Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes

Abstract

Historic Japanese culture evolved from at least two distinct migrations that originated on the Asian continent. Hunter-gatherers arrived before land bridges were submerged after the last glacial maximum (>12,000 years ago) and gave rise to the Jomon culture, and the Yayoi migration brought wet rice agriculture from Korea beginning $2,300 years ago. A set of 81 Y chromosome single nucleotide polymorphisms (SNPs) was used to trace the origins of Paleolithic and Neolithic components of the Japanese paternal gene pool, and to determine the relative contribution of Jomon and Yayoi Y chromosome lineages to modern Japanese. Our global sample consisted of >2,500 males from 39 Asian populations, including six populations sampled from across the Japanese archipelago. Japanese populations were characterized by the presence of two major (D and O) and two minor (C and N) clades of Y chromosomes, each with several sub-lineages. Haplogroup D chromosomes were present at 34.7% and were distributed in a U-shaped pattern with the highest frequency in the northern Ainu and southern Ryukyuans. In contrast, haplogroup O lineages (51.8%) were distributed in an inverted U-shaped pattern with a maximum frequency on Kyushu. Coalescent analyses of Y chromosome short tandem repeat diversity indicated that haplogroups D and C began their expansions in Japan $20,000 and $12,000 years ago, respectively, while haplogroup O47z began its expansion only $4,000 years ago. We infer that these patterns result from separate and distinct genetic contributions from both the Jomon and the Yayoi cultures to modern Japanese, with varying levels of admixture between these two populations across the archipelago. The results also support the hypothesis of a Central Asian origin of Jomonese ancestors, and a Southeast Asian origin of the ancestors of the Yayoi, contra previous models based on morphological and genetic evidence.

Genetic insights into the origins of Tibeto-Burman populations in the Himalayas

“…Northeast Asia is the major contributor to both Tibet (63.4%) and Tamang (59.7%) whereas Newar (44.7%) and Bhutan (41.1%) received equivalent percentages, followed by Kathmandu (22.3%). These results corroborate studies indicating a shared common ancestry between Tibet and the Northeast Asian collections of Japan and Korea by a variety of marker systems, including classical, 61,62 autosomal, 63 Y-chromosome 1,12,64,65 and mtDNA. 12,64,66,67 On the genetic origins of the Tibeto-Burman populations of the Himalayas T Gayden et al…”

“…On the other hand, previous Y-chromosome studies characterizing the Tibetan people 4,11,12 argue for Central Asian genetic contributions to account for the presence of Asian-specific YAP (Y Alu polymorphism) chromosomes (D-M174) in the plateau. Haplogroup D-M174 lineages are found at appreciable frequencies in the Andaman Islands of the Indian Ocean 13 but only minimally in all East Asian populations with the exception of Japan.…”

“…Haplogroup D-M174 lineages are found at appreciable frequencies in the Andaman Islands of the Indian Ocean 13 but only minimally in all East Asian populations with the exception of Japan. 1,4,11,12,14,15 Distinctive D-M174 subclades are observed in the Andaman Islands (D-M174*) and Japan (D2-M55), whereas Tibetans exhibit haplogroups D1-M15 and D3-P47.…”

Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data

“…This possible genetic continuity is corroborated by Y chromosome DNA analysis of the modern Ainu. Y chromosomal DNA haplogroup D1b, which is considered to be a strong candidate for the Jomon paternal lineage, was observed at high frequency in the modern Ainu (Hammer et al, 2006; Tajima et al, 2004). …”

“…The first is that almost all of these studies (Hammer et al, 2006; Harihara, Hirai, & Omoto, 1986; Harihara et al, 1988; Horai et al, 1996; Jinam et al, 2015, 2012; Tajima et al, 2004) were based on modern‐day samples. Historically, after the Meiji government started sending settlers to Hokkaido as a national policy in 1869 (Fumoto, 2004), an enormous number of mainland Japanese migrated to Hokkaido, and their apparent genetic influence on the modern‐day Ainu was confirmed by a genome‐wide single‐nucleotide polymorphism (SNP) analysis by Jinam et al (2012).…”