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

Continuing the discussion from Michael Behe's "Billiard Shot" model:

Indeed, but there are several more things you’re not considering. You appear to be reflexively trying to defend an assumption that I’m questioning instead of being scientific.

I don’t see any reason to consider that. Are you really trying to claim that none of the ancestors of these mice have ever lived among colors darker than beige? If so, how do you know that?

Only for the one population studied. They don’t know about the other populations they mentioned. Is there only one locus that controls the black/yellow switch?
Here’s a black C57BL/6J mouse:

Here’s a C3H mouse:

If they have pups together, will they be black?

That’s simply false. See Figure 1A. They caught one black mouse on the light rocks at Pincate.

Even if you weren’t misrepresenting the data and the frequency had been 0 of a massive sample of 43 mice, why would that suggest that the mutations were new ones?

Yes, but that says nothing about whether the alleles were around before or after the selection or whether other loci were involved. You might want to reconsider whether your assertion about black being dominant is generally true.

A unique allele. You’re trying to establish that they mutated after the populations diverged, remember? That’s the only fact even suggestive of new mutations; it doesn’t necessarily follow from that fact, but I suspect you know that or at least suspect it. They also could be caused by founder effects in small populations descended from a much more polymorphic population.

None of the four things you allegedly considered, even leaving out the things you didn’t, demonstrates anything of the sort to this mouse geneticist. Can you try to explain more and assert less?

That’s quite the talent you have there. My mind reading skills are nowhere close to yours.

With that being said, let’s discuss what I did consider. I will mainly be working from this PNAS paper:

First, is the black coat color allele dominant in the genetic background of the wild population? The evidence in the paper seems to back this up:

Every black mouse at the Pinicate locale had 4 specific polymorphisms. Every one of them. On top of that, the black allele was dominant:

All heterozygotes were black. On top of that, the coloration was discrete:

There wasn’t a spectrum of intermediate coloration. They were either light or black.

To summarize these points, the black allele was dominant in this wild population which is a very common feature for dark coloration alleles in mice and other organisms. All heterozygotes were black, and all black mice had 4 specific non-synonymous mutations in the mc1r gene in the Pinacate locale.

Could this allele act differently in a different genetic background? Anything is possible. However, we are talking about the wild population they looked at, and in that genetic background the black allele was dominant. Is it possible that there is some very rare allele in the wild population that they missed? Again, anything is possible, but I can only go with the info in the paper. If there is such an allele then it is either rare or geographically limited, both of which can’t explain the distribution of coat color.

Now let’s look at the geographic distribution of coat color. Fig 1 from the paper:

image

They trapped 18 mice in traps on black basalt, and 16 of those were black mice. In lighter colored desert in the immediate vicinity to the basalt flows, they trapped 11 mice and only 1 had dark fur. The other 10 had light fur. At two sites distant from the Pinacate locale (Avra and Portal) they trapped 20 mice and all were light colored.

If this dominant black allele is not seeing strong negative selection in the light colored desert regions then we would expect to see about 75% of mice with dark fur. We don’t. In regions 100’s of km away from the black basalt regions we see zero black mice. Could they have missed some? That is certainly possible, but given that 16 of 18 mice trapped in the Pinacate locale were black mice this seems very unlikely. The authors also reported that there was sufficient admixture between the populations so that we should see the black allele in the light colored desert regions if there was a lack of negative selection against the allele:

Now, one thing that is a bit hazy is the age of the lava flows. I dug up this info years ago, so I am going from memory. I remember the age of the lava flows being recent, which further supports the emergence of the black allele in the brown population. I will spend some time digging that up later if needed. However, there is more info in the paper that supports the conclusion that the black allele is a recent addition to the population:

Lastly, the mc1r mutations linked to black fur coloration at the Pinacate locale is not seen at the black basalt lava flows at Armendaris locale, located 100’s of km away from the Pinacate locale.

To me, and to the authors of the paper, this suggests independent genetic adaptations to the black basalt environments that emerged in the brown coat colored population.

These are the things I considered. For the most part, I am echoing the conclusions drawn by the authors in the PNAS paper. You can call them my assertions, but they are the conclusions found in the paper.

I am too; that should have been obvious, as I already pointed out above that you misrepresented the data shown in Fig. 1A.

The only work you are doing here is goalpost moving.

Here’s your claim from which you are trying to divert attention:

New mutation. Let’s keep our eye on that ball.

This is very relevant to my point that current educational practices fail miserably to teach people that the reservoir of existing variation is ~1000000-fold larger than the number of new mutations per generation.

You seem to be a poster boy for this failure, as you immediately claimed that the mutation was new and allowed the mice to take up a new niche.

My point is that there is no evidence for your claim that the mutation was new.

You still haven’t presented any.

It obviously was for the only population they studied in detail. I’m disputing your more general claim that black alleles are dominant. They aren’t.

What does that have to do with your claim that the mutation occurred after the selection was present?

I’m quite familiar with the locus, thanks. What does that have to do with your claim that the mutation occurred after the selection was present? Are the progeny of a C57BL/6 x C3H cross discretely colored?

I’d like to see some support for that claim for mice.

Straw man. I’m not claiming that they missed anything. I’m claiming that you don’t know when the mutation occurred. There’s no reason for the adjective “new.”

This is about selection acting on the huge reservoir of existing variation, remember?

You seem to be either very confused or are deliberately obfuscating. I’m challenging your claim that the mutation was a new one.

Yes. As I noted, that falsifies your misrepresentation of the data:

But they did. Why did you do misrepresent the data?

So what? I’m disputing your claim that the mutation is new. How does that relate to your claim?

There’s obviously strong selection. How does that even suggest, much less demonstrate, that the mutation is new?

That has nothing to do with whether the allele was already present in the ancestral population. Of course the allele has become fixed. When did a mutation produce that allele, Taq? There’s no evidence that it happened after the mice encountered the basalt flows.

It says “the recent action of positive selection.” It doesn’t say “a new mutation.”

I agree that the frequency of the black allele has been increased by selection, but that wasn’t your claim. Your claim was that it was a new mutation:

Why are you pretending that you claimed something very different?

Anyway, you are certainly demonstrating that even scientists don’t see the ratio of existing to new variation clearly.

Where will I find your assertion that the mutation is new in the paper? I don’t see any problems with the paper; only with your claim that the mutation is new.

This is why we need to teach students that Darwin only observed existing variation. This is why teaching about mutation first makes students susceptible to pseudoscientific propaganda.

There were zero black mice in the Avra Valley and Portal locales which were the areas I was referring to. I didn’t misrepresent the figure at all.

Ok.

The allele can’t survive in the light colored desert environments, as shown by the lack of black mice at the Avra Valley and Portal locales. Therefore, the recent positive selection evidences a recent emergence of the allele.

I never made any such claim. I said that the black allele is dominant, meaning the black allele under consideration in the wild population that is under consideration.

Such strong negative selection would have removed the allele from the population. It would have nearly zero chance of surviving long term in the population.

Added in edit:

Also from the paper:

Yes, you did:

That was not true, and there’s no reference to Avra Valley and Portal.

Even if you weren’t misrepresenting the data and the frequency had been 0 of a massive sample of 43 mice, why would that suggest that the mutations were new ones?

You really have trouble admitting an error or unwarranted exaggeration, don’t you?

So what? Are they reproductively isolated?

Stop with the “emergence” waffling. You claimed that the mutation is new. There’s no evidence for that, you realize it, but rather than coming clean, you’re handwaving and obfuscating.

There were several wild populations considered in this paper. They don’t know what loci or alleles are involved in the others. Hence my question, which you haven’t answered.

Really? Is the frequency of the allele zero? Is the sample large enough to conclude that?

And how did you determine that the population is completely reproductively isolated from populations with the black allele? Why did they find a black mouse at Pincate if the negative selection is so strong?

I don’t disagree with the paper. The evolution was very rapid. There’s just no evidence to support your claim that the mutations are new, no matter how much you wave your hands. I already explained this and you didn’t respond. How come?

Look at the figure:

image

Look at the pie chart for the Avra Valley and Portal locales. Notice that the entire pie is white. This means that all of the mice trapped at those locations were light colored. Where are those locales? Away from the Pinacate locale, just as I described.

The sample size is large enough to strongly evidence the elimination of the dominant black allele from the population, especially given the strong gradient of coat color right next to the black basalt islands. This isn’t the only study on these mice. Perhaps a survey of other papers would produce the n you are looking for.

I have responded in several posts thus far.

I have. YOUR false statement made no reference to Avra Valley and Portal:

I have. You did not cite them in your false statement.

Show me how you determined that statistically. What’s the probability that 0 of 43 means 0 of thousands?

And even then, you haven’t shown any evidence for the complete reproductive isolation required.

There’s simply no evidence to support your claim that any of these mutations are new.

Not to most of my questions, while presenting nothing to support your claim that the mutations are new. You’re literally working from the false ID assumption!

Here are a couple you might want to address, if your ego will allow you to:

I was referring to the Avra Valley and Portal locales when I said “away from the Pinacate locale”. My apologies for not being explicit. I had assumed that when people looked at the figure and saw two locales away from the Pinacate locale with all light colored mice they would know what I was talking about. Apparently, I assumed incorrectly.

Would this evidence change your views at all? If not, I don’t see a reason to pursue it.

The evidence:

  1. Strong selection against the black allele away from the black basalt islands that would have a strong chance of eliminating the black allele from the ancestral population.

  2. The young age of the black basalt islands (< 1 million years).

  3. The convergent phenotype of different genetic mutations in different genes between two separate black populations of mice.

I only claimed that there is strong evidence that the black allele would be eliminated from the population due to strong negative selection. I’m not playing the “no black swans” game. If you don’t find the evidence compelling then there is nothing more I can do.

Statistics isn’t the evidence, and the paper even notes that the populations aren’t isolated. You could just admit that you see my point.

You don’t know the colors of the background(s) on which the ancestral population lived.

Why would that distinguish between new and preexisting alleles? That makes no sense.

Different alleles. How does that suggest new mutations?

That doesn’t matter at all unless there is complete reproductive isolation. Is there?

You’re just throwing things out and not explaining why you allegedly find any of them compelling, or moving the goal posts.

You could, though, just admit that you don’t have evidence to support your unwarranted, hasty (ID creationist) assumption that mutation happens after selection. We all make mistakes.

It’s really hard to eliminate alleles, even dominant ones.

The paper says that there is gene flow between the mice on the black basalt and the mice in the adjacent light colored desert. In fact, I cited that evidence in an earlier post. However, I don’t think they looked at gene flow between the Pinacate locale and the Avra Valley and Portal locales. I don’t think the Pinacate locale is isolated from the Avra Valley and Portal populations, but given your propensity for wanting exact language I didn’t leap to that conclusion.

With that said, do you agree that the Pinacate population is not isolated from the other locales?

If the desert has been around much longer than the black basalt lava flows, would you agree that this is good evidence?

It suggests independent mutations in separate geographic locations that weren’t able to spread through the population, even though there appears to be a lack of reproductive isolation. The barrier to the spread of these alleles is the light brown desert between the lava flows. Given the young age of the lava flows, it suggests new mutations at each of these sites.

I never said that mutations happen after selection. Where did you get that from? You need the mutation before it can be selected. That seems rather straightforward. What I am saying is that the mutations causing black fur emerged in the light colored population surrounding the black basalt flows. Normally, those alleles would be quickly eliminated from the population. However, if they occur near a black basalt flow then the black mice can move into those environments and thrive. That’s the scenario I am laying out.

Found a nice picture of the Pinacate lava fields, just for some context:

I know. That fact alone should have been sufficient for you to pause, reconsider, and retract your claim.

I don’t want language, I want evidence. It’s a science thang.

Are there no dark regions in the desert?

Why not multiple alleles in the ancestral population?

I don’t see how the young age of the lava flows suggests new mutations instead of selection for existing alleles. Can you explain?

I’m saying that you have zero evidence that allows you to distinguish between that and:

An allele already present in the ancestral population resulting in black fur allowed the mice to take up a new niche in environments dominated by black basalt rocks.

“Emerged” is a weasel word.

What you said is that they are new. I’m saying that you have no evidence that demonstrates that they weren’t present in the ancestral population and then “emerged.” There are terms in genetics that are more accurate, ya know.

Only if there was no flow between that population and others that live in darker habitats AND there were no dark habitats before the lava flows existed.

Those seem like two mighty big assumptions to me.

Why?

There are black basalt lava flows.

Because there is strong negative selection against black phenotypes outside of the black basalt lava flows.

I have presented that evidence. You have rejected it, which puts us at a sticking point. I guess we can see of others want to chime in.

Because gene flow provides a reservoir for the black allele.

I mean before the lava flows.

But there is gene flow.

You have presented evidence, but none of it supports your claim that these are new alleles.

That is objectively false. I have not rejected any of it. I reject your interpretation of it.

We’re at a sticking point because you refuse to explain how any of the evidence is inconsistent with the hypothesis that the alleles were present in the ancestral population.

So you’re claiming to know, and I’m claiming there’s insufficient evidence to support your claim. I would think that, as a scientist, you would present your hypothesis and evidence as a scientist would.

But you’re not doing either. Why not just admit that we don’t know?

Again, strong selection will eliminate the black allele even with gene flow. If gene flow is spreading black alleles, then why don’t we see these alleles in between the two lava flows, and why don’t we see the mc1r mutations at both locations?

Already did that in multiple posts.

How so? We know for a fact that the fitness of black homozygotes on a tan background is >0.

Does fitness have to be 0 in order for an allele to be removed from a population?

The fact that the mc1r mutations conferring black coat color in the Pinacate population is not found in the Armendaris population is, in my opinion, strong evidence that the allele is quickly eliminated outside of those black basalt regions. Pinacate is a resevoir for the black alleles, and yet even with gene flow those mc1r mutations can’t make it to other parts of the species range. The same for the alleles for black fur in the Armendaris population.

Here is another paper that should answer a lot of our questions:

https://www.nature.com/articles/6800600

I am looking it over now, and would love to hear your comments.

No, but it’s more likely. Gene flow is the more important factor.

How do you remove an allele that has high fitness in a neighboring, interbreeding population, even if we make the false assumption that fitness on black/brown backgrounds is 100/0 for black mice and 0/100 for brown mice?

Thanks.

Figure 2 already shows that that coat colors are not discrete, indicating plenty of polymorphism as I would expect. That was why I asked you whether you were claiming that there were no dark regions in the desert.

Are you aware of the number of loci that affect coat color in mice and other mammals that have active switching between black and yellow pigment to give the base agouti color?

In this study, there were four pairs of populations for which light and melanic mice were found in close geographic proximity (Table 4). We found substantial gene flow in several of these comparisons. The population migration rate was highest between PIN and TUL ( Nm >60) and also high in KNZ and AFT ( Nm =8). Both of these estimates of gene flow are higher than those that typically lead to population differentiation. This pattern can also be observed in the phylogenetic tree (Figure 4), where individuals from these populations are intermingled along the tips.

How likely would it be to eliminate alleles in subpopulations given these data?