Campbell, Biology 6th Ed - Chapter 25, pgs 484-507
Campbell, Biology 7th Ed - Chapter 25, pgs 491-509
Phylogenetics- a discipline of evolutionary biology which seeks to accurately
depict the evolutionary relationships among living and non-living taxa.
Homology/homologs- when traits are similar due to shared ancestry (the trait was
inherited from a shared ancestor).
Synapomorphy – a derived trait shared by taxa due to common ancestry. A derived
Analogy/analogs – when traits are similar due to convergent evolution; the
traits were not inherited from a common ancestor.
Taxa- general term for a taxonomic group (e.g. species, genera, families).
Sister taxa are those presented as most-closely related in a phylogeny.
Clade- a group in a phylogenetic tree which begins with a node (ancestor) and
includes everything more distal to the node (all descendents of the ancestor).
Monophyletic group- a proper clade; that is, a group which contains a common
ancestor and all descendents of that ancestor (and no non-descendents).
Paraphyletic group- a group which contains a common ancestor and some, but not
all, descendents of that ancestor.
Phylogenetics and Phylogenies
Phylogenetics is a discipline that aims to determine the true evolutionary
relationships among organisms (The Tree of Life). Evolutionary biologists
use a type of diagram, called a cladogram, to represent these evolutionary
relationships or phylogenies. Cladograms (or phylogenetic trees) are
sequentially branching trees. In these diagrams, you can gain information of the
temporal pattern of diversification and shared ancestry.
Nodes on the trees (where branches meet) represent the common (shared) ancestor
of all taxa beyond the node. If two taxa share a closer node than either share
with a third taxon, then they share a more recent ancestor (they are
more-closely related). Cladograms usually do not contain information about
absolute time (e.g. in millions of years), but phylogenetic trees can be drawn
which do depict the timing of events.
Reference the cladograms below, and make sure you understand how the following
terms relate to the cladograms: sister taxa, node, branch, ancestor,
descendent, most recent common ancestor.
Classification of organisms into the hierarchical system you are familiar with
(e.g. Kingdom, Phylum, Class, etc.) is what the field of Taxonomy focuses on.
Evolutionary biologists today believe that classification should represent true
evolutionary relationships among organisms. Therefore, phylogenies are widely
used for classification, and understanding the accurate phylogenetic
relationships of organisms is important.
Taxa are best classified according to
In these monophyletic groups, an ancestor (node) and all descendents are
included. For example, “mammals” are a monophyletic group when we include the
most recent common ancestor (MRCA) of all known mammals. “Reptiles” are not a
monophyletic group if we exclude birds, since the MRCA of all reptiles is also a
common ancestor of birds. Without birds included, “reptiles” is a
group. Groups are
when they include multiple taxa, but not the common ancestors.
Phylogenetic relationships are established by analyzing homologous traits.
are traits which are similar in two taxa because of shared ancestry. In
are similar because of
of the two traits rather than inheritance from a shared ancestor. If we want to
determine the accurate phylogeny of taxa, we need to concentrate on traits which
are similar due to shared ancestry while ignoring analogies.
Because traits are constantly modified throughout evolutionary history, some
components of a trait may be homologous, while others are analogous. For
example, wings in birds and bats are analogous and due to convergent evolution.
However, certain components of wings are homologous – e.g. finger and humerus
Homologies are considered derived or ancestral depending on what clade you are
(synapomorphies=shared, derived characters) are new to a clade of interest
(first seen in ancestor of clade).
(symplesiomorphies=shared, ancestral characters) arose before the common
ancestor of the clade.
When determining phylogenetic relationships, we look only at the derived
Synapomorphies which define clades are often included in cladograms, as seen in
the examples below.
Deuterostomy is a synapomorphy (derived homology) of the clade containing
chordates and echinoderms.
Multicellularity is a symplesiomorphy (ancestral
homology) of the same clade.
Hair is a derived homology of all mammals.
Having a backbone is an ancestral
homology of all mammals.
A backbone is a derived homology for the vertebrate clade.
Principle of Parsimony
is employed when using homologies to make a phylogeny. This principle favors the
hypothesis that requires the fewest or simplest assumptions to explain an
observation. In phylogenetics, the principle of parsimony invokes the minimal
number of evolutionary changes to infer phylogenetic relationships. For example,
it is more parsimonious to infer that a vertebral column evolved only once in a
common ancestor of all living vertebrates than to infer that it evolved multiple
times, once for fish, once for amphibians, etc. The first option requires fewer
The Principle of Parsimony states that trait origination is much less likely
than trait inheritance in an ancestor-descendent relationship. The single
origination and subsequent evolutionary inheritance of a trait is more likely
than multiple originations of the same trait. When determining a phylogeny, we
look at a number of traits in our taxa which are 1) not similar, 2) similar due
to homology, or 3) similar due to convergence (analogy). Parsimony is invoked to
construct a phylogeny that minimizes the number of changes in these traits
(maximizes homology and minimizes analogy). In essence, we minimize the number
of “tick marks” we have to make on the cladogram (see “tick marks” in the
synapomorphy examples above.
For more advanced detail on how phylogenies are determined and cladograms made,
For a quiz on phylogenetics,
then go to the "Readings" link in the left hand column, then click on
“Phylogenetic Systematics exercise” on the main screen.
What can be
learned from phylogenies and homologies?
There is a single phylogeny for all of life.
Based on homologies seen in all life forms (e.g. nucleic acids, metabolic
pathways), it is most parsimonious to conclude that all of life as we know it
(currently and historically) shares a common ancestor.
You can find out more about efforts to determine the true tree of life here:
This link shows you what important taxa originated during different periods of
geologic time -
Humans are a third chimp
DNA homology suggests that humans are more closely related to living chimps than
either are to other living primates.
Birds are dinosaurs.
Based on traits common with mammals (e.g. endothermy), it was long thought that
birds were more closely related to mammals than to other vertebrates. When
looking at various skull and hip characteristics, however, birds share more
traits with certain lineages of dinosaurs. When evidence arose that some
dinosaurs had beak-like traits and feathers, it became clear that these bird
traits were all homologous with dinosaurs and that the clade of living birds
was, in fact, within the clade of dinosaurs.
A cladogram of the phylogenetic relationships of dinosaurs and birds.
A cladogram of all reptiles, including birds.
Origin of traits
Phylogenetics is used to identify where in a phylogeny traits first evolved.
Once we have established an accurate phylogeny, we can make “tick marks” on a
cladogram to indicate where a trait first appeared. These marks are usually
placed on the branch before the MRCA of all taxa which share the trait. For
example, we know that whales and their relatives (cetaceans) all have long,
torpedo-shaped bodies. The closest relatives of cetaceans, the artiodactyls
(e.g. cows, deer) do not have this body shape. Therefore, we know that this body
shape must have arisen on the branch between the common ancestor of cetaceans
and artiodactyls and the MRCA of all known cetaceans.
- Construct a tree of the following taxa:
- How easily (evolutionarily speaking) do you think it is for diet to change
compared to number of limbs in an organism? What would happen if we made a
phylogeny of mammals based on diet? Do you think it would accurately reflect
true evolutionary relationships?
- How do we know that there is one Tree of Life?
- Based on vertebrate evolutionary relationships, are the dorsal fins of
dolphins and sharks homologous or analogous?
- Is the group currently recognized as Fish monophyletic or paraphyletic? You
may want to refer to a text to look at a phylogeny of jawless, cartilaginous,
and bony fish and tetrapods.
- What does a node in a cladogram represent?