Biology Reference
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under selection. Data also support the hypothesis that much molecular varia-
tion is essentially (nearly) neutral. The debate thus is over how
many
, and
which
, molecular variants are selectively neutral or nearly neutral.
Moritz and
Hillis (1990)
suggest that each molecular marker should be tested for neutrality.
They also note that, because most departures from neutrality are locus-specific,
selection will have relatively minor effects on analyses if many different loci are
studied.
12.3.4 Homology and Similarity
A fourth issue concerns terminology.
Homology
is an important concept in biol-
ogy and historically has had the precise meaning of “having a common evolu-
tionary origin” (
Reeck et al. 1987
). However, homology has been used in a more
loose sense when comparing protein and nucleic-acid sequences. Protein and
nucleic-acid sequences from different organisms have been called homologous
when they are
similar
. According to the traditional definition of homology,
amino-acid or nucleotide sequences are either homologous, or not. They cannot
exhibit a “level of homology” or “percent homology.”
Reeck et al. (1987)
point
out that using homology to mean similarity can cause three different problems.
First, sequence similarities may be called homologies, but the sequences are
not
evolutionarily related
, which is inconsistent. Second, similarities (again called
homologies) are discussed but evolutionary origins are not, which can lead the
reader to believe that coancestry is involved when it is not. Third, the similarities
(called homologies) are used to support a hypothesis of evolutionary homology.
The problem is that although similarity is easy to document, a common evolu-
tionary origin usually is more difficult to establish, especially if fossil evidence
is lacking. Several evolutionary processes other than homology could account
for sequence similarities, including
convergent evolution
, that is the indepen-
dent evolution of the same characteristic in separate branches of a phylogenetic
tree. When in doubt, it is better to talk about “percentage similarity” of DNA
sequences.
12.4 Molecular Methods for Molecular Systematics and Evolution
Systematics studies conducted prior to the 1960s primarily utilized morpho-
logical and behavioral attributes as characters, although cytogenetic characters
were used in some cases (
Mayr 1970, White 1973, 1978
). In the 1960s, electro-
phoresis of proteins began to provide new characters after
Lewontin and Hubby
(1966)
demonstrated that protein-coding genes often are polymorphic (have
more than one allele) and that gel electrophoresis of proteins could reveal the
