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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!