I also enjoyed reading your analysis of the problem.
> In other words, other than point 4, based on several assumptions it seems
> likely that the HW equilibrium holds. Is there any other way to test it
> empirically? (I tried a search for population AND genetics AND opsin* and
> didn't find anything that seemed relevant).
Agreed, though genetic drift should be modeled in this case. See
explanations of Ne.
(I'll assume the alleles were tested for their approximate divergence
> The argument is stated...
> There are several different alleles present in the wild population
>> This implies selection pressure for individuals that carry several
> alleles in order to maintain heterogeneity in the population
> (reference to another paper that says... "therefore there must be
> selection pressure to maintain the alternative alleles...").
> The most likely explanation is that colour vision is advantageous because
> it allows us to see fruit better.
>> ... It's the 2nd bit I don't follow. I can think of numerous scenarios by
> which I think the alleles could be established and maintained in the
> absence of selection pressure. So colour vision could just have happened
> by chance and there's no need to think up explanations of why it's useful
> to us on this evidence, at least. I brought up the X-chromosome issue, as
> I wasn't sure if the HW equilibrium applied to genes inherited in this
> fashion, and if not, then it would eliminate my dilemma. I can't see
> straight out why genes shouldn't be in H-W equilibrium if on the
> X-chromosome, though.
Definitely. The 2nd bit about "seeing fruit" is a conjecture -- I'm sure we
can come up with other stories to explain maintenance of the alleles. Of
course, as you said, the colour vision did happen by chance, a mutation.
However, it is much more likely that selection would maintain these alleles
over time than by chance (this has been simulated, see Nei's book (1987)).
The locus on the X-chromosome adjusts the model somewhat since they are
neither inherited in a diploid nor a haploid manner. I know this is modeled
but I would have to search for the exact information. Either way the
important forces, considering the age of the alleles, is selection and