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Biology of Organisms
Comparative Biology
•  Uses phylogenetic relationships to study
the features that unite and distinguish
different groups.
•  Allows us to understand everything in
biology from genes to behavior to anatomy
to ecology to distributions in a holistic
manner.
•  Why is an
introduction to
life’s diversity
important?
Comparative Biology
Escherichia coli
Saccharomyces cerevisiae
Caenorhabditis elegans Drosophila melanogaster
Xenopus laevis
Mus musculus
Arabidopsis
thaliana
Zea mays
Danio rerio
•  This is why we can
study human diseases
using mouse models.
•  This is why principles of
genetics derived from
fruit flies are
generalizable.
•  This all goes back to the
unity of life.
Macaca mulatta
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Comparative Biology
•  Some of the most
exciting recent
discoveries in
biology include the
elucidation of
common genetic
elements of animal
development.
•  HOX genes.
Biology of Organisms
•  Interactions between
life’s diversity
underlie essentially
all of biology.
•  How many
interactions are
going on here?
Biology of Organisms
•  Interactions between
life’s diversity
underlie essentially
all of biology.
•  How might this be
relevant to your
future interests?
•  Medicine?
ic
zo
oMes
zoic
Cenozoic
Humans
leo
Pa
Colonization
of land
Today,
Module 1:
Animals
Origins,
History, &
Unity of Life
Origin of solar
system and
Earth
4
1
Proterozoic
Bil
lio
2
ns
of
Archaean
a
ye
rs
ag
3
Prokaryotes
o
Multicellular
eukaryotes
Single-celled
eukaryotes
Atmospheric
oxygen
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What is life?
•  What would we look for in a life form?
•  What defines life?
•  It’s been around for 3.8-3.5 billion years
What is life?
•  Reproduction
–  Oldest rocks are 4.0-3.8 billion years
•  Any thoughts?
Asexual
What is life?
•  Reproduction
•  Metabolism:
–  the set of chemical
reactions that occur
in living organisms
that manage the
material and energy
resources of the cell.
Sexual
What is life?
•  Reproduction
•  Metabolism
•  Organization
–  Non-random
–  Hierarchies
–  Emergent properties
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What is life?
• 
• 
• 
• 
What is life?
Reproduction
Metabolism
Organization
Growth &
Development
• 
• 
• 
• 
Reproduction
Metabolism
Organization
Growth &
Development
•  Homeostasis
–  Heritability
–  Cells
–  Regulating internal
environment
What is life?
• 
• 
• 
• 
• 
• 
Reproduction
Metabolism
Organization
Growth & Development
Homeostasis
Responds to the
environment
–  Temperature, moisture,
sunlight, substrate
What is life?
• 
• 
• 
• 
• 
• 
Reproduction
Metabolism
Organization
Growth & Development
Homeostasis
Responds to the
environment
•  Evolution, Adaptation, &
Extinction
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III. A hierarchy
of organization
•  From atoms to
grasslands
•  There are increasing
levels of complexity
IV. Emergent Properties
atom
tissue
organ
–  An upside-down pyramid
of increasing structural
and functional
complexity.
•  At each increasing
level, the whole is more
than the sum of its parts
molecule
cell
population
organism
•  With increasing complexity
the hierarchical level
becomes more than the sum
of its parts.
•  These are known as
emergent properties.
•  These are novel properties
that emerge from
interactions at lower levels.
•  How is this cathedral termite
mound an example of an
emergent property?
organ system
ecosystem
biome
IV. Emergent Properties
•  As biologists, to
understand the whole
we need to break it
down and examine its
parts.
•  Reductionist
perspective.
•  But we always must
keep in mind that when
we do this that the
whole loses its
emergent properties.
organelle
V: Correlation: structure,
function, diversity
•  Divergence through
evolution.
–  a.k.a. descent with
modification.
•  Organisms have
both a shared
ancestry and new
attributes.
Mammalian Forelimb
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V: Correlation: structure,
function, diversity
•  The pentamerous
(five-digit)
arrangement of the
mammalian forelimb
indicates homology.
V: Correlation: structure,
function, diversity
•  This pentamerous
arrangement has
been subsequently
been modified
through adaptation.
–  Features that are
similar as a result of
descent.
Mammalian Forelimb
VI. Unity in diversity
•  Sometimes it is
difficult to see unity
in diversity.
•  What, for example,
could a
hummingbird and a
mushroom have in
common?
VI. Unity in diversity
•  Fungi and Animals
diverged some 965
million years ago!
•  Evolution will, of
course, obscure
these relationships.
•  But they are all part
of the hierarchy of
life.
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VI. Unity in diversity
•  Over 1.5 million
species are named.
•  But more than 98%
of all species that
have ever existed
have become
extinct.
•  This also obscures
relationships.
VII: Pattern & Process
•  Pattern: Description of the WHAT?
•  Process: Description of the HOW?
•  This course will mainly be about the
description.
•  Because we must know what exists
before we attempt to explain
VI. Unity in diversity:
Phylogenetics and Taxonomy
•  The study of
diversity is known as
SYSTEMATICS.
•  Phylogenetics is the
practice of
elucidating
relationships.
•  Taxonomy is the
practice of naming
organisms.
•  Classification
arranges organisms.
I. Fossils & Sedimentation
•  Fossils are the most
readily observable
record of the history
of life.
•  Key to the field of
macroevolution.
•  Paleontology is the
study of fossils.
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I. Fossils & Sedimentation
•  Unfortunately, the
fossil record is both
biased and
incomplete.
•  Why would it be
biased?
I. Fossils & Sedimentation
•  Unfortunately, the
fossil record is both
biased and
incomplete.
•  Why would it be
biased?
•  Why would it be
incomplete?
I. Fossils & Sedimentation
•  Taphonomic
conditions must be
appropriate.
I. Fossils & Sedimentation
•  Taphonomic
conditions depend
upon:
•  Geological
processes
•  Type of fossil
•  Age of fossils
–  These are the
conditions that
permit decaying
organisms to
become fossilized.
Will this wombat skeleton fossilize?
Shales are particularly good
for preserving fossils
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I. Fossils & Sedimentation
•  Geological Processes
•  Most fossils are found in
sedimentary rock.
•  How are sediments
formed? What are the
implications of this for the
abundance of fossils?
•  Also mineralized amber
and ice.
I. Fossils & Sedimentation
I. Fossils & Sedimentation
•  Types of Fossils
•  The vast majority are of
hard parts. Why?
I. Fossils & Sedimentation
•  Types of Fossils
•  Types of Fossils
•  The vast majority are of
hard parts. Why?
•  Trace fossils provide
information on
interactions, ecology,
behavior, functional
morphology.
•  How?
•  These are rare!
–  Soft tisues are broken
down by bacteria and
fungi
–  Hard parts become
mineralized.
•  This includes animals
AND plants.
Dinosaur tracks
Leaf-mining
insects
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I. Fossils & Sedimentation
I. Fossils & Sedimentation
•  Ages of Fossils
•  Ages of Fossils
•  Older fossils are much
more rare.
•  Why?
•  Older fossils are much
more rare.
•  More opportunity for
geological processes to
obscure or destroy:
weathering, subduction,
etc.
•  Older rocks are rarer.
Stromatolites
Fossilized
stromatolite
I. Fossils & Sedimentation
•  The rarity of appropriate
taphonomic conditions
results in this bias and
incompleteness.
•  Despite this, the fossil
record provides
remarkable insights into
the history of life on
earth.
“eBay insect fossil is new species”
Stromatolites
Fossilized
stromatolite
II. Dating of major events
•  How do
paleontologists
estimate fossil/strata
ages?
–  Relative
–  Absolute
One second before the
end of the dinosaurs…
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II. Dating of major events
•  Relative dating:
•  Usually older fossils at bottom of strata,
younger towards top.
II. Dating of major events
•  Absolute dating.
•  Radioactive elements:
isotopes that decay at a
constant rate.
•  The ratio of these
versus the stable
isotopes that they decay
into gives us a metric of
the age that the
sediment was formed
–  or the fossil itself if any
organic Carbon is lucky
enough to be preserved.
II. Dating of major events
Common isotope ratios used in radiometric dating
II. Dating of major events
•  Generalizations:
•  Index fossils help
correlate ages of
strata over wide
areas.
•  Based on welldocumented fossils
of short-lived (but
abundant) species.
Viviparus glacialis is an index fossil for 2.3-1.8 mya
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III. The Geological Time Scale
IV. Major Episodes
The geologic record
is divided into the
Archaean, the
Proterozoic, and the
Phanerozoic eons.
•  A combination of:
–  Relative dating
–  Absolute dating
–  Major events in the history of life
•  Give us the Geological Time Scale
–  You should become familiar with the
names, dates, and major events in this
time scale.
The Archaean: 4.6-2.5 bya
•  Probably absent of life
until 3.5 bya (first rocks
3.8 bya)
•  Prokaryotes appear (3.5
bya)
•  Massive increase in
Oxygen (of biological
origin) and first
significant extinction at
end of Archaean 2.5
bya
I highly recommend
that you study Table
25.1 from your book!
Stromatolites
Fossilized
stromatolite
The Archaean &
Proterozoic together
are commonly known
as the Precambrian
Era
The Proterozoic: 2500-542 mya
•  First Eukaryotes and
multicellular
organisms appear.
•  Familiarize yourself
with pages 516-517
and figure 25.9 in
the textbook for this.
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The Proterozoic: 2500-542 mya
•  First Eukaryotes and
multicellular organisms
appear.
•  Low diversity early
(Snowball Earth)
•  Later characterized by the
“Ediacaran” or “Vendian”
biota.
•  Mass extinction of these
forms at the end of this
boundary.
•  Why?
The Paleozoic Era: 542-251 mya
•  Began with the Cambrian
Explosion.
•  Sudden appearance of
modern animal phyla in the
fossil record.
•  Localized fossils and DNA
evidence suggest earlier
origins (Conway Morris’
long fuse).
•  BUT the explosion refers to
their widespread
emergence and dominance.
Phanerozoic: 542 mya-present
•  The Phanerozoic
encompasses multicellular
eukaryotic life
•  The Phanerozoic is divided
into three eras: the
Paleozoic, Mesozoic, and
Cenozoic
•  Major boundaries between
geological divisions
correspond to extinction
events in the fossil record
The Paleozoic Era: 542-251 mya
•  Major features:
–  Colonization of land
–  Appearance of
vascular plants
–  Origins of seed
plants
–  Diversification of
insect orders
–  Radiation of
vertebrates
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The Paleozoic Era: 542-251 mya
•  Ended with the
PERMIAN extinction.
•  Correlated with
formation of PANGEA.
The Paleozoic Era: 542-251 mya
•  Ended with the PERMIAN
extinction.
•  Correlated with formation of
PANGEA.
•  Correlated with high levels of
volcanism.
•  Loss of approximately 90%
of all animal species.
•  Transition into the Mesozoic
Era
Continental Drift
•  The movement of
earth’s continents
relative to each other.
•  Based on the theory
of plate tectonics.
•  Tectonic plates move
in relation to each
other causing
continental drift,
earthquakes,
volcanoes,
mountain-building,
and oceanic trench
formation
The Mesozoic Era: 251-65mya
•  Divided into three
Periods:
–  Triassic (251-200 mya)
–  Jurassic (200-145 mya)
–  Cretaceous (145-65
mya)
•  End of each
characterized by
extinctions
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The Mesozoic Era: 251-65mya
•  Characterized by rise and
dominance of
Gymnosperms (Triassic
and Jurassic).
•  Rise, diversification, and
extinction of most
dinosaur groups.
•  Origins and early
diversification of mammals
and Angiosperms.
The Mesozoic Era: 251-65mya
•  Ended with Cretaceous
Extinction
The Mesozoic Era: 251-65mya
•  Ended with Cretaceous
Extinction.
•  Significant evidence for
massive impact event at
Chicxulub crater in the
Yucatán Peninsula.
A split second before the
extinction of the dinosaurs
The Mesozoic Era: 251-65mya
•  Ended with Cretaceous
Extinction.
•  Significant evidence for
massive impact event at
Chicxulub crater in the
Yucatán Peninsula.
•  Worldwide Iridium layer at
Cretaceous-Tertiary
boundary (a.k.a. K-T
boundary).
•  Extinction of 50% of all
marine and terrestrial
species, including all but
one lineage of dinosaurs.
Cenotes in the Yucatán indicate
the rim of the ancient crater
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The Cenozoic Era: 65mya-present
•  Divided into two
periods:
What is the objective of
systematics?
–  Paleogene (65-23
mya)
–  Neogene (23myapresent)
•  Rise of angiosperms,
mammals, and
extreme diversification
of insects.
A. Objectives of Taxonomy
A. Objectives of Taxonomy
Small canine teeth;
language
1.  Sort and identify
organisms into
species.
• 
This includes the
unique derived
characteristics that
distinguish them.
Cranial features;
brain size; brain
morphology
1.  Sort and identify
organisms into
species.
• 
This includes the
unique derived
characteristics that
distinguish them.
Presence of a
chin
Advanced toolmaking
Dimensions of pelvis;
upright gait; s-shaped spine
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A. Objectives of Taxonomy
Skull balanced upright
on vertebral column
1.  Sort and identify
organisms into
species.
• 
• 
This includes the
unique derived
characteristics that
distinguish them.
This includes
giving a name to
undescribed
species.
Reduced hair
cover
Elongated
thumb and
shortened
finger;
Limb length
Species:
Panthera
pardus
A. Objectives
of Taxonomy
Genus: Panthera
1.  Sort and identify
organisms into
species.
2.  Arrange (classify)
species into broader
hierarchical
taxonomic categories
• 
• 
Family: Felidae
Order: Carnivora
Class: Mammalia
From genera to
domains
What is our
classification?
Phylum: Chordata
Kingdom: Animalia
Bacteria
1. 
• 
• 
Provides the most
information.
Becomes
predictive.
Archaea
B. How to classify--the rationale
B. How to classify--the rationale
1.  Classification
should as much as
possible reflect
evolutionary
history.
Domain: Eukarya
2. 
Classification should as
much as possible reflect
evolutionary history.
Single taxon should be
composed of all species
derived from a common
ancestor.
1. 
2. 
3. 
Older:
Family Pongidae
Subfamily Ponginae
Family
Hominidae
This is known as
monophyletic
Contrast older notion of
primate families Pongidae
+ Hominidae vs current
notion of Hominidae
Illustrates concepts of
paraphyly and polyphyly
Tribe Pongini
Current:
Hominidae
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B. How to classify--the rationale
B. How to classify--the rationale
• 
Paraphyletic: A taxon that does not include all of
the descendants of the most recent common
ancestor.
C. The Importance of Homology
•  Structures that
share a common
ancestor.
–  forelimb of tetrapods.
–  opposable thumb of
primates
–  flower of
angiosperms
•  These provide
information into
relationships via
monophyly.
• 
Polyphyletic: A taxon that includes members
derived from two or more ancestors. Note that this
is part of a continuum with paraphyletic.
C. The Importance of Homology
•  Similar structures
that do not share a
common ancestry
are analogous or
are homoplasies.
•  These result from
convergent
evolution.
•  Are not informative
to relationships.
Informative to
adaptation.
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PHYLOGENETICS
•  The study of evolutionary relatedness
between organisms.
•  (Contrast with taxonomy)
•  Without phylogenetics, comparative
biology would not exist and diversity
would make no sense.
PHYLOGENY
•  Graphical representation of the evolutionary
history of a group as expressed in terms of
relatedness.
•  Classifications based on phylogenies are
known as natural classifications.
•  Phylogenies are based on shared, derived
(or unique) homologous features. These
are known as synapomorphies.
Phylogenies Phylogenies Change through time
Change through time
Change through time
Change through time
Change through time
Relative position is the only thing that matters!
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Sister groups Nodes, Tips, Internodes The two taxa on either side of a split Lancelet
(outgroup)
Lamprey
Fish
Vertebral
column
Hinged jaws
Four walking legs
Amphibians
Reptiles
Amniotic egg
Mammals
Hair, mammary glands, 3 bones in the middle ear
Outgroups Polytomies When resolu<on of the branching diagram is difficult Not part of the group in ques<on, but is closely related to the group Lancelet
(outgroup)
Lamprey
Fish
Vertebral
column
Hinged jaws
Four walking legs
Amphibians
Reptiles
Amniotic egg
Mammals
Hair, mammary glands, 3 bones in the middle ear
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Terminology •  Phylogenies are based on shared, derived (or unique) homologous features. These are known as apomorphies. •  Synapomorphies are traits that are unique, derived, and indicate rela<onships. They denote clades. •  Autapomorphies are traits that are unique and derived, but do not indicate rela<onships. They denote <ps. •  Plesiomorphies are traits shared by a number of groups, and are inherited from ancestors older than the last common ancestor. They do not denote clades. Synapomorphies, Autapomorphies, & Plesiomorphies Lancelet
(outgroup)
Lamprey
Fish
Vertebral
column
Hinged jaws
Four walking legs
Amphibians
Reptiles
Amniotic egg
Mammals
Hair, mammary glands, 3 bones in the middle ear
Lancelet
(outgroup)
Lancelet
(outgroup)
Lamprey
Lamprey
Fish
Vertebral
column
Fish
Vertebral
column
Hinged jaws
Four walking legs
Amphibians
Reptiles
Amniotic egg
Mammals
Hair, mammary glands, 3 bones in the middle ear
Phylogenetic tree: Endothermic vertebrates with hair, mammary glands, three
bones in the middle ear (etc.) are all related and thus called MAMMALS.
Hinged jaws
Four walking legs
Amphibians
Reptiles
Amniotic egg
Mammals
Hair, mammary glands, 3 bones in the middle ear
Is the vertebral column a defining feature of mammals? How or how not?
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Lancelet
(outgroup)
Lancelet
(outgroup)
Lamprey
Lamprey
Fish
Vertebral
column
Fish
Vertebral
column
Hinged jaws
Four walking legs
Amphibians
Reptiles
Amniotic egg
Mammals
Hair, mammary glands, 3 bones in the middle ear
NO! This is a shared ancestral trait or plesiomorphy. At what level does this become
an synapomorphy?
Understanding the branching diagram
•  Recall that species
arise from a splitting of
an ancestral (parent)
population
(speciation);
•  Thus, all life could be
represented by
millions of such
branches going back
to the first organisms.
Hinged jaws
Four walking legs
Amphibians
Reptiles
Amniotic egg
Mammals
Hair, mammary glands, 3 bones in the middle ear
Tree-thinking questions: Which is most closely related to a fish: amphibians,
reptiles, or mammals? Which is most evolved: amphibians, reptiles, or mammals?
Understanding the branching diagram
•  Recall that species
arise from a splitting of
an ancestral (parent)
population
(speciation);
•  Thus, all life could be
represented by
millions of such
branches going back
to the first organisms.
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Understanding the branching diagram
•  Recall that species
arise from a splitting of
an ancestral (parent)
population
(speciation);
•  Thus, all life could be
represented by
millions of such
branches going back
to the first organisms.
Understanding the branching diagram
All the way
to the
relationships
linking all
species of
cats
(Johnson et
al 2006)
D. CHARACTERS
• 
• 
A set of alternative
conditions (character
state) that are
considered able to
evolve one to another.
Must search for and
evaluate homologous
structures.
–  Must follow Recognition
Criteria of Homology:
1.  Similarity in position
2.  Detailed resemblance
3.  Continuance through
intermediate forms
D. CHARACTERS
• 
• 
A set of alternative
conditions (character
state) that are
considered able to
evolve one to another.
Must search for and
evaluate homologous
structures.
–  Must follow Recognition
Criteria of Homology:
1.  Similarity in position ✔
2.  Detailed resemblance
3.  Continuance through
intermediate forms
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D. CHARACTERS
D. CHARACTERS
• 
• 
• 
A set of alternative
conditions (character
state) that are
considered able to
evolve one to another.
Must search for and
evaluate homologous
structures.
• 
–  Must follow Recognition
Criteria of Homology:
–  Must follow Recognition
Criteria of Homology:
1.  Similarity in position ✔
2.  Detailed resemblance ✖
3.  Continuance through ✖
intermediate forms
1.  Similarity in position ✔
2.  Detailed resemblance ✖
3.  Continuance through
intermediate forms
D. CHARACTERS
•  Types of
Characters:
–  Must be products of
evolutionary process
–  Must be heritable
–  What kinds of things
fall under this?
A set of alternative
conditions (character
state) that are
considered able to
evolve one to another.
Must search for and
evaluate homologous
structures.
•  Morphological
Characters
•  Physiological
characters
•  Molecular characters
•  Behavioral characters
•  Ecological characters
•  Geographic characters
D. CHARACTERS
A simple rule for
hypothesis testing
•  The more data, the
better!
–  This applies to testing
phylogenetic
relationships as well:
the more characters,
the better
–  Also, the more
character systems, the
better.
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Phylogenetic Analysis
•  How do we reconstruct phylogenetic
trees?
•  Based on using characters to test
hypotheses of phylogenetic
relationships.
•  Remember that the branching diagram
is the hypothesis.
Phylogenetic Analysis
1.  A set of data
(character X taxon
matrix)
2.  A set of possible
evolutionary trees
3.  A means of
evaluating the
alternative trees
given the data.
•  Identify homologous
characters and
delineate alternative
character states.
Phylogenetic Analysis
1.  A set of data
(character X taxon
matrix)
2.  A set of possible
evolutionary trees
3.  A means of
evaluating the
alternative trees
given the data.
Phylogenetic Analysis
1.  A set of data
(character X taxon
matrix)
2.  A set of possible
evolutionary trees
3.  A means of
evaluating the
alternative trees
given the data.
•  These are the
alternative
hypotheses.
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Phylogenetic Analysis
1.  A set of data
(character X taxon
matrix)
2.  A set of possible
evolutionary trees
3.  A means of
evaluating the
alternative trees
given the data.
•  Based on distribution of using
shared derived characters
(apomorphies) to identify
clades.
•  Evaluated based on maximum
parsimony or maximum
likelihood as the optimality
criterion.
Which tree is preferred?
•  Parsimony
•  Maximum-likelihood
•  We will spend time in lab on
these AND your book is
quite thorough with this (pp
542-547)
•  We should first investigate
the simplest explanation for
observed character state
distributions.
•  Minimizes the number of
evolutionary events on a
tree.
•  Maximizes apomorphic
characters while mimizing
homoplasious characters.
Which tree is preferred?
•  Parsimony
•  Maximum-likelihood
•  We will spend time in lab on
these AND your book is
quite thorough with this (pp
542-547)
How would we draw a phylogeny
of these lizards with only the
information we have right here?
C
A
B
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Which tree is preferred?
•  Parsimony
Which tree is preferred?
A
–  Data matrix & alternative
hypotheses.
•  Parsimony
A
–  Minimize character
changes on the trees.
B
B
C
C
B
Tail
black
Legs
blue
Back
orange
Front
red
A
C
A
C
B
B
Tail
black
Legs
blue
Back
orange
Front
red
C
B
A
C
A
C
B
B
Which tree is preferred?
•  Parsimony
Which tree is preferred?
•  Parsimony
A
–  Minimize character
changes on the trees.
–  Minimize character
changes on the trees.
–  Do so for every
character.
B
C
B
Tail
black
A
B
A
C
A
Legs
blue
Back
orange
Front
red
C
Tail
black
A
B
A
C
B
C
B
A
C
A
Legs
blue
Back
orange
Front
red
A
C
C
A
C
B
B
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Which tree is preferred?
•  Parsimony
–  Minimize character
changes on the
trees.
–  Do so for every
character.
–  Count the number of
changes.
–  Which is most
parsimonious?
A
B
C
B
A
Which tree is preferred?
•  Parsimony
•  Maximum-likelihood
•  We will spend time in lab on
these AND your book is
quite thorough with this (pp
542-547)
C
C
A
•  Similar, but now
optimality no longer
based on principle of
parsimony.
•  Optimality based on
specified model of
evolution.
•  Generally applied to
molecular data.
•  Uses external
information.
B
Testing evolutionary hypotheses
Using Phylogenies
Mapping evolutionary transitions
Some horned lizards squirt blood from their eyes when attacked by canids.
How many times has blood-squirting evolved?
•  Now that you have a tree, what can you
do with it?
–  Testing hypotheses about evolution
–  Learning about the characteristics of
extinct species and ancestral lineages
–  Classifying organisms (later)
Blood squirting?
No
Yes
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Testing evolutionary hypotheses
Testing evolutionary hypotheses
Mapping evolutionary transitions
Mapping evolutionary transitions
Some horned lizards squirt blood from their eyes when attacked by canids.
How many times has blood-squirting evolved?
This phylogeny suggests a single
evolutioary gain and a single loss
of blood squirting
Blood squirting?
No
Yes
But a new phylogeny using
multiple characters
suggests that blood squirting
has been lost
many times in the evolution of
this group
Our interpretation of
these evolutionary
scenarios depends on
phylogeny
Leaché and McGuire. Molecular Phylogenetics and Evolution 39: 628-644
Testing evolutionary hypotheses
Reconstructing ancestral characters
This phylogeny also shows how we
can use data from living species to
infer character states in ancestral taxa
?
?
Testing evolutionary hypotheses
Mapping evolutionary transitions
How many times has venom
evolved in squamate reptiles?
Once in the large “venom
clade”
Groups within this clade then
evolved different venom types
e.g., different proteins found in
Snakes versus Gila monsters
Ancestral state could be blue, purple,
or intermediate…outgroup comparison
indicates blue is most parsimonious
Leaché and McGuire. Molecular Phylogenetics and Evolution 39: 628-644
Even non-venomous lizards in
this clade (Iguania) share
ancestral toxins
Fry et al. (2006) Nature 439: 584-588
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Testing evolutionary hypotheses
Testing evolutionary hypotheses
Convergence and modes of speciation
Coevolution
What can this phylogeny tell us about homology/analogy and
speciation?
Lake Tanganyika
Aphids and bacteria are
symbiotic
Lake Malawi
Given this close relationship,
we might expect that
speciation in an aphid would
cause parallel speciation in
the bacteria
1.
Similarities between each pair are
the result of convergence
2.
Sympatric speciation more likely
than allopatric speciation
When comparing phylogenies
for each group we see
evidence for reciprocal
cladogenesis (but also
contradictions)
Clark et al. (2000)
Testing evolutionary hypotheses
Testing evolutionary hypotheses
Geographic origins
Geographic origins
Where did domestic corn
(Zea mays maize)
originate?
Where did humans
originate?
A
B
Each tip is one of 135
different mitochondrial
DNA types found among
189 individual humans
Populations from
Highland Mexico are at
the base of each maize
clade
African mtDNA types are
clearly basal on the tree,
with the non-African types
derived
Vigilant et al. (1991) Science
Matsuoka et al. (2002)
Suggests that humans
originated in Africa
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The power of Phylogenetic
Biology
Phylogenetics and Dinosaur behavior
•  From understanding physiological
processes to identifying endangered
species.
•  To understanding dinosaur behavior…
(?!)
Belinda Chang and colleagues began by reconstructing a
phylogeny of vertebrates using numerous genes.
Phylogenetics and Dinosaur behavior
Phylogenetics and Dinosaur behavior
They then sequenced a rhodopsin gene from all of these
species and tested their photoactive properties.
Using this information, they reconstructed what the ancestral
protein looked like.
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Phylogenetics and Dinosaur behavior
Phylogenetics and Dinosaur behavior
They then synthesized this protein, expressed it in a mammalian cell line
tissue culture, and tested its photoactive properties.
The photoactive properties were significantly red-shifted from modern birds,
suggesting that early archosaurs hunted at dawn and dusk!
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