Lecture 4: Phylogeny and the Tree of Life

Campbell:

Chapter 26
 All life is interconnected by descent

Bacterium Amoeba Pine tree Rattlesnake Humans

How to determine the pattern of descent?

 Systematics - field of biology dealing with
diversity and evolutionary history of life

Includes Taxonomy: DINC

Description
Identification
Nomenclature
Classification
Goal:
– Determine Evolutionary History (Phylogeny) of Life
 Description
= assign features

Character = a feature (e.g., “petal color”)

Character states = two or more forms of a

character (e.g., “red,” “white”).
 Identification
= associate an unknown with a known
How? One way:
Taxonomic Key, e.g.,
Tree
Leaves simple …….………………………… Species A
Leaves pinnate …….………..…..…..…… Species B
Herb
Flowers red …….…………………………… Species C
Flowers white …….…………………..…… Species D
 Nomenclature
Naming, according to a formal system.

Binomial: Species are two names (Linnaeus):

E.g., Homo sapiens

Homo = genus name
sapiens = specific epithet
Homo sapiens = species name
 Nomenclature
Hierarchical Ranks:
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
 Classification
• Placing objects, e.g., life, into some type of
order.

• Taxon = a taxonomic group (plural = taxa).

 How to classify life
• Phenetic classification

– Based on overall similarity

– Those organisms most similar are classified more

“closely” together.
 Phylogenetic classification
• Based on known (inferred) evolutionary
history.

• Advantage:
– Classification reflects pattern of evolution
– Classification not ambiguous
 lineage
or clade
TIME

Cladogram or Phylogenetic Tree

= representation of the history of life

 TAXA

A B C D E F

lineage
or clade
TIME

Cladogram or Phylogenetic Tree

 TAXA

A B C D E F

TIME

speciation

Cladogram or Phylogenetic Tree

 Ingroup – group studied

Outgroup – group not part of

ingroup, used to “root” tree
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
 Apomorphy (derived trait)
 = a new, derived feature
E.g., for this evolutionary transformation

scales --------> feathers

(ancestral feature) (derived feature)

 Presence of feathers is an apomorphy

for birds.
Taxa are grouped by apomorphies
Apomorphies are the result of evolution.

Taxa sharing apomorphies

underwent same evolutionary history
should be grouped together.
 Principle of Parsimony
That cladogram (tree) having the fewest number
of “steps” (evolutionary changes) is the one
accepted.

Okham’s razor: the simplest explanation, with

fewest number of “ad hoc” hypotheses, is
accepted.
 Other methods of phylogeny
reconstruction:

• Maximum Likelihood or Bayesian

analysis
–Uses probabilities
–Advantage: can use evolutionary
models.
 TAXA

A B C D E F
apomorphy
(for Taxon D)

apomorphies
(for Taxa B & C)
TIME

apomorphy
(for Taxa B,C,D,E,F)

Cladogram or Phylogenetic Tree

 Sequentially group taxa by
shared derived character states (apomorphies)
TAXA Lancelet
(outgroup)

Leopard
Lamprey

Tuna
Vertebral column Tuna
0 1 1 1 1 1
(backbone) Vertebral
column
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) egg 0 0 0 0 1 1
Amniotic egg Leopard
Hair 0 0 0 0 0 1
Hair

(a) Character table (b) Phylogenetic tree

Fig. 26-11
DNA sequence data – most important type of data

Deletion
2

Insertion
Fig. 26-8a
 DNA sequence data - alignment

Fig. 26-8b

Each nucleotide position = Character

Character states = specific nucleotide
 Homology

• Similarity resulting from common

ancestry.

–E.g., the forelimb bones of a bird,

bat, and cat.
 Homoplasy (analogy)
• Similarity not due to common ancestry

• Reversal – loss of new (apomorphic)

feature, resembles ancestral (old)
feature.

• Convergence (parallelism) – gain of new,

similar features independently.
 Convergent evolution:
spines of cacti & euphorbs

Cactus Euphorb
 Ranunculales
Proteatales
Sabiales

Buxales
Trochodendrales
Gunnerales
Dilleniales
Saxifragales
Vitales
Zygophyllales
Celastrales
Malpighiales *
Oxalidales
Euphorbs

Fabales
Fabids

Rosales
Cucurbitales
Fagales
Geraniales
Rosids

Myrtales
Crossosomatales
Picramniales
euphorb spines

Sapindales
Malvids

Huerteales
Brassicales
Eudicots

Malvales
Core Eudicots

Berberidopsidales
Santalales
Caryophyllales
*
Cacti

Cornales
Ericales
Garryales
Boraginales
Gentianales
Lamiids

Lamiales
Convergent evolution:

Solanales
Aquifoliales
Angiosperm
cactus spines
Asterids

Escalloniales
spines of cacti & euphorbs

Asterales
(after APGIII 2009)
Eudicot Relationships

Dipsacales
Paracryphiales
Campanulids

Apiales
Bruniales
 Leg-less lizards Snake
Both examples of reversal within
legged leg-less
Tetrapods: snakes lizards lizards

loss of a derived feature – forelimbs. * *

Example of convergence relative to one
*= loss of legs
another!
Independently evolved. gain of legs (Tetrapods)
 Convergent evolution:
wings of some animals evolved independently
Fig. 26-7

Convergent evolution:
Australian “mole” and N. Am. “mole”
 Ancestral gene
Gene Duplication
can occur! Ancestral species

Speciation with
divergence of gene

Orthology –
Orthologous genes
genes
Species A Species B
(a) Orthologous genes
homologous

Species A

Gene duplication and divergence

Paralogy –
genes not
Paralogous genes
Species A after many generations homologous
(b) Paralogous genes
Fig. 26-18
 Monophyletic Group
• a group consisting of:
–a common ancestor +
–all descendents of that common
ancestor
 TAXA

A B C D E F

monophyletic
group

TIME

common ancestor
(of taxon D, E, & F)

common ancestor
(of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

 TAXA

A B C D E F

monophyletic
group

TIME

common ancestor
(of taxon D, E, & F)

common ancestor
(of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

 TAXA

A B C D E F

monophyletic
group

TIME

common ancestor
(of taxon D, E, & F)

common ancestor
(of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

 TAXA

A B C D E F

monophyletic
group

TIME

common ancestor
(of taxon D, E, & F)

common ancestor
(of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

 TAXA

A B C D E F

monophyletic
group

TIME

common ancestor
(of taxon D, E, & F)

common ancestor
(of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

 TAXA

A B C D E F

TIME

speciation

Cladogram or Phylogenetic Tree

 TAXA
C
A BB FC DE ED FA

TIME

speciation

Cladogram or Phylogenetic Tree

Cladograms can be “flipped” at nodes, show same
relationships
Fig. 26-13

One can date divergence times with molecular clock and fossils

Drosophila

Lancelet

Zebrafish

Frog

Chicken

Human

Mouse

PALEOZOIC MESOZOIC CENOZOIC

542 251 65.5 Present
Millions of years ago
 Relationship
• = recency of common ancestry

i.e., taxa sharing a common ancestor

more recent in time are more closely related
than those sharing common ancestors more
distant in time.
 Example:
• Are fish more closely related to sharks or to
humans?
 Shark Fish Humans

TIME
 Shark Fish Humans

TIME

common ancestor of
Fish and Humans

common ancestor of
Sharks, Fish, and Humans
 Vertebrata
Osteichthyes

Shark Fish Humans

TIME monophyletic
group
common ancestor of
Fish and Humans

common ancestor of
Sharks, Fish, and Humans
 Example:
• Are crocodyles more closely related to lizards
or to birds?
 Lizards &
Lizards &
Turtles
Turtles Snakes
Snakes Crocodyles
Crocodiles Birds
Birds
 "Reptilia"
Lizards &
Lizards &
Turtles
Turtles Snakes
Snakes Crocodyles
Crocodiles Birds
Birds
 Is “E” more closely related to “D” or to “F”?
Is “E” more closely related to “B” or to “A”?
Is “E” more closely related to “B” or to “C”?

TAXA
C B F E D A
A B C D E F

TIME

speciation

Cladogram or Phylogenetic Tree

 Is “E” more closely related to “D” or to “F”?
Is “E” more closely related to “B” or to “A”?
Is “E” more closely related to “B” or to “C”?

TAXA
C B F E D A
A B C D E F

TIME

speciation

Cladogram or Phylogenetic Tree

Answers: F, B, neither (equally to “B” & “C”)
 Paraphyletic group
• Consist of common ancestor but not all
descendents

• Paraphyletic groups are unnatural, distort

evolutionary history, and should not be
recognized.
 "Reptilia"
Lizards &
Lizards &
Turtles
Turtles Snakes
Snakes Crocodyles
Crocodiles Birds
Birds
“Reptilia” here paraphyletic

"Reptilia"
Lizards &
Lizards &
Turtles
Turtles Snakes
Snakes Crocodyles
Crocodiles Birds
Birds
Re-defined Reptilia monophyletic

Reptilia
Lizards &
Lizards &
Turtles
Turtles Snakes
Snakes Crocodyles
Crocodiles Birds
Birds
 Reptilia
Dinosaurs
Dinosaurs
Lizards &
Lizards &
Turtles
Turtles Snakes
Snakes Crocodyles
Crocodiles Birds
Birds
† † †
 Importance of a name:
Did humans evolve from apes?
Orangatan Gorilla
Orangutan Chimpanzees Humans
Chimpanzees
 Pongidae
“Great Apes” Hominidae
Orangatan Gorilla Chimpanzees
Orangutan Chimpanzees Humans
 Pongidae
Pongidaeor
Hominidae
“Great Apes”
Orangatan Gorilla
Orangutan Chimpanzees Humans
Chimpanzees
 Pongidae or
Hominidae

Orangatan Gorilla
Orangutan Chimpanzees Humans
Chimpanzees
 Pongidae or
Hominidae

Orangatan Gorilla
Orangutan Chimpanzees Humans
Chimpanzees
 We are human, but
we are also apes.

• We share unique human features.

• We also share features with other apes

(and with other animals, plants, fungi,
bacteria, etc.).

• Humans didn’t evolve from apes, humans

are apes.
 All of life is interconnected
by descent.
TAXA

A B C D E F

lineage
or clade
TIME

Cladogram or Phylogenetic Tree

There are no “higher” or “lower”
species.
TAXA

A B C D E F

lineage
or clade
TIME

Cladogram or Phylogenetic Tree

 Importance of systematics & evolution:

1) Foundation of biology - study of biodiversity

2) Basis for classification of life
3) Gives insight into biological processes:
speciation processes
adaptation to environment
4) Can be aesthetically/intellectually pleasing!