Literature DB >> 19411596

Constructing genomic maps of positive selection in humans: where do we go from here?

Joshua M Akey1.   

Abstract

Identifying targets of positive selection in humans has, until recently, been frustratingly slow, relying on the analysis of individual candidate genes. Genomics, however, has provided the necessary resources to systematically interrogate the entire genome for signatures of natural selection. To date, 21 genome-wide scans for recent or ongoing positive selection have been performed in humans. A key challenge is to begin synthesizing these newly constructed maps of positive selection into a coherent narrative of human evolutionary history and derive a deeper mechanistic understanding of how natural populations evolve. Here, I chronicle the recent history of the burgeoning field of human population genomics, critically assess genome-wide scans for positive selection in humans, identify important gaps in knowledge, and discuss both short- and long-term strategies for traversing the path from the low-resolution, incomplete, and error-prone maps of selection today to the ultimate goal of a detailed molecular, mechanistic, phenotypic, and population genetics characterization of adaptive alleles.

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Year:  2009        PMID: 19411596      PMCID: PMC3647533          DOI: 10.1101/gr.086652.108

Source DB:  PubMed          Journal:  Genome Res        ISSN: 1088-9051            Impact factor:   9.043


  111 in total

1.  TRPV6 exhibits unusual patterns of polymorphism and divergence in worldwide populations.

Authors:  Joshua M Akey; Willie J Swanson; Jennifer Madeoy; Michael Eberle; Mark D Shriver
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Review 2.  The evolutionary significance of cis-regulatory mutations.

Authors:  Gregory A Wray
Journal:  Nat Rev Genet       Date:  2007-03       Impact factor: 53.242

3.  Integration of biological networks and gene expression data using Cytoscape.

Authors:  Melissa S Cline; Michael Smoot; Ethan Cerami; Allan Kuchinsky; Nerius Landys; Chris Workman; Rowan Christmas; Iliana Avila-Campilo; Michael Creech; Benjamin Gross; Kristina Hanspers; Ruth Isserlin; Ryan Kelley; Sarah Killcoyne; Samad Lotia; Steven Maere; John Morris; Keiichiro Ono; Vuk Pavlovic; Alexander R Pico; Aditya Vailaya; Peng-Liang Wang; Annette Adler; Bruce R Conklin; Leroy Hood; Martin Kuiper; Chris Sander; Ilya Schmulevich; Benno Schwikowski; Guy J Warner; Trey Ideker; Gary D Bader
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

Review 4.  The locus of evolution: evo devo and the genetics of adaptation.

Authors:  Hopi E Hoekstra; Jerry A Coyne
Journal:  Evolution       Date:  2007-05       Impact factor: 3.694

5.  From genotype to phenotype: systems biology meets natural variation.

Authors:  Philip N Benfey; Thomas Mitchell-Olds
Journal:  Science       Date:  2008-04-25       Impact factor: 47.728

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

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

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

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

Review 8.  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

9.  Population genetic diversity of the NAT2 gene supports a role of acetylation in human adaptation to farming in Central Asia.

Authors:  Hélène Magalon; Etienne Patin; Frédéric Austerlitz; Tatyana Hegay; Almaz Aldashev; Lluís Quintana-Murci; Evelyne Heyer
Journal:  Eur J Hum Genet       Date:  2007-11-28       Impact factor: 4.246

Review 10.  Genome-wide scans for loci under selection in humans.

Authors:  James Ronald; Joshua M Akey
Journal:  Hum Genomics       Date:  2005-06       Impact factor: 4.639

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  208 in total

1.  Genome-wide detection of natural selection in African Americans pre- and post-admixture.

Authors:  Wenfei Jin; Shuhua Xu; Haifeng Wang; Yongguo Yu; Yiping Shen; Bailin Wu; Li Jin
Journal:  Genome Res       Date:  2011-11-29       Impact factor: 9.043

Review 2.  Genetic contributions to behavioural diversity at the gene-environment interface.

Authors:  Andres Bendesky; Cornelia I Bargmann
Journal:  Nat Rev Genet       Date:  2011-11-08       Impact factor: 53.242

Review 3.  Recent advances in understanding the role of nutrition in human genome evolution.

Authors:  Kaixiong Ye; Zhenglong Gu
Journal:  Adv Nutr       Date:  2011-11-03       Impact factor: 8.701

Review 4.  Molecular spandrels: tests of adaptation at the genetic level.

Authors:  Rowan D H Barrett; Hopi E Hoekstra
Journal:  Nat Rev Genet       Date:  2011-10-18       Impact factor: 53.242

5.  Signatures of positive selection apparent in a small sample of human exomes.

Authors:  Jacob A Tennessen; Jennifer Madeoy; Joshua M Akey
Journal:  Genome Res       Date:  2010-08-06       Impact factor: 9.043

6.  Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations.

Authors:  Pavlos Pavlidis; Jeffrey D Jensen; Wolfgang Stephan
Journal:  Genetics       Date:  2010-04-20       Impact factor: 4.562

7.  Colloquium paper: gene-culture coevolution in the age of genomics.

Authors:  Peter J Richerson; Robert Boyd; Joseph Henrich
Journal:  Proc Natl Acad Sci U S A       Date:  2010-05-05       Impact factor: 11.205

8.  Adaptive selection of an incretin gene in Eurasian populations.

Authors:  Chia Lin Chang; James J Cai; Chiening Lo; Jorge Amigo; Jae-Il Park; Sheau Yu Teddy Hsu
Journal:  Genome Res       Date:  2010-10-26       Impact factor: 9.043

Review 9.  The epigenomic interface between genome and environment in common complex diseases.

Authors:  Christopher G Bell; Stephan Beck
Journal:  Brief Funct Genomics       Date:  2010-11-08       Impact factor: 4.241

10.  Fine-scale recombination rate differences between sexes, populations and individuals.

Authors:  Augustine Kong; Gudmar Thorleifsson; Daniel F Gudbjartsson; Gisli Masson; Asgeir Sigurdsson; Aslaug Jonasdottir; G Bragi Walters; Adalbjorg Jonasdottir; Arnaldur Gylfason; Kari Th Kristinsson; Sigurjon A Gudjonsson; Michael L Frigge; Agnar Helgason; Unnur Thorsteinsdottir; Kari Stefansson
Journal:  Nature       Date:  2010-10-28       Impact factor: 49.962

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