Jomon: Paleolithic Contingent in Modern Japanese

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Jomon: Paleolithic Contingent in Modern Japanese Feb 21, 2019 18:40:02 GMT

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Post by Admin on Feb 21, 2019 18:40:02 GMT

Allele sharing analysis
Allele sharing analysis using 5392 SNP sites (Figure 3a) showed that the Ainu had the highest percentage of allele sharing with the Sanganji Jomon, followed by the Ryukyuan, the mainland Japanese and CHB, similar to the projection of PC1 in Figure 2b. Using the HGDP East Eurasian data set with 7081 SNP sites (Figure 3b), the mainland Japanese had the highest allele sharing with the Sanganji Jomon. Interestingly, southern East Eurasians (green bars) had slightly higher allele-sharing percentages than northern East Eurasians (blue bars), although we have to be careful with the effect of post-mortem changes.

Figure 3

Allele sharing between Sanganji Jomon and modern humans. Vertical line indicates the frequency of having the same allele with the Sanganji Jomon. (a) Comparison with Japanese Archipelago populations and Chinese Beijing (CHB) based on 5392 SNP sites with PB, (b) comparison with HGDP East Eurasians, Sahulians and Native Americans based on 7081 SNP sites with PB. Colors blue, green, brown and violet indicate northern East Eurasians, southern East Eurasians, Sahulians and Native Americans, respectively.

TreeMix analysis
We constructed maximum-likelihood population trees (ML tree) using TreeMix to investigate the phylogenetic relationship and the presence of admixture events between Sanganji Jomon and other human populations. When three migration events were assumed, the gene flow from Sanganji Jomon to JPT (modern Japanese) appeared (Figure 4) (bootstrap probability=42%). The directionality of this gene flow event was as expected, however, the inferred gene flow from Karitiana to Mal’ta MA1 (Supplementary Results S2; Supplementary Figures S16b-j and S17c-j), was in the reverse direction to what was reported by Raghavan et al.23 who used a much larger sequence data. This result might have been caused by using a relatively small SNP data set. We therefore used only modern human data, and reran TreeMix. We used a much larger 0.7 million SNP loci data. However, the resulting tree showed some anomalous gene flow directions; from Papuans to Denisovans (bootstrap probability=98%) and CEU to Papuans (bootstrap probability=86%), whereas the tree topology was consistent with that of Figure 4 (see Supplementary Figure S19). The reason for this anomaly may be that some filtering steps between our analyses and Reich et al.16 and Meyer et al.19 are different, and/or homozygous diploid genotypes in individual genome (that is, Denisovan, Papuan and so on) were used instead of their original genotype, though gene flow from Mal’ta MA1 to Karitiana correctly appeared in both all sites and transversion only when we add Mal’ta MA1, Karitiana and Ust’-Ishim to the large SNP loci data (data not shown).

Figure 4

Phylogenetic analysis I. TreeMix tree with gene flows. A comparison of Sanganji Jomon, 1000 Genomes Project worldwide populations, Papuan, Karitiana, Mal’ta MA1, Ust’-Ishim and Denisovan based on 43 310 all sites. Denisovan was used as the outgroup, and three gene flow events were estimated. The tree was drawn by using MEGA6.38 Red colored values (only those higher than 90% are shown) are bootstrap probabilities (%) for their adjacent internal branch. Arrows were manually added to this tree, and colors of migration weight (ratio of gene flow) follow TreeMix outputs. Values inside arrows are the ratio of gene flow. Bootstrap probabilities (%) of the gene flow from Sanganji Jomon to JPT, Karitiana to the root of European and Mal’ta MA1, and LWK to European, estimated out of 1000 bootstrap replicate TreeMix outputs, are 42%, 86% and 0.4%, respectively.

Last Edit: Feb 21, 2019 18:40:21 GMT by Admin

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Jomon: Paleolithic Contingent in Modern Japanese Feb 22, 2019 18:29:45 GMT

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Post by Admin on Feb 22, 2019 18:29:45 GMT

Distance matrix-based analysis
We constructed neighbor-joining trees (Figure 5a and Supplementary Figure S20) from distance matrices, and the Native American diverged after the divergence of the Sanganji Jomon from the modern East Eurasians in these trees. This is consistent with Figure 4, although the bootstrap probability to support this branching pattern was only 64% in Figure 5a. We also drew a Neighbor-Net network using the same distance matrix (Figure 5b and Supplementary Figure S21). Major splits are consistent with the neighbor-joining tree (Figure 5a), and split X clustered the Sanganji Jomon and JPT. This split confirms the admixed nature of the mainland Japanese inferred from the PCA and TreeMix analyses. See Supplementary Results S3 for more detailed analysis using Neighbor-Net.

Figure 5

D-statistic analysis
In agreement with the PCA and TreeMix results, the D-statistic test also suggested genetic affinity of the Sanganji Jomon with the East Eurasians, especially with the mainland Japanese, compared with non-East Eurasians (Figure 6a and b). This reflects the genetic continuity between the Jomon and the mainland Japanese, and support the hypothesis of an early divergence of the Jomon with the ancestor of modern East Eurasians (Supplementary Figure S23). See also Supplementary Results S4 for additional analyses using D-statistics.

Figure 6
D-statistic tests of Sanganji Jomon and worldwide humans. (a) Comparison of Sanganji Jomon, 1000 Genomes Project worldwide populations, Mal’ta MA1 and Ust’-Ishim based on 15 549 transversion sites. (b) Comparison with HGDP East Eurasians and Native Americans and SGVP Malay population based on 7439 SNPs.

The genetic relationship between Sanganji Jomon and the archaic humans were then investigated. Genetic affinities between Neanderthal and non-African, and between Denisovan and Sahulian were previously reported.15, 16, 19, 22 The test of ((Sanganji Jomon, San), Altai Neanderthal) implies genetic affinity of the Jomon people with Neanderthals, but the degree was not much different from the other non-Africans (Supplementary Figure S31). Compared with the other East Eurasians, Sanganji Jomon did not show additional similarities with the Denisovans.

Our results show that the populations genetically closest to Sanganji Jomon are those that live on the Japanese Archipelago. The current Japanese population is widely accepted to be a result of admixture of indigenous Jomon and later migrant people, whereby the latter were agricultural people that came from continental Asia into the Japanese Archipelago probably via the Korean Peninsula during and after the Yayoi era. Until now, this hybridization scenario has not been verified directly at the genomic level. Our result based on PCA, TreeMix and neighbor-joining trees, Neighbor-Net networks, and D-statistic tests clarified that the Jomon people genetically contributed to the modern Japanese Archipelago populations. The genetic similarity would not be explained by contamination from Japanese archipelago populations during experiments, because the direction of gene flow estimated in TreeMix tree was from Jomon to JPT, not from JPT to Jomon (Figure 4), and the D((KHV or CHS, CHB) Jomon) value in D-statistic tests (Figure 6a) was not negative with significant Z-score (JPT was genetically closer to CHB than to CHS or KHV). Furthermore, if there was contamination from modern Japanese, the Jomon would be genetically closer to CHB than to CHS and KHV, leading to negative D-values and probably significant Z-scores. Therefore, we can conclude that the modern Japanese Archipelago populations are the admixture of the Jomon people and other populations with genetic affinities with modern Northeast Asians. This result is consistent with the conclusion based on the genetic analyses of modern human populations.1 However, it is difficult to pin-point the geographic origins of the candidate populations because of lack of genetic data of relevant ancient populations.

The amount of genetic contribution from the Jomon people varied among the Japanese Archipelago populations (Figures 2b and 3a and Supplementary Figure S15). The Ainu and the Ryukyuan share more alleles with the Jomon than the mainland Japanese, suggesting smaller genetic contributions from continental populations in those two populations than for the mainland Japanese, in agreement with previous findings.1, 2, 4, 13, 46, 47, 48, 49, 50 This supports the dual-structure model of Hanihara,3, 50 which is a widely accepted theory that explains the history of the three current populations that inhabit the Japanese Archipelago, and which predicts that the mainland Japanese are more admixed with agricultural continental people than the Ainu and the Ryukyuan, with major admixture occurring in and after the Yayoi period.

PC1 values of some Ainu individuals were similar to that of Sanganji Jomon, whereas PC2 separated the Ainu people from Sanganji Jomon (Figure 2b). It is probable that the ancestors of the Ainu people experienced admixture with other population(s) (for example, continental population(s) not used in the current study) after the Jomon period, and they are thus genetically differentiated from the Jomon people.51 The candidate population is the Okhotsk people, who inhabited the Northeastern costal area of the Hokkaido region, Japan, from the 5th to 13th century. They were morphologically close to modern southern Siberians such as the Nivkhi and Ulchi people,52, 53, 54, 55 who were not included in the current study. Recent studies suggest that the descendants of the Hokkaido Jomon people had admixed with the Okhotsk people and became ancestors of the modern Ainu.56, 57, 58, 59

Jinam et al.2 recently estimated the proportion of the Jomon ancestry in the mainland Japanese using the f4-ratio test35 under a specified phylogenetic scenario. The estimated proportion of Jomon ancestry differs depending on the compared populations and were within the range of 13–21%. Jinam et al.2 also used ADMIXTURE60 and found that the mainland Japanese was best explained by two ancestry components. One of them has very high proportions in many Ainu individuals, and is considered to be Jomon ancestry if we assume that the Ainu people are largely descendants of the Jomon. The average proportion of this Jomon component in the mainland Japanese was 17%, which is within the range of f4-ratio test results.2 The same genome-wide SNP data were also used for ABC analysis, and the highest likelihood model estimated the admixture proportion from the Jomon ancestry to the mainland Japanese to be 36% (22–53%, 95% confidence interval).50 We used TreeMix for estimating Jomon ancestry proportions in this study, and the frequency was 12% as shown in Figure 4. We note that it is possible that the frequency was underestimated if the Jomon people had some population substructure and the northern Jomon including the Sanganji Jomon only indirectly contributed to the modern Japanese, and/or if there are contamination during experiments from the Japanese Archipelago populations. Previously, the proportion of the Jomon component in the modern mainland Japanese was estimated to be 35% based on partial mtDNA sequences of modern human populations46 and 23–40% based on application of a demographic model of population admixture.61 Although the Jomon admixture proportion is still debatable, we would like to conclude that the Jomon component in the mainland Japanese is probably lower than 20%.

Journal of Human Genetics volume 62, pages 213–221 (2017)

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Jomon: Paleolithic Contingent in Modern Japanese May 15, 2019 18:47:19 GMT

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Ancient DNA prescreening, dating, and sequencing by high-throughput sequencers
Initially, we extracted DNA of twelve individuals from three sites (Fig.S1), which were
accompanied by remains associated with the Jomon culture. The endogenous DNA content for ten out
of twelve individuals were less than 1.0%, indicating poor preservation of DNA, while those of two
individuals, IK002 and HG02, were more than 1.0% (Table S1). From those remaining two
individuals, only the ~2,500 years old IK002 (Text S1) exhibited typical ancient DNA damage
patterns[16–18](Fig.S2), and was therefore selected for further sequencing. A total of 29
double-stranded sequencing libraries were generated using DNA extracted from the teeth and petrous
bone of IK002, yielding endogenous DNA contents ranging from 1.14 to 19.09% (Table S2 &Text
S2). The libraries were sequenced to average coverages of 1.85-fold for autosomal genome and
146-fold for mitochondrial genome, with low estimated contamination rate of 0.5% (95% CI:
0.01-2.2%, Fig.S3) [19]. We found IK002 to be assigned to mitochondrial haplogroup N9b1, which is
rare among present-day Japaneses people (< 2.0%) , but typically found in previous studies of Jomon
mtDNA[20,21].

Fig. 1: Genetic structure of present-day and ancient Eurasian and Ikawazu Jomon.
A, Principal component analysis (PCA) of ancient and present-day individuals from worldwide
populations after the out-of-Africa expansion. Grey labels represent population codes showing
coordinates for individuals. Coloured circles indicate ancient individuals.

Testing whether IK002 is the direct descendant of the Upper Paleolithic people in the Japanese
archipelago
To make inferences on the genetic relationship of IK002 with geographically diverse human
populations, we merged the IK002 genomic data with a diverse panel of previously published ancient
genomes[22–28], as well as 300 high-coverage present-day genomes from the Simons Genome
Diversity Project (SGDP)[29]. We extracted genotypes for a set of 2,043,687 SNP sites included in
the “2240K” capture panel[30]. First, we characterized IK002 in the context of worldwide populations
after the out-of-Africa expansion using principal component analysis (PCA)[31,32]. We found that
IK002 clusters between present-day Southeast and East Asians and the Upper-Paleolithic human
remain (40 kya) from Tiányuán Cave[28,33](Fig.1A). Second, when using a smaller number of SNPs
(41,264 SNPs) including the present-day Ainu [34] from Hokkaido (Fig.S1), IK002 clusters with the
Hokkaido Ainu (Fig.S4), supporting previous findings that they are direct descendants of the Jomon
people[14,34–41]. Thus, the PCA plot showed that IK002 is slightly different from present-day people
in East Eurasia and Japan except for the Hokkaido Ainu.

Subsequently, we carried out model-based unsupervised clustering using ADMIXTURE[42]
(Fig.S5). Assuming K = 10 ancestral clusters (Fig.1B), an ancestral component unique to IK002
appears, which is the most prevalent in the Hokkaido Ainu (average 79.3%). This component is also
shared with present-day mainland Japanese as well as Ulchi (9.8% and 6.0%, respectively) (Fig.1C).
Thus, the results of ADMIXTURE showed the strong genetic affinity between IK002 and the
Hokkaido Ainu.

C, Maximum-likelihood phylogenetic tree (TreeMix) with bootstrap support of 100% unless indicated
otherwise. The tree shows phylogenetic relationship among present-day Southeast/East Asians,
Northeast Siberians, Native Americans, and ancient East Eurasians. Mbuti are the present-day
Africans; Ust’Ishim is an Upper-Paleolithic individual (45 kya) from Western Siberia (Fu et al.,
2014); Mal’ta (MA-1) and Sunghir is Upper-Paleolithic individuals (24 kya and 34 kya) (Raghavan et
al., 2014; Sikora et al., 2017), and Loschbour is a Mesolithic individual from Central Siberia
(Lazaridis et al., 2014); La368 is a pre-Neolithic Hòabìnhian hunter-gatherer (8.0 kya) in Laos and
Önge is the present-day hunter-gatherers in the Andaman island, both of who are from Southeast Asia
(McColl et al., 2018); Tiányuán is an Upper-Paleolithic individual (40 kya) in Beijing, Chaina;
Kusunda are the present-day minority people in Nepal; Chokhopani is an Iron-age individual (3.0 –
2.4 kya) and Sherpa are the present-day minority people, both of who are in Tibet (Jeong et al., 2016);
Han, Ami and main-island Japanese are the present-day East Asians (Mallick et al., 2016); Devils
Gate Cave is a Neolithic individual (8.0 kya) in the Primorye region of Northeast Siberia, and
Shamanka and Lokomotive are Early-Neolithic individuals (8.0 kya) from Central Siberia,
respectively (Damgaard et al. 2018); USR1 and Clovis are late-Paleolithic individuals (11.5 kya and
12.6 kya) in Alaska and Montana, respectively (Moreno-Mayar et al., 2018, Rasumussen et al., 2014).
Coloured arrows represent the migration pathways and signals of admixture among all datasets. The
migration weight represents the fraction of ancestry derived from the migration edge.
Fig. 2: Exploring genetic affinities of IK002 within Northeast Siberians and Southeast/East Asi

We next used ALDER[43] to investigate the timing of admixture in populations with Jomon
ancestry. Using IK002 and present-day Han Chinese as source populations, we estimate the admixture
in modern Japanese to date to between 42 and 57 generations ago (~1,200 - 1,700 years ago assuming
29 years / generation), consistent with previous estimates[44] (Table S3). For the Ulchi we estimate a
more recent timing (8-33 generations ago) consistent with the higher variance in Ikawazu Jomon
admixture proportions, albeit with overall weaker statistical support[7]. Finally, using IK002 and
present-day Japanese as source populations, we detect very recent (2-4 generations ago) admixture for
the Hokkaido Ainu, likely a consequence of still ongoing gene flow between the Hokkaido Ainu and
mainland Japanese.

To further explore the deep relationships of Jomon and other Eurasian populations, we used
TreeMix[45] to reconstruct admixture graphs of IK002 and 18 ancient and present-day Eurasian and
Native American groups (Fig.1C & Fig.S6). We found the IK002 lineage placed basal to the
divergence between ancient and present-day Tibetans[7,29] and the common ancestor of the
remaining ancient/present-day East Eurasians[29,46] and Native Americans[47,48]. These genetic
relationships are stable across different numbers of migration incorporated into the analysis. Major
gene flow events recovered include the well-documented contribution of MA-1 to the ancestor of
Native Americans[47], as well as a contribution of IK002 to present-day mainland Japanese (m=3~6;
Fig.S6). IK002 can be modelled as a basal lineage to East Asians, Northeast Asia/East Siberians, and
Native Americans, supporting a scenario in which their ancestors arrived through the southern route
and migrated from Southeast Asia towards Northeast Asia[6,49]. The divergence of IK002 from the
ancestors of continental East Asians therefore likely predates the split time between East Asians and
Native Americans, which has been previously estimated at 26 kya[47]. Thus, the TreeMix strongly
supported that IK002 is the direct descendant of the people who brought the Upper Paleolithic stone
tools 38,000 years ago into the Japanese archipelago.

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Jomon: Paleolithic Contingent in Modern Japanese May 16, 2019 4:31:40 GMT

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Testing the impacts of the northern route migration into East Asia
Taking advantage of the earliest divergence of the IK002 (Fig.1C & Fig.S6), we address a question
if the Upper-Paleolithic people who took the northern route of the Himalayas mountains to arrive east
Eurasia made genetic contribution to populations migrated from Southeast Asia. Under the
assumption that MA-1 is a descendant of a northern route wave, we tested gene flow from MA-1 to
IK002, as well as to the other ancient and present-day Southeast/East Asians and Northeast
Asians/East Siberians by three different forms of D statistics: D(Mbuti, MA-1; X, Ami), D(Mbuti, X;
MA-1, Ami), and D(Mbuti, Ami; X, MA-1).

Fig. 2: Exploring genetic affinities of IK002 within Northeast Siberians and Southeast/East Asians,
respectively. Three different D values are plotted with different colors; D(Mbuti, MA-1; X, Ami) in
red, D(Mbuti, X; MA-1, Ami) in cyan, and D(Mbuti, Ami; X, MA-1) in green. Error bars show 3
standard deviation, and the vertical dotted and dashed lines indicate D = 0 and D = -0.2, -0.1, 0.1, and
0.2.

The first D statistics (shown as red in Fig.2) provides results consistent with previous findings on
the prevalence of MA-1 ancestry in the present-day Northeast Asians/East Siberians (Z < -3; Table
S4)[23], while none of Southeast/East Asians, except for Oroqen, shows a significant deviation from
zero. The tree relationships observed in Fig. 1C are confirmed from the other two different forms
between Ami and all of the tested populations with some variation that is mostly explained by the
MA-1 gene flow (cyan and green in Fig.2, Table S5 & Table S6). Therefore, we concluded that no
gene flow from MA-1 to the ancient/present-day Southeast/East Asians including IK002 was detected.

Remnant Jomon-related ancestry in the coastal regions of East Asia
The basal divergence of IK002 (Fig.1C) suggests a negligible contribution to later ancient and
present-day mainland East Asian groups. To further test this prediction we conducted f4 statistics with
the form of (Mbuti, IK002; X, Chokhopani). If IK002 were a true outgroup to later East Asian groups,
this statistic is expected to be zero for any test population X. However, we find that together with
Japanese, present-day Taiwan aborigines (Ami and Atayal), as well as minorities in the
Okhotsk-Primorye region (Ulchi and Nivhk) also showed a significant (Z < -3) excess of allele
sharing with IK002. Populations in the inland of the eastern part of the Eurasian continent on the other
hand were consistent with forming a clade with Chokhopani (Fig.3), suggesting the presence of
remnant Ikawazu Jomon-related ancestry in present-day coastal populations in East Asia. The signal is
also present in the Neolithic individuals from Devil’s Gate Cave in the Primorye region (Z < -3;
Fig.S7a), suggesting that at 8 kya IK002-related ancestry in the region had already been largely but
not completely replaced by later migrations. Interestingly, the genetic affinity to IK002 was found,
thus, only in the coastal region but not in the inland for both ancient and present-day populations
(Fig.3).

Discussion
This study takes advantage of whole-genome sequence data from the 2,500-years old Jomon
individual, IK002, dissecting the origins of present-day East Asians. IK002 is modelled as a basal
lineage to East Asians, Northeast Asians/East Siberians, and Native Americans (basal East Eurasians:
bEE)(Fig.4), supporting a scenario in which their ancestors came through south of the Himalayas
mountains and migrated from Southeast Asia towards the north[6,49]. We clearly show the early
divergence of IK002 from the common ancestor of the other ancient and present-day East Eurasian
and Native Americans (Fig.1C). Given that the split between the East Asian lineage and the Northeast
Asians/East Siberian and Native American lineage was estimated to be 26 kya[47], the divergence of
the lineage leading to IK002 is likely to have occured before this time but after 40 kya when the
Tiányuán appeared (Fig.4). Therefore, our results support the archaeological evidence that the Jomon
are direct descendants of the Upper-Paleolithic people who started living in the Japanese archipelago
38 kya.

Here, we use the MA-1 ancestry as a proxy for ancestral populations who took the northern route
of Himalaya mountains to come to East Eurasia. The fine stone tool, i.e., microblade, is a
representative technology that was originally developed around Lake Baikal in Central Siberia during
the Upper-Paleolithic period[8]. This microblade culture also reached the Hokkaido island ~25 kya
and the mainland of the Japanese archipelago ~ 20 kya (Text S5). If this culture was brought by demic
diffusion, IK002 may still retain the MA-1 ancestry. However, we find no evidence on the genetic
affinity of MA-1 with ancient and present-day Southeast/East Asians including Devil’s Gate Cave
(8.0 kya), Chokhopani (3.0 – 2.4 kya), and IK002 (2.5 kya) (Fig.2). Therefore, we conclude that
MA-1 gene flow occurred after the divergence between the ancestral populations of Northeast
Asians/East Siberians (NS-NA) and East Asians (Fig.4): namely, East Asians originated in Southeast
Asia without any detectable genetic influence from the ancestor who took the northern route. There
are two hypothetical possibilities to explain the contradiction between genome data and
archaeological records. The first possibility is that MA-1 may not be a direct ancestor who invented
the microblade culture. The second is that, if the assumption is correct, then the northern-route culture
was brought to the Japanese archipelago by the NS-NA population who must have had substantial
gene flow from MA-1. The first and second possibilities can be examined by obtaining genome data
of the Upper-Paleolithic specimens hopefully accompanying with microblade excavated from around
Lake Baikal and from the Primorye region, respectively.

The genome of the Ikawazu Jomon (IK002) strongly supports the classical hypothesis concerning
peopling history in the Japanese archipelago. The PCA plot and phylogenetic tree showed that the
present-day Japanese fell in the cluster of present-day East Asians (e.g., Han Chinese) but not
clustered with IK002 (Fig.1A & C), while a signal of gene flow was detected from IK002 to
present-day Japanese (Fig.1C & S6). The PCA and ADMIXTURE showed the close relationship
between IK002 and the Hokkaido Ainu even in the genome-wide structure reflected by linkage blocks
(Fig.S4 & 5). These results fit the hypothesis that the Ainu and the Jomon share the common ancestor:
the present-day mainland Japanese are the hybrid between the Jomon and migrants from the East
Eurasian continent, and the Hokkaido Ainu have less influence of genetic contribution of the
migrants[35,40](Text S5).

IK002 gave new insights into the migration route from south to north in East Eurasia. The f4
statistics suggest that both the ancient and the present-day East Asians are closer to IK002 than
Chokhopani (ancient Tibetans, 3.0 – 2.4 kya) in the coastal region but not in the inland region (Fig.3
& Fig.S7). There are two explanations for the genetic affinity to IK002: (1) the earliest-wave of
migration from south to north occurred through the coastal region, and/or (2) the migration occurred
in both the coastal and inland regions, but the genetic components of the earliest-wave were drowned
out by back-migration(s) from north to south occurred in the inland region. In the early migration of
anatomically modern humans, the route along the coast has been primarily thought to be important
[3,50–53]. The use of water craft could support such explanation for the expansions through the
islands and the coastal region[3], which supports the first explanation. There could be, however,
potential criticisms: such archaeological evidence of craft boat is hardly found. Ulchi and Nivkh show
significantly negative values of f4 statistics (Z = -4.541 and -10.148, respectively). This could be an
influence of the Hokkaido Ainu who are likely to be direct descendants of the Jomon people. The
ancestor of the Ainu people could have admixed with the Okhotsk people[54] who were
morphologically close related to Ulchi and Nivkh currently inhabit in the the Primorye region[55–57],
which are supported by mtDNA[58,59] and genome-wide SNP data (Matsumae et al., unpublished
data). The second explanation is that the track of the earliest-wave was erased in the inland but left
over in the coastal region. Taiwan aborigines (Ami and Atayal) and Igorot are the Austronesian
minorities. Taiwan aborigines are thought to have come from the East Eurasian continent 13.2 +/- 3.8
kya[60], though the origin of Igorot is not well known.

Last Edit: May 16, 2019 5:08:32 GMT by Admin

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Jomon: Paleolithic Contingent in Modern Japanese May 23, 2019 18:03:44 GMT

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Post by Admin on May 23, 2019 18:03:44 GMT

More than two decades after researchers discovered the 3,800-year-old remains of "Jomon woman" in Hokkaido, Japan, they've finally deciphered her genetic secrets.

And it turns out, from that perspective, she looks very different from modern-day inhabitants of Japan. The woman, who was elderly when she died, had a high tolerance for alcohol, unlike some modern Japanese people, a genetic analysis revealed. She also had moderately dark skin and eyes and an elevated chance of developing freckles.

Surprisingly, the ancient woman shared a gene variant with people who live in the Arctic, one that helps people digest high-fat foods. This variant is found in more than 70% of the Arctic population, but it's absent elsewhere, said study first author Hideaki Kanzawa, a curator of anthropology at the National Museum of Nature and Science in Tokyo. [Photos of Samurai: The Last Century of Japanese Warriors]

This variant provides further evidence that the Jomon people fished and hunted fatty sea and land animals, Kanzawa said.

"Hokkaido Jomon people engaged in [not only] hunting of ... land animals, such as deer and boar, but also marine fishing and hunting of fur seal, Steller's sea lions, sea lions, dolphins, salmon and trout," Kanzawa told Live Science. "In particular, many relics related to hunting of ocean animals have been excavated from the Funadomari site," where the Jomon woman was found.

Who is Jomon woman?
Jomon woman lived during the Jomon period, also known as Japan's Neolithic period, which lasted from about 10,500 B.C. to 300 B.C. Though she died more than three millennia ago — between 3,550 and 3,960 years ago, according to recent radiocarbon dating — researchers found her remains only in 1998, at the Funadomari shell mound on Rebun Island, off the northern coast of Hokkaido.

But Jomon woman's genetics have remained a mystery all these years, prompting researchers to study her DNA, which they extracted from one of her molars. Last year, the researchers released their preliminary results, which helped a forensic artist create a facial reconstruction of the woman, showing that she had dark, frizzy hair; brown eyes; and a smattering of freckles.

Her genes also showed that she was at high risk of developing solar lentigo, or darkened patches of skin if she spent too much time in the sun, so the artist included several dark spots on her face.

"These findings provided insights into the history and reconstructions of the ancient human-population structures in east Eurasia," said Kanzawa, who was part of a larger team that included Naruya Saitou, a professor of population genetics at the National Institute of Genetics in Japan.

Now, with their study slated to be published in the next few weeks in The Anthropological Society of Nippon's English-language journal, Kanzawa and his colleagues are sharing more of their results. Jomon woman's DNA shows, for example, that the Jomon people split with Asian populations that lived on the Asian mainland between 38,000 and 18,000 years ago, he said.

It's likely that the Jomon people lived in small hunter-gatherer groups, likely for about 50,000 years, Kanzawa noted. Moreover, Jomon woman had wet earwax. That's an interesting fact because the gene variant for dry earwax originated in northeastern Asia and today up to 95% of East Asians have dry earwax. (People with the dry earwax variant also lack a chemical that produces smelly armpits.)

Despite her differences from the modern Japanese population, Jomon woman is actually more closely related to today's Japanese, Ulchi (the indigenous culture of eastern Russian), Korean, aboriginal Taiwanese and Philippine people than these populations are to the Han Chinese, Kanzawa said.