Introduction to interpreting evolutionary trees and related vocabulary
One of Darwin's contributions was to depict the diversification of life using an
evolutionary tree, or phylogeny. Let's start with the example shown in the phylogeny
below.
1. Various lineages of organisms are
descended from common ancestors. In the
example, birds share a common ancestor with
dinosaurs and then those two groups
collectively share a more remote common
ancestor with crocodiles, and those three
collectively share an even more remote
common ancestor with lizards plus snakes,
which diverged from each other
subsequently. These parts of this tree are
well known. Others parts of the tree are still
poorly known. Some data suggest that
mammals diverged before the radiation of
reptiles (turtles through dinosaurs on the
phylogeny), while other data suggest that
turtles or {lizards+snakes} diverged first.
From here on, we'll assume mammals
diverged first, then turtles, then the
{lizard+snake} branch.
turtles
lizards
snakes
crocodiles
dinosaurs
birds
mammals
2. It is often helpful to map character changes
Character 1 2
on a phylogeny. As examples, consider two
A C
characters: 1. having continuous skull bone
between the eye and the nostril (A) versus
A C
having an opening in that place (B); and 2.
coldbloodedness (C) versus
warmbloodedness (W). Character evolution
A C
is reconstructed on the phylogeny shown to
the right. To do this, one looks for a branch
B C
in the tree where a change in character would
1
explain the distribution of character states in
B ?
all the taxa. For character 1, there is a single
place in the tree, marked with a solid bar
2 ?
labeled 1: a change from no opening to
B W
2
having an opening along this lineage and
inheritance of the opening in all descendants
above this point would result in crocodiles,
A W
dinosaurs and birds having the opening. The
opening is a shared derived character, or
synapomorphy, of the group {crocodiles+dinosaurs+birds}. With some characters it is
not possible to explain the character distribution with a single change. For character 2,
two changes are required: warmbloodedness evolved in both the lineage leading to
mammals and the lineage leading to birds. Since we do not know whether dinosaurs
were warmblooded or not (just from these data), we can't say whether
turtles
lizards
snakes
crocodiles
dinosaurs
birds
mammals
warmbloodnessness arose before the dinosaur-bird split or afterwards. At any rate, it
seems there was convergent evolution in warmbloodedness. The following words are
essential vocabulary for speaking of character evolution.
homology – a character that is similar due to common ancestry
synapomorphy – shared derived character, e.g., being on land for tetrapods
symplesiomorphy – shared ancestral character, e.g., being in the water for fishes +
sharks
homoplasy – a similarity between two kinds of organisms that is not due to common
ancestry
convergence – separate evolution in different lineages of a feature that ends up being
similar
reversal – changing back to a previous state
One can use phylogenies to judge whether a similarity should be interpreted as a
homology or a homoplasy, and (less easily) whether a homoplasy should be interpreted as
a convergence or a reversal. The most frequently used criterion for making these
judgments is parsimony, which in this context means choosing the explanation that
requires the fewest changes in character state.
3. Parsimony is also the most frequently used criterion for judging among various
possible trees: one choose the tree that requires the fewest steps, i.e., the smallest number
of changes in state for all the characters used to infer the tree. There are many other
methods for phylogenetic inference, most notably various maximum likelihood methods
that model the processes of molecular evolution. If there were no homoplasy, inferring
the tree would be easy (the similarities would tell you directly which trees were possible),
but before you have the tree you cannot tell which similarities are homologies and which
are homoplastic. The solution is to get a large number of presumably independent
characters and go with the preponderance of evidence on the argument that common
ancestry is the cause that most coordinates nested patterns of similarity.
4. Branching pattern (the sequence of common ancestors) does not necessarily represent
overall similarity or relative difference. Overall similarity can be inflated due to
convergent evolution, and when rates of evolution are unequal some lineages may
diverge while others remain relatively similar. In the diagram below, the lineage that led
to {C+D} diverged radically, while the lineages leading to A and to B remained static.
AB
C D
AB
C D
Notice on the right that one might well group A and B together, although their most
recent common ancestor is more remote than the common ancestor of B and {C+D}. In
our previous example, the birds have evolved physiologically and anatomically very far
(some would say) from the living reptiles (turtles though crocodiles). A group that
contains a common ancestor and all of its descendants is monophyletic; it’s a whole
branch of the tree of life. A group that excludes some of the descendants of its common
ancestor is paraphyletic; {A+B} is paraphyletic by the exclusion of {C+D}. Traditional
taxonomy was not developed based on a rigorous knowledge of phylogeny, so taxa
(classes like Reptilia, orders, families, genera, etc.) cannot be presumed to be
monophyletic. Cladistics refers to branching pattern. Someone who argues that taxonomy
should be revised to only recognize monophyletic groups is a “cladist.” Phenetics refers
to overall similarity. Phyletics refers to the length of branches on the phylogeny.
5. There is free rotation around any node.
turtles
turtles
birds
lizards
dinosaurs
snakes
crocodiles
crocodiles
snakes
dinosaurs
lizards
birds
mammals
mammals
This means you have to be careful when viewing large complicated trees. They may look
different but convey the same branching pattern.
6. Phylogenies can be based on morphology, or molecules, or combinations of data sets.
Morphology might sometimes be very helpful if complex structures tend to evolve when
groups-to-be are formed and then somehow become locked in place and made to be
conservative. Phylogenetic conservatism is a prominent feature of biodiversity.
Nevertheless, in principle one can get very large amounts of information by using
molecular markers, so at present molecular approaches are adding greatly to our
resolution of the tree of life.
7. Fossils can be included in a phylogenetic reconstruction. Since generally DNA cannot
be gotten from fossils, fossils are probably best used in conjunction with a phylogeny
whose superstructure is based on extant organisms. The value of adding fossils is much
like the value of adding additional extant organisms. We could have inferred the
relationships of birds, lizards, and mammals without knowing about crocodiles, but
adding crocodiles tells us a bit more about the transition. Crocodiles are a link between
lizards and birds. Dinosaurs are another link. When one finds a new link, one can add that
“missing link”, and it improves one’s inferences about the branching pattern and about
character evolution. The one way in which adding fossils is not just like adding an extant
missing link, is that they allow one to date the appearance and disappearance of forms in
the fossil record.
8. Methods such as parsimony can be used to infer branching pattern without rooting the
tree. Rooting is done by outgroup comparison, by referring to organisms that are thought
to be (just) outside one’s focal group, sharing a most recent common ancestor with the
focal group that is more remote than the most recent common ancestors of all the species
within the group. To know that one’s outgroups are not part of one’s focal group,
someone must have already done at least a crude phylogenetic analysis of the larger
group. By stepping inward, obvious relationships can be used in conjunction with more
character data to resolve closer and closer relationships.
9. Although we can infer a great deal of the tree of life, we are very far from having
complete resolution.