Extended Data Fig. 6: Admixture graph model.
From: Genomic insights into the formation of human populations in East Asia
This figure is the same as Fig. 2 except we show the fitted genetic drifts on each lineage. We used all available sites in the dataset comprising 1,237,207 SNPs, restricting to transversions only to confirm that the same model fit (Supplementary Information section 3). We started with a skeleton tree that fits the data for Denisovan, Mbuti, Onge, Tianyuan and Luxembourg Loschbour and one admixture event. We grafted on Mongolia East Neolithic, Late Neolithic farmers from the Upper Yellow River, Liangdao 2, Japan Jomon, Nepal Chokhopani, Taiwan Hanben and Late Neolithic farmers from the West Liao River in turn, adding them consecutively to all possible edges in the tree and retaining only graph solutions that provided no differences of |Z| < 3 between fitted and estimated statistics (maximum |Z| = 2.95 here). We used the MSMC and MSMC2 relative population split time estimates to constrain models. Deep splits are not well constrained because of the minimal availability of data on East Asian populations from the Upper Paleolithic. a, Locations and dates of the East Asian individuals used in model fitting, with colours indicating whether the majority ancestry is from the hypothesized coastal expansion (green), interior expansion south (red) and interior expansion north (blue). The map is based on the ‘Google Map Layer’ from ArcGIS Online Basemaps (map data ©2020 Google). The grey circles represent sampled populations and white circles represent unsampled hypothesized nodes. b, In the model visualization, we colour lineages modelled as deriving entirely from one of these expansions, and also colour populations according to ancestry proportions. Dashed lines represent admixture (proportions are marked), and we show the amount of genetic drift on each lineage in units of FST × 1,000.
