Post by djoser-xyyman on May 9, 2014 20:26:39 GMT -5
I am now getting my head around this new analytical technique. I am under the impression that DNATribes is currently using a similar technique
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Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data - Joseph K. Pickrell (Nov2012)
Author Summary
However, it has long been recognized that, since populations from the same species exchange genes, simple bifurcating trees may be an incorrect representation of population histories. We have developed a method to address this issue, using a model which allows for both population splits and gene flow. In application to humans, we show that we are able to identify a number of both previously known and unknown episodes of gene flow in history, including gene flow into Cambodia
We infer that the Mozabite are the result of admixture between an African and a Middle Eastern population (with about 33% of their ancestry from Africa), and that Middle Eastern populations also have African ancestry (Palestinians and Bedouins: w~13% from Africa; Druze: w~6%). This is consistent with previously reported admixture proportions from these populations [43,55]. Additionally, we identify the known European ancestry in the Maya (w~12%) [21], and infer that the Uyghur and Hazara populations are the result of admixture between west Eurasian and East Asian populations (w~46% and 47% from west Eurasia, respectively) [20,21,56]. Several additional migration events in the human data have not been previously examined in detail, but are consistent with previous clustering analysis of these populations [7,20,21]. These include migration from Africa to the Makrani and Brahui in Central Asia (w~5%) and from a population related to East Asians and Native Americans (which we interpret as likely Siberian) to Russia (w~11%). Two inferred edges were unexpected. First, perhaps the most surprising inference is that Cambodians trace about 16% of their ancestry to a population equally related to both Europeans and other East Asians (while the remaining 84% of their ancestry is related to other southeast Asians). This is partially consistent with clustering analyses, which indicate shared ancestry between Cambodians and central Asian populations [7]. To confirm that the Cambodians are admixed, we turned to less parameterized models. The predicted admixture event implies that allele frequencies in Cambodia are more similar to those in African populations than would be expected based on their East Asian ancestry. To test this, we used three-population tests [37]. We tested the trees [African, [Cambodian,Dai]] for evidence of admixture in the Cambodians (Methods). When using any African population, there is strong evidence of admixture (when using Yoruba, Z~{7:0 [p~1|10{12]; when using Mandenka, Z~{7:3 [p~1|10{12]; when using San, Z~{4:8 [p~8|10{7]).
Finally, we infer an admixture edge from the Middle East (a population related to the Mozabite, a Berber population from northern Africa) to southern European populations (w~22%). This migration edge is the one edge that is not consistent across independent runs of TreeMix on these data (Figure S8). In particular, an alternative graph (albeit with lower likelihood) places the Mozabite as an admixture between southern Europe and Africa (rather than the Middle East and Africa), and does not include an edge from the middle East to southern Europe. We thus hesitate to interpret this result, except to note that the relationship between northern African, the Middle East, and southern Europe involves complex patterns of gene flow that merit further investigation [43,57].
For example, in the human data, note that we see no evidence of the documented gene flow from Neandertals to all non-African populations [39] (Figure 3B). The reason for this is that the large number of populations with admixture can be accommodated in the tree by allowing the branch from Neandertals to Africans to be slightly underestimated (additionally, by using
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What does it all mean? The researchers are getting really good at deciphering direction of migration. From the above they concluded “recent” Africans migrated to Cambodia, Bedouins, Druze, Makrani and Brahui(Harrapan Valley of India).
For the Mozabite, they see evidence of North Africans to Europe. There ares also similarities between North Africans and some Middle East Populations. Thery are unsure on the direction. They are leaning towards the Saharan/Basal EEF as DNATribes.
This is going to be a great year. A revealing year.
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Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data - Joseph K. Pickrell (Nov2012)
Author Summary
However, it has long been recognized that, since populations from the same species exchange genes, simple bifurcating trees may be an incorrect representation of population histories. We have developed a method to address this issue, using a model which allows for both population splits and gene flow. In application to humans, we show that we are able to identify a number of both previously known and unknown episodes of gene flow in history, including gene flow into Cambodia
We infer that the Mozabite are the result of admixture between an African and a Middle Eastern population (with about 33% of their ancestry from Africa), and that Middle Eastern populations also have African ancestry (Palestinians and Bedouins: w~13% from Africa; Druze: w~6%). This is consistent with previously reported admixture proportions from these populations [43,55]. Additionally, we identify the known European ancestry in the Maya (w~12%) [21], and infer that the Uyghur and Hazara populations are the result of admixture between west Eurasian and East Asian populations (w~46% and 47% from west Eurasia, respectively) [20,21,56]. Several additional migration events in the human data have not been previously examined in detail, but are consistent with previous clustering analysis of these populations [7,20,21]. These include migration from Africa to the Makrani and Brahui in Central Asia (w~5%) and from a population related to East Asians and Native Americans (which we interpret as likely Siberian) to Russia (w~11%). Two inferred edges were unexpected. First, perhaps the most surprising inference is that Cambodians trace about 16% of their ancestry to a population equally related to both Europeans and other East Asians (while the remaining 84% of their ancestry is related to other southeast Asians). This is partially consistent with clustering analyses, which indicate shared ancestry between Cambodians and central Asian populations [7]. To confirm that the Cambodians are admixed, we turned to less parameterized models. The predicted admixture event implies that allele frequencies in Cambodia are more similar to those in African populations than would be expected based on their East Asian ancestry. To test this, we used three-population tests [37]. We tested the trees [African, [Cambodian,Dai]] for evidence of admixture in the Cambodians (Methods). When using any African population, there is strong evidence of admixture (when using Yoruba, Z~{7:0 [p~1|10{12]; when using Mandenka, Z~{7:3 [p~1|10{12]; when using San, Z~{4:8 [p~8|10{7]).
Finally, we infer an admixture edge from the Middle East (a population related to the Mozabite, a Berber population from northern Africa) to southern European populations (w~22%). This migration edge is the one edge that is not consistent across independent runs of TreeMix on these data (Figure S8). In particular, an alternative graph (albeit with lower likelihood) places the Mozabite as an admixture between southern Europe and Africa (rather than the Middle East and Africa), and does not include an edge from the middle East to southern Europe. We thus hesitate to interpret this result, except to note that the relationship between northern African, the Middle East, and southern Europe involves complex patterns of gene flow that merit further investigation [43,57].
For example, in the human data, note that we see no evidence of the documented gene flow from Neandertals to all non-African populations [39] (Figure 3B). The reason for this is that the large number of populations with admixture can be accommodated in the tree by allowing the branch from Neandertals to Africans to be slightly underestimated (additionally, by using
===
What does it all mean? The researchers are getting really good at deciphering direction of migration. From the above they concluded “recent” Africans migrated to Cambodia, Bedouins, Druze, Makrani and Brahui(Harrapan Valley of India).
For the Mozabite, they see evidence of North Africans to Europe. There ares also similarities between North Africans and some Middle East Populations. Thery are unsure on the direction. They are leaning towards the Saharan/Basal EEF as DNATribes.
This is going to be a great year. A revealing year.
