Skin/Eye/Hair Pigmentation of Indo-Aryans and their Ancestors.

[VishwamitraSunuh]

Hello, I want to understand why Indo-Aryans despite being from North East Europe and Corded ware were Darker in pigmentation while later Sintasta and Andronovo were supposed to be lighter ?


I am quoting Genetiker as it seems he is the only guy who's deceleration of pigmentation of ancient and Modern Population is Online.
https://genetiker.wordpress.com/pigmentation/

the Chain of Migration starts from Yamnaya culture who were as we know it Swarthy tall people from modern day ukraine. the 2nd Stage comes at Corded Ware culture who were mixture of Yamnaya with Majority blonde and Blue eyed population of Gobular culture yet i was surprised to see that Corded Ware culture's samples are overwhelmingly Dark haired and eyed.

according to Genetiker out of 17 samples only 3 had blond and dark blond hair and only 2 had light eyes. maybe this is the result of higher 75% Yamnaya like ancestry?

but, Fatyanovo, an offshoot of CWC culture had 21% blue eyes and similar number of people with light hairs according to Razib.
https://www.brownpundits.com/2020/07...of-the-aryans/

we see the Similar Results at Poltavka and Abashevo culture as all Poltavka samples have Dark hair and eyes and Abashevo provides 10 samples and out of those 10 only one wad blond/dark blond and light eyed.

his calling for Sintasta and Andronovo is simlar as well as out of 2 samples one is Dark and another one is Dark blond/Brown and have brown eyes, Andronovos have 4 samples out of which only one is light haired and eyed rest being dark pigmented.

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from the above sampling we see that even though Fatyanovo(Pre-Proto-Aryan) and Sintasta(Proto-Aryan) are claimed by others as having at lest 25% blue eyed, we see that population in between had very low number of those features, what is the reason behind this ?

is it safe to assume that they maintained same frequency of those features even after they migrated into Central Asia ?

please let me know what you think.

[VishwamitraSunuh]

also, we have mention of Aryas calling non-Aryans as Dark, red eyed people with flat noses and curly hairs but they didn't describe themselves themselves as having blond hair or light eyes but they called themselves White or Fair so those blond features were long gone by the time they Migrated into India, main Rigvedic gods such as Agni, Shiva, Vishnu are called White as Moon and Camphor with Black hairs. Brahmins with Black hair etc in Vedas and (post vedic literature).

maybe because of mixing with Central Asian population and Indus Neolithic Populations they lose those features but as their Contribution was still 50% to 70% Sintasta like i assume they still probably Resumed Fatyanovo who were ancestors of Sintasta with same Dark Hair/Eye Pigmentation chain.

[Kulin]

To quote, we simply do not know. However, it is certain that the populations that migrated to Central Asia, and subsequently to South/West Asia were significantly darker than their earlier CWC counterparts, as well as sister populations. The % of light eyes nor hair can however not be determined with certainty but looking at pigmentation alleles this is the case, as is indicated by people like Razib. There was also a latter selection event in Europe, that increased the frequency of light eyes/hair (as well as traits like lactose tolerance), though the magnitude of change is unknown or debatable.

[ThaYamamoto]

Could it possibly have something to do with WSHG ancestry?

[cardinale389]

I don't think you can compare ancient populations to modern groups. Ancient people are always darker than their modern counterparts.

[pmokeefe]

The evolution of skin pigmentation associated variation in West Eurasia
Dan Ju, Iain Mathieson
Significance
Some of the genes responsible for the evolution of light skin pigmentation in Europeans show signals of positive selection in present-day populations. Recently, genome-wide association studies have highlighted the highly polygenic nature of skin pigmentation. It is unclear whether selection has operated on all of these genetic variants or just a subset. By studying variation in over a thousand ancient genomes from West Eurasia covering 40,000 y, we are able to study both the aggregate behavior of pigmentation-associated variants and the evolutionary history of individual variants. We find that the evolution of light skin pigmentation in Europeans was driven by frequency changes in a relatively small fraction of the genetic variants that are associated with variation in the trait today.

Abstract
Skin pigmentation is a classic example of a polygenic trait that has experienced directional selection in humans. Genome-wide association studies have identified well over a hundred pigmentation-associated loci, and genomic scans in present-day and ancient populations have identified selective sweeps for a small number of light pigmentation-associated alleles in Europeans. It is unclear whether selection has operated on all of the genetic variation associated with skin pigmentation as opposed to just a small number of large-effect variants. Here, we address this question using ancient DNA from 1,158 individuals from West Eurasia covering a period of 40,000 y combined with genome-wide association summary statistics from the UK Biobank. We find a robust signal of directional selection in ancient West Eurasians on 170 skin pigmentation-associated variants ascertained in the UK Biobank. However, we also show that this signal is driven by a limited number of large-effect variants. Consistent with this observation, we find that a polygenic selection test in present-day populations fails to detect selection with the full set of variants. Our data allow us to disentangle the effects of admixture and selection. Most notably, a large-effect variant at SLC24A5 was introduced to Western Europe by migrations of Neolithic farming populations but continued to be under selection post-admixture. This study shows that the response to selection for light skin pigmentation in West Eurasia was driven by a relatively small proportion of the variants that are associated with present-day phenotypic variation.

Here's another fairly recent review (paywalled, unfortunately):
The Evolutionary History of Human Skin Pigmentation
Jorge Rocha
PMID: 31363820 DOI: 10.1007/s00239-019-09902-7
Abstract
Skin pigmentation is a complex, conspicuous, highly variable human trait that exhibits a remarkable correlation with latitude. The evolutionary history and genetic basis of skin color variation has been the subject of intense research in the last years. This article reviews the major hypotheses explaining skin color diversity and explores the implications of recent findings about the genes associated with skin pigmentation for understanding the evolutionary forces that have shaped the current patterns of skin color variation. A major aspect of these findings is that the genetic basis of skin color is less simple than previously thought and that geographic variation in skin pigmentation was influenced by the concerted action of different types of natural selection, rather than just by selective sweeps in a few key genes.

The Rocha paper is more focussed on the inter-continental level, as opposed to the the intra-Eurasian theme of the OP.
rocha2019.jpg
Fig. 4 Allele frequencies at 5 genes/SNPs associated with skin color
variation exemplifying the variety of selection patterns underlying
skin pigmentation differences across populations: parallel shifts
in allele frequencies from standing variation (HERC2/rs6497271);
selective sweeps in proto-Eurasians (KITLG/rs642742); selection on
standing variation in proto-Eurasians (DDB1/rs11230664); selective
sweeps in Europeans (SLC24A5/rs1426654), and selective sweeps
in Asians (OCA2/rs1800414). a = Botswana Khoisan; b = West Africans;
c = East Africans; d = Australo-Melanesians; e = East Asians;
f = Europeans. Alleles associated with darker skin are shown in black

Also, here's an old thread about skin pigmentation:
https://anthrogenica.com/showthread....-of-human-skin

My sense from a quick scan of the literature on modern skin pigmentation genetics is that it is still a area of active research. Inferences about ancient populations may be challenging. What might be more tractable is to focus on specific alleles known to be correlated with pigmentation phenotypes, instead of trying to infer ancient phenotypes per se?

[DMXX]

My sense from a quick scan of the literature on modern skin pigmentation genetics is that it is still a area of active research.

This is the take-home message.

Phenotype's a combination of genotype, environment and time. The selective pressures affecting pigmentation may be both direct and indirect. The vitamin D-health-latitude pressure is an example of the direct. For indirect, that's an open question - It may emerge in the future that the up-regulation of promoter or silencer areas of the genome through other factors (e.g. exposure to heavy metals).

The Scytho-Siberians were, from memory, predominantly light-eyed and light-haired (~60%). So, as Kulin suggests, it may be the case that, by the Iron Age, those populations residing in latitudes comparable to (or above) the Abashevo-Sintashta-Petrovka area continued to be subject to the same selective pressures that had affected them (in comparison to Yamnaya-Khvalynsk-Repin).

Certainty (or, at least, a reasonable truncation of the possibilities) will only arrive once a sufficient number of Sintashta-Petrovka samples and the entirety of the Andronovo archaeological horizon is sampled.

It may emerge, for instance, that the n=17 Sintashtans that Razib had analysed just so happened to be slightly darker-pigmented than the actual cohort from 2200-2000 B.C.
It may well be the case that, even within Sintashta, the early founders (~2200 B.C.) were darker-pigmented than those who'd branched off to form Federovo/Alakul (i.e. Andronovo).

We're dealing with fairly low density population clusters in this discussion, so genetic drift could've well occurred in an irregular manner throughout their spatiotemporal expansion into Asia.

I personally don't have any opinion on this topic - Insufficient data to wed one's self to any particular idea.

[Alain]

I think the early Indo-Aryans had a skin tone similar to today's Tatars or Romanians, as far as the hair is concerned, I think there were also blonde individuals but also light eyes such as blue / green / gray and gradations and of course brown eyes and also dark hair . See today's populations in South Central Asia at Kalash, Nuristani ... But of course as mentioned a lot of time has passed and we need more results from this period! And certainly when the early Indo-Aryans immigrated to the subcontinent, they mixed up with the local population, which also had a climatic aspect, a darker skin is an advantage in these latitudes and even early steppe people were never quite pale, but rather later by selection in northern Europe.

[pmokeefe]

The OP and and some of the other posts seem focussed on Steppe, Indo-Aryan contributions to pigmentation. However in the Mathieson article, focussed on Europe, it seems like there is also a significant signal from early farmer ancestry:

Most notably, a large-effect variant at SLC24A5 was introduced to Western Europe by migrations of Neolithic farming populations but continued to be under selection post-admixture. This study shows that the response to selection for light skin pigmentation in West Eurasia was driven by a relatively small proportion of the variants that are associated with present-day phenotypic variation.

...

Mesolithic hunter-gatherers carried fewer light pigmentation alleles than Early Farmer or Steppe ancestry populations. This difference (0.091 score units) was similar to the difference between Mesolithic hunter-gatherers and Early Upper Paleolithic populations (0.097 score units). We tested for evidence of change in score over time within groups while controlling for changes in ancestry, finding no significant change within hunter-gatherer or Early Farmer populations (P = 0.32; P = 0.29). Steppe ancestry populations, however, exhibited a significant decrease (P = 0.007), with a steeper slope than that of Early Farmer or hunter-gatherer (P = 0.004 and P = 0.08, respectively).

...

Few of the skin pigmentation loci show extreme PBS values (Fig. 3), and even fewer show evidence of divergent frequencies across ancient groups (SI Appendix, Fig. S10). On the Early Farmer and Steppe ancestry branches, but not the hunter-gatherer branch, the SLC24A5 locus exhibited the strongest signal (Fig. 3 B and C), indicating selection at the locus in both Early Farmer and Steppe source populations. The RABGAP1 locus also exhibited an elevated signal of selection in Early Farmer and Steppe, which remained when using a 40-SNP window size (SI Appendix, Fig. S11 B and C). In all three ancestry groups, we observed an elevated PBS at the OCA2 locus, with the most extreme value on the hunter-gatherer branch. However, unlike the SLC24A5 variant, neither of these SNPs (rs644490 and rs9920172) showed a substantial effect of ancestry from the individual SNP regression analysis. As a whole, the PBS values of the 170 skin pigmentation SNPs do not significantly deviate from the genome-wide distribution of PBS for any of the ancient source populations (SI Appendix, Fig. S12).

...

We find little evidence of parallel selection on independent haplotypes at skin pigmentation loci, suggesting that that differences in allele frequency across ancestry groups were mostly due to genetic drift. One exception is that the light allele at SLC24A5 was nearly fixed in both Early Farmer and Steppe ancestry populations due to selection. However, even for this variant we observe a signal of ongoing selection in our data even after admixture with hunter-gatherers, indicating continued selection after admixture. This is analogous to the rapid selection at the same locus for the light allele introduced via admixture into the KhoeSan, who now occupy southern Africa

...

In the ancient populations, we found an elevated PBS signal around rs9920172 that was most prominent in hunter-gatherers but also elevated in Early Farmer and Steppe ancestry populations (Fig. 3), suggesting a relatively early episode of selection in West Eurasians.

The Mathieson article is focussed on Europe, hopefully in the future we will see studies on this level for other regions including South Asia.

[Coldmountains]

To quote, we simply do not know. However, it is certain that the populations that migrated to Central Asia, and subsequently to South/West Asia were significantly darker than their earlier CWC counterparts, as well as sister populations. The % of light eyes nor hair can however not be determined with certainty but looking at pigmentation alleles this is the case, as is indicated by people like Razib. There was also a latter selection event in Europe, that increased the frequency of light eyes/hair (as well as traits like lactose tolerance), though the magnitude of change is unknown or debatable.

I am a bit sceptical about fully reconstructing phenotypes from ancient genotypes. In the recently Fatyanovo preprint Iron Age and Medieval Estonanians were predicted as having around 20% intermediate dark + black skin, what sounds at first unrealistic. I think we not fully understand how light phenotypes are and were coded in dna.

But we can for sure say that steppe Proto-Indo-Iranians had light phenotpes but signficantly less in frequency than modern day North Europeans who are in terms of overall genetic affinity (indirect affinity) the closest modern day population to them. How the share of these phenotypes was exactly and from where it arrived (GAC, Steppe, HGs...) can not be said for now without more reserch but it seems these kind of phenotypes were selected significantly in mixed EEF-HG cultures like GAC who had set of samples with a high share of predicted light phenotypes.