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The great pruning, and the great synthesis

Gene Expression
By Razib Khan
May 9, 2012 9:11 AMNov 19, 2019 10:02 PM


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Sahul 10,000 years ago

John Hawks has a very long rumination

on the story of blonde Melanesians

which came out last week. If I can read between the lines I think some of the implications dovetail with John's thesis in his 2007 paper on adaptive acceleration

. But I'll leave the deep reading of tea leaves to those better versed in such affairs. Rather, I will comment on two issues. The first is specific. I believe that the TYRP1 R93C allele responsible for blonde hair among the Solomon Islanders is going to be found to be the same one responsible for blonde hair around New Guinea

and among some Australian Aboriginals

. There are several reasons why I suspect this. First, these Oceanian populations do seem to be a distinctive clade. There are some disagreements among geneticists as to whether they are the descendants of the first settlers of Oceania in totality, or whether they're a compound lineage

. The natural historical details need to be teased apart, but there's no doubt that they're a distinct and separate phylogenetic lineage in relation to other human populations (with some admixture from Austronesians in the case of Melanesians). Second, the phenotype of rather light hair, and dark skin, is striking and parallel among all these populations. It is not entirely impossible that random genetic drift could stumble upon an architecture which results in such a suite of characteristics, but I'm generally skeptical of this possibility of having occurred several times in the same human lineage, when it seems relatively rare in other populations (the loci associated with light eyes and light hair in Eurasians seem to have some effect on skin color as well, so it is difficult, though not impossible, to have  very dark skin and light hair). Third, as noted in John's post, this seems an "old" variant. A new mutation which rose rapidly in frequency should have a lot of associated markers flanking it (ergo, high linkage disequilibrium). Again, we need to take into account the joint information here; there seem several Oceanian populations where the allele is at high, but still minor, frequency (assuming it is the same allele). Oceanian populations, especially those verging toward Melanesia, have low effective population sizes. If this is an old variant I am curious as to why it has not fixed in any of the daughter populations (recall that if it did fix, and admixture recently drove it below ~100 percent, there would be a lot of linkage disequilibrium). Therefore, I think we have to seriously consider the possibility that balancing selection is maintaining this polymorphism in the Oceanian populations. This does not entail that the selection is targeting the hair color phenotype, though it may. In his post John Hawks seems to suggest that ancient variation in pigmentation, phenotypic and genotypic, may be somewhat different from what was the norm in Eurasia over the past 10,000 years. Rather than focusing on this issue, I will rather put forward a proposition of only moderate boldness, and lay out my own suspicion of what the next few years will tell us about the human past. First, let us set the stage. Between 100,000 and 15,000 years ago modern humans spread out across the world, to every continent where they reside today. There were several "touch & go" moments. The Toba

event may have been one, and the Last Glacial Maximum

perhaps another. Human populations waxed & waned. Because of low densities, and resultant barriers to gene flow, many of the deep phylogenies evident in the mtDNA and Y chromosomal record date to this period. It does not seem that modern human expanded rapidly from one or two populations ~15,000 years ago. Mitochondrial Eve tells us that is not so. As I have stated before the "state of the art" in 2005 would have ended with this story. By about ~15,000 years ago, as Amerindians reached the precipice of the New World, pre-Columbian patterns of genetic variation were settling in. I do not believe that this story holds up. It does not seem to accurately describe how the 20 percent of the world's population which is South Asian came to be

. More precisely, there was always a peculiar discordance in the uniparental lineages for South Asians; the maternal line was closer to East Eurasians, the paternal close to West Eurasians. The autosomal data, which looked at the whole genome, indicated a moderately closer affinity to West Eurasians, though as a function of geography (northwest to southeast) and caste (high to low). These conundrums are solved by a recent admixture of >10,000 years before past. But it is not simply the existence of particular sets of humans. The patterns of genetic variation in Africa today are very new, and owe little to the Last Glacial Maximum. Rather, it seems that the Bantu expansion wiped clean much of Sub-Saharan Africa of pre-existent variation. The Khoisan, Pygmies, and Hadza being the remnants of vast numbers of pre-Bantu populations, which seem to have had marginal effect on the genetics of East African Bantus. The two cases above illustrate dual dynamics which I believe shaped the nature of modern human genetic variation in the early Holocene: the great pruning and the great synthesis. The great pruning consists of the marginalization and assimilation of vast amounts of cultural diversity, and perhaps genetic diversity as well. It seems likely that the Pygmies and Khoisan have archaic admixture not found in other Africans, while Oceanians have archaic admixture not found in other humans. If it were not for geography, and the practice of horticulture, the populations of Near Oceania may have suffered the fate of the Negritos of Malaysia and the Philippines. But speaking of Negritos, the Andaman Islanders, and South Asians, illustrate the second aspect: the great synthesis. South Asians are a compound in part descended from the cousins of the Andaman Islanders. In The First Farmers

Peter Bellwood lays out an elegant model of demic diffusion from core agriculture hearths, which explains the modern linguistic and genetic patterns we see around us. As an extreme null hypothesis it is useful, but I think we need to be cautious about taking a stylized fact too literally. Bellwood's thesis came close to positing ancient agricultural apartheid. But mtDNA remains imply strongly that women of local lineages were absorbed into expanding populations (a result which is eminently plausible given historic patterns). Racial purity

has never been high on the list of human male "to-do's." There is a moderate probability that within the next few years other Eurasian populations will be seen to be similar to South Asians in their origin: products of a dialectic between the conqueror and the conquered, between the intruder and the indigene. Finally, in the shadows, and poorly understood from what I can glean, is the third dynamic which comes to the fore in the receding tide of the action of the great pruning and synthesis: the sons of the soil who manage to dodge the fate of being pruned from the human tree by finding a different strategy of survival

. Obviously this is not the whole story. The Columbian Exchange

is one chapter, which post-dates the prehistoric prunes and synthesis, though it echoes them in many ways. The expansion of the Han Chinese is another story which post-dates the period to which I allude. But these stories are known and counted. What I am suggesting here is that in the near future dynamics only faintly recollected will begin to move to out of the shadows, because they have left an imprint in our genes.

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