57 Journal of Human Genetics 787-795 (December 2012)
The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations
Japanese Archipelago Human Population Genetics Consortium
The Japanese Archipelago stretches over 4000 km from north to south, and is the homeland of the three human populations; the Ainu, the Mainland Japanese and the Ryukyuan. The archeological evidence of human residence on this Archipelago goes back to >30 000 years, and various migration routes and root populations have been proposed. Here, we determined close to one million single-nucleotide polymorphisms (SNPs) for the Ainu and the Ryukyuan, and compared these with existing data sets. This is the first report of these genome-wide SNP data. Major findings are: (1) Recent admixture with the Mainland Japanese was observed for more than one third of the Ainu individuals from principal component analysis and frappe analyses; (2) The Ainu population seems to have experienced admixture with another population, and a combination of two types of admixtures is the unique characteristics of this population; (3) The Ainu and the Ryukyuan are tightly clustered with 100% bootstrap probability followed by the Mainland Japanese in the phylogenetic trees of East Eurasian populations. These results clearly support the dual structure model on the Japanese Archipelago populations, though the origins of the Jomon and the Yayoi people still remain to be solved.The Yayoi people arrived in Japan from Korea immediately following the Jomon period in Japan around 900 BCE to 800 BCE. They brought with them the core of what would become the modern Japanese language, cavalry warriors, and the rice farming method of food production used on the mainland. The precise Korean culture on the then balkanized Korean penninsula that was ancestral to the Yayoi is disputed, but linguistically there were not a Tibeto-Burman people although they were a people who had experienced considerable Chinese cultural influence.
The culture created by the fusion of the Yayoi superstrate and the Jomon substrate upon the arrival of the Yayoi in Japan did not include all of Japan's main Honshu Island until about 1000 CE or later.
The genetic evidence shows that while the Jomon language and much of its culture was wiped out on Honshu, that a very substantial proportion of the genetic ancestry of the modern Japanese people is Jomon in comparison to other historically or archaeologically attested encounters between hunter-gatherer populations and farmers. The Jomon had pottery long before they were farmers, contrary to the experience in the Fertile Crescent where there was a long pre-Pottery Neolithic period, and in most other places.
The Ainu and Ryukuan ethnic minorities in Japan are widely believed to have significantly more indigineous Japanese (i.e. Jomon) ancestry and less Yayoi ancestry than the majority ethnicity in Japan. This autosomal genetic study appears to confirm this conclusion.
But, the genetics of the Ainu come with a twist. The Ainu appear to have another ancestral component not present in the also Jomon derived Ryukuan people. The obvious guess in the absence of the closed access paper, based on uniparental data available about the Ainu, would be that this other component is some now existing or now extinct or moribund Northeast Asian Paleo-Siberian popuation.
The Jomon are also very notable for being the apparent source of Y-DNA haplogroup D, a paternal lineage that is virtually absent in mainland East Asia and Southeast Asia, which is absent outside Tibet and the Andaman Islands except for trace to moderate frequencies similar to the Tibetan rather than to Japanese populations in North Asia. Y-DNA haplogroup D is more closely related to Y-DNA haplogroup E, which is the predominant Y-DNA haplogroup in modern Africa, than to any of the other Eurasian Y-DNA haplogroups. This suggests that the members of this migration wave may have been part of a migration wave distinct from that of the main Out of Africa migration that was ancestral to most of the rest of Eurasia.
There are two possible "two wave" scenarios. In one, the people of the Y-DNA haplogroup D came first and were brought to extinction by a later wave of migration in the remainder of East Eurasia, Australia, Melanesia and Oceania who arrived in Australia and Papua New Guinea not later than 45,000 years ago. In the other scenario, the people of Y-DNA haplogroup D were a secondary wave of out of Africa migration to Asia that was left with the territory that the first wave populations didn't occupy, didn't want, or couldn't defend, not later than about 30,000 years ago when Japan and Tibet were first populated, which is still well before the last glacial maximum ca. 20,000 years ago.
In the latter scenario, which I think is more likely, the Y-DNA haplogroup D people could have migrated either via a coastal maritime "Southern route" along the Southern coast of mainland Asia, or via a "Northern route" travelling to Tibet and Japan via Central Asia and/or Siberia and then migrating from Tibet to the parts of South Asia and Andaman Islands where Y-DNA haplogroup D is now found from Tibet. I am increasingly coming around to the Northern route, rather than the maritime coastal Southern route as the more plausible of the two possibilities. Other routes, such as a migration first to South India, then to Tibet, and from Tibet onto Japan are possible, but not necessarily persuasive since the archaeological evidence points to Tibet being populated from the direction of China, rather than India.
However, there is strong circumstantial evidence to suggest that the original Y-DNA haplogroup D people overwhelmingly had mtDNA haplogroup M. Neither Y-DNA haplogroup D nor mtDNA haplogroup M (or its descendants) are associated with any West Eurasian populations. So, if this D/M population did migrate via a Northern route, it is not easy to explain why they left no West Eurasian relic populations.
"But, the genetics of the Ainu come with a twist. The Ainu appear to have another ancestral component not present in the also Jomon derived Ryukuan people".
Y-DNA C1 also seems to be pre-Yayoi, although as far as I know it is mainly Ryukyu. That would mean it was Y-DNA D who came in with the 'Northeast Asian Paleo-Siberian popuation'.
"the people of Y-DNA haplogroup D were a secondary wave of out of Africa migration to Asia that was left with the territory that the first wave populations didn't occupy, didn't want, or couldn't defend, not later than about 30,000 years ago when Japan and Tibet were first populated"
To me the most likely expalnation as well.
"I am increasingly coming around to the Northern route, rather than the maritime coastal Southern route as the more plausible of the two possibilities".
Much more plausible. D is not present anywhere along any likely 'coastal route' between the Andamans and Japan. Mind you it is not present through any inland route between Africa and East Asia either, but let's not forget we have had an ice age which would have eliminated a percentage of the population along any such route.
"However, there is strong circumstantial evidence to suggest that the original Y-DNA haplogroup D people overwhelmingly had mtDNA haplogroup M".
I actually disagree with that although if we confine our observation to the Andamans we would come to that conclusion. In northeast Asia I suspect D is associated with mt-DNA N9 and A. I have no idea of how that fits with Ryuku/Ainu mt-DNAs but according to the McDonald map mt-DNA Y (part of N9) is particularly dominant in the Nivkh, just to the north of Japan. To me the Japanese M mt-DNAs look to be associated with Y-DNA O.
"So, if this D/M population did migrate via a Northern route, it is not easy to explain why they left no West Eurasian relic populations".
No problem if D was not origianlly associated with M but simply picked up M from along the shoreline as they moved out to the Andaman Islands.
"That would mean it was Y-DNA D who came in with the 'Northeast Asian Paleo-Siberian popuation'."
The private Japanese subclades of D have not been found at even trace levels in mainland Asia and split off at a quite basal position from other D subclades in the branching tree, while C1 is common on mainland Asia. So, this is not a plausible assumption.
"I actually disagree with that although if we confine our observation to the Andamans we would come to that conclusion."
This is based also on the likely pre-LGM mtDNA of Tibet (with other mtDNA having identifable more recent sources) and on the likely provenance of O in the Yayoi era.
N9 could easily be a post-LGM arrival to North Asia in the post-LGM repopulation of the region. You get M in Japan by extracting out the probably more recent Paleo-Siberian and Yayoi era contributions and seeing what remains.
"while C1 is common on mainland Asia"
Are you sure? I wasn't aware of that. I was sure it was confined to Japan. And that is what Wikipedia says:
"Haplogroup C-M8, an ancient but at present extremely rare lineage, is specific to the Japanese and Ryukyuan populations of Japan, among whom it occurs with a frequency of about 5% or less".
No mention of anywhere else.
"The private Japanese subclades of D have not been found at even trace levels in mainland Asia and split off at a quite basal position from other D subclades in the branching tree"
But the various D haplogroups have to have a common origin somewhere. And D is more widespread in Japan than is C1. I remember reading some comment on the paper which is the subject of your post that claimed the northern Ainu show evidence of two separate sources. The two Y-DNA haplogroups may represent those separate sources. I'll see if I can find the relevant article.
"N9 could easily be a post-LGM arrival to North Asia in the post-LGM repopulation of the region".
Could be, but that is unlikely. I doubt you've seen the following paper which I came across. I'm surprised that neither Dienekes nor Maju has posted on it (no Europeans involved in the publication?):
The paper separates Chinese mt-DNA into 'southern dominating haplogroups' and 'northern dominating haplogroups'. A and N* (presumably N9) are firmly in the second category. In fact the southern group is totally dominated by R-derived haplogroups R11'B (especially B4) and R9 (especially F1). M7 is the only 'southern' M haplogroup although M7c is placed within the 'northern' group. Figure 5 is the most interesting I think. It shows N and M with completely different distributions. N is concentrated in southeastern China Mainly R of course rather than 'N') while M looks obviously to have entered China from Arunachal Pradesh, not even through as far south as Burma. It's entry cannot possibly have been 'coastal' in any way at all. The northern 'N' outliers shown in the map are presumably A and N9. And here is a little more information on the Ainu. I can't access the article itself:
"You get M in Japan by extracting out the probably more recent Paleo-Siberian and Yayoi era contributions and seeing what remains".
But M rather than N could very easily have been the haplogroup introduced by the 'more recent Paleo-Siberian and Yayoi'. It could be N(xR) who are the more ancient haplogroups in Japan.
You make some fair points. I'll try to consider them in depth when I get a chance.
Actually the maps have given me a rethink. Y-DNA D may well have carried mt-DNA M north from the Tibet/China/India border region. I have always assumed mt-DNA N was first into Japan as it seems to predate M's presence in NE Asia. And Y is extremely common in the Nivkh. However it doesn't necessarily follow at all that it reached Japan at that time.
I found some interesting links on Jomon mt-DNA though. First off from Dienekes, which you obviously saw at the time:
"Haplogroups N9b, D4h2, G1b, and M7a were observed in these individuals, with N9b being the predominant one"
And another link that offers more information but supports the above (and pretty pictures):
I think Ainu people are much closer to Assamese and NE Indians. A book published in 2008 "TONKORI" explains their cultural and linguistic similarities. Also, the Assamese language has about hundreds of words similar to Ainu languages. Eg:-
"kara" in Ainu means to do
"kora" in Assamese also means the same.
"nei" of Ainu has similar uses of "xei" in Assamese.
"Meko" means cat in ainu whereas "Meko-ri" means the same in Assamese.
The musical instruments used by Ainus are also similar to some Assamese instruments like "Tonkori" which is "Tokori" in Assamese.Sword called "Emush" is similar to Assamese/Ahomese sword"Heng-Dang" There are also words which are similar to those used in Tai-Ahom(Extinct language),Tai-Khamti, Bishnuparia, Khasi, Sanskrit, Khampa, etc.
Post a Comment