Literature DB >> 24052086

Recent human adaptation: genomic approaches, interpretation and insights.

Laura B Scheinfeldt1, Sarah A Tishkoff.   

Abstract

The recent availability of genomic data has spurred many genome-wide studies of human adaptation in different populations worldwide. Such studies have provided insights into novel candidate genes and pathways that are putatively involved in adaptation to different environments, diets and disease prevalence. However, much work is needed to translate these results into candidate adaptive variants that are biologically interpretable. In this Review, we discuss methods that may help to identify true biological signals of selection and studies that incorporate complementary phenotypic and functional data. We conclude with recommendations for future studies that focus on opportunities to use integrative genomics methodologies in human adaptation studies.

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Year:  2013        PMID: 24052086      PMCID: PMC4882605          DOI: 10.1038/nrg3604

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  108 in total

1.  An integrative genomics approach to infer causal associations between gene expression and disease.

Authors:  Eric E Schadt; John Lamb; Xia Yang; Jun Zhu; Steve Edwards; Debraj Guhathakurta; Solveig K Sieberts; Stephanie Monks; Marc Reitman; Chunsheng Zhang; Pek Yee Lum; Amy Leonardson; Rolf Thieringer; Joseph M Metzger; Liming Yang; John Castle; Haoyuan Zhu; Shera F Kash; Thomas A Drake; Alan Sachs; Aldons J Lusis
Journal:  Nat Genet       Date:  2005-06-19       Impact factor: 38.330

Review 2.  Q(ST)-F(ST) comparisons: evolutionary and ecological insights from genomic heterogeneity.

Authors:  Tuomas Leinonen; R J Scott McCairns; Robert B O'Hara; Juha Merilä
Journal:  Nat Rev Genet       Date:  2013-02-05       Impact factor: 53.242

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

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

Review 4.  Positive natural selection in the human lineage.

Authors:  P C Sabeti; S F Schaffner; B Fry; J Lohmueller; P Varilly; O Shamovsky; A Palma; T S Mikkelsen; D Altshuler; E S Lander
Journal:  Science       Date:  2006-06-16       Impact factor: 47.728

5.  Statistical tests of neutrality of mutations.

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

6.  Evidence for polygenic adaptation to pathogens in the human genome.

Authors:  Josephine T Daub; Tamara Hofer; Emilie Cutivet; Isabelle Dupanloup; Lluis Quintana-Murci; Marc Robinson-Rechavi; Laurent Excoffier
Journal:  Mol Biol Evol       Date:  2013-04-26       Impact factor: 16.240

7.  Detecting and characterizing genomic signatures of positive selection in global populations.

Authors:  Xuanyao Liu; Rick Twee-Hee Ong; Esakimuthu Nisha Pillai; Abier M Elzein; Kerrin S Small; Taane G Clark; Dominic P Kwiatkowski; Yik-Ying Teo
Journal:  Am J Hum Genet       Date:  2013-05-23       Impact factor: 11.025

8.  Adaptations to climate-mediated selective pressures in humans.

Authors:  Angela M Hancock; David B Witonsky; Gorka Alkorta-Aranburu; Cynthia M Beall; Amha Gebremedhin; Rem Sukernik; Gerd Utermann; Jonathan K Pritchard; Graham Coop; Anna Di Rienzo
Journal:  PLoS Genet       Date:  2011-04-21       Impact factor: 5.917

9.  Genetic adaptation to high altitude in the Ethiopian highlands.

Authors:  Laura B Scheinfeldt; Sameer Soi; Simon Thompson; Alessia Ranciaro; Dawit Woldemeskel; William Beggs; Charla Lambert; Joseph P Jarvis; Dawit Abate; Gurja Belay; Sarah A Tishkoff
Journal:  Genome Biol       Date:  2012-01-20       Impact factor: 13.583

10.  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

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  46 in total

Review 1.  The Genome 10K Project: a way forward.

Authors:  Klaus-Peter Koepfli; Benedict Paten; Stephen J O'Brien
Journal:  Annu Rev Anim Biosci       Date:  2015       Impact factor: 8.923

2.  Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation.

Authors:  Julien Jouganous; Will Long; Aaron P Ragsdale; Simon Gravel
Journal:  Genetics       Date:  2017-05-11       Impact factor: 4.562

3.  Was ADH1B under Selection in European Populations?

Authors:  Quan-Kuan Shen; Xierzhatijiang Sulaiman; Yong-Gang Yao; Min-Sheng Peng; Ya-Ping Zhang
Journal:  Am J Hum Genet       Date:  2016-11-03       Impact factor: 11.025

4.  Population Structure of UK Biobank and Ancient Eurasians Reveals Adaptation at Genes Influencing Blood Pressure.

Authors:  Kevin J Galinsky; Po-Ru Loh; Swapan Mallick; Nick J Patterson; Alkes L Price
Journal:  Am J Hum Genet       Date:  2016-10-20       Impact factor: 11.025

5.  Genetic origins of lactase persistence and the spread of pastoralism in Africa.

Authors:  Alessia Ranciaro; Michael C Campbell; Jibril B Hirbo; Wen-Ya Ko; Alain Froment; Paolo Anagnostou; Maritha J Kotze; Muntaser Ibrahim; Thomas Nyambo; Sabah A Omar; Sarah A Tishkoff
Journal:  Am J Hum Genet       Date:  2014-03-13       Impact factor: 11.025

6.  Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia.

Authors:  Kevin J Galinsky; Gaurav Bhatia; Po-Ru Loh; Stoyan Georgiev; Sayan Mukherjee; Nick J Patterson; Alkes L Price
Journal:  Am J Hum Genet       Date:  2016-02-25       Impact factor: 11.025

7.  Detecting Recent Positive Selection with a Single Locus Test Bipartitioning the Coalescent Tree.

Authors:  Zongfeng Yang; Junrui Li; Thomas Wiehe; Haipeng Li
Journal:  Genetics       Date:  2017-12-07       Impact factor: 4.562

8.  Distance from sub-Saharan Africa predicts mutational load in diverse human genomes.

Authors:  Brenna M Henn; Laura R Botigué; Stephan Peischl; Isabelle Dupanloup; Mikhail Lipatov; Brian K Maples; Alicia R Martin; Shaila Musharoff; Howard Cann; Michael P Snyder; Laurent Excoffier; Jeffrey M Kidd; Carlos D Bustamante
Journal:  Proc Natl Acad Sci U S A       Date:  2015-12-28       Impact factor: 11.205

Review 9.  Inferences of African evolutionary history from genomic data.

Authors:  Marcia Holsbach Beltrame; Meagan A Rubel; Sarah A Tishkoff
Journal:  Curr Opin Genet Dev       Date:  2016-11-01       Impact factor: 5.578

10.  Defective Tibetan PHD2 binding to p23 links high altitude adaption to altered oxygen sensing.

Authors:  Daisheng Song; Lin-sheng Li; Patrick R Arsenault; Qiulin Tan; Abigail W Bigham; Katherine J Heaton-Johnson; Stephen R Master; Frank S Lee
Journal:  J Biol Chem       Date:  2014-04-07       Impact factor: 5.157

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