Encyclopedia of Evolution.pdf - Online Reading Center

cladistics
The above examples used easily visible characteristics to
classify organisms into groups. The characteristics need not
be visible. In fact, many cladistic analyses use DNA sequence
information (see bioinformatics; DNA [evidence for
evolution]). Suppose the scientist has segments of DNA
from three species. If the segment of DNA is 100 nucleotides
in length, this allows 100 characters to be used to test
each cladogram. Nearly every phylogenetic study includes at
least one analysis that uses DNA nucleotides as traits. It is
no easier to use DNA than to use visible characters in cladistic
analysis. The reason is that one cannot compare just any
old piece of DNA of one species with any old piece of DNA
in another, any more than one can make comparisons of just
any visible trait. Just as visible traits must be homologous,
so the DNA segments must be homologous. The investigator
must compare the same gene in all of the species in the analysis.
Further complications arise when one considers that some
mutations exchange one nucleotide for another, while other
mutations add or delete nucleotides, or reverse segments, or
even move segments to different places. Usually, researchers
use certain well-studied DNA sequences rather than trying to
figure a new one out for themselves. In comparisons among
plants, matK (the gene for an enzyme that acts upon the
amino acid tyrosine) and rbcL (the gene for the large subunit
of the enzyme rubisco) are frequently used.
Some analyses use noncoding DNA for phylogenetic
analysis. Researchers may use transposable elements (see
horizontal gene transfer) because homoplasy is very
unlikely to occur with them. It is very unlikely that the same
transposable element would evolve twice: It would neither
insert itself in the same location in the chromosomes of two
different species, nor transfer to a new location without gaining
or losing a few nucleotides in the process. Other analyses
use short or long interspersed sequences in the noncoding
DNA. The figure on page 73 uses the presence or absence of
20 segments of noncoding DNA to construct a cladogram of
mammals. Cows and deer are clustered together, because they
share all of the segments for which information is available.
Whales and hippos are clustered together, because they share
15 of the 17 segments for which information is available.
Whales and cows are not clustered closely together, because
they share only nine of the 17 segments for which information
is available. Camels are not closely related to cows, as
they have none of the 11 DNA segments that cows possess.
Choosing the best cladogram
A computer can generate many possible cladograms for any
set of species that are being compared. Which of these cladograms
is the correct one? The correct one is the one that most
closely matches what actually happened during evolutionary
history. Nobody can know exactly what happened during
evolutionary history; cladists must make an assumption about
which cladogram is best. They often make the assumption
of parsimony (see scientific method), that is, they choose
the simplest explanation. To do this, they choose the cladogram
that requires the fewest number of character changes.
Consider this simplified example in the classification of dogs,
cats, and lions. Since each group has two branches, one could
classify them in three ways:
1. [Dogs] [Cats, Lions]
2. [Dogs, Cats] [Lions]
3. [Dogs, Lions] [Cats]
Cats and lions both have retractable claws; dogs do not.
Cladograms 2 and 3 require that retractable claws should
have evolved twice, separately in cats and lions. Therefore
cladogram 1 is the most parsimonious. It would not be safe
to draw a conclusion based upon just one characteristic (in
this case, retractable claws). Cladograms based on any of a
number of other characteristics would lead to the same conclusion:
Cats and lions form the feline group, while dogs are
part of a separate (canine) group. From this one would conclude
that cats and lions shared a common ancestor that lived
much more recently than the common ancestor of canines
and felines.
It is easy enough to compare the three cladograms that
are possible with three species. However, as more species are
compared, the analysis becomes exponentially more difficult.
When comparing even a slightly larger number of species, the
calculations become so complex that they can only be performed
by a computer. As the number of species in the analysis
increases, even a computer cannot sort through all of the
possibilities. For 10 species, there are more than two million
possible cladograms; for 50 species, there are 3 × 10 76 possible
cladograms. To provide some idea of how large a number
this is, consider that the universe has existed for less than
10 18 seconds! The computer must randomly generate a subset
of several hundred possible cladograms and make comparisons
among them.
Even when a cladistic analysis compares only a few hundred
of the possible cladograms, there may be a large number
of almost equally parsimonious ones. The computer must
then generate a consensus tree that preserves the patterns that
the best cladograms share in common with one another.
Applying cladistics to classification
A cladistic approach to classification would group organisms
together on the basis of the branch points in the cladogram.
A clade (whether it corresponds to a genus, a family,
an order, a class, a phylum, or a kingdom; see Linnaean
system) must consist of all species that share a common
ancestor, and only those species. Such a clade is called monophyletic
(mono- means one). Cladists will not accept a genus,
family, order, class, phylum, or kingdom that includes only
some of the species that have evolved from a common ancestor.
Such a group is called paraphyletic (para- means beside).
Cladists most vigorously reject taxonomic groups that both
omit some species that share a common ancestor and include
some species that do not, a group referred to as polyphyletic
(poly- means many).
A cladistic approach can lead to a different system of
classification than what is traditionally recognized, as in these
examples: