Investigating the Evolutionary History of Life
How are phylogenetic trees useful?
Assumptions
• Mutations that are not expressed are maintained. They
are neutral.
• They should accumulate at a constant rate = the
mutation rate.
• This serves as a molecular clock.
• Kittler et al. (2003,2004) compare genetic differences in
lice between chimpanzees and humans.
Also considered fossil record.
• Common ancestor of chimps and humans – 5.5. mya.
• Able to determine # of base changes during that time
between chimp lice and human lice
– the molecular clock.
• Then applied that rate of change to the difference
between human head lice (Pediculus humanus capitis)
and body lice (Pediculus humanus corporis)
A. Head
B. Body
How are phylogenetic trees useful?
Assumptions
Ethiopian lineage of head lice.
The rate of mutation accumulations between
Chimp lice - Human lice =
Human head lice / Body lice.
Multiply the rate of change by the
number of differences ~ 107, 000 years.
Origin of body lice was not more than
107,000 years ago.
Since Pediculus humanus corporis lives
in clothing (though it feeds on the
body), we can infer that humans began
wearing clothing not more than 107,000
years ago.
Phylogenetic trees existed before OOS, but they were more like organizational charts.
Augustin Augier’s detailed tree of
life for plants in 1801
Jean-Baptiste Lamarck
sketchy diagram for animals
in 1809.
Vestiges of the Natural History of
Creation, anonymously published by
Robert Chambers in 1844, had an
even sketchier one, where fish,
reptiles, and birds are represented
by branches from a path leading to
mammals.
in 1858, just a year before the
Origin of Species, Heinrich Georg
Bronn published a hypothetical
phylogenetic tree labeled with
letters.
Phylogenetic trees existed before OOS, or histories of life.
Indeed, once the tree of life image
became associated with transmutations,
Hitchcock dropped the image from later
editions, since he strongly disagreed with
the transmutation hypotheses of
Lamarck, Haeckel, Darwin and others.
“Paleontological chart” from Edward Hitchcock’s Elementary Geology, first published in 1840.
The first phylogenetic tree
The first real
phylogenetic tree.
The root of the tree –
the common ancestor
The only figure in Darwin’s
Origin of Species
Linking Classification and Phylogeny
 Systematicists depict evolutionary relationships in
branching phylogenetic trees
 Much like a family tree
Ancestors
Me
Sister
Cousin Vinny
Cousin Flossie
Time
Reading a Phylogenetic Tree
• A phylogeny, or evolutionary tree, represents the evolutionary relationships
among a set of organisms or groups of organisms, called taxa (singular: taxon).
• Because no one was present to observe the splitting of taxa from a common
ancestor, many evolutionary biologists consider a phylogenetic tree to be a
hypothesis of those relationships
Reading a Phylogenetic Tree
Tips – descendent species
Node
Root
• The root is the common ancestor of the species in the tree.
• The tips represent the descendant taxa (often species)
• The nodes represent the common ancestor of those descendants.
Reading a Phylogenetic Tree
Sister groups
Outgroup
Node
• Two descendants that split from the same node are called sister
groups.
• The outgroup is a taxa that is outside the group of interest.
It stems from the base of the tree and provides perspective to
the group of organisms being examined.
Character state – One of the variant conditions of a character
(e.g. melanic or typical moth color. Or presence and absence
of a trait. ).
Derived character state - same as apomorphy; a derived
character / trait is inferred to be a modified version of a
more primitive condition of that character and therefore
inferred to have arisen later in the evolution of the clade.
Clade - a group of organisms that share a common ancestor;
lineage; a monophyletic group.
Monophyletic group - terms applied to a group of organisms
that includes an ancestral species and all of its descendants;
e.g. Aves, Mammalia. This group is a complete branch of the
tree of life, the phylogeny of life. Such a branch is called a
clade.
Beak is the character, the state is its length.
State
Character – beak length
Long
Short
Apomorphy – a derived, or evolutionary novel character. It is
context specific.
When all four species are
considered, the presence of the
mask is considered novel relative
to the presence of the ancestral
form.
Plesiomorphy - An original character state for the taxa under
consideration
When just the three species are
considered, the presence of the
mask is considered a pre-existing
trait, or ancestral. This is called a
plesiomorphy.
Apomorphy and plesiomorphy illustrated together
Changed state
Original state
What about primitive and derived
characters?You might hear people
use the term "primitive" instead of
plesiomorphic and "derived" instead
of apomorphic. However, many
biologists avoid using these words
because they have inaccurate
connotations. We often think of
primitive things as being simpler and
inferior — but in many cases the
original (or plesiomorphic) state of a
character is more complex than the
changed (or apomorphic state). For
example, as they have evolved,
many animals have lost complex
traits (like vision and limbs). In the
case of snakes, the plesiomorphic
characteristic is "has legs" and the
apomorphic characteristic is "doesn't
have legs."
A synapomorphy is a trait that is shared by two or more taxa and inferred to
have been present in their most recent common ancestor, whose own ancestor
in turn is inferred to not possess the trait.
The mask is a synapomorphy
because it is shared by the
most recent common
ancestor.
But not this ancestor.
A clade is a grouping that includes a common ancestor and all the
descendants (living and extinct) of that ancestor. Using a phylogeny, it is
easy to tell if a group of lineages forms a clade. Imagine clipping a single
branch off the phylogeny — all of the organisms on that pruned branch
make up a clade.
Taxonomically, an organism accumulates all the names of all
the clades to which it belongs.
A member of the most recent clade is also a member of all the
ancestral (preceding clades).
Evo. Edu. Outreach (2009) 2:303-309
Clade - a group of organisms that
share a common ancestor;
lineage; a monophyletic group.
Transition - a change in
the character state along a
branch.
Note that each one of these groups can be separated by “one snip”.
They are each a clade (monophyletic).
Practice to review – phylogenetic trees
Phylogenetically thinking – birds are dinosaurs.
• Birds evolved from dinosaurs.
• Cannot clip (make a clade) a branch that includes:
a) dinosaurs and b) more dinosaurs without including c) birds.
• Q: Using tree thinking, are all reptiles cold-blooded? Can reptiles be
defined as being cold-blooded?
Evo. Edu. Outreach (2009) 2:303-309
Using tree thinking and the concept of clades,
we can see that Ostriches belong to every
clade preceding them (their ancestors).
Conclusion – Birds are descendants of
dinosaurs.
Evo. Edu. Outreach (2009) 2:303-309
These are all clades (monophyletic)
Depending on how many branches of the tree you are
including however, the descendants at the tips might be
different populations of a species, different species, or
different clades, each composed of many species.
A paraphyletic grouping consists of an ancestral species and
some, but not all, of the descendants.
Note that two scissor snips rules out that this is a clade.
A polyphyletic grouping consists of various taxa with different
ancestors.
Note that the taxa (tips) do not have the same common
ancestor.
Reading Phylogenetic Trees
 Understanding a phylogeny is a lot like reading a
family tree. The root of the tree represents the
ancestral lineage, and the tips of the branches
represent the descendants of that ancestor. As you
move from the root to the tips, you are moving forward
in time.
Evolution.berkeley.edu
Reading Phylogenetic Trees

When a lineage splits (speciation), it is represented as branching on a
phylogeny. When a speciation event occurs, a single ancestral lineage
gives rise to two or more daughter lineages.
Evolution.berkeley.edu
Reading Phylogenetic Trees
 Phylogenies trace patterns of shared ancestry between
lineages. Each lineage has a part of its history that is
unique to it alone and parts that are shared with other
lineages.
Evolution.berkeley.edu
Reading Phylogenetic Trees
 Similarly, each lineage has ancestors that are unique to
that lineage and ancestors that are shared with other
lineages — common ancestors.
Evolution.berkeley.edu
Reading Phylogenetic Trees

Evolution produces a pattern of relationships among lineages that is treelike, not ladder-like.
Evolution.berkeley.edu
Reading Phylogenetic Trees
 Just because we tend to read phylogenies from left to
right, there is no correlation with level of "advancement."
 One form of a trait may be ancestral to another
more derived form, but to say that one is primitive and the
other advanced implies that evolution entails progress —
which is not the case.
 An organism's position on a phylogeny only indicates its
relationship to other organisms, not how adaptive or
specialized or extreme its traits are.
Evolution.berkeley.edu
Reading Phylogenetic Trees
 Just because we tend to read phylogenies from left to
right, there is no correlation with level of "advancement."
Evolution.berkeley.edu
Aristotle's vision of a Great Chain of
Being, above. We now know that
this idea is incorrect.
Reading Phylogenetic Trees
Although mosses branch off early on
the tree of life and share many
features with the ancestor of all land
plants, living moss species are not
ancestral to other land plants. Nor
are they more primitive. Mosses are
the cousins of other land plants.
University of California Museum of Paleontology's
Understanding Evolution (http://evolution.berkeley.edu).
Reading Phylogenetic Trees
 For any speciation event on a phylogeny, the choice of
which lineage goes to the right and which goes to the
left is arbitrary. The following phylogenies are
equivalent:
Evolution.berkeley.edu
Practice Reading Phylogenetic Trees
Building Phylogentic Trees - Outgroups
 Outgroups –An outgroup is a taxa that is related to the groups of interest,
but is known to have branched off earlier in evolutionary history.
1.Provides a root for the tree.
2.Can better estimate polarity – the order of appearance in evolutionary
time – of traits of interest.
Could infer that Kangaroo, Lemur and
Human are more closely related than to Rat
and Mouse.
Building Phylogentic Trees - maximum parsimony.
 Maximum parsimony assumes that the tree that
requires the fewest evolutionary events (appearances
of shared derived characters) is the most likely.
 Computer programs are used to search for trees that
are parsimonious.
 But we can build a simple tree without a computer.
Parsimony is used in cladistics analysis.
• Cladistics is a particular method of hypothesizing
relationships among organisms. Like other methods, it
has its own set of assumptions, procedures, and
limitations.
• The basic idea behind cladistics is that members of a
group share a common evolutionary history, and are
"closely related," more so to members of the same
group than to other organisms.
• These groups are recognized by sharing unique features
which were not present in distant ancestors.
• These shared derived characteristics are called
synapomorphies.
3 Assumptions to Cladistics
What is the outgroup?
1. Change in characteristics occurs in
lineages over time.
2. Any group of organisms is related
by descent from a common
ancestor.
3. There is a bifurcating, or
branching, pattern of lineagesplitting.
3 Assumptions to Cladistics
3. There is a bifurcating, or
branching, pattern of lineagesplitting.
No polytomies.
A polytomy indicates that there is
not enough data to determine
how the lineages are related.
3 Assumptions to Cladistics
3. There is a bifurcating, or
branching, pattern of lineagesplitting.
No polytomies.
Figure 1: Phylogenetic tree of Drosophila
melanogaster species group. Redrawn from
[5]. This phylogeny shows the relationships
among some species in the Drosophila group
in which there is a hard polytomy branch. The
reason could be that the island species D.
mauritiana and D. sechellia branched off from
the mainland species D. simulans in a narrow
timeframe, such that it is impossible to
distinguish which species branched off first
and which second.
A polytomy indicates that there
may not have been enough
time since the divergence of
the two species to separate
them.
Reconstructing trees: A step by step method
1. Choose the taxa whose evolutionary relationships interest
you.
2. Determine the characters and examine each taxon to
determine the character states. Use homologies, not
analogies.
3. Determine the polarity of characters — in other words, figure
out the order of evolution for each character.
4. Group taxa by synapomorphies, not by symplesiomorphies.
Sorting Homology from Analogy
2. Determine the characters and examine each taxon to
determine the character states. Use homologies, not
analogies.
• Homology is similarity due to shared ancestry
• Analogy is similarity due to convergent evolution
• Convergent evolution occurs when similar
environmental pressures and natural selection
produce similar (analogous) adaptations in
organisms from different evolutionary lineages
Sorting Homology from Analogy
• Bat and bird wings are homologous as
forelimbs, but analogous as functional wings –
Why?
Sorting Homology from Analogy
The structural dissimilarities
between a bird wing and bat wing
suggests that they were not
inherited from a common
ancestor with wings.
Independent evolution of a character – the wing.
Bird and bat wings are analogous — that
is, they have separate evolutionary
origins, but are superficially similar
because they have both experienced
natural selection that shaped them to
play a key role in flight.
Analogies are the result of convergent
evolution.
Convergent evolution
Convergent evolution – the independent appearance in different lineages of similar
derived characters.
3. Determine the polarity of characters — in other words, figure out the order of
evolution for each character.
• For example, did the beetle species under consideration all evolve from an ancestor
with five antennal segments — and only later did six evolve, or was it the other way
around?
4. Group taxa by synapomorphies, not by symplesiomorphies.
• Synapomorphies are derived or "changed" character states shared by two
taxa.
• Symplesiomorphies An ancestral character state (i.e., a plesiomorphy)
shared by two or more lineages in a particular clade.
The change here is
from 5 antennal
segments to 6.
This is a grouping
by the ancestral
state – 5 antennal
segments.
Synapomorphies are integral to studying phylogenetic trees because:
a) they identify evolutionary branch points
b) they are nested. As you proceed from the base of the tree to the tips, each branching event adds one
or more shared, derived traits.
Building phylogenetic trees - Cladistics
CHARACTERS
Hinged jaws
Lancelet
(outgroup)
Lamprey
Bass
Frog
Turtle
Leopard
Vertebral
column
(backbone)
TAXA
0
1
1
1
1
1
0
0
1
1
1
1
Four
walking legs
0
0
0
1
1
1
Amnion
0
0
0
0
1
1
Hair
0
0
0
0
0
1
Lancelet
(outgroup)
Lamprey
Bass
Vertebral
column
Frog
Hinged jaws
Turtle
Four walking legs
Amnion
Leopard
Hair
(a) Character table
(b) Phylogenetic tree
Building phylogenetic trees - Activity
Species I
Species III
Species II
Three phylogenetic hypotheses:
I
I
III
II
III
II
III
II
I
Examine and tabulate the molecular data
Technique
Site
1
2
3
4
Species I
C
T
A
T
Species II
C
T
T
C
Species III
A
G
A
C
Ancestral sequence
A
G
T
T
 An ancestral group (outgroup) is included to put the tree in a larger context.
The ancestral sequence is not
shown as an outgroup on this tree,
but its placement can be inferred
to be here.
 Which is the most parsimonious tree?
Phylogenetic Trees as Hypotheses
• The best hypotheses for phylogenetic trees
fit the most data: morphological, molecular,
and fossil
• Phylogenetic hypotheses are modified when
new evidence arises
Phylogenetic Trees as Hypotheses
Difficulties in Creating Phylogenetic Trees
Homoplasy – a character state that has independently
evolved two or more times and does not have a
unique origin.
Types of homoplasy:
• Convergent evolution – we’ve covered this
• Reversals- A derived trait that reverts to the
ancestral (original) state through:
 Mutation
 Selection
Phylogenetic Trees as Hypotheses
This would have been a reversal.
Reversals provide misleading evidence
about the order in a phylogeny and they
can remove similarity that is caused by
descent from a common ancestor.
A reversal – When a derived trait can revert to an ancestral trait either through a
mutation, or selection.