Definitions can indeed be "clunky." I would use the phrase race/ethnicity rather than just race because in common parlance it is a better description. I tend to think that race has been used more in terms of continental origins (Africa, East Asia, Europe, Americas). On that basis, one would not characterize African Americans as a racial group, but rather as an ethnic group. We sort of implied this in the Genome Biology paper. The reason is that African Americans typically have European as well as African ancestry (and possibly other ancestries as well) and are also culturally distinct from Africans. Sort of similar to Latinos - who from a genetic ancestry standpoint can be nearly anything. Hence our use of race/ethnicity.
Just to opine a bit, I think part of the problem is the notion of a causal relationship -- i.e. "dark-skin" or "blackness" causing sickle-cell -- as opposed to a more geographic definition that might encompass people regardless of skin color.
Yes, exactly. Groups living in isolation from each other for long periods of time have acquired many genetic differences. The large majority of those are due to "genetic drift" -- i.e. random fluctuations in gene frequencies. That also includes many genetic variants that code for traits and diseases. But then there are some genetic variants that differ in frequency due to differential selection pressure in different environments. The best examples are for genes that confer resistance to malaria. One of those causes sickle cell disease in those who carry two mutations; those who carry one copy have sickle cell trait, which is generally benign but confers greater resistance to severe malaria infection. Mutations for sickle cell disease are found at pretty high frequency in some African populations, but also found in parts of the middle east and India. Beta thalassemia is another disease where carriers are offered greater protection from malaria. This disease is more common around the Mediterranean (e.g. Greeks).
Then there is G6PD deficiency. Mutations for that are found at increased frequency in parts of Africa, but also in the Middle East. The mutations underlying these disorders generally differ geographically, which is another indication that while the mutations are different ancestrally, they achieved high frequency in different populations for similar reasons (i.e. resistance to malaria). Another more recent example is a gene called ApoL1. There are a couple of genetic variants found in West Africans (and African Americans); when carrying two of these, there is an increased risk for kidney disease if hypertensive. It was shown that these variants likely provide some immunity from African Sleeping Sickness (tsetse fly disease) which may have led to them becoming more common where the disease is prevalent.
Various populations have an increased frequency of genetic diseases, which are often unique. Probably a lot or most of it is just chance, but perhaps not all of it. Proving historical selective advantages can be pretty challenging. So, as I mentioned above, groups living in isolation developed their own genetic (and cultural) profiles. Generally, there is no cause and effect between the traits that differentiate groups. East Asians have dark hair and eat with chopsticks. But there is no causal relationship. You can use a whole variety of different traits to place individuals into the same categories, but those traits may have nothing to do with each other etiologically.
I often hear people say that Africa has the highest genetic diversity in the world. What does that practically mean?
If you sequence the genome of an African individual (pretty much from anywhere except North Africa), you will generally find more locations in their DNA that are variable than for any non-African individual. Why is this the case? Population geneticists believe that the world outside of Africa was initially populated by humans who migrated out of Africa. The presumption is that if the number of such individuals migrating was small, then some of the genetic variation was lost in the process. As I described before, genetic drift (fluctuation in allele frequencies) can happen when a population is small. The random fluctuation means that some alleles increase in frequency and others decrease. The ones that decrease may be lost altogether. You tend to find that the amount of genetic variation decreases along the migration routes out of Africa (more or less by distance from Africa, but of course population bottlenecks can also happen anywhere along the way).
What is the impact of this? As I mentioned before (and above), random fluctuations in allele frequencies can mean that rare alleles that create risk for a disease may increase in frequency, by chance. So some diseases may become more common. But the flip side is that some diseases may also become less common.
One last question. Your paper on assessing genetic contributions to phenotype, seemed skeptical that we would ever tease out a group-wide genetic component when looking at things like cognitive skills or personality disposition. Am I reading that right? Are "intelligence" and "disposition" just too complicated?
Joanna Mountain and I tried to explain this in our Nature Genetics paper on group differences. It is very challenging to assign causes to group differences. As far as genetics goes, if you have identified a particular gene which clearly influences a trait, and the frequency of that gene differs between populations, that would be pretty good evidence. But traits like "intelligence" or other behaviors (at least in the normal range), to the extent they are genetic, are "polygenic." That means no single genes have large effects -- there are many genes involved, each with a very small effect. Such gene effects are difficult if not impossible to find. The problem in assessing group differences is the confounding between genetic and social/cultural factors. If you had individuals who are genetically one thing but socially another, you might be able to tease it apart, but that is generally not the case.
In our paper, we tried to show that a trait can appear to have high "genetic heritability" in any particular population, but the explanation for a group difference for that trait could be either entirely genetic or entirely environmental or some combination in between.
So, in my view, at this point, any comment about the etiology of group differences, for "intelligence" or anything else, in the absence of specific identified genes (or environmental factors, for that matter), is speculation.