Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

Yi, Xin; Liang, Yu; Huerta‐Sánchez, Emilia; Jin, Xin; Cuo, Zha Xi Ping; Pool, John E.; Xu, Xun; Jiang, Hui; Vinckenbosch, Nicolas; Korneliussen, Thorfinn Sand; Zheng, Hancheng; Liu, Tao; He, Weiming; Li, Kui; Luo, Ruibang; Nie, Xifang; Wu, Honglong; Zhao, Meiru; Cao, Hongzhi; Zou, Jing; Shan, Ying; Li, Shuzheng; Yang, Qi; Asan,; Ni, Peixiang; Tian, Geng; Xu, Junming; Liu, Xiao; Jiang, Tao; Wu, Renhua; Zhou, Guangyu; Tang, Meifang; Qin, Junjie; Wang, Tong; Feng, Shuijian; Li, Guohong; Huasang,; Luosang, Jiangbai; Wang, Wei; Chen, Fang; Wang, Yading; Zheng, Xiaoguang; Li, Zhuo; Bianba, Zhuoma; Yang, Ge; Wang, Xiznping; Tang, Shuhui; Gao, Guoyi; Chen, Yong; Luo, Zhen; Gusang, Lamu; Cao, Zheng; Zhang, Qinghui; Ouyang, Weihan; Ren, Xiaoyong; Liang, Huiqing; Zheng, Huisong; Huang, Yi; Li, Jingxiang; Bolund, Lars; Kristiansen, Karsten; Li, Yingrui; Zhang, Yong; Zhang, Xiuqing; Li, Ruiqiang; Li, Songgang; Yang, Huanming; Nielsen, Rasmus; Wang, Jun; Wang, Jian

doi:10.1126/science.1190371

Cited by 1,352 publications

(1,524 citation statements)

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“…Statistics d was obtained either summing across all pairs of populations, that is, a global measure of differentiation, or between population k and their three nearest populations in terms of lowest F ST . This latter statistics is similar to that proposed by Yi et al (2010), and should be more powerful to identify selection than is Akey's statistics (Equation (1)) as it provides a direction to the allele frequency trajectory and reduces noise relative to the global test, where all population pairs are averaged. All populations with N44 were analyzed individually.…”

Section: Resultsmentioning

confidence: 99%

Porcine colonization of the Americas: a 60k SNP story

et al. 2012

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The pig, Sus scrofa, is a foreign species to the American continent. Although pigs originally introduced in the Americas should be related to those from the Iberian Peninsula and Canary islands, the phylogeny of current creole pigs that now populate the continent is likely to be very complex. Because of the extreme climates that America harbors, these populations also provide a unique example of a fast evolutionary phenomenon of adaptation. Here, we provide a genome wide study of these issues by genotyping, with a 60k SNP chip, 206 village pigs sampled across 14 countries and 183 pigs from outgroup breeds that are potential founders of the American populations, including wild boar, Iberian, international and Chinese breeds. Results show that American village pigs are primarily of European ancestry, although the observed genetic landscape is that of a complex conglomerate. There was no correlation between genetic and geographical distances, neither continent wide nor when analyzing specific areas. Most populations showed a clear admixed structure where the Iberian pig was not necessarily the main component, illustrating how international breeds, but also Chinese pigs, have contributed to extant genetic composition of American village pigs. We also observe that many genes related to the cardiovascular system show an increased differentiation between altiplano and genetically related pigs living near sea level.

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Section: Resultsmentioning

confidence: 99%

Porcine colonization of the Americas: a 60k SNP story

et al. 2012

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“…Finding evidence for parallel or convergent adaptation provides strong evidence for a gene's adaptive importance, informs our understanding of constraints to adaptive evolution, and may improve our ability to predict adaptive responses to selection [29,30]. Population genetic approaches have revealed several examples of convergent local adaptation at the molecular level: within the threespine stickleback (Gaterosteus aculeatus) the EBT locus has been involved in repeated adaptation to freshwater habitats [31], two species of European spruce harbor adaptive latitudinal clines at Ft2 and GI genes [32], and EPAS1 and HBB genes show patterns of high altitude adaptation in both dogs [33] and Tibetan humans [34]. Chen et al [32,36] identified a total of 18 genes harboring SNPs with signatures of latitudinal adaptation in the two species but only 2 genes were detected in both species, and Wang et al [33] identified 14 genes with strong signatures of high altitude adaptation in dogs but only 2 targeted in both dogs and humans.…”

Section: Is Local Adaptation Convergent At the Molecular Level?mentioning

confidence: 99%

Advances and limits of using population genetics to understand local adaptation

Tiffin

Ross‐Ibarra

2014

Preprint

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Local adaptation is an important process shaping within species diversity. In recent years, population genetic analyses, which complement organismal approaches in advancing our understanding of local adaptation have become widespread. Here we focus on using population genetics to address some key questions in local adaptation: What traits are involved? What environmental variables are most important? Does local adaptation target the same genes in related species? Do loci responsible for local adaptation exhibit tradeoffs across environments? After discussing these questions we highlight important limitations to population genetic analyses including challenges with obtaining high quality data, deciding which loci are targets of selection, and limits to identifying the genetic basis of local adaptation.

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“…of homozygosity are expected to be the more powerful methods applied to detect these signatures (Yi et al, 2010;Garud et al, 2013;Messer and Petrov, 2013).…”

Section: Moving Towards An Autosomal and Paternal Marker-based Definimentioning

confidence: 99%

Mining the pig genome to investigate the domestication process

et al. 2014

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Pig domestication began around 9000 YBP in the Fertile Crescent and Far East, involving marked morphological and genetic changes that occurred in a relatively short window of time. Identifying the alleles that drove the behavioural and physiological transformation of wild boars into pigs through artificial selection constitutes a formidable challenge that can only be faced from an interdisciplinary perspective. Indeed, although basic facts regarding the demography of pig domestication and dispersal have been uncovered, the biological substrate of these processes remains enigmatic. Considerable hope has been placed on new approaches, based on next-generation sequencing, which allow whole-genome variation to be analyzed at the population level. In this review, we provide an outline of the current knowledge on pig domestication by considering both archaeological and genetic data. Moreover, we discuss several potential scenarios of genome evolution under the complex mixture of demography and selection forces at play during domestication. Finally, we highlight several technical and methodological approaches that may represent significant advances in resolving the conundrum of livestock domestication.

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Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

Cited by 1,352 publications

References 26 publications

Porcine colonization of the Americas: a 60k SNP story

Porcine colonization of the Americas: a 60k SNP story

Advances and limits of using population genetics to understand local adaptation

Mining the pig genome to investigate the domestication process

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