primitive

Characters

(ancestral)

Shared

Derived

Characters

(unique to a clade)

**The sequence of branching in a cladogram then

represents the sequence in which evolutionary

novelties (shared derived characters) evolved

● 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

Ingroup vs. Outgroup

● Characters shared by the outgroup and ingroup

are ancestral characters that predate the

divergence of both groups from a common

ancestor

Cladistic Analysis

Ingroup vs. Outgroup

An outgroup helps identify shared ancestral and

shared DERIVED CHARACTERS (unique to a

clade)

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

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

Mouse

Human

Chicken

Frog

Zebrafish

Lancelet

Drosophila

Present

CENOZOICMESOZOICPALEOZOIC

Millions of years ago

542 251 65.5

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

descendants

-For example, phylogenetic bracketing allows us to

infer characteristics of dinosaurs

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

descendants, including dinosaurs

● The fossil record supports nest building and

brooding in dinosaurs

Phylogenetic Trees as Hypotheses

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

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 (i.e. human ancestral

groups)

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

Molecular Clocks

Molecular Clocks

● A molecular clock uses constant rates of evolution

in some genes to estimate the absolute time of

evolutionary change

● In orthologous genes (genes found in different

species; e.g. cytochrome c for E.T.C.), nucleotide

substitutions are proportional to the time since they

last shared a common ancestor

● In paralogous genes (similar genes found within

one species; e.g. olfactory receptor genes in

humans), nucleotide substitutions are proportional

to the time since the genes became duplicated

● Molecular clocks are

calibrated against

branches whose dates

are known from the

fossil record

● Individual genes vary

in how clocklike they

are

Molecular Clocks

Divergence time (millions of years)

Nu

mb

er o

f m

uta

tio

ns

90

60

30

30 60 90 120

0