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View Full Version : Traits that were Selected for in the last 8,000 years



Krefter
10-13-2015, 12:22 PM
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.

SwampThing27
12-02-2015, 08:14 PM
Do you know what rs7119749 actually does? I can't seem to find any studies on it in regards to pale skin. Even google only brings back 2 pages of results on it and none are helpful. I'm the only one of the four profiles that I manage that's heterozygous. Can't even find an allele frequency database for it.

anglesqueville
12-02-2015, 09:34 PM
rs653178: what is the ancestral allele, C or T ?
edit: risk allele C, so I presume that the ancestral is T, do you confirm?

SwampThing27
12-03-2015, 12:50 AM
rs653178: what is the ancestral allele, C or T ?
edit: risk allele C, so I presume that the ancestral is T, do you confirm?

Surprised the risk allele is C. All four of my profiles are CC.

anglesqueville
12-03-2015, 07:20 AM
rs653178: 6788 The variations are small inside Europe, but the link with hunter-gatherer vs EEF has not completely dissapeared.