Angela
Elite member
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- 21,823
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See:
[h=1]Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure[/h]http://www.pnas.org/content/early/2016/01/20/1513197113
"India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform."
Razib Khan has written a perceptive critique of the paper, in my opinion.
http://www.unz.com/gnxp/south-asians-are-not-descended-from-four-populations/
Even for those with a minimal interest in South Asian genetics, the critique is an important read for highlighting the limitations of Admixture programs. If more people understood this we wouldn't get the absurdity of a recent thread at Anthrogenica which purported to find the most "European" ethnic groups based on Admixture results for things like "West Mediterranean" versus "East Mediterranean" and other nonsense. One would think that all the papers of the last few years had never appeared.
Anyway, here are some pertinent quotes:
"Long-time readers will see the immediate problem: you can’t use ADMIXTURE like this! There is no guarantee that a group that is 100% x actually is in a situation where x corresponds to a genuine discrete ancestral population that existed in reality. That is, these sorts of models push a certain number of ancestral populations, and force individuals into being combinations of those. The model is constrained by the data you are putting into it to generate the results. For example, if I took Uygurs and Europeans, and did a K = 2, the Uygurs may form one cluster, and the Europeans another, at 100% levels. But we know from history and other methodologies that the Uygurs are a recently mixed group (within the last 2,000 years). Nevertheless if you tell the package to assume K = 2 with Uygurs and Northern Europeans, then it will place these into two distinct groups. And in fact, the result tells you something real and significant about the relatedness of the individuals in the data…but it doesn’t tell you necessarily anything about the real population history."
"To repeat, ADMIXTURE does not necessarily give you real population combinations!!! In fact, populations are to some extent a social construct, insofar as they’re just really collapsing the genetic variation which is the result of a particular demographic and pedigree history. "
"Instead of relying on ADMIXTURE so much, they should have also utilized D-stats and f-stats (not as sensitive to drift), as well as TreeMix. I think that would have quickly shown that some of these “pure” groups were mixed. Second, there is the issue of time-since-admixture. They obtained lower values than the 2013 paper. Why? Because they use source populations (and probably the methodology) which are somewhat different from that earlier work. Honestly if some of these populations are compounds, then it doesn’t make sense to necessarily use them as idealized donors in an admixture event."
[h=1]Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure[/h]http://www.pnas.org/content/early/2016/01/20/1513197113
"India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform."
Razib Khan has written a perceptive critique of the paper, in my opinion.
http://www.unz.com/gnxp/south-asians-are-not-descended-from-four-populations/
Even for those with a minimal interest in South Asian genetics, the critique is an important read for highlighting the limitations of Admixture programs. If more people understood this we wouldn't get the absurdity of a recent thread at Anthrogenica which purported to find the most "European" ethnic groups based on Admixture results for things like "West Mediterranean" versus "East Mediterranean" and other nonsense. One would think that all the papers of the last few years had never appeared.
Anyway, here are some pertinent quotes:
"Long-time readers will see the immediate problem: you can’t use ADMIXTURE like this! There is no guarantee that a group that is 100% x actually is in a situation where x corresponds to a genuine discrete ancestral population that existed in reality. That is, these sorts of models push a certain number of ancestral populations, and force individuals into being combinations of those. The model is constrained by the data you are putting into it to generate the results. For example, if I took Uygurs and Europeans, and did a K = 2, the Uygurs may form one cluster, and the Europeans another, at 100% levels. But we know from history and other methodologies that the Uygurs are a recently mixed group (within the last 2,000 years). Nevertheless if you tell the package to assume K = 2 with Uygurs and Northern Europeans, then it will place these into two distinct groups. And in fact, the result tells you something real and significant about the relatedness of the individuals in the data…but it doesn’t tell you necessarily anything about the real population history."
"To repeat, ADMIXTURE does not necessarily give you real population combinations!!! In fact, populations are to some extent a social construct, insofar as they’re just really collapsing the genetic variation which is the result of a particular demographic and pedigree history. "
"Instead of relying on ADMIXTURE so much, they should have also utilized D-stats and f-stats (not as sensitive to drift), as well as TreeMix. I think that would have quickly shown that some of these “pure” groups were mixed. Second, there is the issue of time-since-admixture. They obtained lower values than the 2013 paper. Why? Because they use source populations (and probably the methodology) which are somewhat different from that earlier work. Honestly if some of these populations are compounds, then it doesn’t make sense to necessarily use them as idealized donors in an admixture event."