Sharing Between All Human Populations

We were interested in the distribution of IBD segments among different populations. The main population groups are Africans (AFR), Asians (ASN), Europeans (EUR), and Admixed Americans (AMR), where AMR consist of Colombian, Puerto Rican, and Mexican individuals. Table 1 lists the number of IBD segments that are shared between particular populations. The vast majority (152,120) of the detected IBD segments are shared by Africans (at least one African possesses the segment), of which 93,197 are exclusively found in Africans. Only 19,062 and 10,645 IBD segments are shared by Europeans and Asians, respectively. 1,191 IBD segments are exclusively found in Europeans and 2,522 exclusively in Asians. Admixed Americans share 384 IBD segments with Asians, but 1,900 with Europeans which can be explained by the AMR admixture. If we additionally consider sharing with AFR, we obtain the same figures: 8,322 IBD segments have AFR/AMR/EUR sharing while only 1,196 IBD segments have AFR/AMR/ASN sharing. According to results of the 1000 Genomes Project, individuals with African ancestry carry much more rare variants than those of European or Asian ancestry (2) supporting our finding that most IBD segments are shared by Africans. We found that few IBD segments are shared between two populations (Tab. 1 ``Pairs of Populations'') confirming recently published results (23,2) (see also Section 3.1.2). The relatively large number of shared IBD segments between Africans and Europeans was due to many shared IBD segments between the AFR sub-group ASW (Americans with African ancestry) and Europeans. This tendency was also observed in the 1000 Genomes Project via the fixation index $F_{\mathrm{ST}}$ estimated by Hudson ratio of averages and via shared haplotype length around $f_2$ variants (2). The high content of European DNA segments in ASW is consistent with the finding that in African Americans a median proportion of 18.5% is European (24). We conclude that IBD segments that are shared across continental populations, in particular by Africans, date back to a time before humans moved out of Africa. Consequently, the rare variants that tag these short IBD segments arose before the time humans migrated out of Africa. See Section 9, for a discussion of the question whether rare variants are recent or old.

Table 1: Number of IBD segments that are shared by particular populations.

Single Population						All Populations
AFR	AMR	ASN	EUR			AFR/AMR/ASN/EUR
93,197	981	2,522	1,191			4,132
Pairs of Populations				Triplets of Populations
AFR/AMR	AFR/ASN	AFR/EUR		AFR/AMR/ASN		AFR/AMR/EUR
42,631	615	1,720		1,196		8,322
AMR/ASN	AMR/EUR	ASN/EUR		AFR/ASN/EUR		AMR/ASN/EUR
384	1,901	556		307		933

AFR = Africans (246), AMR = Admixed Americans (181), ASN = East Asians (286), and EUR = Europeans (379).