Sharing of IBD Segments Between Continental Groups

We found that most IBD segments are observed in only one continental group, which are, in most cases, Africans. However, for other continental groups, we saw a considerable sharing of IBD segments across continental groups. The sharing between continental groups seems to contradict statements in other publications. For example, Gravel et al. (23) report that sharing of SNVs between continental groups is low.

Sharing between continental groups has been reported in the publication of the 1000 Genomes Project (2). In our nomenclature, the terms ``low-frequency variants'' and ``rare variants'' from (2) are unified to the term ``rare variants''. The 1000 Genomes Project (2) use the term ``ancestry groups'' to denote EUR, EAS (ASN in our nomenclature), AFR, and AMR according to their Fig. 2b. The authors of the 1000 Genomes Project (2) write:

``By contrast, 17% of low-frequency variants in the range 0.5-5% were observed in a single ancestry group, and 53% of rare variants at 0.5% were observed in a single population (Fig. 2b).''

This means that 83% of the low-frequency variants are shared between continental groups and 47% (almost half) of the rare variants are shared between continental groups.

Another example taken from the 1000 Genomes Project paper (2) is:

``Some sharing patterns are surprising; for example, 2.5% of the $f_2$ FIN-X variants are shared with YRI or LWK populations.''

$f_2$ variants are those variants for which their minor allele is observed in exactly 2 individuals. $f_2$ variants are rarer than most SNVs that tag our extracted IBD segments because, on average, 6 individuals possess an IBD segment. According to (23), sharing between continental groups decreases with rarer variants. Thus, in our extracted IBD segments, we would expect to find sharing between continental groups considerably more often than for $f_2$ variants.

Furthermore, the same publication (2) reports:

``By contrast, between populations with no recent shared ancestry, $f_2$ variants are present on very short haplotypes, for example, an average of 11 kb for FIN-YRI $f_2$ variants (median between ancestry groups excluding admixture is 15 kb), and are therefore likely to reflect recurrent mutations and chance ancient coalescent events.''

This statement also supports our findings of IBD sharing between continental groups, but we could exclude recurrent mutations because IBD segments are shared between multiple individuals.