Genomic insights into a tripartite ancestry in the Southern Ryukyu Islands

Abstract

A tripartite structure for the genetic origin of Japanese populations states that present-day populations are descended from three main ancestors: 1) the indigenous Jomon hunter-gatherers, 2) a Northeast Asian component that arrived during the agrarian Yayoi period, and 3) a major influx of East Asian ancestry in the imperial Kofun period. However, the genetic heterogeneity observed in different regions of the Japanese archipelago highlights the need to assess the applicability and suitability of this model. Here, we analyze historic genomes from the southern Ryukyu Islands, which have unique cultural and historical backgrounds compared with other parts of Japan. Our analysis supports the tripartite structure as the best fit in this region, with significantly higher estimated proportions of Jomon ancestry than mainland Japanese. Unlike the main islands, where each continental ancestor was directly brought by immigrants from the continent, those who already possessed the tripartite ancestor migrated to the southern Ryukyu Islands and admixed with the prehistoric people around 11th century AD, coinciding with the emergence of the Gusuku period. These results reaffirm the tripartite model in the southernmost extremes of the Japanese archipelago and show variability in how the structure emerged in diverse geographic regions.

Decoding triancestral origins, archaic introgression, and natural selection in the Japanese population by whole-genome sequencing

“…We subsequently used qpAdm to estimate contributions of NEA, EA, and Jomon ancestries in each subgroup, following the approach described in prior studies ( 41 , 48 ) (see Materials and Methods). For this analysis, the Chinese Han was designated as representative of EA, while China_WLR_BA_o and China_HMMH_MN were grouped to represent NEA.…”