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SLC24A5 alleles

Many years ago I was perplexed by particular patterns in some genes which have been subject to very strong selection. In particular, the locus SLC24A5 has been subject to a powerful sweep over the last 10,000 years across Western Eurasia, to near total fixation in Europe, but still at high frequencies as far south as India. Yet the derived variant is relatively uncommon in East Asia. Groups which carry the West Eurasian variant, such as the Uyghurs, almost certainly obtained it through admixture processes over the last 10,000 years (in the case of the Uyghurs and various northeast Eurasian ethnicities such as the Mongols, this admixture from West Eurasians is mostly in historical time over the past 2,000 years).

The common sense explanation is that vast regions of interior Eurasia were not highly populated for tens of thousands of years. Even after the Ice Age retreated the Eurasian interior would have been particular inhospitable. Though maps of human migration show where humans have lived at some frequency all across the world, they do not usually show any sign of the density. If densities were low enough in the inter-montane zones of Inner Asia, then for all practical purposes the idea of isolation-by-distance gene flow may not have held for the two antipodes of Eurasia for much of the Pleistocene and early Holocene. So have things changed? I believe so. And it comes down to agriculture, which enabled much higher population densities in areas which were previously simply not feasible areas for hunter-gatherers.

A new paper in Science outlines this for Tibet, Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 B.P.. I’ll quote the relevant sections of the paper:

On the basis of the above evidence, the prehistoric human occupation of the NETP can be subdivided into three phases. During the first phase (pre–5200 cal yr B.P.), hunter-gatherers made occasional forays to altitudes reaching above 4300 masl, presumably tracking game. During the second phase (5200 to 3600 cal yr B.P.), a longstanding tradition of millet farming that had become widely established along the middle and lower reaches of the Yellow River extended upstream into the NETP. Millet farming had spread across the Loess Plateau after 5900 cal yr B.P. (17) and subsequently spread across these lower reaches of the NETP from 5200 cal yr B.P. Toward the end of the second phase (4000 and 3600 cal yr B.P.), two significant additions are observed in the crop repertoire (text S4 and fig. S6). The North Chinese crops of broomcorn and foxtail millet were joined or displaced on some sites by the principal cereals of the Fertile Crescent, barley and wheat. There has been much interest in the chronology and consequences of the meeting of east and west staple crops in prehistory (1820). Here, its notable consequence was to facilitate the sustained settlement of the Tibetan Plateau’s higher altitudes. The importation of wheat and barley enabled human communities to adapt to the harsher conditions of higher altitudes in the Tibetan Plateau, a possibility raised in previous studies (15, 21).

The key addition was barley. During phase three, from around 3600 cal yr B.P., sites can be divided into those that lie above or below 2500 masl. In the lower-altitude group, the longstanding crops, broomcorn and foxtail millet, are joined by barley as a third component in an otherwise traditional dietary repertoire. In the higher-altitude group, however, the frost-sensitive millet is absent, and the cold-tolerant barley has moved to a primary position (Fig. 2D). Alongside the presence of wheat (also relatively cold-tolerant) and sheep, the diet at these high altitudes has clearly been transformed, but in a manner that enabled sustained settlement at unprecedented altitudes.

There’s been a lot of interesting work on the genetics of Tibetans recently, from altitude adaptation from archaics, to the inference that a great deal of Tibetan ancestry is actually shared with the Han and other lowland groups in the past three to four thousand years. These results make more sense if you realize that the arrival of more advanced agricultural techniques reshaped the possibilities of habitation for humans at higher densities. In fact, it is almost certainly no coincidence that it is during the period of agriculture that the great fusions between the disparate “branches” of the human family tree came back together; higher population densities across huge areas mean that de facto gene flow no go zones disappeared.

• Category: Science • Tags: Genetics, Tibet 
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  1. anon • Disclaimer says:

    During the second phase (5200 to 3600 cal yr B.P.)

    Given how relatively recent that is it makes me wonder how recently Yetis survived in mountainous regions.

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    Regarding yetis, seems obligatory to link this one:
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  2. #1, crossed my mind :-)

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  3. Polynices says:

    During the second phase (5200 to 3600 cal yr B.P.)
    Given how relatively recent that is it makes me wonder how recently Yetis survived in mountainous regions.

    Regarding yetis, seems obligatory to link this one:

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  4. In the Chinese histories, the earliest of which might be dated to 1100, the Chinese occupied only about 10% of China, in the North Central area (near the Yellow River upstream from its mouth) , with other peoples who were most likely Sino-Tibetan living to their north, east, and west. (To South were various other peoples, probably Hmong-, Thai-, Viet-, and Cambodian-like). These peoples are sometimes enemies and sometimes allies but are clearly different political units and somewhat different in culture. Some of these people (e.g. the Qiang) always have been suspected of being Tibeto-Burman, though they also intermarried with Chinese and took leadership positions at times. Some seem to have been absorbed by the Chinese, while others just disappeared or migrated away. My guess is that non-Chinese were the majority of the population in the area and that Chinese gained dominance by combined political, military, and economic superiority.

    In short, the separation of Chinese and other Sinitic and Sino-Tibetan peoples probably was not complete even in 800 BC. And even the Shang dynasty (1500-1100), recognized as ancestral by the Chinese, doesn’t seem to have been culturally very similar to the Chinese of 800 BC and later.

    In short, relatively recent common Chinese / Tibetan ancestry isn’t really at all unlikely when you look at the documentary record.

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  5. Well it is the skin colour knock out allele isn’t it?

    “Divergent natural selection caused by differences in solar exposure has resulted in distinctive variations in skin color between human populations. The derived light skin color allele of the SLC24A5 gene, A111T, predominates in populations of Western Eurasian ancestry. To gain insight into when and where this mutation arose, we defined common haplotypes in the genomic region around SLC24A5 across diverse human populations and deduced phylogenetic relationships between them. Virtually all chromosomes carrying the A111T allele share a single 78-kb haplotype that we call C11, indicating that all instances of this mutation in human populations share a common origin. The C11 haplotype was most likely created by a crossover between two haplotypes, followed by the A111T mutation. The two parental precursor haplotypes are found from East Asia to the Americas but are nearly absent in Africa. The distributions of C11 and its parental haplotypes make it most likely that these two last steps occurred between the Middle East and the Indian subcontinent, with the A111T mutation occurring after the split between the ancestors of Europeans and East Asians.”

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  6. Razib – Do you think it would be possible to reconstruct these population densities using homozygousity of ancient DNA samples, or some other method that relies purely on genetics?

    It would think the demographic turnover at the transition from the Middle Paleolithic to the Upper Paleolithic may have had similar combination of climate/technology at work.

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  8. ohwilleke says: • Website

    One of the notable aspects of the population genetics of Tibet is that it is one of the rare reservoir of non-Japanese Y-DNA D (a sister clade to predominantly African Y-DNA E), specifically DE*, D*, D1 and D3, all of which are very old based on mutation rate estimates (D2 found in Japan is about 20,000 years younger in common ancestor than D1 and D3).

    DE* is also found in Northwest and West Africa.

    D* is also found in non-Chinese Tibeto-Burmese language speaking populations outside Tibet, in speakers of languages that belong to the same family as Thai and Laotian (Tai-Kadai), in Andamanese Islanders, and in small numbers in North Asians and Pacific Ocean Islanders.

    D1 is also found among the Han Chinese, non-Chinese Tibeto-Burmese language speaking populations outside Tibet, speakers of the languages that belong to the same family as Thai and Laotian, and speakers of the Hmong-Mien languages of Southeast Asia. “The southern ethnic populations (Daic and Hmong-Mien) form a relatively separate cluster from Tibetan and Tibeto-Burman populations in the D1-M15 sub-haplogroup.” The are a few Northeast Asian subtypes in the Tibeto-Burmese subtypes of subhaplotype D1, but are no Andamanese or Japanese peoples.

    D3 is also found among the Han Chinese and other Tibeto-Burmese langauge speakers, with D3* found in Tibet but not elsewhere.

    Given the gene pool in Tibet, this original Y-DNA D population was probably accompanied by women who were mtDNA M16.

    In Japan, the original bearers of Y-DNA D2 were probably accompanied by women of mtDNA M7 (also found in South Siberia, Korea and Southeast Asia).

    The Andamanese (an uncontacted population, completely until the last couple hundred years, on islands between SE Asia and India that probably arrived ca. 20kya) are Y-DNA D* and mtDNA M2.

    The unsolved question is whether Tibet is a source for the Y-DNA in the North or in the South, and from what direction its own Y-DNA D originated.

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  9. Regarding the parallel linguistic evidence, I’m reminded of Blench and Post’s tentative conclusion that all three of the major “national-level” Trans-Himalayan (a.k.a. Sino-Tibetan) languages, to wit Chinese, Burmese, and Tibetan, should be grouped together into a sub-sub-sub-node of the family. That is, the three famous Trans-Himalayan languages are genetically much closer to each other than to the vast bulk of the rest of the family (see Blench and Post “Rethinking Sino-Tibetan phylogeny from the perspective of North East Indian languages”). Blench and Post don’t give this sub-sub-sub-node a name, but I call it Sino-Burmo-Bodic when I’m feeling conservative or Zhouic if I’m feeling creative. You could also call it “narrow Sino-Tibetan” or “narrow Tibeto-Burman”. Van Driem has a similar hypothesis which he calls Sino-Bodic (he does not include Lolo-Burmese as especially close to Sinitic and Tibetan).

    I read a paper recently by Scott DeLancey in which he lays out a hypothesis of the origins of Proto-Sinitic. According to the paper, he’s building on similar ideas that have been discussed since the 70s, but it was all new to me. DeLancey emphasises the unusual linguistic environment of ancient China, in which relatively quite advanced city-states competed for power on the plains back well into prehistory. The result was a dramatic level of language contact, with a high percentage of L2 speakers, over a long period time under conditions that could change gradually or suddenly. The basic idea of his hypothesis is that when this environment first starts to come into historical view with the Shang kingdom as the dominant power, the Shang ruling class spoke a language that was not Sinitic. Instead, it most likely had a Hmong-Mien-like basis with heavy admixture from Tai, Austronesian, and Viet-Muong. This would mean that the language behind the earliest Chinese characters was not Chinese per se. The Zhou were a western vassal state and DeLancey argues that they were linguistically distinct, speaking a Sino-Tibetan language (“Sino-Burmo-Bodic” or “Zhouic” by my terminology for Blench and Post’s ideas). The Zhou language would have been strongly influenced by the Shang language and, over time, as the Zhou became more powerful, it would have begun to influence nearby languages. In other words, it moved gradually from substratum to superstratum. When the Zhou finally became the dominant power (ca. 2,800 years ago), they would have been a fundamentally Sino-Burmo-Bodic-speaking ruling class ruling a highly varied but primarily Hmong-Mien (or other SE Asian)-speaking populace, with literacy associated with the latter; and, crucially, both languages having already influenced each other for centuries. What resulted from this stew was Proto-Sinitic (see DeLancey “The Origins of Sinitic”).

    I believe Beckwith argues that both the Shang and the Zhou, as well as the early Qiangs were all led by Indo-European-speaking élites, but it’s harder to see how that’s plausible.

    I speculated in a previous comment on this blog ( that, since it seems likely that Trans-Himalayan (a.k.a. Sino-Tibetan)-speakers were the first to settle permanently on the plateau but common Han-Tibetan genes are much too recent to reflect that event, probably the Sherpa-like archaic population of the plateau were already Trans-Himalayan speakers from a much more distant branch of the family and their language was later replaced by that of Sino-Burmo-Bodic conquerors … this would have been not so long before Sino-Burmo-Bodic first became dominant on the central plain of China.

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  10. basically OT: it only occurred to me recently that mon/mron looks like an old ancestral Sino-Burmo-Bodic root word or wanderwort meaning “southerners who are not quite the same as us”. Possible examples are the Mons of Burma (southern foreigners from the perspective of the invading Burmese), the Mönpas of the Himalayas (southern foreigners to the Tibetans), and the “southern Man” (Old Chinese mˤro[n] per Baxter and Sagart) of the Sichuan area (southern foreigners to the ancient Chinese such as Liu Bei and Zhuge Liang), and perhaps also the ethnonyms “Hmong”, “Mien”, and “Muong”. (I seem to recall seeing a Tibetan example with mr- similar to the Old Chinese, but I can’t quite remember where exactly – could be wrong about that.

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