Coat color evolution--is there evidence for new mutations?

[Mercer (John Mercer)]

@T_aquaticus

I am setting up two scenarios and determining which observations we would expect to see in each. It is hypothesis A and B. Let me label them as such:

Hypothesis A : Let’s say that there were no black alleles in the pocket mouse population that spread out into the deserts of Arizona and New Mexico. Once they had established themselves, the populations at each of the two sites acquired new mutations that produced the black phenotype.

If the mutations occurred after the lava flows, then the time between now and the time of divergence of all of the alleles, both black and beige, shown in the paper must be less than a half-million years. Much less, since the sample is so small and there are almost certainly other polymorphisms that are being missed.

Correct?

Hypothesis B : Let’s say that the black allele was present in the original population that spread out into the desert. Chances are, we would have a mixture of different genotypes for the black phenotype at both sites. Therefore, you would expect to see different genotypes for black fur at the same sites.
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That’s not very realistic, given what we know from the house mouse and the gradient of color observed in the paper you just found.

Hypothesis C: The founding population was as polymorphic as house mice, with multiple alleles at multiple loci. This allowed them to inhabit multiple niches in the desert, even darker ones like shady, north-facing cliffs. Different black alleles and different black/yellow loci (such as Agouti, the first place the PNAS paper’s authors looked) are likely to have been selected on different flows because of founder effects.

This predicts that calculated divergence times for pairs of alleles will be longer than the age of the lava flows.

@Mercer

Here’s something that I have been waiting for you to acknowledge: if this was a new mutation, shouldn’t it only differ from WT by a single residue?

If it is new then it should have less divergence than the brown genotypes, and it does.

1. Divergence also is dependent on selection.
2. When we address divergence, we have to address both tines of the fork.

So given the mouse germline mutation rate, how long has it been since all of those alleles in the PNAS paper diverged from a common ancestor?

Your hypothesis predicts that the time has to be less than the age of the lava flows.

Why are there four substitutions, all of which change charge? What’s more likely: four simultaneous new mutations or a long history of selection?

@T_aquaticus

It could be one adaptive mutation with the other three hitching a ride.

Could be, but then the divergence time must be far longer if 3 additional neutral missense mutations occurred and became fixed by drift. That time would be more than sufficient to falsify hypothesis A.

So which is more likely?

@Mercer

We’re discussing your unsupportable assumption that it was a new one.

You didn’t say new one.

No, you did:

@T_aquaticus

A new mutation resulting in black fur allowed the mice to take up a new niche in environments dominated by black basalt rocks.

Evolution rarely needs new mutations for rapid selection and fixation, because there is polymorphism in healthy populations.

@Mercer

Who’s to say that the black allele wasn’t the WT in the founding population before it colonized the desert?

If that were the case then I would expect to see the black mc1r allele at both black lave sites. We don’t. We see different genotypes for the same phenotype.

Now we’re getting somewhere. Could any allele be credibly called WT in the founding population?

@T_aquaticus

Just in case you missed it from above:

I didn’t miss it. You’re missing the fact that selection fixing an adaptive substitution, no matter how rapid, has no bearing on the age of that substitution.