Biology Reference
In-Depth Information
the number of mutations along a branch or an estimate of the time the evo-
lutionary process took; as we shall see, these estimates are often represented
as proportional to the length of the branches along one graph axis.
This introductory section has presented the simple tree structure,
which is the basis of phylogenetics, and introduced some basic terminol-
ogy. In the sections that follow, let us go to the heart of the matter.
2. Homology and Homoplasy: Look-alikes
are Not Necessarily Closely Related
2.1. Characters and Their States
The first step in any phylogenetic analysis is to identify and observe com-
parable characters displayed by the taxa or genes to be analyzed. In nature,
these characters can be morphological (e.g. color of the tail, presence or
absence of a bony endoskeleton, number of legs, etc.) or molecular
(e.g. the nucleotidic base or the amino acid at a specific position of a gene
or a protein). The phylogenetic model states that two comparable char-
acters should present states which, on the one hand, tend to be similar
due to a common evolutionary origin (their cenancestor) and, on the
other hand, tend to be dissimilar due to evolutionary divergence from
this common origin.
It is rarely possible to make a meaningful statement regarding the
phyletic history of a number of taxons just by analyzing the evolution of a
single character. Generally, the larger the number of homologous characters
for a given set of taxons, the better the phylogenetic analysis (We will
explain further the meaning of “homologous” in Sec. 2.2). This can
translate into a fairly large dataset which is best displayed in the form of
a matrix of the states of characters, where a row corresponds to a taxon,
and a column to a character. If the characters within any taxon have a nat-
ural linear or sequential order (as in DNA or a protein), each row within
the matrix is called a sequence of characters.
d
In Fig. 2, a number of
d
Often, characters in a sequence are called sites.
