If you read evolgen, you’ve probably been following the race riots that Wilkins started. It’s pretty much died down now, and it was more a debate about semantics rather than an actual scientific disagreement. This is usually the case in evolutionary biology — take, for example, the neutralist-selection debate or the recent junk DNA fun we had here at evolgen. I have refrained from offering my opinion on Wilkins’s post due to my poor understanding of human population genetics (as evidenced by my attempt to discuss marketing BiDil to African Americans), but I have a few comments I would like to make. You can find them below the fold.

Before my opinion, a quick recap. It all started when John Wilkins wrote his opinion about race in humans, arguing that it is not biologically meaningful (defending the Lewontin thesis). PZ Myers then posted in agreement with Wilkins, and Jason Malloy disagreed in the comments. Razib, who knows more about human population genetics than any armchair scientist should, provided a nice argument for why Lewontin is wrong, and the Contingency Table took a look at some of the articles Wilkins cited to show they don’t actually support his argument. My conclusion (based on something Razib wrote): what one person is willing to call race, another wants to label as population structure. Oh, and some people think Lewontin is an idealist who believes in a homogenous population of all humans. I’m going to try to stay as neutral as possible. This post is mostly an attempt to request feedback from my readers and encourage a discussion of the data, rather than opinions.

First of all, I’m going to refer to populations rather than races. If you want, you can think of them as metapopulations or some other nested population structure. Either way, we’re using the word population. Let’s assume we have no a priori assumptions regarding our populations. Now, it’s not very practical to identify populations based on fixed alleles between the populations because there won’t be very many of those. Instead, we should employ a probabilistic approach where certain alleles tend to be found in one population versus another. If we genotype individuals at multiple loci, we can construct our populations using an assignment test. This is what Jonathan Pritchard’s Structure program does. In this algorithm, the most probable model tends to be over-split into many populations, but we can constrain the method to find no more than 3, 4, 5 or any other number of populations.

I think everyone involved will agree that we can recover our predefined “races” using an assignment test. The races have been reproductively isolated (to some extent) allowing for the neutral alleles to reach different frequencies in the different populations. Determining whether these differences are meaningful beyond population structure requires a bit more work. First off, we must define what we mean by meaningful. I would argue that meaningful requires some sort of physiological, anatomical, or other phenotypic difference between the populations.

Are there such differences? Well, duh. Human populations have different skin colors, tolerance to types of food, resistance to pathogens, facial characteristics, body types, etc. None of these differences seem contentious, but when we start dealing with behavior or intelligence, supremacist undertones permeate the conversation. Most of the aforementioned differences are due to natural selection, and that makes them poor markers for recovering population structure — if selection regimes are similar in multiple populations, allele frequencies may be similar due to convergent or parallel evolution rather than recent common ancestry. But these loci are what make our populations biologically different.

So, we must first determine our populations using neutral loci, and then examine non-neutral alleles to see which ones differ between the populations. We can examine the polymorphism around a locus to determine whether alleles differ between populations because of selection or population structure. Also, genes that suggest different population structure than most of the other loci in the genome may have their pattern due to selection.

That’s what I think; sadly, I’m not familiar enough with the data from humans to tell you what they reveal. My (limited) understanding is that the majority of human genetic diversity can be found in African populations. African populations differ from each other at both neutral alleles (revealing population structure within Africa) and non-neutral loci (revealing biologically meaningful differences). My argument has always been that the current races (as defined in the United States) are inappropriate because they marginalize the diversity found within Africa. If each race were to contain the same amount of diversity, we would need to split Africans into multiple races. Those who are more familiar with these areas of research, please correct me where I am wrong.