2,000 years of Yayoi – Japanese are gaikokujin!

By Razib Khan | May 4, 2011 11:49 pm

A new paper in Proceedings of the Royal Society dovetails with some posts I’ve put up on the peopling of Japan of late. The paper is Bayesian phylogenetic analysis supports an agricultural origin of Japonic languages:

Languages, like genes, evolve by a process of descent with modification. This striking similarity between biological and linguistic evolution allows us to apply phylogenetic methods to explore how languages, as well as the people who speak them, are related to one another through evolutionary history. Language phylogenies constructed with lexical data have so far revealed population expansions of Austronesian, Indo-European and Bantu speakers. However, how robustly a phylogenetic approach can chart the history of language evolution and what language phylogenies reveal about human prehistory must be investigated more thoroughly on a global scale. Here we report a phylogeny of 59 Japonic languages and dialects. We used this phylogeny to estimate time depth of its root and compared it with the time suggested by an agricultural expansion scenario for Japanese origin. In agreement with the scenario, our results indicate that Japonic languages descended from a common ancestor approximately 2182 years ago. Together with archaeological and biological evidence, our results suggest that the first farmers of Japan had a profound impact on the origins of both people and languages. On a broader level, our results are consistent with a theory that agricultural expansion is the principal factor for shaping global linguistic diversity.

I don’t know the technical details of linguistics to comment, but the alignment between the linguistic model and archeology is pretty impressive to me. There’s a 95% confidence interval which can push the time back to 4,000 years, so there’s some fudge factor too. The basic technique is borrowed from phylogenetics. This is pretty clear when you notice that one of the algorithms seems to be the same one used in the rice genomics paper. Nick Wade covers the paper in The New York Times, so no need for me to give a blow-by-blow in a domain where I don’t have much insight anyway.


Dienekes Pontikos really likes these results and the method which they use. He, rightly in my opinion, believes that they lend more credence to the thesis promoted in the early 2000s using the same technique that the last common ancestor of Indo-European languages is very far back in time. I’m skeptical of this model, at least in its simple general form, but these results do push me into thinking that that model is more plausible. But to really understand this stuff I probably need to teach myself some rudimentary linguistics, so I guess we’ll see.

More broadly this gets to the question: did farming spread through demographic expansion or cultural diffusion? Obviously it’s not an either/or. There’s a small residual of Amerindian ancestry in American whites, so there was some diffusion through genetic assimilation. The Xhosa tribe of South Africa seem to have ~20% Khoisan ancestry. They’re the group on the Bantu farming frontier, the last before the Bantu toolkit ceased to be effective and the Khoisan managed to maintain their hold before the whites arrived. Some of the admixture is from pastoralist Khoi, but some of it may also be from hunter-gatherer Bushmen. But here’s my issue at this point: what are the examples where we know that hunter-gatherers picked up agriculture? The instances of Japan and the Bantu expansion are two where we’re now rather sure that it was demographic expansion and replacement. Was it so different in the past? I think it may have been insofar as farming was less advanced a cultural toolkit in terms of its ability to overpower hunter-gatherers. And yet still I am becoming more convinced of the thesis of that farming spread through procreation, not propagation. My hesitation is mostly due to the reality that our understanding of the past is so clouded as a fundamental matter.

CATEGORIZED UNDER: Anthroplogy, Culture
  • RK

    Wow, Razib, “gaikokujin”? I’ve never known you to be so P.C.

  • Charles Nydorf

    I do a lot using classical comparative reconstruction to work back from dialects to a common ancestor. When I’m lucky, there are old written texts against which I can check my results. What I have found is that the classical method tends to ascribe derived features to the common ancestor because it views parallel independent innovations as more implausible than they are. The method also tends to favor, too strongly,shorter, simpler paths of transformation from ancestral to modern forms and so tends to imply overly short chronologies. From what I can judge the same assumptions are built into this model so I would not take the date of the last common ancestor too literally.

  • Garvan

    ADMIXTURE results on the Pan Asian (my own tests) and “ref” database that you encouraged readers to try do not appear to support a replacement of of the Jomon people by Yoyoi people. The Ryukyuan sample form the Pan Asian sample stands out as population with a single color in the analysis, while the mainland Japanese population looks like it is derived from 20% Koreans. The better distribution of populations in the ‘ref’ data set including northern populations do conflict with this picture.

    20% Korean does not sound like an agricultural era replacement, but it is consistent with a language change.

    Or else the Yoyoi and the Jomon people were from related populations?

    Are there outer explanations that I do not consider?

    Garvan

  • Onur

    Garvan, to test the replacement theory you should at least compare Japanese with both Koreans and unadmixed Ainu (I don’t know if you used any Ainu sample in your Pan-Asian tests). Of course, the ideal is using ancient DNA.

  • jb

    Razib, I’ve been reading this blog regularly, and I’m still not clear on how well the most recent genetic studies align with what I think is the simple story you get just by eyeballing the people of Europe. The simple story says that, while farming may have allowed the first farmers to demographically overwhelm their neighbors, the replacement was more complete in southern Europe, because the climate was a better match to Anatolia, and because there was easy access from the sea. This explains in a general way why southern Europeans are darker than northern/eastern Europeans — they look more like the people of the Middle East because a greater portion of their ancestry comes from the Middle East.

    I’ve been telling people this story since I read Colin Renfrew’s “Language & Archaeology” years ago. It’s a very satisfying story, because it explains something that people can actually see with their own eyes. But now I keep reading about “near total replacement”. How can this be reconciled with the fact that people from different parts of Europe look so noticeably different? I can think of several possibilities, but I’m curious what you think about this.

  • Koreansentry

    well, does Buyeo-Baekje-Gaya sing any bells?
    Early Yayoi Japanese settlers were directly off-shoot from Gaya related Haan tribes of Korean peninsula from archeological to genetical POV. And then Baekje Kingdom of Korea sent large sum of immigrants to Yamatai (Yamato state). Yamatai kingdom or chiefdom expanded all over southern Japan by end of 5th century, during Baekje’s 4th century period, Yamatai was just small chiefdom state. Modern Japanese language contain a lot of Sino-words and Jomon words but their context is closer to Middle Korean language than anyone suggesting later arrival of settlers to Japan could well have been ancient Koreans tribes from Korean peninsula. Btw, both Gaya and Baekje were disappeared from Korea after Silla kingdom of Korea overran them.

  • http://3lbmonkeybrain.blogspot.com/ Mike Keesey

    “[W]hat are the examples where we know that hunter-gatherers picked up agriculture?”

    Not sure about this, but … eastern North America? Some of the native tribes were already practicing agriculture when the European settlers arrived (famously illustrated in the story of Thanksgiving).

    Could be examples in Papua New Guinea as well.

  • DK

    “approximately 2182 ago”

    LOL. But what if it was approximately 2153.5 years ago?

  • http://washparkprophet.blogspot.com ohwilleke

    A study that confidently tells us that with highly calibrated Japanese languages data from the era of Japanese ethnogenesis supported by data established by other means, isn’t all that impressive. Among other things, it doesn’t have to deal with the complications involved in that hypothesis that language changes fast upon initial divergence from a prior language and in periods of contact with other languages, as opposed to period of gradual random change over time. This analysis basically leapfrogs the language formation period for Japanese.

    Genetically, Japan is probably one of the best examples of a case where a pure replacement model doesn’t fit well. While there was obviously a major recent genetic contribution form East Asia, there was also clearly a substantial strata that is earlier, presumably the Jomon.

    The harder question for Japanese is where proto-Japanese in a larger perspective. The mainstream positions are either that the origin is so obscure, perhaps because related languages are extinct, that it is impossible to know (hence making it a language isolate), or that it is a relation of the Northeast Asian origin Altaic language (together with Korean). The connections from from lexical similarities (particularly in the minority of Japanese words that aren’t borrowed) and in residues of Altaic language features in Old Japanese.

    The linguistic data don’t match the recent genetic contribution from East Asia. Rather than looking like the Asian component of Altaic populations, it looks more or less Chinese genetically.

    The most sensible way to reconcile these facts, in my view, would be that an ethnically Chinese-esque population in Korea was conquered by a thin Altaic language superstrate population that left a strong linguistic mark, leading to language shift, but not a strong genetic mark (a la Hungary and Turkey), and that the language shifted population then moved onto Japan as the Yaoyi.

    Naiively, one might think that Japanese was changed by Jomon influences, making it hard to peg, but the lexical data suggest only only about 1% of Japannese words have that origin, and given that Ainu is still a living (if not very healthy) language, that estimate is credible. Cultural replacement was stronger than genetic replacement.

    Another example that might be comparable to Japan is hunter-gatherers picking up agriculture would be Northern Scandinavia and the Northern and Eastern parts of the former Soviet Union.

  • Onur

    there was also clearly a substantial strata that is earlier, presumably the Jomon

    Where is the evidence that it was substantial?

    The most sensible way to reconcile these facts, in my view, would be that an ethnically Chinese-esque population in Korea was conquered by a thin Altaic language superstrate population that left a strong linguistic mark, leading to language shift, but not a strong genetic mark (a la Hungary and Turkey), and that the language shifted population then moved onto Japan as the Yaoyi.

    That may also explain why Korea has a supposedly Altaic tongue despite genetic affinity to Chinese.

    Another example that might be comparable to Japan is hunter-gatherers picking up agriculture would be Northern Scandinavia and the Northern and Eastern parts of the former Soviet Union.

    But those transitions all happened during modern times.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Wow, Razib, “gaikokujin”? I’ve never known you to be so P.C.

    there are always kommissars complaining in the comments if i put stuff in titles. of course, if i am P.C., i get anti-kommissars complaining.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    But now I keep reading about “near total replacement”. How can this be reconciled with the fact that people from different parts of Europe look so noticeably different? I can think of several possibilities, but I’m curious what you think about this.

    i think there were several independent replacements. but weak confidence.

    Are there outer explanations that I do not consider?

    you need a ‘jomon’ outgroup. you don’t have one. the main issue with using okinawa is that it’s an isolated island. i can imagine that it’s just got issues with isolation allowing it create its own cluster, kind of like sardinia can.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Genetically, Japan is probably one of the best examples of a case where a pure replacement model doesn’t fit well. While there was obviously a major recent genetic contribution form East Asia, there was also clearly a substantial strata that is earlier, presumably the Jomon.

    i’ve read the uniparental stuff, but it doesn’t really show up in the autosome IMO too much. the jomon that is.

  • http://washparkprophet.blogspot.com ohwilleke

    “Where is the evidence that it was substantial?”

    Japanese specific mtDNA haplogroup frequency, Japanese specific Y-DNA haplogroup frequency and phylogeny, autosomal admixture component frequency. At least 40% of Japanese Y-DNA and 22% of Japanese mtDNA has a clear Jomon signature. We know from ancient DNA some of the mtDNA haplogroups that were common in the Jomon (also here) and can compare those frequencies to those found in modern populations.

    The autosomal signal isn’t as strong, but is still there – in my view the ancestral population/eigenvector methodology is is probably underestimating the Jomon component, perhaps because its differences from more recent populations may be fairly subtle at the level of detail examined (e.g. K=15). While uniparental market and autosomal marker frequencies don’t have to match, normally one would expect the Y-DNA frequencies to be lower rather than higher that autosomal frequencies in subjected populations that have their languages virtually obliterated, not elevated.

    There are lots of reasons that autosomal and uniparental frequencies get out of parity with each other. But, given the magnitude of the disconnect and the fairly short time period that it would have to have arisen during (2000 years give or take), one needs a pretty compelling story to explain why this disconnect arose, if there isn’t a good technical reason for the autosomal data to be off. We know to a high degree of certainty that the uniparentals have to be patriline or matriline ancestry informative. The autosomal data don’t give us phylogeny information in the same way.

    “That may also explain why Korea has a supposedly Altaic tongue despite genetic affinity to Chinese.”

    Agreed. The genetic and lingustic case that the Yayoi’s closest surviving population outside Japan are the Koreans is a strong one, although on the genetic front, it is hard to know how much of that is attributable to Japanese occupation of Korea in recent times. Koreans are more different from the Chinese than one might naiively expect given their proximity, however.

    “those transitions all happened during modern times.”

    Outside Southern Japan, we are talking 40 generations or less. In Southern Japan were are talking 80 generations. Northern Scandinavia and parts of the former Soviet Union converted to agriculture and pastoralism pre-1000 CE, switched back when the little ice age hit then, and then coverted to agriculture and/or pastoralism again in the late middle ages. The transitions aren’t exactly identical in era, but they aren’t orders of magnitude different either.

  • Matt

    Not sure about this, but … eastern North America? Some of the native tribes were already practicing agriculture when the European settlers arrived (famously illustrated in the story of Thanksgiving).

    This is a bit of a tangent to this, but in Mesoamerica, I think there isn’t really any sign of a “first farmer” dominant language group amongst the pre-Columbian agricultural populations, which is interesting. That’s my impression, someone like German Dzeibel would probably be in a better position to confirm or deny.

    The most sensible way to reconcile these facts, in my view, would be that an ethnically Chinese-esque population in Korea was conquered by a thin Altaic language superstrate population that left a strong linguistic mark, leading to language shift, but not a strong genetic mark (a la Hungary and Turkey), and that the language shifted population then moved onto Japan as the Yaoyi.

    Assuming that the idea is that the Altaic conquerors had the same advantages that later Turkic conquerors did, this seems like the bizarro world Kurgan Hypothesis where it happens at the opposite end of Eurasia! My understanding is that nomadic pastoralism is late in East Eurasia, so I’m not sure if I can credit this kind of expansion so early (which it seems like must be to be before a Japanese-Korean divergence), and it seems to rely on that being operative (unless there’s some other means for a group of non-farmers to take control over a group of farmers).

    It seems like there might be some kind of detectable Sino-Tibetan substrate in Korean if this is the case, though this would not necessarily be true and could be hard to distinguish from lanaguage contact.

    This probably isn’t the best post on which to place this comment, but I will say that I haven’t seen how an identification of Indo-European with the early Neolithic and Neolithic expansion is reconciled by the fact that the first attested written languages, presumably from the central part of the expanding, i.e. Sumerian, Elamite, Minoan, aren’t Indo-European. It’s hard to imagine Indo-European was specifically replaced in just these places.

  • Onur

    Andrew, thanks for the links, but I think uniparental studies, especially those of contemporary populations or of a very limited number and/or territorial range of ancient DNA samples, don’t tell much about ancient population movements and relationships. In East Asian autosomal studies, Japanese, Koreans and Han Chinese usually show up genetically pretty close to each other, with Koreans showing up in the middle of Han Chinese and Japanese in accordance with geography. For example, see:

    http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003862

    In that paper, the authors note: “With respect to population groups derived from very populous groups, the data indicate that Japanese and Korean were very closely related, as were Korean and Han Chinese”. They also note: “These studies also provide data supporting the derivation of many other EAS groups from a Han expansion (including She, Japanese, Dai, Lahu and Miao).” We can of course replace the phrase “Han expansion” with “rice farmer expansion” for more accuracy.

    As for the transitions to agriculture and pastoralism in northern Fenno-Scandinavia and northern and eastern parts of the former Soviet Union, they overwhelmingly began around 1500 CE at the earliest, in other words, during the modern era in Europe.

  • Onur

    they overwhelmingly began around 1500 CE at the earliest, in other words, during the modern era in Europe

    I think they were triggered both by the compulsions from European colonists (mostly Russians) and by the fact that advantages of a settled and agriculture-based populational lifestyle increased more than ever with the emergence of modernity.

  • http://washparkprophet.blogspot.com ohwilleke

    “they overwhelmingly began around 1500 CE at the earliest, ”

    By late middle ages, I’m suggesting roughly 1100-1400 CE, not very far in time in the greater scheme of things, particularly when it comes to degree of admixture genetically.

    “Assuming that the idea is that the Altaic conquerors had the same advantages that later Turkic conquerors did, this seems like the bizarro world Kurgan Hypothesis where it happens at the opposite end of Eurasia! My understanding is that nomadic pastoralism is late in East Eurasia, so I’m not sure if I can credit this kind of expansion so early (which it seems like must be to be before a Japanese-Korean divergence), and it seems to rely on that being operative (unless there’s some other means for a group of non-farmers to take control over a group of farmers). ”

    The Kurgan hypothesis (which is the leading theory by far among linguists) has horse domestication and the development of the core elements of the Indo-European culture developing around 3500 BCE in the Pontic-Caspian steppe. Kurgan hypothesis conquerers date to ca. 2500 BCE under that hypothesis in many of the places where they became prominent (e.g. India and Iran and Greece). People presumed to be Indo-European Tocharians reach the Tarim Basin around 2200 to 1900 BCE.

    The earliest language that could have split from a common proto-Altaic to be something associated with Korean or pre-Korean would be the language of the kingdom of Gojoseon in Northern Korea (which was a predecessor to some of the Three Kingdoms era states of Korea in the first millenium CE) which tradition says was founded in 2333 BC, but archaeological evidence and Chinese histories support from around 1500 BCE, and was a kingdom fused from a federation of smaller states around the 7th century BCE. A Japanese split from Korean would be ca. 700 BCE to 300 BCE. Korean as distinct from predecessor pre-Korean languages is usually dated to around 0 CE, although there is dispute concerning which of the three Kingdom languages is most closely associated with what emerged as a Korean language.

    The 1500 BCE to 600 BCE timing for Gojoseon divergence from other Altaic languages (it might be a sister language of the language of the Xianbei in Manchuria and Eastern Mongolia), is actually a quite good fit, chronology wise, to the arrival of nomadic pastoralism and Bronze age technology in that part of the world, probably with significant borrowings of technology and horses from far eastern Indo-Europeans. It is quite a bit later than in the West. Some of the parallel Chinese chronology would be as follows:

    244BC: First mention of Xiongnu, a nomadic pastoralist state North of China that the Great Wall was built to keep out. Traces of Xiongnu culture seem to be present from the 700 BCE, however, and the Zhukaigou culture of Inner Mongolia/Ordos enters the Bronze Age ca. 1500 BCE or perhaps a few hundred years earlier, around the same time as the Gojoseon to the east and is a candidate for a proto-Altaic urheimat.

  • http://www.tron.ru/ainu/historical/ Rechkabo Kakuhoningen

    We’re talking about Japan and its language. It is based on two elements – the language of arrivals from Korea zemledeltskev and Ainu. Explore the Japanese language without borrowing from the Ainu people is wrong. Ainu language does not apply to the Altaic group, he is much older and it has other roots. Conclusion – if you study the development of language, the right to study the Altaic language and its offspring – the whale

  • http://washparkprophet.blogspot.com ohwilleke

    @19 The evidence that the Japanese language has received much linguistically from Ainu is not well supported. Only about 1% of Japanese words have Ainu roots and it does not appear to have borrowed much gramatically or phonetically either. Probably the main Ainu impact would be those changes in Japanese from the predecessor language associated with having a large population of adult language learners for a few generations – basically a tendency to drop elaborations. Ainu may have some minor areal influences from Altaic but I would agree that its language family is genuinely an isolate with only the very most remote connection to any of the other living language families the exist in the world.

    Of course, Japanese also owes a great deal to Chinese. It is the source of about half of all Japanese words, its more commonly used set of number words, and its written language. Indeed, since Japanese and Chinese use the same ideograms in many instances, even when the spoken Japanese word differs from the Chinese one, it isn’t entirely incorrect to describe the status quo in Japan as stable bilingualism with a Japanese spoken language that used modified Chinese characters to express itself phonetically in writing and a Chinese literary language that does not have a Chinese oral counterpart in Japanese society.

    (Japanese religious beliefs likely integrate simultaneously multiple traditions with different origins – Shinto beliefs and folk animist/shamanism with origins that appear to resemble Chinese folk religion, Buddhism, and Confucian philosophy, all in their own place integrated seamlessly.)

    Modern Japanese also borrows more from English than it does from Ainu.

    Of course, since this is non-mysterious and involves well established borrowings in the historic era, we don’t think of Japanese language borrowings from Chinese, English and other languages as the “genetic origin” of Japanese. We think of the origins of Japanese as being the Yayoi language whose “wago” root words make up about a third of the Japanese lexicon and which provided the starting point for modern Japanese grammar and phonetics. It is this part of the source for the Japanese language that has Altaic affinities.

  • Justin Giancola

    Might you know how much of Korean is borrowed from Chinese? One would think a similar proportion if not more.

  • Time Traveler

    Justin Giancola

    Korean and Japanese have Chinese loan words in nouns and adjectives, but not grammar. It is similar to how English has French loan words, but are different grammar wise.

  • Time Traveler

    Some thoughts to add.

    Japanese reaction to this paper is obviously very unhappy, accusing the Tokyo University researchers of liberal bias, but the standard Japanese response is to reiterate the current leading theory on Yayoi origin. Yes, Yayoi came from Southern Korean Peninsula, but they weren’t ancestors to modern-day Korean and the peninsula Yayois went extinct by later-arriving Korean invaders from Siberia/Manchuria while Yayois prospered in Japan. Koreans would not be arriving in Japan until 4th century and their migration peaked in 7th Century, but Japanese estimate their numbers were no more than 250K.

    As for Korean origin, there has been significant progresses made in this department, and the current leading theory holds that Koreans are an off-shoot of Evenki, based on linguistic analysis which only became active after the fall of Soviet Union and found the closest match to Korean language nouns(native words, not Chinese-loan words). This theory is widely held in both Japan and Korea, and you can actually read lines like “Those Evenkis(Referring to Koreans) kicked out and massacred peaceful Yayois from the peninsula!” in Japanese news portals and message boards discussing this news. Why supposedly “Altaic” Koreans picked up rice farming is that their first settlement weren’t the Peninsula or even Manchuria, but Inner Mongolia and Shangdong Province based on archeological evidences, then relocated to Manchuria and then the Korean Peninsula after a series of conflicts with Chinese dynasties moving up from the Yellow River.

  • Justin Giancola

    thanks Time Traveler, but hoping for an estimate like half the words or something like that.

    I like how they try and ignore the studies that basically show that Koreans and Japanese are like the equivalent to the Irish and Scottish, to be played off Chinese and English respectively. Slightly different admixures but rooted in the same.

    Even with the language origins it’s neat to see the parallels in the far east and far west!

  • Time Traveler

    Justin Giancola

    “Slightly different admixures but rooted in the same.”

    Not necessarily. The biggest genetic contributors of Japanese ethnicity is Jomon(aka Ainu), followed by Southern Chinese. Koreans make up only 25% or so, although that 25% was enough to introduce Altaic grammar as bases of Japanese language.

    Korean gene-pool by contrast is majority Altaic(Evenki and Manchu), Scythian(Surname Kim is of Scythian origin based on genetic study and artifacts and are different from the rest of Altaic Koreans), 30% Chinese(Descendants of Han Dynasty colonists who were overrun by Koreans, but contributed in introduction of Chinese cultural product of writing, literature, and government system), and less than 1% Jomon.

    Basically, Jomon is the secret ingredient of Japanese gene pool, while Scythian is the secret ingredient of Korean gene pool, and you can actually tell them apart just by looking at these people as they physically look different.

  • Onur

    Time Traveler, what are the bases of your claims? None of the ancestry percentages you give seem plausible to me; I have seen nothing remotely similar to them in the literature.

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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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