W. Ko, et al., "Genetic origins and admixed ancestry characterization of Japanese people."
A modern human population found at a certain geographic location is often descended from multiple ethnic groups owning to the complex migration history of human expansion. In Japan, although it has been studied extensively over the past decades, the genetic origins of Japanese people remain controversial.
Current genetic evidence supports a dual model which suggested that the Japanese people are constituted mainly by an early settlement of human populations during the Upper Paleolithic period (i.e., Jomon people) followed by an admixture event with the people migrated from the Korean peninsula around 2300 year ago (i.e., Yayoi people).
However, the genetic origin(s) of the native Jomons remains unclear. Tracing the genomic signatures of admixture history can not only reveal the unknown human migration events but also provide critical information that can facilitate the genetic profiling of disease susceptibility, which is critical for the success of personalized medicine. Here, we analyzed a combined dataset of the whole genome SNP genotyping data from 2,277 individuals sampled globally across >100 populations for a total of 19,290 SNPs (after intersecting the two datasets). We performed principle component analysis to project individuals onto a series of orthogonal axes to reveal the genetic structure among diverse ethnic groups.
After separating the genetic components contributed from the populations representing the Yayoi, we identified several candidate populations that share common non-Yayoi ancestry with the modern Japanese people. Our results suggest that the genetic origins of Jomons may consist of multiple migration events from both Southeast and Northeast Asia. Surprisingly, we also identified an additional migration wave from the Hmong population.
We assigned local ancestry (LA) on the phased chromosomes of the mainland and Okinawa Japanese by performing RFmix (which used the identified candidate ancestral populations to infer the LA tracts in admixed chromosomes by finding the most likely sequence of ancestries through maximum a posterior estimation). Because an ancient population admixture would allow more recombination events to break LA tracks into shorter segments than a recent admixture event, our results of the LA track-length distributions differ significantly between the Yayoi, Hmong, and Jomon ancestries (in descending order), suggesting that the Hmong migration may have occurred before the Yayoi migration.