Understanding and Creating Phylogenetic Trees

Investigating the Evolutionary History of Life
How are phylogenetic trees useful?
• 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?
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
in 1858, just a year before the
Origin of Species, Heinrich Georg
Bronn published a hypothetical
phylogenetic tree labeled with
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
Cousin Vinny
Cousin Flossie
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
• 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
• Two descendants that split from the same node are called sister
• 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
Beak is the character, the state is its length.
Character – beak length
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
Plesiomorphy - An original character state for the taxa under
When just the three species are
considered, the presence of the
mask is considered a pre-existing
trait, or ancestral. This is called a
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
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
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
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
Note that the taxa (tips) do not have the same common
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.
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.
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
Reading Phylogenetic Trees
 Similarly, each lineage has ancestors that are unique to
that lineage and ancestors that are shared with other
lineages — common ancestors.
Reading Phylogenetic Trees
Evolution produces a pattern of relationships among lineages that is treelike, not ladder-like.
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.
Reading Phylogenetic Trees
 Just because we tend to read phylogenies from left to
right, there is no correlation with level of "advancement."
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
Practice Reading Phylogenetic Trees

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