https://www.biorxiv.org/content/biorxiv/early/2019/05/30/653279.full.pdf
S1.4 Admixture analysis
We performed an admixture analysis to complement out analysis of kinship andFST. We used theAdmixture software [62] to inferK= 7ancestry clusters from the Final dataset (see Table S1).The admixture proportions can be visualized as stacked barplots on Fig. S3, where individualsare ordered just as in the kinship matrix of the main text. These seven infered ancestry clusterscorrespond approximately with the 11 subpopulations we constructed based on geography and othercriteria (Section S1.1) as follows (Fig. S3):
•Cluster 1 corresponds toSAfrica.•Cluster 2 corresponds toMAfrica.•Cluster 3 corresponds toEurope,NAfrica,MiddleEastandCaucasus.•Cluster 4 corresponds toSAsia.•Cluster 5 corresponds toEAsiaandNAsia.•Cluster 6 corresponds toAmericas.•Cluster 7 corresponds toOceania.
We typically see that each ancestry cluster is concentrated in a certain geographical region, and this ancestry is also present to a lesser extent in neighboring regions and diminishes with geographical distance from its point of greatest concentration. This again argues for a complex population structure where relatedness at the population level falls on a continuum rather than taking on discrete values.The most notable geographic discontinuities in ancestry were observed for cluster 3, which is roughly West Eurasian ancestry. Unusually high proportions of this ancestry are observed inmost individuals of two sub-subpopulations of the Kamchatka Peninsula in Russia (Aleut and Aleut_Tlingitin subpopulation NAsia), as well as the fourAmericassub-subpopulations from Canada (Chipewyan,Cree,Algonquin, and Ojibwa) and Chilote from Chile (Fig. S3). We also observed an unusual reduction of cluster 5 ancestry in Aleut and Aleut_Tlingit relative to its closestNAsia sub-subpopulations, and unusually low levels of cluster 6 ancestry in Chipewyan,Cree,Algonquin,Ojibwa, and Chilote relative to the rest of Americas sub-subpopulations. These data point to likely recent European admixture in those individuals
S1.4 Admixture analysis
We performed an admixture analysis to complement out analysis of kinship andFST. We used theAdmixture software [62] to inferK= 7ancestry clusters from the Final dataset (see Table S1).The admixture proportions can be visualized as stacked barplots on Fig. S3, where individualsare ordered just as in the kinship matrix of the main text. These seven infered ancestry clusterscorrespond approximately with the 11 subpopulations we constructed based on geography and othercriteria (Section S1.1) as follows (Fig. S3):
•Cluster 1 corresponds toSAfrica.•Cluster 2 corresponds toMAfrica.•Cluster 3 corresponds toEurope,NAfrica,MiddleEastandCaucasus.•Cluster 4 corresponds toSAsia.•Cluster 5 corresponds toEAsiaandNAsia.•Cluster 6 corresponds toAmericas.•Cluster 7 corresponds toOceania.
We typically see that each ancestry cluster is concentrated in a certain geographical region, and this ancestry is also present to a lesser extent in neighboring regions and diminishes with geographical distance from its point of greatest concentration. This again argues for a complex population structure where relatedness at the population level falls on a continuum rather than taking on discrete values.The most notable geographic discontinuities in ancestry were observed for cluster 3, which is roughly West Eurasian ancestry. Unusually high proportions of this ancestry are observed inmost individuals of two sub-subpopulations of the Kamchatka Peninsula in Russia (Aleut and Aleut_Tlingitin subpopulation NAsia), as well as the fourAmericassub-subpopulations from Canada (Chipewyan,Cree,Algonquin, and Ojibwa) and Chilote from Chile (Fig. S3). We also observed an unusual reduction of cluster 5 ancestry in Aleut and Aleut_Tlingit relative to its closestNAsia sub-subpopulations, and unusually low levels of cluster 6 ancestry in Chipewyan,Cree,Algonquin,Ojibwa, and Chilote relative to the rest of Americas sub-subpopulations. These data point to likely recent European admixture in those individuals