High-coverage genome sequencing of Yayoi and Jomon individuals shed light on prehistoric human population history in East Eurasian
Koji Ishiya et al.
August 12, 2024
Abstract
Our high-coverage genome provides interesting insights into the evolution of copy number polymorphisms related to the dietary styles of ancient Japanese people.
The copy number estimates of the amylase gene for the Yayoi individual were comparable to those of present-day East Asians who have diets high in starch. This suggests that the population in the middle Yayoi period may have already adapted to high-starch diets, which may have been related to paddy rice agriculture introduced from the continent.
Furthermore, the individual from the initial Jomon period showed high amylase copy numbers comparable to those from modern East Eurasia, including modern Japanese. This suggests that some Jomon people may have consumed a high-starch diet then.
1. Introduction
In the Japanese Archipelago, >30-fold high-coverage ancient genomes have been obtained only from Hokkaido (Kanzawa-Kiriyama et al., 2019), which is relatively cold and has a higher latitude than mainland Japan.
To enhance the quality of ancient human genetic resources in this region, we obtained high-coverage genomes of individuals from two different periods in the Japanese archipelago. These high-coverage genome sequences allow inferences of several copy number polymorphisms and diploid genotyping and demographic inferences from the individual genome, which have not been reported in previous ancient genomes in this region.2. Materials and
Methods
2.1 Archeological sites
The height of the bar plot indicates the average coverage in the autosomal genome. The colored bars are the high-coverage ancient human genomes (Doigahama and Iyai1) reported in this study.
2.1.2 Doigahama site
The Doigahama site is a cemetery ruin from the early to middle-Yayoi period located on Doigahama beach and is part of southwestern Honshu, Japan
以下のmethod各項目省略
3. Results
3.1 High-coverage ancient genomes from prehistoric Japan
IY1 is one of the oldest buried human remains in the Initial Jomon period in the Japanese archipelago. The Doigahama site, from which the DO individual was excavated, is also known as a site for migratory Yayoi people, and the individual could be a representative genomic resource for migratory Yayoi people.
shotgun-sequenced genomes showed high coverage (IY1: autosome-avg. 67.94-fold; DO: autosome-avg. 46.82-fold) (Table 1
Biological sex was estimated from the read ratio (Ry) mapping to sex chromosomes as female for IY1 (Ry=0.001) and male for DO (Ry=0.090) (Table 1).
Maternal mitochondrial haplogroups of IY1 and DO were N9b and D4b2b1, respectively (Table 1).
3.2 Genetic relationships with worldwide populations
The results (PC1 and PC2) showed that the two individuals (IY1 and DO) were located close to the present-day East Asian population, but the two principal components differentially characterized IY1 and DO.
In PC3 and PC4, we were able to distinguish Jomon from other Eurasian populations. IY1, an initial Jomon individual from the mainland, was located near previously reported Jomon individuals close to the Late Jomon individuals from the mainland (ca. 1500-1000 BC).
PC3,4
3.3 Ancestral contexts of Jomon and Yayoi individuals
To infer the ancestral components of the Jomon and Yayoi individuals, model-based unsupervised clustering analysis was performed using ADMIXTURE (Figure 3). We found that the Jomon and Yayoi individuals shared the same components found in the present-day Japanese population yet were also shown to have several different components (Figure 4). The blue component (P1) observed in Yayoi was not observed in the Jomon individuals.
Nonetheless, it was observed at a high frequency in ancient Northeast Asia (ANEA), mainly in Mongolia and the Baikal region. A green component (P4) was also observed in the high-coverage Mainland Jomon IY1 and Hokkaido Jomon (F23).
3.4 Ancestral contexts of Jomon and Yayoi individuals
Comparison of copy number of AMY1A gene. This figure outlines the estimated copy number polymorphisms in the AMY1A gene. The distribution of copy number polymorphisms of the gene is compared between low-starch (Yakut) and high-starch (Japanese) dietary populations in Northeast Asia. The lines indicate the cumulative percentage of copy number polymorphisms in each population. The vertical lines show the estimated copy number of AMY1A in each ancient individual.
The copy number of AMY1A in La Braña 1, a Mesolithic European hunter-gatherer from the La Braña-Alintero site in Spain, was estimated to be approximately five (Olalde et al., 2014). These results may be related to the different dietary styles of the hunter-gatherer Jomon individuals of IY1 and the Mesolithic Period European hunter-gatherers who lived in the Japanese archipelago.
3.8 Archaic ancestry inference in Jomon genome
4. Discussion
だらだら長いのでメモ省略。
Koji Ishiya et al.
August 12, 2024
縄文1個体、弥生1個体のみの分析である。両サンプルとも前者は偶然、後者は恐らくは選んだ結果、船泊縄文サンプル並みのデータが得られたようである。
図の12が強烈な印象に残った。分析が正しいのであれば、縄文人は既に少なくとも20世代に渡ってでんぷん質を多く含む食事（多分、栽培栗が主たるカロリー源？）をしていた可能性が高いか？又は、縄文人の時点で既にヤクート人等々とは遺伝的には異なり、反復回数が既に多かった？（食事内容という環境の影響よりも先に遺伝的に相違していた）のどちらかである
また、前者であれば、縄文時代に長野県付近では既に雑穀栽培・焼畑による陸稲栽培がなされていた可能性すら示唆する。ただし、著者らも結論を出せていない。
縄文時代に雑穀栽培があったかどうかについては、自称考古学者は、30年前から二転三転しており、今のところ、想像と憶測どまりであるものの、一部地域では縄文土器からは雑穀栽培の痕跡らしきものは確認されている。ただし、連中はいい加減であるからして、確定しえない。
分析が正しいのであれば、縄文時代の長野県では、でんぷん質を多く含む食事がされていた可能性が高いものの、1個体のみである
図の12が強烈な印象に残った。分析が正しいのであれば、縄文人は既に少なくとも20世代に渡ってでんぷん質を多く含む食事（多分、栽培栗が主たるカロリー源？）をしていた可能性が高いか？又は、縄文人の時点で既にヤクート人等々とは遺伝的には異なり、反復回数が既に多かった？（食事内容という環境の影響よりも先に遺伝的に相違していた）のどちらかである
また、前者であれば、縄文時代に長野県付近では既に雑穀栽培・焼畑による陸稲栽培がなされていた可能性すら示唆する。ただし、著者らも結論を出せていない。
縄文時代に雑穀栽培があったかどうかについては、自称考古学者は、30年前から二転三転しており、今のところ、想像と憶測どまりであるものの、一部地域では縄文土器からは雑穀栽培の痕跡らしきものは確認されている。ただし、連中はいい加減であるからして、確定しえない。
分析が正しいのであれば、縄文時代の長野県では、でんぷん質を多く含む食事がされていた可能性が高いものの、1個体のみである
Abstract
Our high-coverage genome provides interesting insights into the evolution of copy number polymorphisms related to the dietary styles of ancient Japanese people.
The copy number estimates of the amylase gene for the Yayoi individual were comparable to those of present-day East Asians who have diets high in starch. This suggests that the population in the middle Yayoi period may have already adapted to high-starch diets, which may have been related to paddy rice agriculture introduced from the continent.
Furthermore, the individual from the initial Jomon period showed high amylase copy numbers comparable to those from modern East Eurasia, including modern Japanese. This suggests that some Jomon people may have consumed a high-starch diet then.
1. Introduction
In the Japanese Archipelago, >30-fold high-coverage ancient genomes have been obtained only from Hokkaido (Kanzawa-Kiriyama et al., 2019), which is relatively cold and has a higher latitude than mainland Japan.
To enhance the quality of ancient human genetic resources in this region, we obtained high-coverage genomes of individuals from two different periods in the Japanese archipelago. These high-coverage genome sequences allow inferences of several copy number polymorphisms and diploid genotyping and demographic inferences from the individual genome, which have not been reported in previous ancient genomes in this region.2. Materials and
Methods
2.1 Archeological sites
2.1.1 Iyai-rock shelter site
The site has been reported to be an archaeological site dating from the Initial Jomon to the Late Yayoi period, with an open-sloping terrace extending from the interior of the shelter to the front space.
2.1.2 Doigahama site
The Doigahama site is a cemetery ruin from the early to middle-Yayoi period located on Doigahama beach and is part of southwestern Honshu, Japan
2.2 Experimental samples
We used Jomon individual IY1 from the Iyai-rock shelter site, and Yayoi individual DO from the Doigahama site as samples for whole-genome analysis.
Radiocarbon dating indicates that IY1 has a calibrated date of 8,300-8,200 calBP (Kondo et al., 2018), which is the later part of the Initial Jomon period. The DO showed a radiocarbon date of 2,306-2,338 calBP (Mizuno et al., 2021), which belongs to the Middle Yayoi period (Figure 1B).
2.3 Sequence analysis
hg19/GRCh37 using bwa aln以下のmethod各項目省略
3. Results
3.1 High-coverage ancient genomes from prehistoric Japan
IY1 is one of the oldest buried human remains in the Initial Jomon period in the Japanese archipelago. The Doigahama site, from which the DO individual was excavated, is also known as a site for migratory Yayoi people, and the individual could be a representative genomic resource for migratory Yayoi people.
shotgun-sequenced genomes showed high coverage (IY1: autosome-avg. 67.94-fold; DO: autosome-avg. 46.82-fold) (Table 1
Biological sex was estimated from the read ratio (Ry) mapping to sex chromosomes as female for IY1 (Ry=0.001) and male for DO (Ry=0.090) (Table 1).
Maternal mitochondrial haplogroups of IY1 and DO were N9b and D4b2b1, respectively (Table 1).
3.2 Genetic relationships with worldwide populations
The results (PC1 and PC2) showed that the two individuals (IY1 and DO) were located close to the present-day East Asian population, but the two principal components differentially characterized IY1 and DO.
In PC3 and PC4, we were able to distinguish Jomon from other Eurasian populations. IY1, an initial Jomon individual from the mainland, was located near previously reported Jomon individuals close to the Late Jomon individuals from the mainland (ca. 1500-1000 BC).
PC3,4
3.3 Ancestral contexts of Jomon and Yayoi individuals
To infer the ancestral components of the Jomon and Yayoi individuals, model-based unsupervised clustering analysis was performed using ADMIXTURE (Figure 3). We found that the Jomon and Yayoi individuals shared the same components found in the present-day Japanese population yet were also shown to have several different components (Figure 4). The blue component (P1) observed in Yayoi was not observed in the Jomon individuals.
Nonetheless, it was observed at a high frequency in ancient Northeast Asia (ANEA), mainly in Mongolia and the Baikal region. A green component (P4) was also observed in the high-coverage Mainland Jomon IY1 and Hokkaido Jomon (F23).
3.4 Ancestral contexts of Jomon and Yayoi individuals
メモ省略
3.5 Ancestral demographic changes
To estimate the population size transitions that occurred in the past, we performed demographic inferences based on the Coalescent Theory.
メモ省略
3.6 Genetic remnants from Jomon and Yayoi lineages
The LD decay of IY1 and DO is 72.34 ± 6.82 gen, and that of IY1 and Han is 56.77 ± 3.66 gen, suggesting that the contribution to the modern Japanese population may be more significant from continental immigrants at the Yayoi periods.
3.7 Estimation of CNVs in AMY1 gene
Figure 12Comparison of copy number of AMY1A gene. This figure outlines the estimated copy number polymorphisms in the AMY1A gene. The distribution of copy number polymorphisms of the gene is compared between low-starch (Yakut) and high-starch (Japanese) dietary populations in Northeast Asia. The lines indicate the cumulative percentage of copy number polymorphisms in each population. The vertical lines show the estimated copy number of AMY1A in each ancient individual.
The copy number of AMY1A in La Braña 1, a Mesolithic European hunter-gatherer from the La Braña-Alintero site in Spain, was estimated to be approximately five (Olalde et al., 2014). These results may be related to the different dietary styles of the hunter-gatherer Jomon individuals of IY1 and the Mesolithic Period European hunter-gatherers who lived in the Japanese archipelago.
3.8 HLA haplotypes of DO and IY1
メモ省略3.8 Archaic ancestry inference in Jomon genome
メモ省略
4. Discussionだらだら長いのでメモ省略。
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