Lecture 4: Phylogeny and the Tree of Life

Campbell & Reece:

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 . Species A
Leaves simple . Species B
Leaves pinnate ....... Species C
Herb
Flowers red . Species D
Flowers white ... Species E

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.

Problem with phenetic classification:

Can be arbitrary,
e.g., classify these:

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

lineage
or clade
TIME

Cladogram or Phylogenetic Tree

TAXA

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

Taxon C
ANCESTRAL
LINEAGE

Taxon D

Taxon E
Taxon F
Common ancestor of
taxa AF

Polytomy

Sister
taxa

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.
Okhams 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

E
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

Tuna

Leopard

Lancelet
(outgroup)

Vertebral column
(backbone)

Hinged jaws

Lamprey

Tuna
Vertebral
column
Salamander
Hinged jaws

Four walking legs

1
Turtle

Four walking legs

Amniotic (shelled) egg

Hair

Amniotic egg

(a) Character table

Leopard
Hair

(b) Phylogenetic tree

Fig. 26-11

DNA sequence data most important type of data

1

Deletion

Insertion
Fig. 26-8a

DNA sequence data - alignment

3

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

Convergent evolution:
spines of cacti & euphorbs

euphorb spines

cactus spines

Leg-less lizards
Both examples of reversal within Tetrapods:
loss of a derived feature forelimbs.
Example of convergence relative to one another!
Independently evolved.

Snake
snakes

legged
lizards

leg-less
lizards

*
*= loss of legs

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

Species A

Orthologous genes

Species B

(a) Orthologous genes

Orthology
genes
homologous

Species A
Gene duplication and divergence

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

Paralogy
genes not
homologous

Common ancestry
TAXA

TIME
common ancestor
(of taxon D, E, & F)
common ancestor
(of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

Monophyletic Group
a group consisting of:
a common ancestor +
all descendents of that common ancestor

TAXA

monophyletic
group

TIME
common ancestor
(of taxon D, E, & F)
common ancestor
(of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

TAXA

monophyletic
group

TIME
common ancestor
(of taxon D, E, & F)
common ancestor
(of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

TAXA

monophyletic
group

TIME
common ancestor
(of taxon D, E, & F)
common ancestor
(of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

TAXA

monophyletic
group

TIME
common ancestor
(of taxon D, E, & F)
common ancestor
(of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

TAXA

monophyletic
group

TIME
common ancestor
(of taxon D, E, & F)
common ancestor
(of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

TAXA

TIME
speciation

Cladogram or Phylogenetic Tree

TAXA

C
A

BB

FC

DE

ED

TIME
speciation

Cladogram or Phylogenetic Tree

Cladograms can be flipped at nodes, show same
relationships

FA

Fig. 26-13

One can date divergence times with molecular clock and fossils
Drosophila

Lancelet

Zebrafish

Frog

Chicken

Human

Mouse
PALEOZOIC
542

MESOZOIC
251

Millions of years ago

CENOZOIC
65.5

Present

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

TIME

Fish

Humans

Shark

Fish

Humans

TIME
common ancestor of
Fish and Humans

common ancestor of
Sharks, Fish, and Humans

Vertebrata
Osteichthyes
Shark

TIME

Fish

Humans

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?

Turtles

Lizards &
Snakes

Crocodyles

Birds

"Reptilia"
Turtles

Lizards &
Snakes

Crocodyles

Birds

Paraphyletic group
Consist of common ancestor but not all
descendents
Paraphyletic groups are unnatural, distort
evolutionary history, and should not be
recognized.

"Reptilia"
Turtles

Lizards &
Snakes

Crocodyles

Birds

Reptilia here paraphyletic

"Reptilia"
Turtles

Lizards &
Snakes

Crocodyles

Birds

Re-defined Reptilia monophyletic

Reptilia
Turtles

Lizards &
Snakes

Crocodyles

Birds

Reptilia
Turtles

Lizards &
Snakes

Dinosaurs
Crocodyles

Birds

Importance of a name:
Did humans evolve from apes?

Orangatan Gorilla

Chimpanzees Humans

Pongidae
Hominidae
Great Apes
Orangatan Gorilla Chimpanzees Humans

Pongidae
Pongidaeor
Hominidae
Great
Apes
Orangatan Gorilla

Chimpanzees Humans

Pongidae or
Hominidae
Orangatan Gorilla

Chimpanzees Humans

Pongidae or
Hominidae
Orangatan Gorilla

Chimpanzees Humans

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 didnt evolve from apes, humans
are apes.

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!

E.g., schistosomiasis

Schistosomiasis:
knowledge of species
diversity and evolutionary
history of primary host can
aid in controlling parasite
(Schistosoma, a fluke)

Phylogeny of Oncomelania snails

All of life is interconnected

by descent.
TAXA

lineage
or clade
TIME

Cladogram or Phylogenetic Tree

There are no higher or

lower species.
TAXA

lineage
or clade
TIME

Cladogram or Phylogenetic Tree