CHAPTER 5
The Tree of Life
Classification and
Phylogeny
Taxonomic Practices
• Taxonomy
– Naming and classification of organisms
• Binomial System of Nomenclature
– Developed by Linnaeus
– Either composed of Latin or Latinized
(conjugation and gender specific endings
from latin)
Taxonomic Practices
• No two species can have the same Binomial
name
– Can have the same genus name for different
organisms only for a single plant and single
animal lineage
• Priority
– the valid name of a taxon is the oldest available
name proposed
– If it is found that what is considered 2 species
actually is just one, the oldest name must be
used, and the newer name is considered a junior
synonym
Taxonomic Revision
• Species placed in different genera and are shown to
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be closely related may be shifted to the same genus,
yet retain their species epithets
A species may be removed from a genus and placed
into a different one if it is shown not to be closely
related
Forms originally described as different species may
prove to be the same species and be synonymized
New species may be described
These general rules also apply to higher taxa above
the level of genus (families, orders, etc.)
Phylogeny
• Hypothesis of evolutionary relationships
• Phylogenetic tree = graphical summary
of evolutionary history
• We have been using trees throughout
the semester
– Now we will examine how to construct them
– Remember: Phylogenies, in almost all
cases, are only estimates
Phylogenetics
• Under Darwin’s hypothesis of common
descent  Species in the same genus
stem from a recent ancestor
• Hierarchical classification reflects not a
mystical ordering of the universe, but
rather a real historical process
Phylogenetics Terms
• Monophyletic Group
– All members are believed to stem
from a single common ancestor,
and the group includes this
common ancestor
• Paraphyletic Group
– Group that is monophyletic
except that some descendents of
the common ancestor have been
removed
• Polyphyletic Group
– consisting of unrelated lineages,
each more closely related to
other lineages not placed in the
taxon
Paraphyletic Groups
Birds
Lizards
Crocodilians
Snakes
Turtles
Mammals
Reptiles are paraphyletic
Class Reptilia should
include Class Aves
Polyphyletic Groups
Wasps
Reptiles
Birds
Spiders
Protists
Bacteria
Winged organisms are polyphyletic
Phenetics
• Also called Numerical Taxonomy
• Mostly developed by Charles Michener
& Robert Sokal
• Looks at the overall similarity of
species based on all characters
• Trees reconstructed with this method
are called PHENOGRAMS
• A phenogram does not necessarily
represent phylogenetic relationships
Phenetics
• The problem with phenetics is that
similarity in itself is not a reliable
guide to phylogenetic relationships
1. Shared derived characters due to
common ancestry
2. Shared ancestral characters relative to
same species
3. Share similar feature but they are not
homologous  HOMOPLASY
Phenetics
• Thus, if shared ancestral characters or
homoplasious characters outnumber
similarities due to shared derived
characters the phenogram will not
often portray the true phylogeny
Cladistics
• Willi Hennig (1950), published in US in
1966
• Argued that classification should
rigorously reflect phylogenetic
relationships and NOT the degree of
adaptive divergence or overall
similarity
Cladistics
• Contends that only 1 type of evidence
provide information about phylogenetic
relationships
– Homoplasious characters DO NOT
– Simlarities based on shared ancestral
characters DO NOT
– Characters unique to a single taxon
(autapomorphies) DO NOT
– Shared derived characters DO
Cladistics
• Evidence that species share a more
recent ancestor with each other than
either do with other species is provided
only by shared derived characters 
Synapomorphies
• These are assumed to be evidence of
this character evolving in the common
ancestor of these two species
Cladistics
• Remember: a shared derived character
provides evidence that species are a
monophyletic group only if it is
UNIQUELY derived
– ie. Only evolved once within the group you
are studying as a whole!
• The Cladistic Principle
– Monophyly is defined by the presence of
shared uniquely derived character states
Vocabulary of Cladistics
• PLESIOMORPHY – ancestral or
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primitive character state
SYMPLESIOMORPHY – shared
ancestral character state
APOMORPHY – derived or ‘advanced’
character state
SYNAPOMORPHY – shared derived
character state
AUTAPOMORPHY – derived character
not shared (unique to species or group)
Cladistic Methods
• Techniques that identify monophyletic
groups based on synapomorphies
• Synapomorphies define evolutionary
branching points
• Autapomorphies and ancestral
characters do not
• Must be able to identify homology of
traits and direction of change through
time
Cladistic Methods
• Several methods used to identify polarity
– Most commonly used is the outgroup
method
– The character state of the target taxa is
compared with that of a relative that
diverged earlier
– Outgroup represents the ancestral state
– Identify outgroup from other phylogenetic
studies or fossil data
– Good to use several outgroups at once
Cladistic Methods
• When no convergence, parallelism, or
reversal occurs all synapomorphies are
congruent
• When all nodes are not congruent try to
minimize homoplasy
• Tree made using synapomorphies is a
cladogram
– Clade is a monophyletic group
Cladograms VS. Phylograms
• Cladogram
– Only shows you the relationships between
taxa
– Branch lengths provide no data!
• Phylogram
– Shows you relationships AND the amount
of change (evolution) inferred along each
branch
– Therefore, branch lengths are very
important!
Cladograms VS. Phylograms
Species A
Species A
Species B
Species B
Species C
Species C
Species D
Species E
Species D
Species E
Species F
Species F
5 changes
Cladistics  Parsimony
• Parsimony – explanation requiring the fewest
•
undocumented assumptions should be
preferred over more complicated hypotheses
that require more assumptions for which
evidence is lacking
Cladistic Tree or Most Parsimonious Tree 
‘the best estimate of phylogeny is the one
that requires the least number of steps (or
character state changes) to explain the
observed variation
Parsimony:
Preliminary Information
• Generally the ancestral character state is
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assumed to be the one that is most widely
distributed among taxa outside the group of
interest
Outgroups invaluable information for
inferring relationships among the members
of the monophyletic ‘ingoup’ under study
Allows inferences about plesiomorphic and
apomorphic characters  We can infer the
directional trends or Polarity of Evolution
Parsimony and Phylogeny
• Most closely related taxa should have
the most traits in common
– Assume that traits are independent,
heritable, and variable in target taxa
– Traits may be DNA sequence, presence or
absence of skeletal elements or floral
parts, mode of embryonic development,
etc.
– Traits scored in different taxa must be
homologous
Parsimony and Phylogeny
• Evolutionary relationships should only
be reconstructed from traits that are
similar because they are derived from a
common ancestor = Homology
– Shared derived characters of all members
of a group
– Synapomorphy
• Synapomorphies are used to decide where
branches should be on a phylogeny
Homology
• Homologous features are derived from a
common ancestor
– Organs of 2 organisms are homologous if they
have been inherited (& perhaps modified) from a
single organ of a common ancestor
• A character may be homologous among
species but a character state may not
– 5 toed state is homologous in humans and lizards
but the 3 toed state is not homologous in Guinea
pigs and Sloths
– The wings of birds and those of bats are not
homologous, although their forelimbs in general
are homologous structures
Homology
• The features of organisms almost
always evolve from pre-existing
features of their ancestors
– Unlikely that features arise de novo from
nothing
Examples of Synapomorphies which
define groups of Fossil Birds
Parsimony and Phylogeny
• There are also traits that are derived
along a single lineage
– Autapomorphy
– The same traits may be independently
derived in different lineages
• Seal and penguin flippers
• Natural selection favors similar adaptations
in similar habitats
• Convergent evolution
Parsimony and Phylogeny
• Traits may revert to ancestral form
because of mutation or selection
– This may destroy phylogenetic signal and
lead to reconstruction of misleading
relationships
• Convergence and Reversal and
collectively known as Homoplasy
Parsimony and Phylogeny
• Homoplasy
– Creates noise in the data
– Some characters give conflicting
information about relationships
– Systematists try to minimize homoplasy in
a data set
– Choose characters that evolve slowly
relative to age of taxa
Parsimony and Phylogeny
• Parsimony minimizes total amount of
evolutionary change in a tree
• Synapomorphies are usually more
common than convergence and
reversal
• Most parsimonious trees minimize
homoplasy to give best estimate of
phylogeny
Phylogeny of Whales
• Whales and dolphins are in order Cetacea
• Synapomorphy is loss of posterior limbs
• Because whales are highly evolved for
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aquatic life, assigning relationships with
other mammals is difficult
Phylogenetic studies have found that
whales are closely related to artiodactyls
– and... Guess what.... We have whale fossils
with hind limbs!!!!!
Whales as the
“sister” taxon
or clade to a
monophyletic
clade of
Artiodactyls
Phylogeny of Whales
• Recent molecular studies suggest that
traditional cetacean + hippo clade is
more likely than artiodactyl + cetacean
clade
• Suggests that some traits for aquatic
life shared among hippos and whales
are not convergent but homologous
Synapomorphies
• Must test which phylogeny is more
likely to be true
Phylogeny of Whales
• Which characters should be used to
reconstruct the phylogeny?
– Morphological characters
• Skeleton
– Molecular characters
• Allozymes, DNA sequences, etc...
– For fossils only morphological characters
can be used
– Morphological characters difficult to use
because taxonomic expert needed
Phylogeny of Whales
• Which characters should be used to
reconstruct the correct phylogeny?
– Many molecular characters can be scored
rapidly
– Homoplasy difficult to identify
• Only four bases: G, A, T, C so reversals or
homoplasy is likely to occur
• Often best to use both types of
characters
Phylogeny of Whales
• Astragalus
– Small bone towards rear of the foot (proximally
positioned in the hind limb)
– Important character in mammal systematics
– Its shape and characteristics divides artiodactyls
from perissodactyls
– If whales are sister to all artiodactyls specialized
astragalus evolved only once
– If whales are sister to hippos, two evolutionary
steps are needed
• Whales lack an astragalus
– Whale + hippo is less parsimonious
Phylogeny of Whales
• Extinct whales with legs have features
of astragalus similar to artiodactyls
• Support for whales as artiodactyls
• Systematists use more than one
character when reconstructing trees
– Must minimize homoplasy over all
characters
– Gatesy used DNA sequence data
• Also found support for whale + hippo clade
Phylogeny of Whales
• In the molecular data set some characters
are parsimony informative, some are
autapomorphic and some are invariant
– Only synapomorphies used
– Most synapomorphies support the overall
phylogeny but one does not
– One synapomorphy supports whale + hippo clade
– Let’s find the most parsimonious solution for
entire tree
Patterns of Speciation That Make
Reconstructing Phylogenies Difficult
Phylogeny of Whales
• How do we find the best tree?
– With a small number of taxa you can evaluate all
possible trees
• Exhaustive search
– With more taxa the amount of possible trees
increase exponentially
– For 8 taxa in artiodactyl tree there are 10,395
possibilities!!!
– Must use a shortcut method to evaluate trees
– Although faster, such shortcut methods open the
possibility of not actually finding the best tree...
Exhaustive Search
Sequences
Number of unrooted, binary trees
4
3
5
15
6
105
7
945
8
10,395
9
135,135
PAUP* can evaluate
approx. 108,000 trees/s
using parsimony for a
problem with 21 sequences
each about 900 nt long.
10
2,027,025
11
34,459,425
12
654,729,075
13
13,749,310,575
14
316,234,143,225
15
7,905,853,580,625
16
213,458,046,676,875
17
6,190,283,353,629,375
18
191,898,783,962,510,625
19
6,332,659,870,762,850,625
20
221,643,095,476,699,771,875
This run would just
about be finished had
we started it at the
time prokaryotes
diverged from eukaryotes (about 2.5
billion years ago!)
Phylogeny of Whales
• How do we evaluate confidence in a
tree?
– Is whale + hippo tree substantially better
than whale + artiodactyl tree?
– Can view slightly suboptimal trees (less
parsimonious) to see how much difference
there is
– Bootstrapping statistically evaluates how
much support data contains for nodes
• Repeated sampling to see if tree differs
from chance
Phylogeny of Whales
• How do we evaluate confidence in a
tree?
– Bootstrap values are percentages of the
number of times the same branch arose
after repeated sampling
– Bootstrap support over 70% indicates that
the correct relationship was probably
found
– Investigators usually report any bootstrap
value over 50%
Phylogeny of Whales
• Other reconstruction methods
– Parsimony is not the only criterion for
reconstructing phylogenies
– Maximum likelihood assumes a particular
model of sequence evolution and
estimates the most likely tree given the
model of evolution and the dataset
• Uses all data, even autapomorphies and
invariant sites
• Can only be used for molecular data
– Morphological data cannot be modeled
Phylogeny of Whales
• Other reconstruction methods
– Distance methods (=Phenetic)
• Neighbor joining and UPGMA
• Based on clustering technique
• Based on overall similarity
• Not a cladistic method
• Uses differences (distances) among
character states to group taxa
Example of Distance
Methods
The % difference is
calculated between all
DNA sequences then
used to make the tree
by connecting pairs of
species with the lowest
distances
NOTICE, this appears
to be a Phylogram,
although they did not
give a scale bar for
changes...
Phylogeny of Whales
• It is useful to use a variety of tree
reconstruction methods
• If methods are congruent you have
more confidence in your
reconstructions
Using Phylogenies to Answer
Questions
• Phylogenies can be useful tools to
answer important evolutionary
questions
• One must always question the methods
used to reconstruct the phylogeny to
be confident in the results
Using Phylogenies to Answer
Questions
• Once a phylogeny is reconstructed with
confidence, it can be used to answer
evolutionary questions
• Hawaiian fruit flies
– Very high diversity
– Must have radiated quickly to produce
500+ species in only 5-6 million years
• Age of oldest island Kauai
• Molecular clock dates species as older
Using Phylogenies to Answer
Questions
• Molecular Clock
– It is hypothesized that molecular change
happens at a steady rate
– If this is so, you should be able to use
know dates to calibrate a molecular clock
and be able to discern the ages of
branching events
• Calibrate with fossils or geologic events
Using Phylogenies to Answer
Questions
• Molecular Clock
– Clocks for a variety of taxa (especially
mammals and birds) have been estimated
to ‘tick’ at a rate of 2% sequence
divergence per million years for
mitochondrial genes
• However, Different genes evolve at different
rates
– Other scientists have challenged the clock
and found that molecular change does not
always happen in a clocklike fashion
Using Phylogenies to Answer
Questions
• Hawaiian fruit flies
– Beverly and Wilson estimated a molecular
clock for Hawaiian fruit flies
– Found that some species are 42 million
years old
– How is this possible?
– Hawaiian Islands are dynamic
• Islands rise and subside
• Have been islands over that geologic hot
spot for a long time
Using Phylogenies to Answer
Questions
• Mesozoic Birds
– Because of branching order some extinct
birds must have lived much earlier than
fossils depict
– Paleontologists predicted several fossil
species would be found
– Xu found an early Cretaceous
dromaeosaurid bird from the dates
predicted
Using Phylogenies to Answer
Questions
• Phylogenetic systematics can aid in
classification of taxa
• Phylogenetic and evolutionary species
concepts require that taxa be
monophyletic
• Many traditional classifications are not
based on monophyly
– Order Artiodactyla is not monophyletic
• Order Cetacea should be sunk to family
level
Using Phylogenies to Answer
Questions
• Paraphyly example
– The true phylogeny of reptiles includes
birds
– Birds are autapomorphic reptiles
– Birds are the sister group to crocodilians
– To fix the classification to contain only
monophyletic groups:
• Reduce class Aves to order
• Or raise other orders of reptiles to classes
– Turtles, crocdilians + birds, squamates,
tuataras
Paraphyletic Groups
Birds
Lizards
Crocodilians
Snakes
Turtles
Mammals
Reptiles are paraphyletic
Class Reptilia should
include Class Aves
Current Taxonomy of Great Apes and Humans
-Family Pongidae – Gorillas, Chimps, Orangutans
-Family Hominidae – Humans
Is this really a valid taxonomy???
Proposed
Classification
(that no-one
ever started
using!!!)
Using Phylogenies to Answer
Questions
• Coevolution
– Leaf-cutting ants and fungi they farm
• Leaf cutters grow fungus on leaves that
they cut for food
• 200 ant species of tribe Attini each farm a
different fungus species
• Did the two groups cospeciate?
– Phylogenies should be congruent
• Hinkle found congruence on all branches
but one
• Fungi were domesticated more than once
Using Phylogenies to Answer
Questions
• Spread of AIDS
– Suspicion that a Florida dentist infected
his patients with HIV in 1990
– Difficult to know because some patients
had other risk factors
– Reconstructed a phylogeny of the HIV of
all his patients and other local people
– Phylogeny proved that dentist had infected
several of his patients but not others
Testing Biogeographic Hypotheses
The two primary hypotheses of the spread of Homo around the world
reduce to phylogenetic hypotheses
•Clear from fossil evidence that the genus arose in Africa, but how did modern
humans get to every other continent?
•Was it a single exodus from Africa that replaced existing lineages (either through
competition or direct combat) - the African replacement hypothesis
•Or was it multiple origins of modern humans from the ancient lineages that had
originally colonized each part of the globe? The multi-regional hypothesis
Phylogenies to Identify Parallel
Speciation and Adaptive Radiations
Trunkdweller
Twigdweller
Trunkdweller
Twigdweller
tree-top
tree-top
Island 1
Island 2
Common Ancestor
Using Phylogenies to Examine Evolution
of Female Choice & Intersexual Selection
Water Mites
– Net-stance must have evolved first and then male trembling
after for the sensory exploitation hypothesis to be true
– Examine phylogeny to see probable order of evolution of
the trait