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Angela
18-03-16, 22:15
Human adaptation and population differentiation in the light of ancient genomes

See:
http://www.nature.com/ncomms/2016/160318/ncomms10775/full/ncomms10775.html

The supplement:
http://www.nature.com/ncomms/2016/160318/ncomms10775/full/ncomms10775.html#supplementary-information

"The influence of positive selection sweeps in human evolution is increasingly debated, although our ability to detect them is hampered by inherent uncertainties in the timing of past events. Ancient genomes provide snapshots of allele frequencies in the past and can help address this question. We combine modern and ancient genomic data in a simple statistic (DAnc) to time allele frequency changes, and investigate the role of drift and adaptation in population differentiation. Only 30% of the most strongly differentiated alleles between Africans and Eurasians changed in frequency during the colonization of Eurasia, but in Europe these alleles are enriched in genic and putatively functional alleles to an extent only compatible with local adaptation. Adaptive alleles—especially those associated with pigmentation—are mostly of hunter-gatherer origin, although lactose persistence arose in a haplotype present in farmers. These results provide evidence for a role of local adaptation in human population differentiation."

I've only skimmed the paper and the supplement, but from what I can see their argument is not based on finding the linked snps to these adaptations in any of the ancient samples, but to finding background haplotypes that might have given rise to these snps.

The ancient genomes they examined were Loschbour, Stuttgart, and Ust-Ishim.

It certainly makes sense that a background haplotype for digestion of animal milk might be present in farmers, and that one for lighter skin might be present in people from more northern latitudes (SLC45A2). That doesn't explain why the actual derived version is present in Anatolian farmers, if not specifically in Stuttgart.

There's also the East Asian light skin alleles to explain. The authors maintain that they can't pick up a signal of selection for them because there has been more drift among East Asians. I have to reread that section.

7645

Tomenable
20-03-16, 17:15
and that one for lighter skin might be present in people from more northern latitudes (SLC45A2). That doesn't explain why the actual derived version is present in Anatolian farmers

I've suggested this before, pointing specifically to Eastern HGs (EHG) as those largely responsible for spreading SLC45A2 derived allele.

As for how did it get to Anatolia:

Analysis of uniparental markers shows that there was either gene flow between EHG and Anatolia, or some shared common ancestry.

Y-DNA haplogroup J and mtDNA haplogroup H were present - albeit at low frequencies - both in Russian EHG and in Anatolian ENF.

Y-DNA haplogroup R1 - surely common among EHG - could also be present in Anatolian ENF, in the form of R1b1c-V88 subclade.

As for how did it get to SHGs:

SHG were basically a mixture between WHGs and EHGs, so they were lighter-pigmented than WHG, but darker than EHG.

Tomenable
20-03-16, 17:34
As for Lactase Persistence - there is no evidence of LP in people of Yamnaya culture - see this article by Mathieson:

http://mathii.github.io/review/2015/06/14/lactase-persistence-and-ancient-dna

On the other hand, it was present (green) in Battle Axe, Corded Ware, Kyjatice, Bell Beaker and Srubnaya cultures:

http://mathii.github.io/assets/images/LCT_imputation_results%20v8.png

Northern_LNBA = Battle Axe
Central_LNBA = Corded Ware
Hungary_BA = Kyjatice culture

All of those cultures (including CWC) were apparently admixed by an EEF or EEF-like population, unlike Yamna folks:


We didn’t find any evidence for LP in early farming populations like the LBK, or in early Bronze age steppe populations like the Yamnaya. In as-yet unreported data, we find a few copies of the allele in the Srubnaya - a later steppe population who seem to have some European Farmer-like ancestry.
Srubnaya was related to Sintashta, and both were EEF-admixed:

https://en.wikipedia.org/wiki/Sintashta_culture#Genetics

https://en.wikipedia.org/wiki/Srubna_culture


Allentoft et al. (2015) also found close autosomal (https://en.wikipedia.org/wiki/AuDNA) genetic relationship between peoples of Corded Ware culture (https://en.wikipedia.org/wiki/Corded_Ware_culture) and Sintashta culture:


The close affinity we observe between peoples of Corded Ware and Sintashta cultures [...] suggests similar genetic sources of the two, which contrasts with previous hypotheses placing the origin of Sintashta in Asia or the Middle East. Although we cannot formally test whether the Sintashta derives directly from an eastward migration of Corded Ware peoples or if they share common ancestry with an earlier steppe population, the presence of European Neolithic farmer ancestry in both the Corded Ware and the Sintashta, combined with the absence of Neolithic farmer ancestry in the earlier Yamnaya (https://en.wikipedia.org/wiki/Yamna_culture), would suggest the former being more probable.[14] (https://en.wikipedia.org/wiki/Sintashta_culture#cite_note-Allentoft_.26_Sikora-14)

Tomenable
20-03-16, 18:50
It certainly makes sense that a background haplotype for digestion of animal milk might be present in farmers

One thing to remember is that mutations emerge by pure chance - not when someone needs them. It's not like I domesticate a cow and suddenly as a "reward" for my feat ("subduing a beast"), I get a mutation allowing me to drink milk. These things are unrelated. Lactase persistence could as well first emerge in hunters, but it was not going to be useful for them because they didn't have milk.

LP mutation could predate domestication of animals, but it became useful only after milk became available to humans.

And probably this is why selection sweep of LP mutation happened only after people with LP acquired cows/goats/horses.

Angela
21-03-16, 00:53
My point was perhaps poorly worded, but I do understand how evolution works. I've certainly tried to explain it often enough on this Board including the fact that selection, both natural and societal, works on mutations that arise haphazardly. Let's say that the existence of the background haplotype for LP in people who would go on to domesticate animals and use their milk seems almost providential. As to your other point about it, if you're going to accept the genetic and statistical analysis of these authors for their conclusion that the background haplotype for SLC42A5 appears in WHG, I don't really see how you can argue that the background haplotype for LP isn't found in "farmers" (but not in WHG). That wouldn't be very consistent, would it?

I'm a bit frustrated both with this paper and the prior Mathiesen et al one. Both come from people from the Reich Lab and yet the difference in terms of the clarity of presentation of the data and and even more of the writing from the Lazaridis and Haak papers is pretty big. I don't know if it's because of less command of English writing skills or if it's because they know a lot more than they're willing to tell us right now.

It's not that I think that the background haplotype for the SLC42A5 mutation couldn't have been present in the EHG, because I don't see any reason why it couldn't. It's just that these authors have at their fingertips the EHG genomes and the Anatolian Neolithic genomes. They know more than anyone that both of these populations did possess the derived alleles for this snp, so why wouldn't they have checked them to see if they possessed the "background haplotype"? I think they must have done it, which is why I don't understand why they didn't say so.

I don't know, maybe they have other older genomes and the earliest appearance of the "background" haplotype is in some WHG related population which may have fed into both some Anatolian farmers and their descendants (although it doesn't appear in Stuttgart) and EHG? Or perhaps they're now able to more successfully model EHG as WHG plus some ANE?I really don't know and I don't see how it much matters. I'm sure they'll let us know eventually.

What we do know is that at a time when derived SLC42A5 was appearing spottily in western Eurasia, all the Anatolian farmers were already derived for SLC 24A5. (Someone should check but I don't think all the SHG were derived for it, not that I think we know for certain that they actually contributed to modern Europeans anyway. I do think the 3 EHG were derived for it.) That may indicate that SLC24A5 derived occurred first or at least spread to fixation first. (CHG already had it as well and is very old.) WHG didn't have it.

SLC42A5 derived seems to have occurred later or at least definitely swept to fixation later. One of the most interesting questions for me is why? What caused the sweep to happen when it did? Also, why does the derived allele for that snp show up in Anatolian farmers and the EHG but not in the WHG whom the study authors maintain are the population in which the background haplotype first appeared? Indeed, why do the WHG not even have the derived allele for SLC24A5 to any real degree? As I've pointed out before, the EEF seem to have gotten "darker", to put it into colloquial terms, when they got to Europe and mingled with the WHG. If the Anatolian farmers had the derived SLC42A5 (as they do), but the EHG didn't, one could speculate that it did indeed have something to do with the new diet adopted after the change to agriculture causing selection on a new mutation on this background haplotype, a mutation that occurred in people in Anatolia with a bit of WHG like ancestry, but not in the WHG themselves. As it stands, I honestly don't know.

I do find the fact that a snp can sweep to fixation so relatively quickly when it is advantageous for some reason to be absolutely fascinating.

I guess we'll have to wait until some more of the Reich Lab's post doctoral fellows (and those of other labs) have gotten a chance to publish.

Greying Wanderer
21-03-16, 11:11
@Angela

Yes the fact there are two alleles with similar effects (at least on the surface) but seem to have taken very different paths is an interesting mystery.

If it is the case and allele SLC45A2 (i think? for some reason i constantly mix up the labels) wasn't just another northern depigmentation gene then you might think it's primary effect was something else and the depigmentation was a secondary effect.