Cladistics





Cladistics (or phylogenetic systematics) is a branch of biology that
determines the evolutionary relationships between living things based on
derived similarity. Cladistics differs from phenetics, which groups
organisms based on overall similarity, and from more traditional approaches
based on "key characters".

Based on a wide variety of information, which includes genetic analysis,
biochemical analysis, and analysis of morphology, relationship trees called
"cladograms" are drawn up to show different possibilities.

A cladogram showing the relationship between various insect groups using
horizontal parallel lines joined by vertical lines. In some cladograms of
this type, the length of the horizontal lines indicates the amount of time
that has passed since the last common ancestor between two groups or species.

A cladogram showing the relationship between various plant groups using
intersecting diagonal lines.

In a cladogram, all organisms lie at the endpoints, and each split is
ideally binary (two-way). Each branch, whether it only contains one item or
a hundred thousand, is called a clade. A correct cladogram should have all
the organisms contained in any one clade share a unique ancestor for that
clade, one which they do not share with any other organisms on the diagram.
Each clade should be set off by a series of characteristics that appear in
its members but not in the other forms it diverged from. These identifying
characteristics of a clade are called synapomorphies (shared, derived
characters). For instance, hardened front wings are a synapomorphy of
beetles, while circinate vernation, or the unrolling of new fronds, is a
synapomorphy of ferns.

Cladistic Methods

Typically, an analysis begins by collecting information on certain features
of all the organisms in question, and then deciding which versions were
present in their common ancestor (plesiomorphies) and which have been
derived since (apomorphies). Usually this is done by considering some
outgroup of organisms we know are not too closely related to any of the
organisms in question. Only apomorphies are of any use in characterising
cladistic divisions.

Next, different possible cladograms are drawn up and evaluated. Clades are
typically drawn so that they can have as many synapomorphies as possible.
The idea is that a sufficiently large number of characteristics should be
large enough to overwhelm any examples of convergent evolution. In other
words, there are many ways in which plants and animals, etc., may evolve
features that resemble each other because of environmental conditions. A
well-known type of convergent evolution is insect mimicry, in which some
insects that are edible come to superficially resemble other insects that
are inedible, and so escape being eaten.

In practice, neutral features like exact ultrastructure (a term for
extremely fine structure, microscopic or molecular composition of cellular
structure) tend to do just that, to provide evidence for real relationships
even when the appearance of organisms makes it otherwise difficult. When
equivalent possibilities turn up, one is usually chosen based on the
principle of parsimony: the most compact arrangement is likely the best (a
variation of Occam's razor). Another approach, particularly useful in
molecular evolution, is maximum likelihood, which selects the optimal
cladogram that has the highest likelihood based on a specific probability
model of changes.

Cladistics has taken a while to settle in, and there is some questioning
over in just what sort of circumstances cladistics is applicable. In
particular, apomorphies are not always easy to distinguish and data are
often unavailable thanks to a sparsity of available forms or a lack of
knowledge of characters, and these may invalidate cladograms. There is also
concern that use of widely different data sets, for instance structural
versus genetic characteristics, may produce widely different trees. However,
by and large cladistics has proven a useful and coherent extension of other
methods and has gained general support.

As DNA sequencing has become easier, phylogenies are increasingly often
constructed with the aid of molecular data. Computational systematics allows
the use of these large data sets to construct objective phylogenies. These
can more accurately filter out true synapomorphy from parallel evolution.

Cladistics does not assume any particular theory of evolution, only the
background knowledge of descent with modification. Thus, cladistic methods
can be, and recently have been, usefully applied to non-biological systems,
including determining language families in historical linguistics and the
filiation of manuscripts in textual criticism.

Cladistic Classification

A recent trend in biology since the 1960s, called cladism or cladistic
taxonomy, is to require taxa (named groups in a taxonomy) to be clades. In
other words, cladists argue the classification system should be reformed to
eliminate all non-clades (paraphyletic and polyphyletic groups). In fact,
some cladists have argued for entirely abandoning the Linnaean system of
ranked taxa in favor of clades. A formal code of phylogenetic nomenclature,
the Phylocode[1], is currently under development for a cladistic taxonomy
that abandons the Linnaean structure.

A true clade is considered to be monophyletic, or containing one (and only
one) complete evolutionary grouping deriving from one common ancestor. When
a named group is found to contain more than one evolutionary line, it is
termed polyphyletic. For example, the once-recognized group Pachydermata was
found to be polyphyletic because an elephant and a rhinoceros were each
found to be more closely to non-pachyderms than either to each other.
Biologists consider groups that turn out to be polyphyletic to be errors in
classification, often occurring because converges or other homoplasy was
misinterpreted as homology.

If a named group is found to include some but not all of the descendants of
the ancestor on which the group is based, it is termed paraphyletic.
Paraphyletic groups are usually created when organisms are groups on the
basis of plesiomorphies instead of apomorphies. Classic examples of
paraphyly include Pisces (fishes), whose descendants include tetrapods
(amphibians, reptiles, birds, and mammals), and Reptilia, whose descendants
include birds; however, neither tetrapods nor birds are included in the
groups named Pisces and Reptilia, respectively. Most paraphyletics groups,
however, were erected at the genus level, because species were grouped on
overall similarity prior to a cladistic analysis.

The denial of recognition to paraphyletic groups has been very controversial
in biology and remains so among a number of more traditional evolutionary
taxonomists. They feel that abandonment of paraphyly leads to loss of
information in the classification system about significant changes in
organisms' morphology, ecology, or life history. Accordingly, they argue
that the notions of clade and taxon should be kept distinct, and that
paraphyletic taxa are necessary if every group is going to be broken down
completely into subgroups. In fact, evolutionary taxomonists such as Peter
Ashlock include paraphyly under the term monophyletic, reserving the term
holophyletic for the strict sense of monophyletic.

Cladists counter that "significant changes" recognized by evolutionary
taxonomists are often too subjective to be a basis for classification.