> Please forgive my ignorance, but I still cannot understand how a gene can
> CHANGE and still be exactly the same gene. It seems to me that you can't
> loose here.
I didn't say that a gene can change and still be exactly the same gene. In
fact I said the exact opposite: "Of course if genes change then so can their
mutation rates, but **if they change they are technically no longer the same
genes they were before they changed**." I'll say that again: a gene that
changes is no longer the same as it was before. So a gene that changes is
NOT exactly the same gene. If a gene changes then it becomes a new gene, and
so may have a new mutation rate. But if a gene does not change then it stays
the same old gene and its mutation rate does not change.
> The definition that I've learned and that is in Futuyma's textbook says:
> "Allele: One of the several forms of the same gene, presumably differing
> by mutation of the DNA sequence, and capable of segregating as a unit
> Mendelian factor. ... ...DNA sequence variants, that may differ at
> several or many sites, are usually called haplotypes."
Ah, now I understand the source of your confusion. In the above definition
the phrase "one of several forms of the same gene" refers to the fact that
they all produce the same basic product, though the products may differ
slightly depending upon the mutation involved. It does not literally mean,
however, that the alleles are all the same gene. The phrase "capable of
segregating as a unit Mendelian factor" tells us that each allele can be
treated as a separate inheritable unit, subject to Mendelian laws just like
any other gene. If in fact alleles were literally all the same gene then
they could not act as separable Mendelian units, because they would be
indistinguishable. An allele is fundamentally a separate gene, so it can
have its own mutation rate.
> I've never read a paper where the authors referred to different haplotypes
> of the same gene as different "genes." Since this is not my area of
> expertise (I'm a behavioral ecologist), I recognize that I may be wrong.
This is because they usually are not thinking in terms of strict Mendelian
inheritence, but in terms of the product being produced. This is one of
those cases in science where the scientists themselves use the wrong phrasing
and nomenclature for convenience, but are nonetheless well aware of what they
really mean. It can, however, be confusing to someone who is not familiar
with the subject.
Kevin L. O'Brien