Literature DB >> 26228473

Population genetic studies in the genomic sequencing era.

Hua Chen1.   

Abstract

Recent advances in high-throughput sequencing technologies have revolutionized the field of population genetics. Data now routinely contain genomic level polymorphism information, and the low cost of DNA sequencing enables researchers to investigate tens of thousands of subjects at a time. This provides an unprecedented opportunity to address fundamental evolutionary questions, while posing challenges on traditional population genetic theories and methods. This review provides an overview of the recent methodological developments in the field of population genetics, specifically methods used to infer ancient population history and investigate natural selection using large-sample, large-scale genetic data. Several open questions are also discussed at the end of the review.

Keywords:  Allele frequency spectrum; Demography; Linkage disequilibrium; Natural selection; Population genetic inference

Mesh:

Year:  2015        PMID: 26228473      PMCID: PMC4790258          DOI: 10.13918/j.issn.2095-8137.2015.4.223

Source DB:  PubMed          Journal:  Dongwuxue Yanjiu        ISSN: 0254-5853


  97 in total

1.  Comparative population genomics of maize domestication and improvement.

Authors:  Matthew B Hufford; Xun Xu; Joost van Heerwaarden; Tanja Pyhäjärvi; Jer-Ming Chia; Reed A Cartwright; Robert J Elshire; Jeffrey C Glaubitz; Kate E Guill; Shawn M Kaeppler; Jinsheng Lai; Peter L Morrell; Laura M Shannon; Chi Song; Nathan M Springer; Ruth A Swanson-Wagner; Peter Tiffin; Jun Wang; Gengyun Zhang; John Doebley; Michael D McMullen; Doreen Ware; Edward S Buckler; Shuang Yang; Jeffrey Ross-Ibarra
Journal:  Nat Genet       Date:  2012-06-03       Impact factor: 38.330

2.  The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations.

Authors:  Gabor T Marth; Eva Czabarka; Janos Murvai; Stephen T Sherry
Journal:  Genetics       Date:  2004-01       Impact factor: 4.562

3.  Inference of population genetic parameters in metagenomics: a clean look at messy data.

Authors:  Philip L F Johnson; Montgomery Slatkin
Journal:  Genome Res       Date:  2006-09-05       Impact factor: 9.043

4.  Asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size.

Authors:  Hua Chen; Kun Chen
Journal:  Genetics       Date:  2013-05-11       Impact factor: 4.562

5.  Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Authors:  F Tajima
Journal:  Genetics       Date:  1989-11       Impact factor: 4.562

6.  The hitch-hiking effect of a favourable gene.

Authors:  J M Smith; J Haigh
Journal:  Genet Res       Date:  1974-02       Impact factor: 1.588

7.  Statistical tests of neutrality of mutations.

Authors:  Y X Fu; W H Li
Journal:  Genetics       Date:  1993-03       Impact factor: 4.562

8.  Population structure and eigenanalysis.

Authors:  Nick Patterson; Alkes L Price; David Reich
Journal:  PLoS Genet       Date:  2006-12       Impact factor: 5.917

9.  The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation.

Authors:  Jonathan K Pritchard; Joseph K Pickrell; Graham Coop
Journal:  Curr Biol       Date:  2010-02-23       Impact factor: 10.834

10.  A map of rice genome variation reveals the origin of cultivated rice.

Authors:  Xuehui Huang; Nori Kurata; Xinghua Wei; Zi-Xuan Wang; Ahong Wang; Qiang Zhao; Yan Zhao; Kunyan Liu; Hengyun Lu; Wenjun Li; Yunli Guo; Yiqi Lu; Congcong Zhou; Danlin Fan; Qijun Weng; Chuanrang Zhu; Tao Huang; Lei Zhang; Yongchun Wang; Lei Feng; Hiroyasu Furuumi; Takahiko Kubo; Toshie Miyabayashi; Xiaoping Yuan; Qun Xu; Guojun Dong; Qilin Zhan; Canyang Li; Asao Fujiyama; Atsushi Toyoda; Tingting Lu; Qi Feng; Qian Qian; Jiayang Li; Bin Han
Journal:  Nature       Date:  2012-10-03       Impact factor: 49.962

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  4 in total

1.  Accelerated evolution of constraint elements for hematophagic adaptation in mosquitoes.

Authors:  Ming-Shan Wang; Adeniyi C Adeola; Yan Li; Ya-Ping Zhang; Dong-Dong Wu
Journal:  Dongwuxue Yanjiu       Date:  2015-11-18

2.  A Computational Approach for Modeling the Allele Frequency Spectrum of Populations with Arbitrarily Varying Size.

Authors:  Hua Chen
Journal:  Genomics Proteomics Bioinformatics       Date:  2020-03-13       Impact factor: 7.691

3.  Draft genome of the gayal, Bos frontalis.

Authors:  Ming-Shan Wang; Yan Zeng; Xiao Wang; Wen-Hui Nie; Jin-Huan Wang; Wei-Ting Su; Newton O Otecko; Zi-Jun Xiong; Sheng Wang; Kai-Xing Qu; Shou-Qing Yan; Min-Min Yang; Wen Wang; Yang Dong; Dong-Dong Wu; Ya-Ping Zhang
Journal:  Gigascience       Date:  2017-11-01       Impact factor: 6.524

4.  Mitochondrial Haplogroup Classification of Ancient DNA Samples Using Haplotracker.

Authors:  Kijeong Kim; Dong-Han Kim; Kyung-Yong Kim
Journal:  Biomed Res Int       Date:  2022-03-18       Impact factor: 3.411

  4 in total

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