Japanese Emperors: Y-DNA Haplogroup D1b1a2

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Japanese Emperors: Y-DNA Haplogroup D1b1a2 Nov 3, 2019 18:34:29 GMT

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Historical Japanese emperors belonged to Y-DNA Haplogroup D1b1a2, which is the imperial Y-DNA lineage. Y-DNA haplogroups can be inherited from a father to his son and the old succession rule maintained this Y-DNA lineage for 2,000 years. Haplogroup D originated in East Africa along with Haplogroup E, which descended from the paragroup DE. D-M174 is dominant in Japan, the Andaman Islands, and Tibet, whereas E-M96 is relatively common in Africa and the Middle East.

The subclades of DE continue to confound investigators trying to reconstruct the migration of humans because, while they are common in Africa and East Asia, they are also largely absent between these two regions. As the paragroup DE(xD,E), including DE*, is extremely rare, the majority of DE male lines fall into subclades of either D-CTS3946 or E-M96. D-CTS3946 is suggested to have originated in Africa, though its most widespread subclade, D-M174, likely originated in Asia – the only place where D-M174 is now found. E-M96 is more likely to have originated in East Africa.

Abstract
The Jomon and the Yayoi are considered to be the two major ancestral populations of the modern mainland Japanese. The Jomon people, who inhabited mainland Japan, admixed with Yayoi immigrants from the Asian continent. To investigate the population history in the Jomon period (14,500–2,300 years before present [YBP]), we analyzed whole Y-chromosome sequences of 345 Japanese males living in mainland Japan. A phylogenetic analysis of East Asian Y chromosomes identified a major clade (35.4% of mainland Japanese) consisting of only Japanese Y chromosomes, which seem to have originated from indigenous Jomon people. A Monte Carlo simulation indicated that ~70% of Jomon males had Y chromosomes in this clade. The Bayesian skyline plots of 122 Japanese Y chromosomes in the clade detected a marked decrease followed by a subsequent increase in the male population size from around the end of the Jomon period to the beginning of the Yayoi period (2,300 YBP). The colder climate in the Late to Final Jomon period may have resulted in critical shortages of food for the Jomon people, who were hunter-gatherers, and the rice farming introduced by Yayoi immigrants may have helped the population size of the Jomon people to recover.

Introduction
Archaeological studies have shown that the Japanese prehistory is divided into three periods: the Paleolithic period (older than 14,500 years before present [YBP]), the Jomon period (14,500-2,300 YBP), and the Yayoi period (2,300-1,700 YBP)1. One of the most important events in Japanese history is the transition from subsistence food production activities such as hunting and gathering to farming rice at the beginning of the Yayoi period. The advanced rice farming is thought to have been introduced to mainland Japan (we use the term “mainland Japan” to distinguish Honshu, Shikoku and Kyusyu from Hokkaido and Okinawa in this paper), inhabited by the Jomon people, by the Yayoi immigrants who came from the Asian continent.

At present there are two minor populations and one major population in the Japanese archipelago: the Ainu who mainly live in Hokkaido (a minor population); the mainland Japanese (the major population); and the Ryukyuan who mainly live in Okinawa (a minor population). The prevailing hypothesis on the origins of the Japanese is “the dual structure model,2” where the present-day Japanese population is formed by an admixture between indigenous Jomon people and Yayoi immigrants who migrated from continental East Asia (Fig. 1). According to this model, modern mainland Japanese should have genomic components derived from both the Jomon people and those originating from the Yayoi immigrants. Genetic studies, using genome-wide single nucleotide polymorphism (SNP) data, basically supported the above model3,4,5,6. A recent study of ancient DNA extracted from the remains of Jomon individuals who had lived in mainland Japan (Fukushima Prefecture) 3,000 YBP suggested that (1) the Jomon people were strongly divergent from the current East Asians (Fig. 1), (2) the Ainu people are most closely related to the Jomon people among the three Japanese populations, and (3) ~12% of the genomic components of the modern mainland Japanese were derived from the Jomon people7. Genetically, the mainland Japanese are closely related to Koreans, followed by Han Chinese, and finally by other Continental East Asians3. These findings suggest that a large number of Yayoi immigrants came mainly through the Korean Peninsula to mainland Japan, and the mainland Japanese still retain genomic components from the Jomon people. Thus, there is a possibility that the historical change in the population size of the historic Jomon people, who lived in mainland Japan, could be estimated from genomic data from the modern mainland Japanese.

Figure 1

In the current work, we estimated the change in population size of the Jomon people in the Late to Final Jomon period by using whole Y-chromosome sequences of Japanese males living in mainland Japan. Specifically, we identified a phylogenetic clade (hereinafter called “clade 1”) specific to Japanese Y chromosomes and largely divergent from ones attributable to the continental East Asians. Y chromosomes in clade 1 appeared to be derived from the Jomon people. The population frequency of clade 1 Y chromosomes was estimated to be ~70% in Jomon males. The Bayesian skyline plot (BSP)8 for Y chromosomes in clade 1 allowed us to infer the historical change in population size of the majority of the Jomon people. Our results suggested that the Jomon people underwent a major decrease in population size at the end of the Jomon period, with a recovery occurring soon after the beginning of the Yayoi period.

Last Edit: Nov 3, 2019 19:44:02 GMT by Admin

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Japanese Emperors: Y-DNA Haplogroup D1b1a2 Nov 4, 2019 18:29:24 GMT

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Results
Phylogenetic Tree of Y Chromosomes
A total of 14 Mb of reliable sites had a call rate greater than 95% on the whole Y-chromosome sequences of 345 Japanese males (depth: 21×), and 28,254 Y-chromosomal SNPs were identified. Initially, a phylogenetic analysis was conducted for 345 Y chromosomes using the 28,254 SNPs. The Japanese Y chromosomes were divided into seven distinct clades in the neighbor-joining (NJ)9 tree (Fig. 2). To further investigate the phylogenetic relationship of East Asian Y chromosomes, a NJ tree of Y chromosomes from 345 Japanese, 47 Koreans10, and 244 East Asians11 was constructed using the 3,006 SNPs (Fig. S1). Although the branch lengths of the NJ tree in Fig. S1 were not correct because of the removal of population-specific variants, the topology was correct. We found a clade that contains only Japanese Y chromosomes in Fig. S1. Table 1 and Fig. 3 show the population frequency of each clade in East Asians. In this study, Japanese analyzed in 1000 Genomes Project are labeled “JPT” (“Japanese in Tokyo”) to distinguish our subjects from mainland Japanese. Incidentally, a total of 838 mitochondrial SNPs were identified from the same subjects (345 Japanese males). However, in contrast to the situation with the Y chromosomes, no clade specific to the Japanese population was found in the NJ tree of mtDNA sequences (Fig. S2).

Figure 2

Y-Chromosome Clades in the Mainland Japanese
The population frequency of Y chromosomes in clade 1 was 35.4% in the mainland Japanese and 35.7% in JPT (Table 1). The genotyping of rs2032626 (rs2032626-G allele is a marker for haplogroup D1b containing YAP+ variant) confirmed that clade 1 corresponded to haplogroup D1b (Fig. S3). Since the population frequencies of Y chromosomes in clades 2 and 3 were observed at relatively high frequencies in East Asians including Japanese (Table 1), a proportion of them seem to have been introduced to the mainland Japanese by Yayoi immigrants. The analysis of SNP markers revealed that Y chromosomes in clades 2 and 3 corresponded to haplogroups O1 and O2, respectively. Haplogroups O1 and O2 have been reported to be frequently observed in East Asians and Southeast Asians12. Clades 4 and 5 were assigned to haplogroup C, and clades 6 and 7 were assigned to haplogroup N.

Figure 3

Frequencies of Seven Y-Chromosome Clades in the Jomon People
Y chromosomes in clade 1 were absent from continental East Asians except for Japanese (Table 1), and the frequency of haplogroup D1b (i.e. clade 1) was reported to be very high (81.3%) in the Ainu12, who have been shown, of the three Japanese populations, to be genetically and morphologically most closely related to the Jomon people7,13. These results strongly suggest that the mainland Japanese Y chromosomes in clade 1 originated from the Jomon people. The frequency of clade 1 in the mainland Japanese population (35.4% in the mainland Japanese and 35.7% in JPT) was much larger than the proportion (12%) of the genomic components of the Jomon people in the modern mainland Japanese, estimated previously by a study of ancient DNA from Jomon individuals7. Thus, the population frequency of clade 1 Y chromosomes must have been much higher in the Jomon people than in the present mainland Japanese.

It was not possible to analytically estimate the population frequencies of seven clades in Jomon people. Instead, to confirm that the majority of Jomon people had clade 1 Y chromosomes, Monte-Carlo simulation, in which the population frequencies of the seven clades in the Jomon people are given by random numbers, was performed (see Material and Methods for details). The clade frequencies in an admixed population were calculated from those in the Jomon population (simulated) and those in Yayoi immigrants (assumed to be Koreans), and then compared with the clade frequencies observed in the current mainland Japanese (our subjects). The distribution of similarity index (SI) for 108 sets of the clade frequencies is shown in Fig. S4. In this analysis, SI decreased, as the difference between the simulated and observed clade frequencies in the mainland Japanese diminished. Only 20 sets (SI <3.24) were selected from 108 sets in order of increasing SI (Fig. 4), and the mean values of the population frequencies of Y chromosomes in clades 1, 2, and 3 were 73%, 14%, and 2%, respectively. This result implies that ~70% of the Jomon people in mainland Japan possessed clade 1 Y chromosomes, whereas the current mainland Japanese clade 3 Y chromosomes were mostly derived from Yayoi immigrants.

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Japanese Emperors: Y-DNA Haplogroup D1b1a2 Nov 5, 2019 18:27:42 GMT

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Figure 4

Bayesian Coalescent Inference of Historical Change in Population Size
To deduce the historical change in the effective male population size of the Jomon people, Bayesian Skyline Plot (BSP) analyses8 were performed using BEAST 2.4.4 for 122 Y chromosomes of mainland Japanese belonging to clade 1 (Fig. 5). In the plot, the effective male population size started to increase gradually after the beginning of the Jomon period (12,500 YBP). Then, the population size decreased at 3,200 YBP (i.e. coalescent events frequently occurred 3,200 YBP as shown in Fig. 5A). Soon after the decrease, the effective population size of clade 1 rapidly increased to the present level. In addition, 68 Y chromosomes of the mainland Japanese in clade 3 were inspected to obtain information on the demography of a proportion of the Yayoi immigrants (Fig. S5). In contrast to the situation with clade 1, no population decrease was observed in the BSP of clade 3, implying that no severe bottleneck occurred when Yayoi immigrants came to the Japanese archipelago. This coincides with the previous observation that ~88% of the genomic components of the modern mainland Japanese were derived from the Yayoi immigrants7.

Figure 5

Coalescent Simulation
In this study, only clade 1 Y chromosomes were used to infer the historical change in population size of Jomon people. Although ~70% of Jomon males are considered to have possessed clade 1 Y chromosomes, the use of such biased samples may prevent us from accurately estimating the time of an historical event. To confirm that the BSP result of the major clade (clade 1) reflects the time when the change in population size occurred, we performed coalescent simulations by fastsimcoal214, assuming that population size was changed three times (i.e., increase of 14,500 YBP, decrease of 3,000 YBP, and increase of 2,000 YBP). Then, the BSP was conducted for simulated chromosomes only in a major clade (frequency of more than 50%). The recent decrease and increase in the population size were successfully detected at the setting times (3,000 YBP and 2,000 YPB) in eight out of 10 simulation runs (Fig. 6, solid lines). As a consequence, the date at which the recent change in population size of Jomon population could be estimated by the BSP for Y chromosomes only in the major clade. However, considering the large difference in date of the population increase between the simulation results and the setting (14,500 YBP) in Fig. 6, the date of population increase around 12,500 YBP in Fig. 5 may not be reliable.

Figure 6

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Japanese Emperors: Y-DNA Haplogroup D1b1a2 Nov 5, 2019 23:43:19 GMT

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Discussion
The present mainland Japanese have two ancestral populations: the indigenous Jomon and the Yayoi immigrants. In order to examine the demographic history during the Jomon period (14,500-2,300 YBP), we conducted a population genetic analysis using Y chromosomes of present-day mainland Japanese. In this study, a monophyletic group (named clade 1), consisting of only Japanese Y chromosomes, was identified in the phylogenetic analysis. Clade 1 was found to correspond to the Y– chromosome haplogroup D1b. This haplogroup, characterized by the insertion of an Alu element called YAP, is frequently observed in Japanese and Tibetans but is absent from other East Asians12,15. Although the lineages of haplogroup D1b in Japanese and Tibetans must have a common ancestor, the absence from Korean and Chinese populations suggests that the divergence of haplogroup D1b occurred before the ancestors of the Jomon people reached the Japanese archipelago. Y chromosomes in clade 1 are considered to have originated almost exclusively from the Jomon people who had inhabited the Japanese archipelago a long time before the Yayoi immigrants arrived. A simple computer simulation suggested that ~70% of the Jomon people carried the Y chromosome belonging to clade 1.

In BSP for Y chromosomes in clade 1, we observed significant decreases in the effective population size of the Jomon people at the end of the Jomon period (Fig. 5). In the Final Jomon Period, there was a cooling trend in Japan with a sea level 1–3 m lower than the present level1. For the first time, we provide genetic evidence that the number of Jomon people decreased simultaneously with the cooling in the Final Jomon Period. Since the Jomon people were hunter–gatherers dependent on wild food, the number of the Jomon people might have decreased due to the shortage of food resources in the colder Final Jomon Period. A previous study16 had reported that a dietary change occurred along with climate change during the Late to Final Jomon period. It has been revealed that the density of archaeological sites declined in the Late to Final Jomon period17, suggesting that a sizeable population decline had occurred in Japan. Our results strongly support the archaeological finding. The effective population size of the Jomon people was estimated to have increased after the beginning of the Yayoi period (i.e., 2,300 YBP) (Fig. 5). The livelihood of the mainland Japanese shifted from nomadic hunter-gatherer to settled agriculturist in the Yayoi period. The rice farming introduced to mainland Japan by Yayoi immigrants, therefore, may have helped the Jomon people to procure food stably and recover their population size.

Since it is known that effective male and female population sizes are different in general18 and the contributions of men and women are often unequal when admixture of two populations occurs19, the population history of Jomon females may be different from that of Jomon males. The ancient mtDNA analysis for Jomon people will add much to our understanding of historical changes in the effective female population size during the Jomon period.

Scientific Reports volume 9, Article number: 8556 (2019)

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Japanese Emperors: Y-DNA Haplogroup D1b1a2 Dec 7, 2019 18:34:57 GMT

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Abstract
Present-day humans outside Africa descend mainly from a single expansion out ∼50,000–70,000 years ago, but many details of this expansion remain unclear, including the history of the male-specific Y chromosome at this time. Here, we reinvestigate a rare deep-rooting African Y-chromosomal lineage by sequencing the whole genomes of three Nigerian men described in 2003 as carrying haplogroup DE* Y chromosomes, and analyzing them in the context of a calibrated worldwide Y-chromosomal phylogeny. We confirm that these three chromosomes do represent a deep-rooting DE lineage, branching close to the DE bifurcation, but place them on the D branch as an outgroup to all other known D chromosomes, and designate the new lineage D0. We consider three models for the expansion of Y lineages out of Africa ∼50,000–100,000 years ago, incorporating migration back to Africa where necessary to explain present-day Y-lineage distributions. Considering both the Y-chromosomal phylogenetic structure incorporating the D0 lineage, and published evidence for modern humans outside Africa, the most favored model involves an origin of the DE lineage within Africa with D0 and E remaining there, and migration out of the three lineages (C, D, and FT) that now form the vast majority of non-African Y chromosomes. The exit took place 50,300–81,000 years ago (latest date for FT lineage expansion outside Africa – earliest date for the D/D0 lineage split inside Africa), and most likely 50,300–59,400 years ago (considering Neanderthal admixture). This work resolves a long-running debate about Y-chromosomal out-of-Africa/back-to-Africa migrations, and provides insights into the out-of-Africa expansion more generally.

HUMAN Y CHROMOSOMEYAP+ Y CHROMOSOMESPHYLOGEOGRAPHYOUT-OF-AFRICA MIGRATION
HUMANS outside Africa derive most of their genetic ancestry from a single migration event 50,000–70,000 years ago, according to the current model supported by genetic data from genome-wide (Mallick et al. 2016; Pagani et al. 2016), mitochondrial DNA (mtDNA) (van Oven and Kayser 2009), and Y-chromosomal (Wei et al. 2013; Hallast et al. 2015; Karmin et al. 2015; Poznik et al. 2016) analyses. The migrating population carried only a small subset of African genetic diversity, particularly strikingly for the nonrecombining mtDNA and Y chromosome where robust calibrated high-resolution phylogenies can be constructed, and in each case all non-African lineages descend from a single African lineage, L3 for mtDNA or CT-M168 for the Y chromosome. Yet there has been a long-running debate about the early spread of Y-chromosomal lineages because their current distributions do not fit a simple phylogeographical model. The CT-M168 branch diverged within a short time interval into three lineages (C-M130, DE-M145, and FT-M89), and just a few thousand years later the lineage DE-M145 further split into D-M174 and E-M96 (Poznik et al. 2016), illustrated in Supplemental Material, Figure S1. Thus, around the time of the expansion out of Africa, between one (CT-M168) and four (C-M130, D-M174, E-M96, and F-M89) of the known extant non-African lineages were in existence (plus additional African lineages). The complexity arises because three of these four early lineages (C-M130, D-M174, and FT-M89) are exclusively non-African, apart from those entering Africa through recent gene flow; while the fourth lineage (E-M96) is largely African, where it constitutes the major lineage in most African populations. The debate began in the absence of reliable calibration, and these distributions were interpreted as arising in two contrasting ways: (1) an Asian origin of DE-M145 (also known as the YAP+ lineage), implying migration of CT-M168 out of Africa followed by divergence into the four lineages outside Africa and then migration of E-M96 back to Africa (Altheide and Hammer 1997; Hammer et al. 1998; Bravi et al. 2000), or (2) an African origin of DE-M145, implying divergence of CT-M168 within Africa followed by migration of C-M130, D-M174, and FT-M89 out (Underhill and Roseman 2001; Underhill et al. 2001). The first scenario requires two intercontinental lineage migrations, while the second requires three and is thus slightly less parsimonious.

An additional very rare haplogroup, DE*, carrying variants that define DE but none of those that define D or E individually, added to this complexity. First identified in 5 out of 1247 Nigerians within a worldwide study of >8000 men (Weale et al. 2003), DE* chromosomes were subsequently reported in a single man among 282 from Guinea-Bissau in West Africa (Rosa et al. 2007) and in 2 out of 722 Tibetans within a study of 5783 East Asians (Shi et al. 2008). While the phylogeographic significance of these rare lineages was immediately recognized, their interpretation was hindered by the incomplete resolution of the phylogenetic branching pattern and the possibility that they might originate from back-mutations at the small numbers of variants used to define the key D and E haplogroups, or genotyping errors rather than representing deeply divergent lineages, plus the lack of a robust timescale. Large-scale sequencing of Y chromosomes has now provided both the phylogenetic resolution and the timescale needed (Wei et al. 2013; Hallast et al. 2015; Karmin et al. 2015; Poznik et al. 2016), so we have therefore reinvestigated the original Nigerian DE* chromosomes using whole-genome sequencing to clarify their phylogenetic position. We then consider the implications for the out-of-Africa/back-to-Africa debate related to Y-chromosomal lineages, and the expansion out of Africa more generally.