This is another response to the recent query by David Steffen regarding the use of
the term "homology." I thought I might as well throw my two cents worth in.
Many molecular biologists commonly use informal arbitrary criteria as
support for statements of the "homology" of two genes. For example, they
might suggest that if two peptide sequences in the same organism were
highly similar (e.g., 85 percent) then one could be confident that the
proteins were "homologous", due to a gene duplication event, as opposed to
similarity due to parallel evolution for similar function.
It seems to me that hypotheses of homology are only relevant to phylogenetic
inference at the level they are proposed to be synapomorphic (shared derived
similarities) on a cladogram. Therefore, it is hopeless to try to provide
evidence for homology by the comparison of two taxa or sequences. The only
interesting evidence one can bring to bear on the issue of common ancestry
is shared "special" similarity relative to one or more outgroup taxa or
sequences. This issue is, I think, distinct from the issue of whether
homology is used as many of us use the term synapomorphy, as a proposal
of homology, or as the actual similarity due to common ancestry which is
ultimately impossible to prove.
With sequence data, there are also problems of specifying the level of
homology. For example, Michael Ghiselin (Syst. Zool. 18: 148-149 (1969)
uses the following hypothetical example:
A Asp-Val-Glu-Met-Ala
B Asp-Pro-Glu-Met-Ala
C Asp-Pro-Thr-Met-Ala
D Gly-Pro-Thr-Met-Ala
E Gly-Pro-Thr-Tyr-Ala
F Gly-Pro-Thr-Tyr-Ser
Ghiselin argues that similarity is a relation between the peptides as
wholes, which decreases from A to F, while homology is a relation between
the parts. He argues, for example, that Asp is hypothesized to be homologous
to Gly in A and F, respectively, given this alignment of the sequences.
He also argues that the peptide sequence A could be homologous to F even
though they are completely dissimilar. One can speak of the correspondence
between nucleotides or amino acids in terms of their position in a sequence
which is hypothesized to be homologous. Although Ghiselin doesn't consider
this use of homology, one more normally may also speak of the shared
similarity of D, E and F at site 1, relative to A, B and C, which could
be a synapomorphy (hypothesis of homology), depending on the outgroup(s)
one selects which in turn determines the cladogram topology. One can also
hypothesize that peptide F is homologous to peptide A, or more precisely,
hypothesize that the shared ancestor of A and F had single protein-coding
gene which is traceable, by descent, to the genes in A and F which produced
these peptides.
Confusing, isn't it?
Doug Eernisse
usergdef at ub.cc.umich.eduusergdef at umichub.bitnet
Museum of Zoology and Dept. of Biology
University of Michigan
