Extended Data Fig. 2: Results from Multi-head Neural ADMIXTURE (K=3 to K=8) on the test set of Chm-22-Sim
For K=3, European (EUR), West Asian (WAS) and South Asian (SAS) are combined within the same cluster, while American (AMR), Oceanian (OCE), and East Asian (EAS) are clustered together, and African (AFR) has its own cluster. These results reflect the genetic similarity between the respective groups due to their Out-of-Africa migration patterns and subsequent gene flow. After increasing to K=5, OCE obtains its own cluster, reflecting the ancient divergence from the others of that population consisting in our study of the Australo-Papuan groups-Native Australian (SGDP), Papuan Highlands (HGDP), Papuan Sepik (HGDP), Bougainville (HGDP), and Dusun (HGDP). As more clusters are incorporated, American (AMR) and EAS obtain their own clusters and OCE is divided between a component found predominantly in OCE and a component characteristic of EAS. The latter likely reflects the later migration of Austronesian speakers from East Asia out into the Pacific Islands, where they contributed their ancestry to the Oceanian inhabitants. A shared component between EUR, SAS and WAS is maintained, independent of the cluster number K. This could be linked to early farmer expansions out of West Asia and into both Europe and South Asia following the birth of agriculture, or to the much later expansion of the Indo-European language family across all of these regions. Other genetic exchanges between these neighboring regions doubtlessly played a role. With a sufficiently high number of clusters, a shared component between WAS and some AFR populations appears, perhaps reflecting North African gene flow.
