Because rare variants are typically recent, their patterns of sharing can reveal aspects of population history. Variants present twice across the entire sample (referred to as f2 variants), typically the most recent of informative mutations, are found within the same population in 53% of cases (Fig. 3a). However, between-population sharing identifies recent historical connections. For example, where one of the individuals carrying an f2 variant is from the Spanish population (IBS) and the other is not (referred to as IBS-X), the other individual is more likely to come from the AMR populations (48%, correcting for sample size) than elsewhere in Europe (41%). Within the East Asian populations, CHS and CHB show stronger f2 sharing to each other (58% and 53% of CHS-X and CHB-X variants respectively) than either does to JPT, but JPT is closer to CHB than to CHS (44% versus 35% of JPT-X variants). Within African-ancestry populations, the ASW are closer to the YRI (42% of ASW-X f2 variants) compared to the LWK (28%), in line with historical information17 and genetic evidence based on common SNPs18. Some sharing patterns are surprising; for example, 2.5% of the f2 FIN-X variants are shared with YRI or LWK populations.
