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recent selection signatures linked to evolution and disease risk of Japanese

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发表于 2018-5-2 14:18 | 显示全部楼层 |阅读模式
Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

Yukinori Okada, Yukihide Momozawa, Saori Sakaue, Masahiro Kanai, Kazuyoshi Ishigaki, Masato Akiyama, Toshihiro Kishikawa, Yasumichi Arai, Takashi Sasaki, Kenjiro Kosaki, Makoto Suematsu, Koichi Matsuda, Kazuhiko Yamamoto, Michiaki Kubo, Nobuyoshi Hirose & Yoichiro Kamatani
Nature Communications
volume 9, Article number: 1631 (2018)
doi:10.1038/s41467-018-03274-0
Received: 09 August 2017
Accepted: 01 February 2018
Published online: 24 April 2018

Abstract
Understanding natural selection is crucial to unveiling evolution of modern humans. Here, we report natural selection signatures in the Japanese population using 2234 high-depth whole-genome sequence (WGS) data (25.9×). Using rare singletons, we identify signals of very recent selection for the past 2000–3000 years in multiple loci (ADH cluster, MHC region, BRAP-ALDH2, SERHL2). In large-scale genome-wide association study (GWAS) dataset (n = 171,176), variants with selection signatures show enrichment in heterogeneity of derived allele frequency spectra among the geographic regions of Japan, highlighted by two major regional clusters (Hondo and Ryukyu). While the selection signatures do not show enrichment in archaic hominin-derived genome sequences, they overlap with the SNPs associated with the modern human traits. The strongest overlaps are observed for the alcohol or nutrition metabolism-related traits. Our study illustrates the value of high-depth WGS to understand evolution and their relationship with disease risk.

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 楼主| 发表于 2018-5-2 14:19 | 显示全部楼层
The top SNPs from the SDS analysis in ADH cluster and BRAP-ALDH2 are in linkage disequilibrium (LD) with functional missense SNPs of ADH1B (Arg47His, rs1229984) and ALDH2 (Glu504Lys, rs671) (r2 = 0.76 and 0.86 in the WGS dataset 1, respectively). These SNPs mediate differences in alcohol metabolism by altering the enzymatic activities of alcohol dehydrogenase and aldehyde dehydrogenase, and have been suggested in evolutional adaptations of global populations including Asians mostly by candidate gene-based approaches22. Our genome-wide analysis initially indicates that both of these alcohol metabolism-related SNPs are under the strongest recent natural selection pressure in the Japanese population.
 楼主| 发表于 2018-5-2 14:20 | 显示全部楼层
本帖最后由 wmch_928 于 2018-5-2 14:22 编辑

发表于 2018-5-4 00:00 | 显示全部楼层
The top SNPs from the SDS analysis in ADH cluster and BRAP-ALDH2 are in linkage disequilibrium (LD) with functional missense SNPs of ADH1B (Arg47His, rs1229984) and ALDH2 (Glu504Lys, rs671) (r2  ...
wmch_928 发表于 2018-5-2 14:19

关于ADH1B (Arg47His, rs1229984) ,宿兵团队8年前已经有过认真的研究,数据很详实,结论是与新石器时期稻米种植人群密切相关,最高频出现在浙江-湖南长江中下游人群,以此为中心扩散,因此可以与我之前认定的his615arg一样,均可视为“神农氏”marker之一(下表数据应该还可以进一步补充完善,比如台湾土著的频度也是很高的):

Population经度纬度Sample SizeLanguageADH1B*47His Frequency
 Zhejiang1213032Han98.5
She1182712Hmong-Mien91.7
 Hunan11027.520Han82.5
 Guizhou1072861Han75.4
Gelo1062710Daic75
Mulam1092412Daic75
Chuang1082333Daic72.7
 Guangxi109249Han72.2
 Jiangsu1193424Han70.8
 Hubei1133041Han70.7
Miao1092629Hmong-Mien70.7
 Guangxi1092616Daic68.7
 Liaonin1244228Han67.9
Shui1082611Daic66.7
Manchu12542.527Altai66.7
 Anhui1183334Han66.2
Tujia1093031Tibeto-Burman66.1
Dong5865.5
Yao1112558Hmong-Mien64.7
 Henan1123456Han64.3
 Hunan11027.542Daic64.3
 Shandong1203790Han63.3
Buyi106.52645Daic63.3
 Shannxi10834.552Han62.5
 Shanxi11237.544Han61.4
Maonan1082515Daic60
 Gansu10536174Han59.8
Yi101.524.530Tibeto-Burman55
Jilin1254414Han50
Bai10025.530Tibeto-Burman50
Dai10023.530Daic43.3
Hani102.52330Tibeto-Burman41.7
Cambodian1051317Austro-Asiatic20.6
 Qinghai9633127Tibeto-Burman20.5
 Rikaze892955Tibeto-Burman16.4
 Changdou973156Tibeto-Burman14.3
Tibetan108814.1
 Dangxiong9130.5816Tibeto-Burman13.1
 Shannan922934Tibeto-Burman11.8
Bulang10023.530Austro-Asiatic1.7
发表于 2018-5-4 00:04 | 显示全部楼层
楚人好酒,可能亦与此相关~
发表于 2018-5-4 09:57 | 显示全部楼层
ADH1B (Arg47His, rs1229984)在Cambodian和Bulang人群中比例很低,而这两个民族都是典型的农业民族,所以ADH1B 应该不是原始农业刚扩散时就跟随扩散的基因。而在在最初的农业扩散后,第二波农业扩散的标志。也就是说,原始农业从长江下游出现后,刚开始沿着山地从长江中游扩散,这部分人群属于后来的蒙高棉语系,这部分人是没有ADH1B 标志的,后来ADH1B诞生后,又分为两支,一部分渡江,一部分留在原地,渡江的就是汉藏语系乃至苗瑶语系,日韩语系,留下的就是百越-南岛语系。
发表于 2018-5-4 12:02 | 显示全部楼层
6# wolfgang
嗯,南亚语人群应该是第一波南下的农夫,彼时稻米酿酒可能还没有发明或还没有普及,第二波是原始南岛语壮侗语苗瑶语濮语人群的大扩散,可能是他们把ADH1B变异扩散到大江南北的
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