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.
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
A
B
C
D
E
F
lineage
or clade
TIME
Cladogram or Phylogenetic Tree
TAXA
A
B
C
D
E
TIME
speciation
Cladogram or Phylogenetic Tree
F
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 A–F
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.
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
apomorphy
(for Taxon D)
apomorphies
(for Taxa B & C)
TIME
apomorphy
(for Taxa B,C,D,E,F)
Cladogram or Phylogenetic Tree
F
Sequentially group taxa by
shared derived character states (apomorphies)
TAXA
Tuna
Leopard
Lancelet
(outgroup)
Vertebral column
(backbone)
0
1
1
1
1
1
Hinged jaws
0
0
1
1
1
1
Lamprey
Tuna
Vertebral
column
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
Hair
0
0
0
0
0
1
Amniotic egg
(a) Character table
Leopard
Hair
(b) Phylogenetic tree
Fig. 26-11
DNA sequence data – most important type of data
1
Deletion
2
Insertion
Fig. 26-8a
DNA sequence data - alignment
3
Fig. 26-8b
4
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
Celastrales
Zygophyllales
Vitales
Saxifragales
Dilleniales
Gunnerales
Trochodendrales
Buxales
Sabiales
Proteatales
Ranunculales
*
Oxalidales
Malpighiales
euphorb spines
Malvids
Ericales
Cornales
cactus spines
*
Angiosperm
Eudicot Relationships
(after APGIII 2009)
Bruniales
Apiales
Paracryphiales
Dipsacales
Lamiids
Asterales
Escalloniales
Aquifoliales
Solanales
Lamiales
Gentianales
Boraginales
Garryales
Rosids
Caryophyllales
Euphorbs
Santalales
Berberidopsidales
Malvales
Brassicales
Huerteales
Sapindales
Fabids
Picramniales
Crossosomatales
Myrtales
Geraniales
Fagales
Cucurbitales
Rosales
Fabales
Convergent evolution:
spines of cacti & euphorbs
Cacti
Eudicots
Core Eudicots
Asterids
Campanulids
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
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
TIME
speciation
Cladogram or Phylogenetic Tree
F
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
Turtles
Lizards &
&
Lizards
Snakes
Snakes
Crocodyles
Crocodiles
Birds
Birds
"Reptilia"
Turtles
Turtles
Lizards &
&
Lizards
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”?
C
A
B
B
TAXA
F
C
E
D
D
E
TIME
speciation
Cladogram or Phylogenetic Tree
A
F
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”?
C
A
B
B
TAXA
F
C
E
D
D
E
A
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"
Turtles
Turtles
Lizards &
&
Lizards
Snakes
Snakes
Crocodyles
Crocodiles
Birds
Birds
“Reptilia” here paraphyletic
"Reptilia"
Turtles
Turtles
Lizards &
&
Lizards
Snakes
Snakes
Crocodyles
Crocodiles
Birds
Birds
Re-defined Reptilia monophyletic
Reptilia
Turtles
Turtles
Lizards &
&
Lizards
Snakes
Snakes
Crocodyles
Crocodiles
Birds
Birds
Reptilia
Turtles
Turtles
Lizards &
&
Lizards
Snakes
Snakes
Dinosaurs
Dinosaurs
Crocodyles
Crocodiles
†
† †
Birds
Birds
Importance of a name:
Did humans evolve from apes?
Orangutan
Orangatan Gorilla
Chimpanzees Humans
Chimpanzees
Pongidae
Hominidae
“Great Apes”
Orangutan
Chimpanzees Humans
Orangatan Gorilla Chimpanzees
Pongidae
Pongidaeor
Hominidae
“Great
Apes”
Orangutan
Orangatan Gorilla
Chimpanzees Humans
Chimpanzees
Pongidae or
Hominidae
Orangutan
Orangatan Gorilla
Chimpanzees Humans
Chimpanzees
Pongidae or
Hominidae
Orangutan
Orangatan Gorilla
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!