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. 2017 Dec 12;8:2062. doi: 10.1038/s41467-017-00663-9

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© The Author(s) 2017

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — Relatedness of the South Africans to other populations estimated on the basis of variant sharing and allelic differentiation. Comparison of variants found by whole-genome sequencing in the a Southeastern Bantu-speakers (SEB) and b Coloured (COL) from this study with the 1000 Genomes Project (KGP) populations using the f ₂ estimate. Only the occurrence of f ₂ variants shared between the South African populations and the KGP populations are shown. The analysis suggests a more recent historical connection between southern and East African Bantu speakers. c Map highlighting the geographic region of southern African hunter–gatherer groups used for comparison in the study. The map was generated using SimpleMappr (http://www.simplemappr.net/). d F_ST values showing comparison between Sotho-speakers (SOT), Xhosa-speakers (XHS), COL populations, and previously studied southern African hunter–gatherer populations. The South African Bantu-speaking groups (SOT and XHS) were found to be closest to the Khwe, whereas the COL was found to be closest to the Nama and ≠Khomani. The y-axis shows the average F_ST value for each comparison. KGP populations used in this analysis along with Color codes are: East Asian (cyan)—Kinh in Ho Chi Minh City, Vietnam (KHV); Chinese Dai in Xishuangbanna, China (CDX); Han Chinese in Bejing, China (CHB): Southern Han Chinese (CHS); Japanese in Tokyo, Japan (JPT), South Asian (orange)—Punjabi from Lahore, Pakistan (PJL); Gujarati Indian from Houston, Texas (GIH); Indian Telugu from the UK; Bengali from Bangladesh (BEB); Sri Lankan Tamil from the UK (STU), European (blue)—Finnish in Finland (FIN); Toscani in Italia (TSI); Iberian Population in Spain (IBS); British in England and Scotland (GBR); Utah Residents (CEPH) with Northern and Western European Ancestry (CEU), Admixed Americans (purple)—Peruvians from Lima, Peru (PEL); Puerto Ricans from Puerto Rico (PUR); Mexican Ancestry from Los Angeles USA (MXL); Colombians from Medellin, Colombia (CLM), West, Central-West African and African descent (green)—Esan in Nigeria (ESN); Americans of African Ancestry in SW USA (ASW); African Caribbeans in Barbados (ACB)—Yoruba in Ibadan, Nigeria (YRI); Gambian in Western Divisions in the Gambia (GWD); Mende in Sierra Leone (MSL); and East African (red)—Luhya in Webuye, Kenya (LWK)