Angela
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Dienekes points us to a new study:
http://www.dienekes.blogspot.com/2015/04/pca-and-natural-selection.html
Fast principal components analysis reveals independent evolution of ADH1B gene in Europe and East Asia
http://biorxiv.org/content/early/2015/04/16/018143?rss=1
"Principal components analysis (PCA) is a widely used tool for inferring population structure and correcting confounding in genetic data. We introduce a new algorithm, FastPCA, that leverages recent advances in random matrix theory to accurately approximate top PCs while reducing time and memory cost from quadratic to linear in the number of individuals, a computational improvement of many orders of magnitude. We apply FastPCA to a cohort of 54,734 European Americans, identifying 5 distinct subpopulations spanning the top 4 PCs. Using a new test for natural selection based on population differentiation along these PCs, we replicate previously known selected loci and identify three new signals of selection, including selection in Europeans at the ADH1B gene. The coding variant rs1229984 has previously been associated to alcoholism and shown to be under selection in East Asians; we show that it is a rare example of independent evolution on two continents. "
A very knowledgeable poster at 23andme states that the coding variant is rs1229984. It had previously been shown to be related to alcoholism and to be under selection in East Asians. The correlation was felt to be with rice agriculture.
"But the variant is not under selection because of alcohol but because of rice:
Rice responsible for Asians' alcohol flush reaction, research finds "Our molecular dating suggests that the emergence of the ADH1B*47His allele occurred about 10,000-7,000 years ago. The geographic distribution of the allele in East Asia is also consistent with the unearthed culture relic sites of rice domestication in China, suggesting that distribution of the alcohol flush mutation can be explained by the origin and expansion of the Neolithic rice culture. This is one of the few cases reported demonstrating the genetic adaptation of human populations to the dramatic changes in agriculture and diet during Neolithic times."
http://www.sciencedaily.com/releases/2010/01/100119213140.htm
http://www.biomedcentral.com/1471-2148/10/15
I actually think we're discovering that there's been a lot of selection because of the Neolithic advance.
See also:rs1229984 T allele is linked with finding alcohol unpleasant, have a reduced risk of alcoholism, and reduced risk for oral/throat cancers:
A=T and G=C
http://www.snpedia.com/index.php/Rs1229984
This study shows it is also under selection in Europeans. Allred has a list of populations that shows the proportion of C ancestral and T derived. All Africans and Native Americans are ancestral C. Han are derived T.
http://alfred.med.yale.edu/alfred/SiteTable1A_working.asp?siteuid=SI000229N
(These links were not found by me.)
Here are some representative numbers that were posted at 23andme. Does it perhaps track with the Neolithic in Europe and the Near East as well?
Ashkenazi 18, 20
Sephardi 16,41
Turks 8,12,17,46
Romanians 10,26
Greeks 8, 16
Italian 0, 5, 5, 6, 12 (I don't know if that 12% is anomalous or not. It's Torino, in northeast Italy.)
Spanish 6, 7, 8
Slovaks 7
Poles 7
The lowest values in Europe seem to be among the Finns (0), Scandinavians, and northwest Europeans.
In the Near East:
Samaritans 88 (Definitely partly because of such strict endogamy.)
Palestinians 6
Armenian 10
Druze 13
Iranians 24,33 (I'm unsure why these would be so high.)
Persians 68 (Perhaps it's a particularly inbred group?)
Does that correlate with high alcoholism rates?
If there is a correlation, it seems to break down with the Russians: 2, 3, 4, 6, 17, 41
That's all from Moscow. Unless perhaps the groups with the higher numbers aren't ethnic Russian?
I think the 0 from the Sardinians might be due to variation within all these populations. The TSI sample from Italy also has O as a value. That's one village northeast of Firenze.
These populations also seem to have pretty high values:
Kalmyks 26
Tatar 12, 19
Ingush 16
Udmurt 12
Mari 11
Perhaps they got some from East Asians and some from European Neolithic.?
I wonder if the same pattern would emerge with mutations that protect against diabetes?
I still don't understand the mechanism.
http://www.dienekes.blogspot.com/2015/04/pca-and-natural-selection.html
Fast principal components analysis reveals independent evolution of ADH1B gene in Europe and East Asia
http://biorxiv.org/content/early/2015/04/16/018143?rss=1
"Principal components analysis (PCA) is a widely used tool for inferring population structure and correcting confounding in genetic data. We introduce a new algorithm, FastPCA, that leverages recent advances in random matrix theory to accurately approximate top PCs while reducing time and memory cost from quadratic to linear in the number of individuals, a computational improvement of many orders of magnitude. We apply FastPCA to a cohort of 54,734 European Americans, identifying 5 distinct subpopulations spanning the top 4 PCs. Using a new test for natural selection based on population differentiation along these PCs, we replicate previously known selected loci and identify three new signals of selection, including selection in Europeans at the ADH1B gene. The coding variant rs1229984 has previously been associated to alcoholism and shown to be under selection in East Asians; we show that it is a rare example of independent evolution on two continents. "
A very knowledgeable poster at 23andme states that the coding variant is rs1229984. It had previously been shown to be related to alcoholism and to be under selection in East Asians. The correlation was felt to be with rice agriculture.
"But the variant is not under selection because of alcohol but because of rice:
Rice responsible for Asians' alcohol flush reaction, research finds "Our molecular dating suggests that the emergence of the ADH1B*47His allele occurred about 10,000-7,000 years ago. The geographic distribution of the allele in East Asia is also consistent with the unearthed culture relic sites of rice domestication in China, suggesting that distribution of the alcohol flush mutation can be explained by the origin and expansion of the Neolithic rice culture. This is one of the few cases reported demonstrating the genetic adaptation of human populations to the dramatic changes in agriculture and diet during Neolithic times."
http://www.sciencedaily.com/releases/2010/01/100119213140.htm
http://www.biomedcentral.com/1471-2148/10/15
I actually think we're discovering that there's been a lot of selection because of the Neolithic advance.
See also:rs1229984 T allele is linked with finding alcohol unpleasant, have a reduced risk of alcoholism, and reduced risk for oral/throat cancers:
A=T and G=C
http://www.snpedia.com/index.php/Rs1229984
This study shows it is also under selection in Europeans. Allred has a list of populations that shows the proportion of C ancestral and T derived. All Africans and Native Americans are ancestral C. Han are derived T.
http://alfred.med.yale.edu/alfred/SiteTable1A_working.asp?siteuid=SI000229N
(These links were not found by me.)
Here are some representative numbers that were posted at 23andme. Does it perhaps track with the Neolithic in Europe and the Near East as well?
Ashkenazi 18, 20
Sephardi 16,41
Turks 8,12,17,46
Romanians 10,26
Greeks 8, 16
Italian 0, 5, 5, 6, 12 (I don't know if that 12% is anomalous or not. It's Torino, in northeast Italy.)
Spanish 6, 7, 8
Slovaks 7
Poles 7
The lowest values in Europe seem to be among the Finns (0), Scandinavians, and northwest Europeans.
In the Near East:
Samaritans 88 (Definitely partly because of such strict endogamy.)
Palestinians 6
Armenian 10
Druze 13
Iranians 24,33 (I'm unsure why these would be so high.)
Persians 68 (Perhaps it's a particularly inbred group?)
Does that correlate with high alcoholism rates?
If there is a correlation, it seems to break down with the Russians: 2, 3, 4, 6, 17, 41
That's all from Moscow. Unless perhaps the groups with the higher numbers aren't ethnic Russian?
I think the 0 from the Sardinians might be due to variation within all these populations. The TSI sample from Italy also has O as a value. That's one village northeast of Firenze.
These populations also seem to have pretty high values:
Kalmyks 26
Tatar 12, 19
Ingush 16
Udmurt 12
Mari 11
Perhaps they got some from East Asians and some from European Neolithic.?
I wonder if the same pattern would emerge with mutations that protect against diabetes?
I still don't understand the mechanism.
