Ainu genetics in their geographical context

Quickies

Timothy A. Jinam et al., Unique characteristics of the Ainu population in Northern Japan. Journal of Human Genetics 2015. Open access → LINK [doi:10.1038/jhg.2015.79]

Abstract

Various genetic data (classic markers, mitochondrial DNAs, Y chromosomes and genome-wide single-nucleotide polymorphisms (SNPs)) have confirmed the coexistence of three major human populations on the Japanese Archipelago: Ainu in Hokkaido, Ryukyuans in the Southern Islands and Mainland Japanese. We compared genome-wide SNP data of the Ainu, Ryukyuans and Mainland Japanese, and found the following results: (1) the Ainu are genetically different from Mainland Japanese living in Tohoku, the northern part of Honshu Island; (2) using Ainu as descendants of the Jomon people and continental Asians (Han Chinese, Koreans) as descendants of Yayoi people, the proportion of Jomon genetic component in Mainland Japanese was ~18% and ~28% in Ryukyuans; (3) the time since admixture for Mainland Japanese ranged from 55 to 58 generations ago, and 43 to 44 generations ago for the Ryukyuans, depending on the number of Ainu individuals with varying rates of recent admixture with Mainland Japanese; (4) estimated haplotypes of some Ainu individuals suggested relatively long-term admixture with Mainland Japanese; and (5) highly differentiated genomic regions between Ainu and Mainland Japanese included EDAR and COL7A1 gene regions, which were shown to influence macroscopic phenotypes. These results clearly demonstrate the unique status of the Ainu and Ryukyuan people within East Asia.

Figure 1. Principal component analysis (PCA) plot after omitting closely related Ainu individuals.

The study detected some differences between Ainu and other East Asians in genes that produce differences in appearance, these are:

Two out of five genes for facial morphology (PAX3 and COL17A1) contain highly differentiated SNPs, as with the hair/tooth morphology gene (EDAR).

Ancient Jomon mtDNA from Japan

Udege family

There is some debate about the connection between the Jomon period (Japan's ceramic but pre-agricultural period, extending between c. 16,000 to 2300 years ago) and the Ainu, as well as Ryukyuans and other peoples, including mainstream Japanese. A new study provides some extra bits of information to fuel the debate:

Hideaki Kanzawa-Kiriyama et al., Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan. Anthropological Science 2013 (advance publication). Open access → LINK [doi:10.1537/ase.121113]

The researchers sequenced ancient mtDNA from Jomon remains from a shell mound of Sanganji (Fukushima), which produced two M7a2, one N9b2 and one (incomplete) N9b* sequences.

Referring to previous similar studies as well, they produced the following tables:

From this data it would appear that the ancient Jomon people would be most closely related to modern Udegey (or Udege) from the Amur region of Eastern Siberia (with the possible exception of the Kanto Jomon, who may be closest to Ryukyuans instead).

The Sanganji sample is included pooled into Tohoku Jomon

The Ainu, it must be said, are next in line after the Udege, and I wonder if recent admixture may be distorting their relation. Another issue is that in such an extensive period of almost all the Holocene and even some millennia into the Pleistocene, there may have been flows and variability also within the Jomons (the Sanganji shell mound is dated to c. 4000-2500 BP, for example).

Whatever the case, it seems clear that N9b was an important matrilineage among ancient Jomon peoples, while M7a (now most common among Ryukyuans) was present but less common, with the Sanganji sample being rather exceptional in this.