One of the distinctive aspects of biology as a science is that
its objects of study, living organisms, have constantly changed through
time. A significant portion of the field of biology is thus devoted to
the investigation of these changes to determine how organisms have evolved,
how the enormous diversity of life on earth has arisen, and how different
organisms are related to one another. These fundamental questions are historical
A powerful approach for answering historical questions in biology
is phylogenetic systematics. The purpose of phylogenetic systematics
is to attempt to reconstruct the historical relationships among organisms.
That is, it attempts to determine (a) the evolutionary pathway by which
modem species arose, (b) how and to what degree they are related, and
(c) what their ancestors may have looked like.
The goal of today's lab is to learn how to apply some of
the methods of phylogenetic systematics, then to use these methods to
examine degrees of relatedness among a group of species. By doing so,
you will be able to make inferences about the course of speciation. Usually
speciation proceeds far too slowly to be observed directly, but many
of the changes that occurred as species diverged are preserved as characteristics
in the organisms presently alive. Using these characteristics and applying
the methods of phylogenetic systematics to determine the one correct
set of evolutionary pathways is a stimulating intellectual challenge.
Evolutionary theory provides an extremely powerful set of guidelines
for thinking about diversity, ancestors, morphological change, and the
relationships among species. For the sake of simplicity, we will assume
that species originate from other species by dichotomous splitting. That
is, during speciation species A gives rise to two new species (no more,
no less), B and C, and at that time the ancestral species, A, is considered
to cease existence (see diagram below), Each of the resulting species now
may gradually change form (evolve) over time, and may itself split into two
new species when conditions for speciation are encountered. As you will see,
these seemingly trivial propositions have some enormous consequences.
How many phylogenetic trees are there?
Suppose you have three species of animals or plants (A, B, and
C) and you wish to know how they are related to each other. Ultimately,
of course, they will share a common ancestor (which we will call ancestor
1), but the three species could have arisen in three different ways,
Given our assumption that evolution proceeds by dichotomous splitting,
then a) only two species can be most closely related to each other, and
b) that pair must have had one additional ancestor (ancestor 2).
Now suppose we discover a new species, D, which we wish to fit
into our existing tree for A, B, and C. Obviously it can be most closely
related to only one of the species we already have. If you drew all the
possible phylogenetic trees that could result from adding species D, you
would have 15 different trees. If you wished to determine phylogenetic
relationships of 4 species, it would be a fairly simple matter to draw
all 15 possible trees and decide, by some subjective argument, which one
you think represents the most likely relationship. The difficulty with
such an approach, however, is that adding even a few more species to the
tree makes the problem quite unmanageable. For instance, with 10 species
there are 282,137,824 possible trees! Clearly, trial and error methods
are ruled out if we are to study and understand the relationships between
even a modest number of species. We will have to adopt a method that approaches
the problem in an organized and rational manner.
How to construct a phylogenetic tree
Deciding on one tree is easy in principle, but quite a mind bender
in practice. All one really needs to do is find, in the collection of
species under consideration, the two species that are most closely related
to each other. These can then be connected by a simple Y-shaped diagram.
One can then proceed to find the next species that is most closely related
to either or both and attach it via an appropriate branch, and so forth
until all species are placed. In practice this procedure has two difficulties.
The first difficulty is in deciding how closely two species are
related, and specifically, which two species are most closely related.
If by relatedness we mean commonality of descent, then the problem can
also be phrased: how do we know which two species share the most recent
There is, as you might guess, a difference of opinion among biologists
about how to determine the "degree of relatedness" of existing species.
One group believes that this should be done on the basis of greatest overall
similarity, taking into account as many characteristics of the organisms
as possible. A second group believes that some characters (e.g. embryonic
ones) are much better indicators of relatedness than others and insist
that classification should emphasize those particular traits. Yet another
group, the phylogenetic systematists, believes that since the sequence
of evolution proceeds from "ancestral" to "derived", and since different
characteristics of an organism are likely to evolve independently, it
is essential to discover which characters of a species are ancestral and
which ones are derived, and then use this information to interpret relationships.
Phylogenetic systematists emphasize that ancestral characters are of no
use in determining relationships among species. Relationships can be discovered
ONLY BY STUDYING DERIVED CHARACTERS. The reason for this assertion will
be discussed below.
The second difficulty arises because every time we join two species,
we in fact "create" a new species in the form of a hypothetical common
ancestor whose characteristics must also be taken into account. In other
words, if we have joined two species A and B, and wish to add a third
species C, we how have to determine whether it is most closely related
to A, or to B, or to the now common ancestor of A and B.
Obviously an cases 1 and 2 we have decided that C is most closely
related to B or A, respectively, while in case 3 it is most closely
related to the common ancestor of A and B. The point is that once we
join two species in a tree we must make a decision about what the common
ancestor looked like. Likewise, adding C to the tree for A and B involves
the creation of an additional common ancestor - either to C and A, and
C and B, or to C and (A and B) - whose characteristics will have to be
taken into account when a fourth species is added to the tree.
Ancestral versus derived
Before continuing we must correct some common misconceptions about
the meanings of "ancestral" and "derived". They do not mean that an ancestral
species is primitive or has primitive characters. When the form (or state)
of a character changes in the course of evolution (e.g. a reduction
in the number of toes from 4 to 3, the initial condition is deemed ancestral
and the new condition is considered derived. Now if evolution proceeds
further (e.g. reduction in number of toes to 2 then the original derived
condition becomes ancestral to the new character state. Hence the character
state "3 toes" is “ancestral” relative to the character state "2 toes",
but it is derived relative to the state "4 toes". It is crucial that you
recognize that a given species invariably has a mixture of both ancestral
(shared with its ancestor) and derived (not shared with its ancestor) character
The importance of derived characters
We now have the information necessary to develop an important
rule to use when we examine the phylogeny of fasteners. Suppose we have
a group consisting of two species, A and B, which share a common ancestor.
Such a group is said to be monophyletic. This group will therefore be characterized
(that is, it can be told apart from all other groups of organisms) by
the features that its members share with their common ancestor. Suppose
we also have a second monophyletic group of species, C and D and their
common ancestor, and suppose further that both of these two groups (A-B
and C-D) are in turn monophyletic, that is, they are linked by a third
Because of their recent common ancestors, A-B and C-D are called
sister taxa. A "natural group" of sister taxa can only be distinguished
from another natural group of taxa by the characters that all the members
of the group uniquely share. And since any character that is unique to
a natural group of taxa must be a derived character (why?), it follows
that group A-B and group C-D (and their respective ancestors) must have
different sets of shared derived characters. This, in turn, implies immediately
that one particular character must always occur in a more ancestral condition
in one group than in the other group. This conclusion is an exercise
in logic, and if it is not intuitively obvious to you, the following
procedure should make it clear.
In Figure A (below) a number of hatch marks have been drawn across
each of the intervals connecting species and ancestors. These marks correspond
to evolutionary "events". That is to say, at each mark one or more of
the characters of the species in question underwent a change. Suppose
that each species in this diagram (A, B, C, and ancestors) possesses 7
analyzable characters a, b, c, d, e, f, g (these could be leg length, body
size, hair color, etc.). If we let each hatch mark represent a change in
a single character, we would get a scheme like the one shown in Figure
B, in which all characters that are primed (e.g. x') represent a derived
character state and all unmarked characters (e.g. x) represent ancestral
states. The important thing to do next is to picture what each of the 7
species in the diagram looks like with respect to characters a - g. This
is shown in Figure C.
The above figures should clarify several of the things we have
mentioned so far.
1) Each species has a mix of ancestral (x) and
derived (x') characters.
2) Each monophyletic group (note that a single
species is a group of one) is defined only by its derived characters.
That is, members of different groups often share ancestral characters.
3) The particular characters that define (i.e.
are unique to) any monophyletic group occur in a more ancestral form
in the sister group. This is the conclusion we were after and which you
can now verify in Figure C.
It should be evident to you now that in order to reconstruct the
phylogeny of a set of organisms it is essential to have both an extensive
list of characters and to determine the ancestral or derived state for
The latter is an important task that you and other phylogenetic
systematists perform because, unless it is done right, your interpretation
of the relationships among the organisms under study will be incorrect.
How can we determine which "state" of a given character is most ancestral?
There are three criteria for identifying an ancestral character.
1) The outgroup criterion. Suppose we could identify a
species that you are certain should be placed outside your group of
interest. It is best to use several. These taxa would be placed onto
your phylogeny by connecting them somewhere below the ancestor for your
entire group in interest. These taxa are called outgroups, and relative
to them, your group of interest is clearly monophyletic. Now recall that
the characters that define a monophyletic group are derived characters
(above), so the characters that define taxa within your group of interest
must derived. By contrast, any characters that members of your group of
interest share with the outgroup must be ancestral, since both groups must
have inherited that character from the ancestor of the entire phylogeny.
With DNA sequence data, only the outgroup criterion can be used for defining
ancestral versus derived characters, so nowadays, this is the primary method
for identifying derived characters.
2) The fossil criterion. Suppose you have a well-preserved
fossil that you are certain is ancestral to your group of interest.
Any characters your group shares with the fossil are ancestral, and
any characters unique to your group of interest are derived. We will
use this criterion because the ancestors of modern fasteners are well
preserved in the fossil record.
3) The ontological criterion. Early development appears
very similar in a wide variety of organisms, with more derived characters
that define different taxa appearing later in development. If this is
true, it follows that derived characters could, in some cases, be identified
if they appear later in an organism’s development.
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