Biology Reference
In-Depth Information
2.2. Homology — A Phylogenetic Hypothesis
Homology is a hypothesis, made when the state of one or more charac-
ters is phylogenetically compared in a number of taxa or sequences. The
basis for a comparison is that there is reason to think that the characters
are derived from a common ancestor. By comparing the amino acids in
column 24 of Fig. 2, we are assuming that they are descendants from an
amino acid present in the cenancestor of all the sequences. The state of
the character is the same (threonine, “T”) in all displayed taxa except
two,
Polypodium vulgare
(where it is a lysine, “K”) and
Taxus baccata
(where it is a serine, “S”). The placement in the same character column
means it is hypothesized that all of these threonines as well as the lysine
and the serine are descendants from the same ancestral amino acid (most
probably a “T”).
More formally, homology is the hypothesis made while defining,
within two different sequences
s
and
t
, the two states
K
s
and
K
t
which
are thought to describe the same character K. This is done because
there is reason to assume that states
K
s
and
K
t
derive from a common
origin
K
0
and are therefore phylogenetically comparable. When a given
character K can be found in two different taxons and their degree of
similarity is due to a common origin, this character is said to be homol-
ogous in the two taxons.
e
Homology, being a hypothesis, can be either true or false. Accordingly,
it does not make sense to state that two quantifiable characters are, say,
79% homologous. They are 79% similar (21% dissimilar); and if this simi-
larity is indeed due to a shared origin, then they are homologous. The same
applies to a set of characters, and by extension also to taxa. Two men who
look strongly similar are not necessarily closely related — similarity is not
homology.
The principle of parsimony, also known as Ockham's razor, states
that, all things being equal, the simplest explanation is best. In phyloge-
netics, the principle of parsimony translates into the following rule:
apart
e
Obviously, there is a difference between the notion of character and of its state;
however, a less rigorous use of terminology, where it is said that so-called “characters”
K
s
and
K
t
are homologous, is so widespread as to be acceptable.
