Surprising Pale pigmentation in Mesolithic Motala HGs

[Augustus]

It's a source, but not THE source. The main specific mutation that causes light skin in Europeans is found all throughout Europe and Asia, and correlates with farming. The farmers in central Europe already have confirmed light skin.




North Western Europeans must have mutations from both farmers and HGs. A bit like someone having 2 separate pigment mutations from both Caucasian and East Asian parents.

[DMXX]

As alan was saying, the sample size is quite small. When it comes to population genetics (especially Y-DNA and mtDNA analysis), I've gravitated towards an arbitrary sample size of at least 50. Now we have a qualitative feel for the findings (HG's had various light pigmentation alleles, a lot of them were homozygous for these, different allele frequencies are found in different groups etc.), more ancient genomes are required to flesh out the quantitative side.

One notable finding in the results is that, for rs4988235 (@MCM6-LCT), which appears to be the primary locus responsible for lactose tolerance in various European (also South Asian to a lesser degree) populations, most of these samples are homozygous for the ancestral variant (GG, thus likely lactose intolerant). That includes the three Samara Yamnaya samples showcased in his table. The only samples with a heterozygous status were Bell Beaker LN I0112 and Unetice EBA I0164. The samples genetiker showcased were all likely lactose intolerant at another influential locus (rs182549 @ MCM6).

This raises several possibilities. For starters, the low sample size likely confounding interpretations. The derived A/T allele at rs4988235 may well have been present in a different part of Yamnaya. Additionally, it may have quickly been selected for at a time after the 3200-2700 B.C. interval in Yamnaya-descended/influenced cultures.

[Augustus]

If Samara had light/yellow hair, and Andronovo samples had some, while Karelia is brown, I wonder if this trait came from across the Urals in Asia.

[DMXX]

Whatever the process, skin tone is today closely related to sunlight in the area. Seems too neat a fit for selection not to be involved. IMO red hair is so closely linked with superfair skin in northern Europe they must be linked genetically somehow.

That's been my suspicion for a while; SLC24A5 is found all over West Eurasia, but MC1R derived mutations seem more prominent the further one goes north or northwest in Eurasia. The distribution pattern of mutations on those genes alone could very well explain the commonality of fair skin in places like West or Central Asia and "superfair" skin in North Europe (South Europe is probably an intermediary between the two). MC1R fits the bill quite well given mutations within the gene cause depigmentation through decreased melanocyte activity.

[Krefter]

Genetiker added the Data for the Spanish Neolithic & Yamnaya genomes. Looks like they were a darker bunch comared to the HGs (both groups negative for all de-pigmentation genes except some instances of SLC24A5). Looks like the implication is that the de-pigmentation genes common in Europeans came from HGs.

Have you already forgotten about LBK_EN, Gok2, and Neolithic Hungarians?

[jeanL]

It's a source, but not THE source. The main specific mutation that causes light skin in Europeans is found all throughout Europe and Asia, and correlates with farming. The farmers in central Europe already have confirmed light skin.




North Western Europeans must have mutations from both farmers and HGs. A bit like someone having 2 separate pigment mutations from both Caucasian and East Asian parents.

That's not what the data is showing. Firstly the map above shows the distribution of rs1426654, which if you look at the map below is found at 100% frequency in populations that aren't fair as a whole:



Before when we only had La Braña, and Loschbour being ancestral while Stuttgart was derived, it did appear that the mutation had been brought over by farmers from the Near East. Then Motala12 appeared to be derived for the mutation, and KO1 also appeared heterozygous for the mutation. Now we have plenty of farmers and Hunter Gatherers and this is what they look like:

SLC24A5, rs1426654, Caucasoid light skin

Hunter Gatherers:

SHG:

Motala HG I0012 AA
Motala HG I0014 AA
Motala HG I0015 GG
Motala HG I0016 GA
Motala HG I0017 AA

EHG:

Karelia HG I0061 AA
Samara HG I0124 AA

Early Farmers:

LBK EN I0025 GG
LBK EN I0026 AA
LBK EN I0046 AA
LBK EN I0054 AA
LBK EN I0056 AA
LBK EN I0057 AA
LBK EN I0100 AA
Spain EN I0410 AA
Spain EN I0412 AA
Spain EN I0413 AA
Starcevo EN I0174 AA

As you can see the mutation is found in both Hunter Gatherers and Farmers, and while it is nearly fixed in farmers, the ancestral state is still found in some farmers(i.e.LBK_EN I0025 ). We don't have any ancient DNA from the Near East to know whether these people carried the mutation or not, nor do we have Ancient DNA from Hunter Gatherers in Southeast Europe where Early Neolithic farmers could have acquired their Hunter Gatherer admixture from. We have KO1 a farmer who looked Hunter Gatherer genetically and he was heterozygous in that mutation. If we assume that AG2 derived state at rs1426654 is not the result of contamination/misreading, then it would appear that the mutation was at least present in Central Asia circa 17,000 ybp, which means that the mutation could have spread with ANE/EHG/SHG carriers. If the mutation is found in Pre-Indo European Near Easterners then perhaps the mutation was widespread and spread both with EHG and farmers, but if it is absent then perhaps the Indo-Europeans are responsible for spreading the mutations in Asia and the Near East.

As for the other mutation rs16891982, here is its distribution:



This mutation is more exclusive to Europeans, and here it is said that having the ancestral state in Europeans translates into having 7x the odds of having dark/black hair, and possibly olive skin. Here is the distribution in ancient samples La Braña, Loschbour and Stuttgart were all ancestral for it at C/C.

Hunter Gatherers:

SHG:

StoraForva11 GG
Motala HG I0011 GG
Motala HG I0012 GG
Motala HG I0013 CC
Motala HG I0014 GC
Motala HG I0015 GG
Motala HG I0016 GG
Motala HG I0017 GG

EHG:

Karelia HG I0061 GC
Samara HG I0124 GG

Early Farmers:

Spain EN I0410 CC
Spain EN I0412 CC
Spain EN I0413 GC
LBK EN I0025 CC
LBK EN I0026 GC
LBK EN I0046 CC
LBK EN I0048 GG
LBK EN I0054 CC
LBK EN I0056 CC
LBK EN I0100 GG

In here we see an interesting pattern, namely that Hunter Gatherers were for the most part derived whereas Early Neolithic farmers were ancestral, thus it is very likely that this mutation arose in European Hunter Gatherers. Now as other have warned the samples sizes are incredibly small, and we are lacking vital ancient DNA from important parts to draw strong conclusions, but what is clear is that a good portion of Scandinavian Hunter Gatherers and also Eastern Hunter Gatherers not only had fair European skin, but were probably blonde and red haired, and that all of them had light eyes.

[Augustus]

As you can see the mutation is found in both Hunter Gatherers and Farmers, and while it is nearly fixed in farmers, the ancestral state is still found in some farmers(i.e.LBK_EN I0025 ). We don't have any ancient DNA from the Near East to know whether these people carried the mutation or not, nor do we have Ancient DNA from Hunter Gatherers in Southeast Europe where Early Neolithic farmers could have acquired their Hunter Gatherer admixture from. We have KO1 a farmer who looked Hunter Gatherer genetically and he was heterozygous in that mutation. If we assume that AG2 derived state at rs1426654 is not the result of contamination/misreading, then it would appear that the mutation was at least present in Central Asia circa 17,000 ybp, which means that the mutation could have spread with ANE/EHG/SHG carriers. If the mutation is found in Pre-Indo European Near Easterners then perhaps the mutation was widespread and spread both with EHG and farmers, but if it is absent then perhaps the Indo-Europeans are responsible for spreading the mutations in Asia and the Near East.

My main proposition is that there isn't simply 1 source for this mutation. I disagree with the possibility that it was spread mainly by IEs. The mutation go way beyond the reaches of IE migrations, and it is heavily centered around the middle east. Some Arabic speaking populations have higher concentrations of it than IE speakers. Also, Northern European populations have more than 1 type of pigment mutation, as some share the Siberian and East Asian pigmentations as well if I'm not mistaken.

Your proposition that the Early Neolithic farmers picked it up from hunter gatherers in SE is very suspect as well. Unless HG in SE had nothing in common autosomally with La brana and Loschbour, this is not the case. As shown by the stutgart samples.

[parasar]

My main proposition is that there isn't simply 1 source for this mutation. I disagree with the possibility that it was spread mainly by IEs. The mutation go way beyond the reaches of IE migrations, and it is heavily centered around the middle east. Some Arabic speaking populations have higher concentrations of it than IE speakers. Also, Northern European populations have more than 1 type of pigment mutation, as some share the Siberian and East Asian pigmentations as well if I'm not mistaken.

Your proposition that the Early Neolithic farmers picked it up from hunter gatherers in SE is very suspect as well. Unless HG in SE had nothing in common autosomally with La brana and Loschbour, this is not the case. As shown by the stutgart samples.

If you are referring to SLC24A5 A, then there is most likely one source for the mutation as the paper from which the figure you posted notes.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820762/
"SLC24A5 in Identity by Descent ... We conclude that all of the 73 phased chromosomes (from Europe, sub-Saharan Africa, Middle East, South Asia, North and Central Asia) with the rs1426654-A allele form a monophyletic group because they share the same haplotype background regardless of their geographic origin. In other words, all carriers of the mutation in our global sample share it by descent."


But SLC24A5 A does not relate to lighter skin much (unlike SLC45A2). About half of Lankan Singhalese have SLC24A5 A, and they are a relatively dark skinned population.
"we generate new allelic data for these two genes from samples of Chinese, Uygurs, Ghanaians, South African Xhosa, South African Europeans, and Sri Lankans (Tamils and Sinhalese). Our data confirm the earlier results and furthermore demonstrate that the SLC45A2 allele is a more specific AIM than the SLC24A5 allele because the former clearly distinguishes the Sri Lankans from the Europeans."
http://www.ncbi.nlm.nih.gov/pubmed/16847698

[Motzart]

Here is a map of the HERC2 gene for blue eyes that the Motala samples & Samara are homozygous for. I think this one is a pretty safe bet for Paleolithic Europe as it shows up in La Brana and Loschbour too.

http://dienekes.blogspot.ca/2008/01/...olor-news.html

SLC24A5/A2 must have arisen some time in the Late Paleolithic given that it appears to have a significant distribution in the Mesolithic and that it is absent in Kotenski/Mal'ta Boy/Ust-Ishim, as to where... who knows. I have always thought it bears a similar distribution to mtDNA H. In my male mind it makes more sense that the Men would be selecting the Women for the phenotypic alleles rather than vice versa, except perhaps in the case of those Scythian Amazon women. This could probably explain the HERC2 distribution too.

here are Genetiker's pigmentation calls for Ust-Ishim and Kotenski

https://genetiker.wordpress.com/2014...-ishim-genome/

https://genetiker.wordpress.com/2014...nki-14-genome/

[Krefter]

Here are two links showing rs12913832 calls in modern pops. Note that all Bell beaker and Corded ware, and most other LN/BA individuals tested for this SNP have at least one A allele meaning they were brown or intermediate eyed.

http://browser.1000genomes.org/Homo_sapiens/Variation/Population?db=core;r=15:28365118-28366118;v=rs12913832;vdb=variation;vf=9124585

https://genetiker.wordpress.com/2013/06/01/frequencies-for-blue-eyes-snp-rs12913832-in-hgdp-populations/