Using rare variation, we are also able to distinguish fine-scale patterns of population structure (Fig. 4, Supplementary Fig. 29 and Supplementary Information 1.9). Broadly, we observe sharing between population groups with shared continental ancestry (whether African, European, Asian or American). Nevertheless, additional patterns emerge. The Amish are unique among the included studies: they exhibit little rare variant sharing with outside groups and also the greatest rare variant sharing within the study—consistent with a marked founder effect. Furthermore, we observe an approximately 4× greater rare variant sharing between African American and Caribbean population groups than between European American population groups, even after correcting for sample size differences (Supplementary Fig. 30).
