Fine-Scale Genetic Structure and Natural Selection Signatures of Southwestern Hans Inferred From Patterns of Genome-Wide Allele, Haplotype, and Haplogroup Lineages.
Fine-Scale Genetic Structure and Natural Selection Signatures of Southwestern Hans Inferred From Patterns of Genome-Wide Allele, Haplotype, and Haplogroup Lineages.
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从全基因组等位基因、单倍型和单倍群谱系模式推断西南汉族的精细遗传结构和自然选择特征
DOI：
10.3389/fgene.2021.727821
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发表时间：
2021
影响因子：
3.7
通讯作者：
He G
中科院分区：
文献类型：
--
作者：
Wang M;Yuan D;Zou X;Wang Z;Yeh HY;Liu J;Wei LH;Wang CC;Zhu B;Liu C;He G
通过传统的常染色体和单亲遗传标记(如短串联重复序列、低密度单核苷酸多态)，汉族人的进化史和混血史得到了广泛的讨论。然而，它们基于高密度等位基因/单倍型共享模式的精细遗传景观(混合场景和自然选择签名)还没有得到深入的表征。在这里，我们收集并生成了来自贵州省四个民族的50个汉族个体的全基因组数据，并将其与3000多个公开可用的现代和古代欧亚人合并，以描述贵州汉族及其邻居的遗传起源和种群混血历史。主成分分析和混合分析结果表明，所研究的四个种群是同质性的，与东亚中部人聚在一起很近。通过在fst和外群f3/f4统计中观察到的遗传分支，进一步证实了贵州种群内的遗传同源性，并与内陆苗族人有很强的遗传亲缘关系。基于qpGraph的系统发育和基于f4的人口学模型表明，贵州汉族与古代黄河谷农与拉家族和江南农民与汉本人的关系很好地吻合。进一步基于ChromoPainter的染色体绘制轮廓和基于Globbetroter的混合签名证实了西南汉族的两个最好的来源匹配，分别来自历史时期不同混合比例的陕北汉族和南方土著。进一步的三向混合模型显示，与所提出的来自东南亚大陆的内陆古代来源相比，东亚南部沿海人对贵州汉族的遗传贡献更大。我们还通过IHS、NSL和IHH等方法在贵州汉族人群中发现了具有较强自然选择特征的候选基因座(如MTUS2、NOTCH4、EDAR、ADH1B和ABCG2)，这些候选基因座与多种复杂疾病的易感性、形态形成、酒精和脂肪代谢有关。总之，我们提供了一个案例和理想的策略来重建贵州汉族详细的人口演化史，从共享的非连锁等位基因、连锁的单倍型和父系和母系的综合角度对一个民族语言特定的目标人群的精细基因组形成提供了新的见解。
The evolutionary and admixture history of Han Chinese have been widely discussed via traditional autosomal and uniparental genetic markers [e.g., short tandem repeats, low-density single nucleotide polymorphisms). However, their fine-scale genetic landscapes (admixture scenarios and natural selection signatures) based on the high-density allele/haplotype sharing patterns have not been deeply characterized. Here, we collected and generated genome-wide data of 50 Han Chinese individuals from four populations in Guizhou Province, one of the most ethnolinguistically diverse regions, and merged it with over 3,000 publicly available modern and ancient Eurasians to describe the genetic origin and population admixture history of Guizhou Hans and their neighbors. PCA and ADMIXTURE results showed that the studied four populations were homogeneous and grouped closely to central East Asians. Genetic homogeneity within Guizhou populations was further confirmed via the observed strong genetic affinity with inland Hmong-Mien people through the observed genetic clade in Fst and outgroup f3/f4-statistics. qpGraph-based phylogenies and f4-based demographic models illuminated that Guizhou Hans were well fitted via the admixture of ancient Yellow River Millet farmers related to Lajia people and southern Yangtze River farmers related to Hanben people. Further ChromoPainter-based chromosome painting profiles and GLOBETROTTER-based admixture signatures confirmed the two best source matches for southwestern Hans, respectively, from northern Shaanxi Hans and southern indigenes with variable mixture proportions in the historical period. Further three-way admixture models revealed larger genetic contributions from coastal southern East Asians into Guizhou Hans compared with the proposed inland ancient source from mainland Southeast Asia. We also identified candidate loci (e.g., MTUS2, NOTCH4, EDAR, ADH1B, and ABCG2) with strong natural selection signatures in Guizhou Hans via iHS, nSL, and ihh, which were associated with the susceptibility of the multiple complex diseases, morphology formation, alcohol and lipid metabolism. Generally, we provided a case and ideal strategy to reconstruct the detailed demographic evolutionary history of Guizhou Hans, which provided new insights into the fine-scale genomic formation of one ethnolinguistically specific targeted population from the comprehensive perspectives of the shared unlinked alleles, linked haplotypes, and paternal and maternal lineages.
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影响因子：
3.7
作者：
Liu Y;Yang J;Li Y;Tang R;Yuan D;Wang Y;Wang P;Deng S;Zeng S;Li H;Chen G;Zou X;Wang M;He G
通讯作者：
He G
影响因子：
9.2
作者：
Chang CC;Chow CC;Tellier LC;Vattikuti S;Purcell SM;Lee JJ
通讯作者：
Lee JJ
对东亚西南部蒙古语和通古斯语人群混合历史的基因组见解
影响因子：
3.7
作者：
Chen J;He G;Ren Z;Wang Q;Liu Y;Zhang H;Yang M;Zhang H;Ji J;Zhao J;Guo J;Zhu K;Yang X;Wang R;Ma H;Wang CC;Huang J
通讯作者：
Huang J
影响因子：
3.7
作者：
Chen, Pengyu;Wu, Jian;He, Guanglin
通讯作者：
He, Guanglin
DOI：
10.1126/science.1243518
发表时间：
2014-02-14
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Hellenthal G;Busby GBJ;Band G;Wilson JF;Capelli C;Falush D;Myers S
通讯作者：
Myers S