Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan
Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan
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DOI：
10.1537/ase.190415
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发表时间：
2019-08-01
影响因子：
0.7
通讯作者：
Shinoda, Ken-ichi
中科院分区：
文献类型：
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作者：
Kanzawa-Kiriyama, Hideaki;Jinam, Timothy A.;Shinoda, Ken-ichi
Fimadomari 绳文人是生活在日本北海道礼文岛的狩猎采集者。 3500-3800年前。在本研究中，我们分别确定了船泊绳文女性 (F23) 和男性 (F5) 的高深度和低深度核基因组序列。我们对 F23 的核 DNA 进行了基因分型，并确定了人类白细胞抗原 (HLA) 1 类基因型和表型特征。此外，在 F23 和 F5 中均发现了 CPTIA 基因的致病性突变。该突变为高脂肪饮食的消耗提供了代谢优势，其等位基因频率在北极人群中超过 70%，但在其他地方不存在。这种变异可能与船泊绳文人的生活方式有关，他们捕鱼和狩猎陆地和海洋动物。我们在 F23 中观察到高血统纯合性 (HBD)，但长度超过 10 cM 的 HBD 束非常有限，这表明北绳文种群的种群规模很小。我们的分析表明，绳文人的人口规模开始减少。五万年前。 F23、现代/古代欧亚人和美洲原住民之间的系统发育关系显示，F23在东欧亚大陆存在深刻的分歧，可能发生在美洲原住民的祖先与东欧亚人分裂之前，但在4万年前的天元分裂之后，表明北绳文人与东欧亚大陆人在基因上长期隔离。有趣的是，我们发现现代日本人以及乙支人、韩国人、台湾原住民和菲律宾人在基因上更接近 F23，而不是汉族。此外，F5的Y染色体属于单倍群D1b2b，这在现代日本人群中是罕见的。这些发现为了解东欧亚大陆古代人类人口结构的历史和重建提供了见解，F23基因组数据可以被视为未来研究的绳文参考基因组。
The Fimadomari Jomon people were hunter-gatherers living on Rebun Island, Hokkaido, Japan c. 3500-3800 years ago. In this study, we determined the high-depth and low-depth nuclear genome sequences from a Funadomari Jomon female (F23) and male (F5), respectively. We genotyped the nuclear DNA of F23 and determined the human leukocyte antigen (HLA) class-1 genotypes and the phenotypic traits. Moreover, a pathogenic mutation in the CPTIA gene was identified in both F23 and F5. The mutation provides metabolic advantages for consumption of a high-fat diet, and its allele frequency is more than 70% in Arctic populations, but is absent elsewhere. This variant may be related to the lifestyle of the Funadomari Jomon people, who fished and hunted land and marine animals. We observed high homozygosity by descent (HBD) in F23, but HBD tracts longer than 10 cM were very limited, suggesting that the population size of Northern Jomon populations were small. Our analysis suggested that population size of the Jomon people started to decrease c. 50000 years ago. The phylogenetic relationship among F23, modem/ancient Eurasians, and Native Americans showed a deep divergence of F23 in East Eurasia, probably before the split of the ancestor of Native Americans from East Eurasians, but after the split of 40000-year-old Tianyuan, indicating that the Northern Jomon people were genetically isolated from continental East Eurasians for a long period. Intriguingly, we found that modern Japanese as well as Ulchi, Korean, aboriginal Taiwanese, and Philippine populations were genetically closer to F23 than to Han Chinese. Moreover, the Y chromosome of F5 belonged to haplogroup D1b2b, which is rare in modern Japanese populations. These findings provided insights into the history and reconstructions of the ancient human population structures in East Eurasia, and the F23 genome data can be considered as the Jomon Reference Genome for future studies.