Echoes of Siberia in Palaeolithic and prehistoric Japan

A 1988 study on distribution of genetic markers of human immunoglobin allotypes among Mongoloid populations revealed for the first time the high frequency of the Gm ab3st gene marker in the Japanese, though at the end of a cline that began with the Baikal Buriats, and that ran among Eskimos, Koryaks, Yakuts, Tibetans, Olunchuns, Tungus, Koreans, Japanese, and Ainus. The study showed that the Japanese people belonged to the northern Mongoloid grouping of people. Other studies (examined below) place many of the early haplogroups in southern Siberia or North Asia, with the remaining of East Asia or Southeast Asian origin:

Characteristics of Mongoloid and neighboring populations based on the genetic markers of human immunoglobulins. Matsumoto H.Hum Genet. 1988 Nov;80(3):207-18:

Since the discovery in 1966 of the Gm ab3st gene, which characterizes Mongoloid populations, the distribution of allotypes of immunoglobulins (Gm) among Mongoloid populations scattered from Southeast Asia through East Asia to South America has been investigated, and the following conclusions can be drawn: 1. Mongoloid populations can be characterized by four Gm haplotypes, Gm ag, axg, ab3st, and afb1b3, and can be divided into two groups based on the analysis of genetic distances utilizing Gm haplotype frequency distributions: the first is a southern group characterized by a remarkably high frequency of Gm afb1b3 and a low frequency of Gm ag, and the second, a northern group characterized by a high frequency of both Gm ag and Gm ab3st but an extremely low frequency of Gm afb1b3. 2. Populations in China, mainly Han but including minority nationalities, show remarkable heterogeneity of Gm allotypes from north to south and contrast sharply to Korean and Japanese populations, which are considerably more homogenous with respect to these genetic markers. The center of dispersion of the Gm afb1b3 gene characterizing southern Mongoloids has been identified as the Guangxi and Yunnan area in the southwest of China. 3. The Gm ab3st gene, which is found with the highest incidence among the northern Baikal Buriats, flows in all directions. However, this gene shows a precipitous drop from mainland China to Taiwan and Southeast Asia and from North to South America, although it is still found in high frequency among Eskimos, Koryaks, Yakuts, Tibetans, Olunchuns, Tungus, Koreans, Japanese, and Ainus. On the other hand, the gene was introduced into Huis, Uyghurs, Indians, Iranians, and spread as far as to include Hungarians and Sardinians in Italy. On the basis of these results, it is concluded that the Japanese race belongs to northern Mongoloids and that the origin of the Japanese race was in Siberia, and most likely in the Baikal area of the Soviet Union.

Related:

The origin of the Japanese race based on genetic markers of immunoglobulin G. Matsumoto H. Proc Jpn Acad Ser B Phys Biol Sci. 2009;85(2):69-82.

This review addresses the distribution of genetic markers of immunoglobulin G (Gm) among 130 Mongoloid populations in the world. These markers allowed the populations to be clearly divided into 2 groups, the northern and southern groups. The northern group is characterized by high frequencies of 2 marker genes, ag and ab3st, and an extremely low frequency of the marker gene afb1b3; and the southern group, in contrast, is indicated by a remarkably high frequency of afb1b3 and low frequencies of ag and ab3st. Based on the geographical distribution of the markers and gene flow of Gm ag and ab3st (northern Mongoloid marker genes) from northeast Asia to the Japanese archipelago, the Japanese population belongs basically to the northern Mongoloid group and is thus suggested to have originated in northeast Asia, most likely in the Baikal area of Siberia.

Distribution of Gm allotypes among the three populations of the Miyako Islands in Okinawa. Uchima E, et al. Nihon Hoigaku Zasshi. 1989 Aug;43(4):310-4. Abstract:

Serum samples from 738 unrelated individuals of three populations in the Miyako Islands were tested for twelve Gm allotypes to investigate the variability of phenotypes and haplotypes. Nine phenotypes observed in these populations as well as mainland Japanese could be explained by the presence of the four Gm haplotypes, ag, axg, ab3st, and afb1b3. A good agreement was obtained in the samples of each populations between the observed and expected frequencies on the basis of the Hardy-Weinberg equilibrium of phenotypes. These populations showed remarkable heterogeneities with one another on the basis of Gm haplotype frequency analysis. Moreover they exhibited no homogeneities with the Ryukyuans nor with the mainland Japanese. Homogeneity was found between the Ainu and the people in Ueno village but not in the other two locations. However, Gm xg haplotype, only detected in the Ainu, was not found in Ueno. These may imply a racial relationship between the Ainu and the inhabitants in Miyako in the remote past. However, there is no certainty that both of Ainu and the people in Ueno derived from the same origin, or that genetic drift due to endogamy in this village took place. The Gm phenotype and haplotype frequencies observed in Miyako show that they belong to the northern mongoloid group characterized by a high frequency of Gm ag and an extremely low frequency of Gm afb1b3. It is therefore reasonable to assume that they came from northern Asia as well as mainland Japanese.

It has also been shown that the majority of haplogroups C and D (mtDNA) subclusters demonstrate a pre-LGM origin and expansion in eastern Asia (unlike most of the southern and northeastern Siberian variants that started to expand after the LGM). The Late Glacial re-expansion of microblade-making populations from the refugial zones in southern Yenisei and Transbaikal region of southern Siberia that started approximately 18 kya has been suggested as a major demographic process signaled in the current distribution of northern Asian-specific subclades of mtDNA haplogroups C and D. It has been shown also that both of these haplogroups were involved in migrations, from eastern Asia and southern Siberia to eastern and northeastern Europe, likely during the middle Holocene.

See:

Origin and post-glacial dispersal of mitochondrial DNA haplogroups C and D in northern Asia. Derenko M. PLoS One. 2010 Dec 21;5(12):e15214.  PDF version

“More than a half of the northern Asian pool of mtDNA is fragmented into a number of subclades of haplogroups C and D, two of the most frequent haplogroups throughout northern, eastern, central Asia and America. Previous studies have proposed that haplogroups C and D originated around 30–50 kya in eastern Asia, from where they subsequently expanded northwards to southern Siberia, and further deep into northern Asia and the Americas, and westwards along the Steppe Belt extending from Manchuria to Europe [14], [15]. It has been also shown that haplogroups C and D were strongly involved in the late-glacial expansions from southern China to northeastern India [16]. In addition, because of their high frequency and wide distribution, haplogroups C and D most likely participated in all subsequent episodes of putative gene flow in northern Eurasia. These include (i) the Paleolithic colonization of Siberia that is associated with the development of macroblade industries (40–30 kya), (ii) further recolonization and possible replacement of early Siberians by microblade-making human populations from the Lake Baikal, Yenisei River, and Lena River basin regions (20 kya), (iii) appearance of pottery-making Neolithic tradition in the forest-steppe belt of northern Eurasia starting at about 14.5 kya and its expanding into the East European Plane (7 kya), (iv) the Neolithic dispersal of agriculture in eastern Asia, (v) the expansion of the Afanasievo and Andronovo cultures (5–3 kya), and (vi) more recent events of gene flow to eastern and central Europe.

The spread of haplogroups C and D

Haplogroups C and D display an extremely wide geographic distribution and high frequencies over most of their range. Haplogroup C peaks over 50% among Yukaghirs of northeastern Asia, central Siberian Yakuts and Evenks as well as East-Sayan Tofalars. Its frequency is persistently above 20% in Altaian, West-Sayan and Baikal region populations and drops to 13% or less among Chukchis, Eskimos and Itelmens in the east, Altaian Kazakhs, Shors, and Oroks in the south, and Khants and Kets in the west. The diminishing line (frequencies under 5%) goes through the Turkic and Finno-Ugric populations of the Volga basin, further south through the populations of the Caucasus and western Asia. In the southern direction the decline of haplogroup C frequency is almost as sharp as in the west direction: it is very common in Mongolia (15%) and most of the populations of central Asia (7–18%), but occurs as rarely as 1–5% in Korea, China, Thailand, Japan, Island southeastern Asia and India. Haplogroup C is detected at a very low frequency in several populations of eastern and central Europe and virtually absent in western Europe and Africa (Table S1).

The second most common haplogroup in all northern Asian populations is haplogroup D, which is also very common in eastern, central Asia and America. Haplogroup D encompasses almost 20% of the total mtDNA variation in most of northern Asia and retains a very high overall frequency in all regional northern Asian groups (11–34%), central Asian (14–20%) and eastern Asian (10–43%) populations (Table S2). Its frequency declines towards the west and south, to 2% or less in India and western Asia, but in the Caucasus, Volga-Ural Region and southeastern Asia is still as high as 5–10%. Interestingly, haplogroup D is also found in some northeastern Europeans, like Karelians, Saami and Scandinavians, while haplogroup C is absent among them (Table S2).

The peopling of northern Asia by anatomically modern humans probably began more than 40 kya, with the first evidence in the Altai region, suggesting the southern mountain belt of Siberia and Middle Siberian plateau as a likely route for this pioneer settlement of northern Asia [33]–[36]. The present-day variation of haplogroups C and D suggests that these mtDNA clades had already expanded before the LGM, with their oldest lineages being present in the eastern Asia. In particular, most of the eastern Asian subclades of haplogroup D show coalescence ages of between 15 and 42 kya, thus suggesting that some of them were already present here before the LGM. As for northern Asia, most of the present-day southern and northeastern Siberian variants of haplogroups C and D started to expand after the LGM. This can be partially ascribed, as in Europe [31], [37]–[39] and southeastern Asia [40], to the (re)colonization processes of areas which were unsuitable for human occupation during the LGM due to aridity and lower temperatures. The Late Glacial re-expansion of microblade-making populations from the small refugial areas in southern Yenisei and Transbaikal region of southern Siberia at the end of the Ice Age from ∼18 kya could be suggested as a major demographic process signaled in the mtDNA by the distribution of northern Asian-specific subclades of haplogroups C and D. The age of haplogroup C5, ∼14–17 kya, supports this postulated arrival after the LGM, as does the age of the D2 and D4b1a2, which date to ∼11–21 kya. However, all northeastern Asian-specific subclades present ages lower than 10 kya, so it is possible that their arrival into the Arctic region of northern Asia occurred later, in Holocene.”

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Complete Mitochondrial DNA Analysis of Eastern Eurasian Haplogroups Rarely Found in Populations of Northern Asia and Eastern Europe Derenko M, PLoS ONE 7(2): e32179. doi:10.1371/journal.pone.0032179

Haplogroup N9a is characteristic of eastern Asian populations, where it is detected at a highest frequencies in Japan (4.6%), China (2.8%), Mongolia (2.1%) and Korea (3.9%). Haplogroup N9a is rare in Taiwan (1.2%) and Island southeastern Asia (1.1%), but appears at greater frequencies in Mainland southeastern Asia (1.5–4.5%). With the comparable frequencies this haplogroup is detected in several populations of northern (0.9%–4.6%) and central Asia (1.2–2.5%), but it is virtually absent in western and southern Asia. Interestingly, haplogroup N9a is rarely found in the Volga-Ural region Tatars (~1%) and Bashkirs (1.5%) as well as in some eastern Europeans, like Russians from southwestern Russia (1.5%) and Czechs (0.6%)….Information from complete mtDNA sequencing reveals that Buryat sample (Br_623) and previously published Japanese sample (HNsq0240) from Tanaka et al. share mutations at nps 11368 and 15090 and therefore belong to a rare N9a8 haplogroup (Figure S3). It should be noted that these two sequences showed deep divergence with each other being characterized by unique sets of seven and six mutations respectively. As follows from phylogenetic analysis data, our Barghut sample (Bt_81) shares transversions at nps 4668 and 5553 with two published Japanese samples and therefore can be ascribed to a previously reported subcluster N9a2a3, Tatar sample (Tat_411G) which is identical to Japanese sample KAsq0018 [21] is a part of N9a2a2, Khamnigan (Khm_36) and Korean (Kor_87) mtDNAs belong to N9a1, whereas Korean (Kor_92) and Buryat (Br_433) variants can be identified as members of N9a3. Interestingly, Russian (Rus_BGII-19) and Czech (CZ_V-44) samples bearing transitions at nps 4913 and 12636 apparently belongs to a new subbranch N9a3a within haplogroup N9a3. Despite the low coalescence time estimates obtained for N9a3a (~1.3–2.3 kya) it is quite probable that its founder had been introduced into eastern Europe much earlier taking into account the age of a whole N9a3 estimated as 8–13 kya and the discovery of a N9a haplotypes in a Neolithic skeletons from several sites, located in Hungary and belonged to the Körös Culture and Alföld Linear Pottery Culture, which appeared in eastern Hungary in the early 8th millennium B.P.

Haplogroups M10, M11 and M13.

Haplogroups M10, M11 and M13 are most common in eastern Asia where they all detected at low frequencies (<5%) [8], [28], . Sporadically these haplogroups have been reported in southern, northern, central and southeastern Asia [8], [21], [30], [32], [36], [47], [48] as well as in eastern Europe – in Russians [49] and Kalmyks [8]. To further elucidate the origin of eastern Eurasian lineages found in mitochondrial gene pools of northern Asians and define more exactly the phylogeny of these rare haplogroups, we have completely sequenced mitochondrial genomes of ten individuals from populations of northern and eastern Asia, and eastern Europe (Figures S4, S5, and S6).

Until now there were only ten completely sequenced M10 subjects. The addition of our Shor sequence (Sh_27) to the tree (Figure S4) gives a branching point for M10a1, defined now by the only transition at np 16129. An Altaian sample (Alt_164) nested with Japanese sample (SCsq0008 [50]) formed a subclade, M10a1a2a, characterized by coding region mutation at np 10529 and back mutation at np 16129. Interestingly, our eastern European M10 mtDNAs (Rus_Vo-78 and Km_27) together with Japanese sequence (ONsq0096 [21]) clustered into another branch, M10a2a, within the second major M10a-subclade, M10a2. It should be noted that the results of mtDNA control region study in central Asian populations demonstrate the presence of M10a2a-haplotypes in Kazakhs at frequency of 0.8% [36]. In general, coalescence time estimate for M10a2a corresponds to 6–11 kya (Table S3), suggesting a relatively recent (post-Neolithic or later) origin and diffusion of M10a2a lineages from central Asia to eastern Europe.

We have also sequenced three complete M11 Siberian mtDNA genomes and compared them with all published M11 complete sequences. Figure S5 displays the reconstructed phylogeny of this haplogroup from which follows that our Buryat sequence (Br_444) fell into subhaplogroup M11a, whereas Altaian mtDNA genome (Alt_33) shared insertion of cytosine at np 459 and transition at np 5192 with Japanese mtDNA (HO1019 [51]) and formed a separate subclade, M11b2, within subhaplogroup M11b. It should be noted that one more subclade, M11b1, characterized by one control region (146) and two coding region (10685 and 14790) transitions can be revealed within M11b….

Haplogroup M9.

Eastern Eurasian haplogroup M9 encompasses two subclades – E and M9a’b, showing a very distinctive geographic distribution. While subhaplogroup E is detected mainly in Island southeastern Asia and Taiwan, haplogroup M9a’b is distributed widely in mainland eastern Asia and Japan and relatively concentrated in Tibet and surrounding regions, including Nepal and northeastern India [31], [45], [46], [48], [52], [53]. It has been proposed recently that haplogroup M9 as a whole had most likely originated in southeastern Asia approximately 50 kya, whereas M9a’b itself spread northward into the eastern Asian mainland about 15 kya, after the LGM. The complete mtDNA sequence analysis and the coalescence time estimates obtained suggest that certain subclades of M9a’b were likely associated with some post-LGM dispersals in eastern Asia, especially in Tibet…Altaian Kazakh (Kz_69) and Kalmyk (Km_79) samples bear transversion at np 10951 and belong to subcluster M9a1b2 revealed recently in southwestern Chinese representatives [53], whereas Korean (Kor_10) mtDNA and complete genome of Vietnamese individual (Kinh_88 [53]) share transition at np 6815 and may therefore represent a new subcluster, M9a4b, within M9a4, distributed both in southeastern Asia and southern and northern China (Figure S7). Interestingly, the remaining of our M9a mtDNA sequences (Br_377, Khm_15, Tv_351c) fall into subclades which were mainly found in Japan (M9a1a1a1), Japan and China (M9a1a1c1a1), southwestern China and Tibet (M9a1a1c1b). Thus, the M9a1a1-lineages revealed in northern Asian populations could be regarded as a traces of northward Late Glacial dispersal(s) originating in southern China about 14–17 kya proposed on the basis of the phylogeographic pattern of haplogroup M9a1a1….the addition of a large number of completely sequenced haplogroup B mtDNAs from northern and eastern Asian populations to available data sets has allowed us to reveal a few new subclusters within the haplogroup B4 (B4b1a3, B4b1a3a, B4c1a2 and B4j) showing predominantly northern Asian distribution. The whole subcluster B4b1a3 showed a coalescent time of approximately 18 to 20 kya, whereas subclusters B4b1a3a and B4c1a3 emerged around 9 to 13 kya and 7 to 8 kya, respectively. As a result, coalescence age estimates placed the origin of subcluster B4b1a3 in the LGM episode, while subclusters B4b1a3a and B4c1a2 are in a more recent post-glacial period (the end of the Pleistocene and the early Holocene). Our findings confirm our previous conclusion that northern Asian maternal gene pool consists of predominantly post-LGM components of eastern Asian ancestry, though some genetic lineages may have a pre-LGM/LGM origin….

The results of our study provided an additional support for the existence of limited maternal gene flow between eastern Asia/southern Siberia and eastern Europe revealed by analysis of modern and ancient mtDNAs previously. Two more mtDNA subclusters which may be indicative of eastern Asian influx into gene pool of eastern Europeans have been revealed within haplogroups M10 and N9a. The presence of N9a3a subcluster only in eastern European populations may indicate that it could arose there after the arrival of founder mtDNA from eastern Asia about 8–13 kya. It is noteworthy that another eastern Asian specific lineage, C5c1, revealed exclusively in some European populations (Poles, Belorussians, Romanians), shows evolutionary ages within frames of 6.6–11.8 kya depending on the mutation rates values [12]. In addition, recent molecular-genetic study of the Neolithic skeletons from archaeological sites in the Alföld (Hungary) has demonstrated high frequency of eastern Asian mtDNA haplogroups in ancient inhabitants of the Carpathian Basin [42]. Specifically, haplogroups N9a and C5 were also revealed in remains, thus indicating that genetic continuity for some eastern Asian mtDNA lineages in Europeans is possible from the Neolithic Period. Prehistoric migrations associated with the distribution of the pottery-making tradition initially emerged in the forest-steppe belt of northern Eurasia starting at about 16 kya and spread to the west to reach the south-eastern confines of eastern European Plain by about 8 kya [60] could be suggested as a potential cause for eastern Asian mtDNA haplogroups appearance in Europe.

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Mitochondrial DNA analysis of Hokkaido Jomon skeletons: Remnants of archaic maternal lineages at the southwestern edge of former Beringia, Adachi, Noboru et al.  American Journal of Physical Anthropology

Volume 146Issue 3pages 346–360November 2011

Abstract:   To clarify the colonizing process of East/Northeast Asia as well as the peopling of the Americas, identifying the genetic characteristics of Paleolithic Siberians is indispensable. However, no genetic information on the Paleolithic Siberians has hitherto been reported. In the present study, we analyzed ancient DNA recovered from Jomon skeletons excavated from the northernmost island of Japan, Hokkaido, which was connected with southern Siberia in the Paleolithic period. Both the control and coding regions of their mitochondrial DNA (mtDNA) were analyzed in detail, and we confidently assigned 54 mtDNAs to relevant haplogroups. Haplogroups N9b, D4h2, G1b, and M7a were observed in these individuals, with N9b being the predominant one. The fact that all these haplogroups, except M7a, were observed with relatively high frequencies in the southeastern Siberians, but were absent in southeastern Asian populations, implies that most of the Hokkaido Jomon people were direct descendants of Paleolithic Siberians. The coalescence time of N9b (ca. 22,000 years) was before or during the last glacial maximum, implying that the initial trigger for the Jomon migration in Hokkaido was increased glaciations during this period. Interestingly, Hokkaido Jomons lack specific haplogroups that are prevailing in present-day native Siberians, implying that diffusion of these haplogroups in Siberia might have been after the beginning of the Jomon era, about 15,000 years before present. Am J Phys Anthropol, 2011. © 2011 Wiley-Liss, Inc.

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Evidence of early settlement in Eurasian Siberia and possible genetic affinity with East Asians:

The following paper is of significance on the issue of evolution of the Upper Paleolithic in Eurasia:

a. it is the oldest full genome of a modern human published for Eurasia, and the authors estimate the age of the Ust’-Ishim bone artifacts to be 49,000 years BP (95% highest posterior den-sity: 31,000–66,000 years BP), consistent with the radiocarbon date

b. the Ust’-Ishim individual represents a population derived from the population involved in the dispersal of modern humans out of Africa

c. “The Y chromosome sequence of the Ust’-Ishim individual is similarly inferred to be ancestral to a group of related Y chromosomes (haplogroup K(xLT)) that occurs across Eurasia today while on the mtDNA side:

“The Ust’-Ishim mtDNA sequence falls at the root of a large group of related mtDNAs (the ‘R haplogroup’), which occurs today across Eurasia (Supplementary Information section 8).”

d. “the finding that the Ust’-Ishim individual is equally closely related to present-day Asians and to 8,000-to 24,000-year-old individuals from western Eurasia”

Qiaomei Fuet al. Genome sequence of a 45,000-year-old modern human from western Siberia Genome sequence of a 45,000-year-old modern human from western Siberia, Nature 514, 445–449 (23 October 2014) doi:10.1038/nature13810 29 August 2014  Published online 22 October 2014

We present the high-quality genome sequence of a ~45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10−9 to 0.6 × 10−9 per site per year, a Y chromosomal mutation rate of 0.7 × 10−9 to 0.9 × 10−9 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10−8 to 3.2 × 10−8 per site per year based on the age of the bone…

Population relationships

About 7.7 positions per 10,000 are heterozygous in the Ust’-Ishimgenome, whereas between 9.6 and 10.5 positions are heterozygous inpresent-day Africans and 5.5 and 7.7 in present-day non-Africans (Supplementary Information section 12). Thus, with respect to genetic diversity,the population to which the Ust’-Ishim individual belonged wasmore similar to present-day Eurasians than to present-day Africans,which probably reflects the out-of-Africa bottleneck shared by nonAfricanpopulations. The Ust’-Ishim mtDNA sequence falls at the root of a large group of related mtDNAs (the ‘R haplogroup’)# see Kivisild below, which occurs today across Eurasia (Supplementary Information section 8). The Y chromosome sequence of the Ust’-Ishim individual is similarly inferred to be ancestral to a group of related Y chromosomes (haplogroup K(xLT))that occurs across Eurasia today6(Supplementary Information section 9). As expected, the number of mutations inferred to have occurred on the branch leading to the Ust’-Ishim mtDNA is lower than the numbers inferred to have occurred on the branches leading to related presentday mtDNAs (Supplementary Fig. 8.1). Using this observation and nine directly carbon-dated ancient modern human mtDNAs as calibration points5,7 in a relaxed molecular clock model, we estimate the age of the Ust’-Ishim bone to be ,49,000 years BP (95% highest posterior density: 31,000–66,000 years BP), consistent with the radiocarbon date.In a principal component analysis of the Ust’-Ishim autosomal genome along with genotyping data from 922 present-day individuals from 53 populations8(Fig. 2a), the Ust’-Ishim individual clusters withnon-Africans rather than Africans. When only non-African populations are analysed (Fig. 2b), the Ust’-Ishim individual falls close to zeroon the twofirst principal component axes, suggesting that it does not share much more ancestry with any particular group of present-day humans.To determine how the Ust’-Ishim genome is related to the genomes of present-day humans, we tested, using D statistics8,whether it shares more derived alleles with one modern human than with another modern human using pairs of human genomes from different parts of the world (Fig. 3).Based on genotyping data for 87 African and 108 non-African individuals(Supplementary Information section 11), the Ust’-Ishim genome shares more alleles with non-Africans than with sub-Saharan Africans(jZj 5 41–89), consistent with the principal component analysis,mtDNA and Y chromosome results. Thus, the Ust’-Ishim individual represents a population derived from, or related to, the population involved in the dispersal of modern humans out of Africa. Among the non-Africans  the Ust’-Ishim genome shares more derived alleles with present-day people from East Asia than with present-day Europeans (jZj 5 2.1–6.4). However, when an 8,000-year-old genome from western Europe (LaBran˜a)9  or a 24,000-year-old genome from Siberia (Mal’ta 1)10 were analysed, there is no evidence that the Ust’-Ishim genome shares more derived alleles with present-day East Asians than with these prehistoric individuals (jZj , 2). This suggests that the population to which the Ust’-Ishim individual belonged diverged from the ancestors of present-day West Eurasian and East Eurasian populations before—or simultaneously with—their divergence from each other. The finding that the Ust’-Ishim individual is equally closely related to present-day Asians and to 8,000-to 24,000-year-old individuals from western Eurasia, but not to presentday Europeans, is compatible with the hypothesis that present-day Europeans derive some of their ancestry from a population that did not participate in the initial dispersals of modern humans into Europe and Asia11.

We also estimated a phylogeny relating the non-recombining part of the Ust’-Ishim Y chromosome to those of 23 present-day males. Using this phylogeny, we measured the number of ‘missing’ mutations in the Ust’-Ishim Y chromosomal lineage relative to the most closely related present-day Y chromosome analysed. This results in an estimate of the Y chromosome mutation rate of 0.76 3 1029 per site per year (95% CI 0.67 3 1029 to 0.86 3 1029 ) (Supplementary Information section 9), significantly higher than the autosomal mutation rate, consistent with mutation rates in males being higher than in females18–20. Finally, using the radiocarbon date of the Ust’-Ishim femur together with the mtDNAs of 311 present-day humans,we estimated the mutation rate of the complete mtDNA to be 2.53 3 1028 substitutions per site per year (95% highest posterior density: 1.76 3 1028 to 3.23 3 1028 ) (Supplementary Information section 8) for mtDNA, in agreement with a previous study5
Neanderthal admixture The time of admixture between modern humans and Neanderthals has previously been estimated to 37,000–86,000 years BP based on the size of the DNA segments contributed by Neanderthals to present-day nonAfricans21.
Thus, the Ust’-Ishim individual could pre-date the Neanderthal admixture. From the extent of sharing of derived alleles between the Neanderthal and the Ust’-Ishim genomes we estimate the proportion of Neanderthal admixture in the Ust’-Ishim individual to be 2.3 6 0.3% (Supplementary Information section 16), similar to present-day east Asians (1.7–2.1%) and present-day Europeans (1.6–1.8%). Thus, admixture with Neanderthals had already occurred by 45,000 years ago. In contrast, we fail to detect any contribution from Denisovans, although such a contribution exists in present-day people not only in Oceania22,23, but to a lesser extent also in mainland east Asia12,24 (Supplementary Information section 17).
The DNA segments contributed by Neanderthals to the Ust’-Ishim individual are expected to be longer than such segments in presentday people as the Ust’-Ishim individual lived closer in time to when the admixture occurred, so there was less time for the segments to be fragmented by recombination. To test if this is indeed the case, we identified putative Neanderthal DNA segments in the Ust’-Ishim and presentday genomes based on derived alleles shared with the Neanderthal genome at positions where Africans are fixed for ancestral alleles. Figure 5 shows that fragments of putative Neanderthal origin in the Ust’-Ishim individual are substantially longer than those in present-day humans.
We use the covariance in such derived alleles of putative Neanderthal origin across the Ust’-Ishim genome to infer that mean fragment sizes in the Ust’-Ishim genome are in the order of 1.8–4.2 times longer than in present-day genomes and that the Neanderthal gene flow occurred 232–430 generations before the Ust’-Ishim individual lived (Supplementary Information section 18; Fig. 6). Under the simplifying assumption that the geneflow occurred as a single event, and assuming a generation time of 29 years16,25, we estimate that the admixture between the ancestors of the Ust’-Ishim individual and Neanderthals occurred approximately 50,000 to 60,000 years BP, which is close to the time of the major expansion of modern humans out of Africa and the Middle East. However, we also note that the presence of some longerfragments (Fig. 5) may indicate that additional admixture occurred even later. Nevertheless, these results suggest that the bulk of the Neanderthal contribution to present-day people outside Africa does not go back to mixture between Neanderthals and the anatomically modern humans who lived in the Middle East at earlier times; for example, the modern humans whose remains have been found at Skhul and Qafzeh…
An Initial Upper Paleolithic individual?
A common mode lfor themodern human colonization of Asia23,28 assumes that an early coastal migration gave rise to the present-day people of Oceania, while a later more northern migration gave rise to Europeans and mainland Asians. The fact that the 45,000-year-old individual from Siberia is not more closely related to the Onge from the Andaman Islands (putative descendants of an early coastal migration) than he is to present-day East Asians or Native Americans (putative descendants of a northern migration) (Fig. 3) shows that at least one other group to which the ancestors of the Ust’-Ishim individual belonged colonized Asia before 45,000 years ago. Interestingly, the Ust’-Ishim individual probably lived during a warm period (Greenland Interstadial 12) that has been proposed to be a time of expansion of modern humans into Europe29,30. However, the latter hypothesis is based only on the appearance of the so-called ‘Initial Upper Paleolithic’ industries (Supplementary Information section 5), and not on the identification of modern human remains31,32. It is possible that the Ust’-Ishim individual was associated with the Asian variant of Initial Upper Paleolithic industry, documented at sites such as Kara-Bom in the Altai Mountains at about 47,000 years BP. This individual would then represent an early modern human radiation into Europe and Central Asia that may have failed to leave descendants among present-day populations29.

 

# The major branches of the Asian mtDNA tree displaying the East Asian–specific haplogroups. The tree is rooted in haplogroup L3. You can see the root of ancestral R haplogroup branching off.   Each haplogroup is indicated by its ancestral haplotype. Informal distinction between the trunks (black), limbs (dark gray), boughs (gray), and twigs (white background boxes) is according to the main text Source: Fig. 2 Toomas Kivisild, et al., The Emerging Limbs and Twigs of the East Asian mtDNA Tree

<img src=”http://mbe.oxfordjournals.org/content/19/10/1737/F2.medium.gif&#8221; alt=”” />

N-M46 or Tat-C (see Racial Reality), the most frequent subclade of N,  is said to have originated 14,000 years ago in Central Asia,  but that it subsequently experienced serial bottlenecks in Siberia(& Pakendorf 2002) , where the haplogroup reached a maximum frequency of approximately 90% among the Yakuts, a Turkic people who live mainly in the Sakha (Yakutia) Republic and also has been detected in 1.4% (1/70) of a sample from Tokushima, Japan (Hammer 2005).
The Tat-C haplogroup was observed at significant frequencies in each of the southern Middle Siberian populations studied. Surprisingly, it reached its highest frequency in the Siberian Eskimos and Chukchi from the Chukotkan peninsula. The Tat-C haplogroup was absent in the Lower Amur and Sea of Okhotsk region populations that have maintained greater geographic and/or linguistic isolation (e.g., the Udegeys, Nivkhs, and Upriver Negidals) and was only detected in the populations likely to have had recent contact or shared origins with the populations of southern Middle Siberia (e.g., the Okhotsk Evenks, Ulchi/Nanai, and Downriver Negidals). Because the Tat-C polymorphism originated on a Y chromosome containing the DYS7C deletion (haplogroup 7C), which was present only in the Middle Siberian Tuvans, Buryats, Tofalars, and Yenisey Evenks, the Tat-C haplogroup probably entered the Lower Amur and eastern Siberia from southern Middle Siberia. This conclusion is consistent with the previous hypothesis that the Tat-C and 7C haplogroups arose in central Asia and migrated west to northern Europe and east to Chukotka (Zerjal et al. 1997). — Source: The Dual Origin and Siberian Affinities of Native American Y Chromosomes Lell et al. 2002
“The network of Tat-C and DYS7C haplotypes revealed that the ancestral Tat-C haplotype (7C[11-11-10-10]) was found only in southern Middle Siberia, indicating that this Y-chromosome lineage arose in that region. Moreover, the limited microsatellite diversity and resulting compact nature of the network indicates that the Tat-C lineage arose relatively recently (Zerjal et al. 1997).
The haplogroup N-M46 has a low diversity among Yakuts suggestive of a population bottleneck or founder effect (& Pakendorf 2002). This was confirmed by a study of ancient DNA which traced the origins of the male Yakut lineages to a small group of horse-riders from the Cis-Baikal area (Crubézy 2010).
***

Examining life in Siberian settlements near Lake Baikal

Below is an excerpt detailing life in the earliest prehistoric Siberian settlements from “A history of Russia, Central Asia and Mongolia” by David Christian. Life of Palaeolithic hunter-gatherers in Japan would likely not have differed much from that of those in Siberia.

“The Malaya Siya site near Lake Baikal is one of the oldest Siberian sites, dating perhaps from 35,000 years ago. There are signs here of the hunting of mammoth, horse, reindeer and other large herbivores. From about 20,000 BP, there appear more modern and more distinctive traditions in western Siberia. At the Afontova Gora site near Krasnoyarsk, people lived in easily portable tents, and wore distinctive styles of clothes, including light caftans, fur boots, and short trousers. The main animal remains here are of reindeer. This is also true of the Mal’ta site, near Lake Baikal, which dates from c. 14,000 BP. It included dwellings partly dug into the ground, made from a framework of large animal bones and reindeer antlers covered with skins or sods. This may have been a winter gathering place for quite large groups. The people of Mal’ta pursued mammoth, as well as woolly rhinoceros, reindeer and many smaller animals. They were also able tailors, making clothing sewn in double layers to shield them from Arctic winds.

There was settlement even in eastern Siberia. This area is of peculiar interest for it was from here that Inner Eurasian peoples began to colonize the Americas sometime late in the upper palaeolithic. The best known east Siberian sites belong to the Dyukhtai culture. These are named after a site in the Middle Aldan Valley, north and east of Lake Baikal that dates from c. 18,000 BP. Y.A. Mochanov, the Soviet archaeologist who has done most work on the Dyukhtai culture, dates the earliest ‘proto-Dyukhtai’ site, at Evanzhtsy, to 35,000 years BP, but most specialists prefer later dates, and some doubt if any eastern Siberian dates are older than 20,000 years. Dyuktai culture shows many similarities with the earliest archaeological evidence from North America, so it is likely that this constituted a core area for the first wave of colonization of ice age North America. Low sea levels during the later ice age would have permitted migrants to travel across a dry Beringian strait.

Differences in the style of stone artefacts in eastern and western Siberia suggests that the two regions were colonized from different zones. The dividing line is the watershed of the Lena and Yenisei rivers. Eastern Siberia was probably colonized from the south, from upper palaeolithic populations of Mongolia or China, while western Siberia may have been colonized from populations of Mongolia or China, while western Siberia may have been colonized from populations of western Inner Eurasia.

All in all, humans managed to settle the upper palaeolithic, with the sole exception of the Arctic shores. It is a reasonable assumption that the increasing number of settlement sites from the upper palaeolithic, and their wider dispersion, implies a substantial increase in Inner Eurasian populations. If we accept that world populations in 10,000 BP were about 10 millions, and assume that Inner Eurasian populations were still much less dense than those of Africa and Outer Eurasia it follows that the population of Inner Eurasia may have grown from several tens of thousands to several hundred thousands, perhaps to half a million.

The hunting methods of the upper palaeolithic were closer to those of modern hunters than to those of the early palaeolithic. The preparation of more and more specialized hunting tools already suggests an increase in planning and cooperation. A narrowing of the range of prey species suggests increased specialization, greater knowledge of particular species, greater knowledge of particular species, and an ability to take even healthy animals more or less at will. In late upper palaeolithic Ukraine, for example, hunting was highly seasonable. Mammoth and furbering animals were hunted in winter, reindeer in the spring, and waterfowl in the summer. North of the Black Sea, organized groups of hunters drove herds of bison to their death.

More complex hunting techniques almost certainly imply the existence of higher levels of social organization. Like modern hunters, upper palaeolithic communities seem to have included stable core groups from which hunting parties regularly split off. The best studied region of upper palaeolithic Inner Eurasia is in modern Ukraine. Here, Olga Soffer has studied about 29 major late upper palaeolithic sites near Kiev. Many have mammoth bones and pits for storage of frozen meat. Linked to these are other, less permanent sites, on high ground, away from the river valleys. These were probably temporary hunting camps. The earliest mammoth bone dwellings appear at Kostenski 11 on the Don, hwere they date from c.20,000 BP. Similar dwellings spread widely in the Dnieper basin, at sites such as Mezhirich, Mezin and Dobranichevka, usually near river valleys. At the spectacular site of Mezhirich on the River Dnieper, there are large concentrations of mammoth bones, along with carefully prepared hearths and many bone or ivory ornaments. Mammoth bones provided a scaffolding over dwellings partly dug into the ground, and covered over with skins. There were about five dwellings, each about 80 m2 in area, and each housing up to ten people. The builders used mammoth bones not just for scaffolding, but also as ‘tent pegs’, in preference to wood, which rots more easily. They forced them deep into the ground and cut sockets into which they inserted wooden poles. They also used mammoth bones as fuel, after splintering them. These settlements were probably winter camps for groups of perhaps 30 people, who may have occupied them for as long as nine months each year.

The relative permanence of these settlements is reflected in the care with which they were built. At the Kostenski 21 site, there were several dwellings along 200 m of the Don river shore, set 10-15 m apart. One dwelling, near marshland, had an area paved with limestone slabs to avoid the damp. There are also objects which seem to have ritual importance, such as the two musk-ox skulls found at Kostenski. Perhaps these were the site of annual gatherings or of ritual activities affirming the unity of related groups.

The inhabitants of these ice age villages lived off frozen stocks of meat kept in storage pits, and thawed out by fire. The meat, most of which came from gregarious herbivores, was hunted in summer and autumn, when the animals were at their fittest. Each year, some of the inhabitants moved out to more temporary summer camps for the hunting season. On returning, they stored meat in pits whose depth suggests they were dug from the top layer of permafrost as it thawed during the brief summers.

Storage may have led to minor inequalities in access to resources ,and perhaps to other forms of hierarchy. At some sites, there are central storage pits, which appear to offer equal to all inhabitants. At Dobranichevka, each dwelling has a circle of two to four storage pits around it. However, at Mezin site, most of the storage pits appear around a single dwelling which also contains art objects, jewellery and shells whose origin is some 800 km to the south. ‘Since…this dwelling was neither a special purpose structure…nor occupied by a greater number of people, the concentration suggests not only higher staus for its residents but also their ability to control considerably greater amounts of surplus.’ If, as modern analogies suggest, hunting was mainly a male activity, then it is entirely possible that there emerged gender inequalities in access to basic resources, including food.

Meat was not the only stored resource in these communities. Their inhabitants also harvested fur-bearing animals and made jewellery from exotic materials. The importance of buildings and objects of symbolic significance suggests that influence and power could also be accumulated and stored. Olga Soffer has argued that rhythmic elements in the design of the Mezhirich buildings, such as the systematic stacking of mandible bones chin side up, then chin side down, suggest that these were early examples of monumental architecture. If so, they may imply the emergence of ‘big men’, who used kinship, gift-giving and personal influence to mobilize the labour and wealth of their neighbours. Certainly, someone had to mobilize the very considerable amount of labour needed to build such structures. Finally, the burials at the Sungir site near Vladimir suggest a degree of status differentiation even before the last glacial maximum. Buried with the boys were spears of mammoth ivory, weapons of stone and ivory, and animal carvings. The youth of the boys shows that status could be inherited in this community, and that points to a structure of ranked families or clans.

Relations between groups became more complex and extensive. Upper palaeolithic communities exchanged goods over large areas. Amber beads, shells and furs are the main ‘imported’ objects found at Ukrainian sites. These almost certainly reached the region through systems of exchange rather than through special expeditions. Some amber had come from as far as 700 km away. Such exchanges imply more regular and systematic contacts between local groups. They hint at increased geographical knowledge and a capacity to exploit larger and more varied territories. They suggest that the ‘reproductive’ group became more significant in the upper palaeolithic.

The scales of such exchanges shows the growing importance of even higher levels of complexity, perhaps involving relations between different reproductive networks, and loosely analogous to tribal networks of the modern world. Some upper palaeolithic art objects suggest the existence of vast networks of contact and exchange. This is true of the Venus figurines which appear from the Pyrenees to the Don at about the late glacial maximum, or the even more astonishing similarities between the cave paintings of southwest Europe and western Mongolia. Indeed, the most likely explanation for the proliferation of art objects in this period is that it reflects increased exchanges of marriage partners, information, fights and perhaps ritual knowledge, all of which would have enhanced the importance of ornamentation that gave a sense of identity to local and regional groups. Ornamentation and decoration provided ways of storing information in the external world, like stone age hard disks. They reflect an intellectual strategy that our own species has developed to a high degree, of expanding the capacity of our brains to store and process information by ‘extruding our minds… into the surrounding world’. So the rich symbolic world that appears in the upper palaeolithic is probably the outer sign of an increasingly rich, complex and perhaps even hierarchical social world. Presumably, like modern small-scale communities, a sense of kinship extending beyond the band would have helped group exchange marriage partners, information and gifts in networks reaching over vast areas.

Under the difficult conditions of the late Ice Age, widespread links between different groups provided insurance in bad times, and information about techniques and resources. As one archaeologist has put it, such exchange networks would have been ‘as necessary for a successful long term adaptation as skin clothing and other technological items that kept out the cold’. Though rare on the Ice Age steppes, contacts between groups would have been vital, and shared symbols would have been necessary to ensure their success. These same contacts may explain the emergence of limited forms of gender and social hierarchy, as they enhanced the political leverage of those individuals with the best external contacts.

Increasing exchanges between different groups allowed modern humans to deal with the harsh environments of Inner Eurasia not as individuals or as bands, but with the collective knowledge of many different groups scattered over large areas. This, in turn, explains the accelerating technological virtuosity of the upper palaeolithic, and the ability to colonize areas of Inner Eurasia that had previously resisted colonization. The successful colonization of most regions of Inner Eurasia during the upper palaeolithic was a spectacular sign of our species’ increasing technological and social virtuosity.

Source: A history of Russia, Central Asia and Mongolia (Blackwell History of the World);  Christian, David  (Wiley-Blackwell); Volume 1, ISBN-10: 0631208143

***

For an excellent account of the lives and legacy of Siberians, see “Mammoth Hunters of the last Ice-Age, their legacy, and “World Surveyor Man” and also:

The Upper Paleolithic of Northern Asia: Achievements, problems, and perspectives. II. Central and Eastern Siberia, Journal of World Prehistory, Volume 4, Number 3 / Sep 1990,  Vitality Larichev et al.  ISSN0892-7537 (DOI 10.1007/BF00974884)

full html version    pdf version here

Abstract  Earlier scholars believed that the Upper Paleolithic of Central and Eastern Siberia appeared very late. However, modern research has shown that not only was there a local Middle Paleolithic, but also there was a very early series of sites in Central Siberia which show both Middle and early Upper Paleolithic traits. These are called the Makarovo horizon and may be 70,000–50,000 years old; features derived from this horizon can be dated to about 30,000 B.P. and can be seen in the early D”uktai culture. The true early Upper Paleolithic is relatively homogeneous in Central and Eastern Siberia and includes artwork. The local Upper Paleolithic reached its florescence in the culture of Mal’ta and Bur’et’, which developed out of local antecedents and which is here reinterpreted in light of recent research (including the artwork, structures, and burials). The final stages of the Upper Paleolithic show considerable variability, perhaps including some exotic traits.

One response to “Echoes of Siberia in Palaeolithic and prehistoric Japan

  1. Fascinating material. I will read the book!

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