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Fire Haired14
13-10-15, 14:30
The focus among posters on Mathieson et al., "Eight thousand years of natural selection in Europe (http://www.biorxiv.org/content/early/2015/10/10/016477.abstract?%3Fcollection=)" has been the genetic-data it provides but the focus of the authors was Natural Selection. Most would consider the genetic-stuff is more interesting, but I have a feeling in the near future ancient DNA research will focus more so on Natural Selection. The Natural selection part of the study isn't difficult to get a basic understanding of at all.

I don't know how strong of an affect each SNP alone has on each trait considering most traits are probably polygenic(determined by many SNPs). But it is still kind of interesting. Many traits under selection in last 8,000 years only apply to someone who lived in a farming lifestyle and first appear with Neolithic farmers. So, Europeans literally adapted a farming. And some traits were under strong selection even in the last 4,000 years, especially lactose tolerance.

There's been a lot of Natural Selection after Yamnaya-types, WHG, EEF mixed with each other

The authors tested if if allele frequencies of 50,000 potentially functional SNPs correlates with ancient ancestry. So, they estimated Yamnaya/EEF/WHG ratios in a set of modern Europeans and allele frequencies in those modern Europeans and in Yamnaya/WHG/EEF. They found potentially functional SNPs don't correlate with ancestry at all, suggesting there's been a lot of Natural Selection going on after those ancient populations mixed with each other.

Polygenic selection on height
http://www.anthrogenica.com/attachment.php?attachmentid=6316&stc=1
They tested 169 SNPs associated with height were tested in ancients/moderns to test for selection of height. The results suggest genetic height in Europeans is a result of natural selection and ancestry. With the little data we have, it suggests short height was selected for in Neolithic Spain and then tall height was selected for in Spain after the Neolithic. Besides that genetic height is mostly due to ancestry. "Steppe" populations were tallest and NW Europeans(GBR, CEU) are intermediate between them and Neolithic Central Europeans.

Genome-wide scan? for SNPs under Natural Selection in last 8,000 years

Through a "scan" of entire genomes the authors found 12 SNPs that have likely been under Natural Selection in the last 8,000 years. I could never understand exactly how they did this. I think they tested the allele frequencies of every single potential functional SNP and checked if allele frequencies in ancient and modern pops showed signs natural selection. Anyways below is a Spreadsheet each of those SNPs by rank 1-12 according to strongest signal of selection and the allele frequencies in ancient/modern Europeans given by the paper. They didn't give allele frequencies for all SNPs and gave allele frequencies for other potentially functional SNPs.

Traits Under Natural Selection in the Last 8,000 years

Only SNPs in the top 7 for signal of selection were given a description of what their potential affect is on humans. Below is a list of those SNPs, a description of their potential affect(highlighted in yellow), and notes on their allele frequencies in moderns/ancients. Also, here's a spreadsheet of allele frequencies in moderns and ancients: Traits Under Natural Selection in the Last 8,000 years (https://docs.google.com/spreadsheets/d/1p-GLilVlQenm9PqdWwURXyer9-xIoeUCPp7M928Wlb0/edit#gid=1514154066).

1: rs4988235: Lactose Tolerance. First appears in Neolithic Spain, Germany, and Sweden(Got this information from sources outside this paper) but was only at modern-like frequencies in a site from Spain. First time a decent amount of the population has this trait is with LN/BA Central Europeans, but was much lower than it is today in most of Europe as recent as 4,000 years ago. Is documented at modern frequencies in Poland by at least the Early Iron age.
2: rs16891982: Pale skin. Existed in Mesolithic Sweden, Russia, and Neolithic Anatolia at relatively high frequency in circa 6000 BC. In circa 3000 BC was slightly higher in Steppe populations than in Neolithic Europe. First reached modern-like frequencies in LN/BA Central Europe in circa 2500 BC. LN/BA Central Europeans had a higher frequency than contemporary people in the "Steppe"(Catacomb), Spain, and Italy.
3: rs2269424: Resistance to leprosy, tuberculosis or other mycobacteria. No frequency data.
4: rs174546: Decreased triglyceride levels.Triglycerides are a type of fat. Unused calories are turned into triglycerides and stored in fat cells for later use. Hunter gatherers had the lowest frequency, Neolithic farmers and LN/BA Central Europeans had the highest, and "Steppe" had intermediate frequencies. Is almost twice as high in all moderns than any ancients, almost 1/3 of moderns have double-derived alleles.
5: rs4833103: Resistance to leprosy, tuberculosis or other mycobacteria. First appears in Neolithic farmers and was equally low among all non-hunter gatherers ancient populations. Is 3-fold higher in SW Europe today and 5-fold higher in NW Europe than in any ancients.
6: rs653178: Celiac disease. Immune response(defensive response) of your body towards gluten(a protein found in wheat, barley, and rye). Interesting none of the Hunter Gatherers had this trait. Neolithic farmers had the highest frequency. First appears in Neolithic farmers and was equally low among all non-hunter gatherers ancient populations. Is 5 to 4 times higher in moderns.
7: rs7944926: Circulating vitamin D levels. Derived allele was higher in all ancients than moderns. Deirved allele was 50%+ in all ancients and barely reaches 25% in moderns.
8: rs7119749: Pale skin. First appears at high frequency in Neolithic farmers, highest in "Steppe" populations. Derived allele was highest in Steppe-pops at ~46% and is 67%+ in moderns.

bicicleur
13-10-15, 15:25
I don't know how strong of an affect each SNP alone has on each trait considering most traits are probably polygenic(determined by many SNPs).

I'm sure this will become a very interesting field in the near future, but this is the reason I haven't studied it yet.
Soon there will come a point where I should join in.

Angela
13-10-15, 16:18
Great idea to separate it out, Fire-Haired. I'll try to study your chart later, but just off the cuff if one looks at the depigmentation snps the steppe levels other than for Sintashta/Andronovo, which is much later (almost 1000 years), and which has additional European farmer ancestry, the SLC42A5 level on the steppe was either lower or the same as the level in Anatolia before the farmers ever came over (depending on whose study you use).

That's extraordinary in itself. I did think, and argue, that the farmers in the Near East must have had derived SLC24A5, but I really didn't think they'd have derived SLC42A5.

It raises the question as to where it (and SLC24A5 for that matter) arose. It can't have been the WHG because they didn't have the derived versions. It can't have been the EHG per se because there's no EHG in the ancient Anatolia farmers. The same would go for the ANE. So, it's a puzzle.

My best guess for the moment is that the early paper that saw it radiating somehow from the region of the greater Caucasus may have been onto something. It looks like it had to be after the WHG like hunter-gatherers left for Europe, however, so that imposes a kind of time restraint.

holderlin
13-10-15, 21:21
6: rs653178: Celiac disease. Immune response(defensive response) of your body towards gluten(a protein found in wheat, barley, and rye). Interesting none of the Hunter Gatherers had this trait. Neolithic farmers had the highest frequency. First appears in Neolithic farmers and was equally low among all non-hunter gatherers ancient populations. Is 5 to 4 times higher in moderns.


This is counter intuitive. It looks like Celiacs, IBS, and colitis susceptibility are hitchhiker effects from higher priority selection for alleles better suited for the agricultural diet. So on average a population will live better on a farming diet, but certain individuals will be unlucky and it will suck. The complexity of biological systems never cease to amaze.

Fire Haired14
14-10-15, 03:14
Great idea to separate it out, Fire-Haired. I'll try to study your chart later, but just off the cuff if one looks at the depigmentation snps the steppe levels other than for Sintashta/Andronovo, which is much later (almost 1000 years), and which has additional European farmer ancestry, the SLC42A5 level on the steppe was either lower or the same as the level in Anatolia before the farmers ever came over (depending on whose study you use).

That's extraordinary in itself. I did think, and argue, that the farmers in the Near East must have had derived SLC24A5, but I really didn't think they'd have derived SLC42A5.

It raises the question as to where it (and SLC24A5 for that matter) arose. It can't have been the WHG because they didn't have the derived versions. It can't have been the EHG per se because there's no EHG in the ancient Anatolia farmers. The same would go for the ANE. So, it's a puzzle.

My best guess for the moment is that the early paper that saw it radiating somehow from the region of the greater Caucasus may have been onto something. It looks like it had to be after the WHG like hunter-gatherers left for Europe, however, so that imposes a kind of time restraint.

I wasn't surprised by Anatolian results. They had basically the same results as Neolithic Central Europeans. We need more EHG, but I'd say most of the two Light skin-mutations have an origin in EEF and Armenian-type ancestors. Sardinians for example, who should be over 70% Neolithic Anatolian, are pretty fair compared to West Asians. Part of the reason I think this is we see the same alleles in West Asians today, just they have a lower frequency of SLC24A5.

It is important to note SLC24A5 in Spain and Italy was nowhere near modern frequencies in 2800 BC. It was still at Neolithic frequencies, and so rose a lot after 2800 BC. I'd say LN/BA folk with R1a-M417 especially, but also other groups like Bell Beaker and in Hungary show similar results, had already gone through the evolutionary event of skin color change. Look at Charchen man, he's a time capsule into Late Neolithic Central-East Europe.
http://www.dandebat.dk/images/6p.jpg

Goga
14-10-15, 03:22
Exactly was I though, he looks partly Mongoloid. Look at his high cheekbones, his teeth and his slanted eyes. His chin is Caucasoid, but everything above looks Mongoloid. Like I said, EHG emerged from Caucasoids + Mongoloids (Finno-Ugric/Uralic/Amerindian)

Angela
14-10-15, 03:24
I wasn't surprised by Anatolian results. They had basically the same results as Neolithic Central Europeans. We need more EHG, but I'd say most of the two Light skin-mutations have an origin in EEF and Armenian-type ancestors. Sardinians for example, who should be over 70% Neolithic Anatolian, are pretty fair compared to West Asians. Part of the reason I think this is we see the same alleles in West Asians today, just they have a lower frequency of SLC24A5.

It is important to note SLC24A5 in Spain and Italy was nowhere near modern frequencies in 2800 BC. It was still at Neolithic frequencies, and so rose a lot after 2800 BC. I'd say LN/BA folk with R1a-M417 especially, but also other groups like Bell Beaker and in Hungary show similar results, had already gone through the evolutionary event of skin color change. Look at Charchen man, he's a time capsule into Late Neolithic Central-East Europe.
http://www.dandebat.dk/images/6p.jpg

Well, we only have two(?) samples from Italy, right? They both had SLC24A5, so I think you meant that the levels for SLC42A5 weren't at current levels, yes?

I don't mean to be annoying, but not everyone is as conversant with these things as you are, and I don't want there to be any confusion.

Fire Haired14
14-10-15, 03:59
Exactly was I though, he looks partly Mongoloid. Look at his high cheekbones, his teeth and his slanted eyes. His chin is Caucasoid, but everything above looks Mongoloid. Like I said, EHG emerged from Caucasoids + Mongoloids (Finno-Ugric/Uralic/Amerindian)


EHG had very little Eastern ancestry. And there's no way he was EHG, he was born in 1000 BC. This is probably what he looked like when alive.
http://i.ytimg.com/vi/BByGe43S-kY/hqdefault.jpg

Fire Haired14
14-10-15, 03:59
Well, we only have two(?) samples from Italy, right? They both had SLC24A5, so I think you meant that the levels for SLC42A5 weren't at current levels, yes?

I don't mean to be annoying, but not everyone is as conversant with these things as you are, and I don't want there to be any confusion.

Yes that's what I meant.

Angela
14-10-15, 04:05
OK. Enough with the amateur anthropology. No one really knows what any of these ancient people looked like...Even reconstructions done by people like Gerasimov are just that...reconstructions.

Let's stick to DNA, shall we.

Tomenable
14-10-15, 17:16
No one really knows what any of these ancient people looked like...

Krefter posted a photo of his mummy, and you say that we don't know how he looked like? :rolleyes2:


Let's stick to DNA, shall we.

Yes we have pigmentation SNPs from Tarim Mummies and they had European pigmentation.

By European pigmentation I mean similar to modern Europeans, not Mesolithic/Neolithic.

Angela
14-10-15, 18:04
I think you mean "a" mummy, not "his" mummy. Sorry, I couldn't resist it. :)

My post was in response to Goga's claim that there are clear "Mongoloid" features evident in the mummy. You cannot make precise claims about what someone looked like from a mummy; that's why people have argued about the reconstructions of the faces of various "other" mummies. However, I certainly don't see any obvious "Siberian" traits in that mummy, although it is possible that in real life there might have been some signs of it. There are certainly people walking around today who are mixed East Asian/West Eurasian who show some East Asian features even if they look more West Eurasian.

It's a fact, however, that Russian scientists have indeed described various ancient samples from eastern Europe as having "Mongoloid" features.So, it's hardly false to say that there are ancient Eastern European populations that may have showed such admixture. I personally wouldn't make such characterizations because it's just too hazy to make such claims from ancient bones and mummies. We do have EDAR in Eastern Europe, so it's not a totally bizarre claim.

If I were inclined to discuss such claims, the Tarim people would not be my first choice of examples of that phenomenon. And, yes, we all know that they had modern European like pigmentation snps. There's no need to keep repeating it. So did other ancient people, btw. Are prizes going to be given out for which group got them first?

MOESAN
16-10-15, 00:39
OK. Enough with the amateur anthropology. No one really knows what any of these ancient people looked like...Even reconstructions done by people like Gerasimov are just that...reconstructions.

Let's stick to DNA, shall we.

we know how their bones were - that said, this man could have had some 'east-asian' genes but I think people forget that when differenciation gradually occurs by isolation, it does not produce immediatly opposed types eveywhere - the "non-europoïd" component among proto-Finnic-Ugric people was not typically "mongoloid" and according to some anthropologists WAS NOT THE RESULT OF A CROSSING between typical "europoids' and typical 'mongoloids'; it was a population "of its own" to say like taht.
That said specialists think the most of first steppic people of Bronze were 'europoids', the mixing occurring later, beginning at iron Age in the Altai region before generalizating in later period until the Caspian banks and influencing peoepe North the Hindu Kush. And left apart some calculators errors, the different sets of genes of ancient populations found today scattered in different ethnic groups don't prove these ancient populations were a mix of these new ethnies! some of thes e genes are the remnant of an old common stage before selection and new mutations; what occurs for autosomals occurs for phoenotypical traits I suppose.

Angela
16-10-15, 01:27
we know how their bones were - that said, this man could have had some 'east-asian' genes but I think people forget that when differenciation gradually occurs by isolation, it does not produce immediatly opposed types eveywhere - the "non-europoïd" component among proto-Finnic-Ugric people was not typically "mongoloid" and according to some anthropologists WAS NOT THE RESULT OF A CROSSING between typical "europoids' and typical 'mongoloids'; it was a population "of its own" to say like taht.
That said specialists think the most of first steppic people of Bronze were 'europoids', the mixing occurring later, beginning at iron Age in the Altai region before generalizating in later period until the Caspian banks and influencing peoepe North the Hindu Kush. And left apart some calculators errors, the different sets of genes of ancient populations found today scattered in different ethnic groups don't prove these ancient populations were a mix of these new ethnies! some of thes e genes are the remnant of an old common stage before selection and new mutations; what occurs for autosomals occurs for phoenotypical traits I suppose.


That's a better way to describe it, I think. Would that explain the EDAR traits not only in SHG but in two of the Afanasievo samples, however? The latter are pretty late.