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

被引:310
作者
Akey, Joshua M. [1 ]
机构
[1] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA
关键词
NONSYNDROMIC HEARING-LOSS; NATURAL-SELECTION; HUMAN-POPULATIONS; SEQUENCE VARIATION; LACTASE-PERSISTENCE; STATISTICAL TESTS; RECENT ORIGIN; COPY-NUMBER; EVOLUTION; SIGNATURES;
D O I
10.1101/gr.086652.108
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:711 / 722
页数:12
相关论文
共 123 条
[1]   PCDH15 is expressed in the neurosensory epithelium of the eye and ear and mutant alleles are responsible for both USH1F and DFNB23 [J].
Ahmed, ZM ;
Riazuddin, S ;
Ahmad, J ;
Bernstein, SL ;
Guo, Y ;
Sabar, MF ;
Sieving, P ;
Riazuddin, S ;
Griffith, AJ ;
Friedman, TB ;
Belyantseva, IA ;
Wilcox, ER .
HUMAN MOLECULAR GENETICS, 2003, 12 (24) :3215-3223
[2]   The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium [J].
Akey, JM ;
Zhang, K ;
Xiong, MM ;
Jin, L .
MOLECULAR BIOLOGY AND EVOLUTION, 2003, 20 (02) :232-242
[3]   Population history and natural selection shape patterns of genetic variation in 132 genes [J].
Akey, JM ;
Eberle, MA ;
Rieder, MJ ;
Carlson, CS ;
Shriver, MD ;
Nickerson, DA ;
Kruglyak, L .
PLOS BIOLOGY, 2004, 2 (10) :1591-1599
[4]   Interrogating a high-density SNP map for signatures of natural selection [J].
Akey, JM ;
Zhang, G ;
Zhang, K ;
Jin, L ;
Shriver, MD .
GENOME RESEARCH, 2002, 12 (12) :1805-1814
[5]   TRPV6 exhibits unusual patterns of polymorphism and divergence in worldwide populations [J].
Akey, Joshua M. ;
Swanson, Willie J. ;
Madeoy, Jennifer ;
Eberle, Michael ;
Shriver, Mark D. .
HUMAN MOLECULAR GENETICS, 2006, 15 (13) :2106-2113
[6]   A haplotype map of the human genome [J].
Altshuler, D ;
Brooks, LD ;
Chakravarti, A ;
Collins, FS ;
Daly, MJ ;
Donnelly, P ;
Gibbs, RA ;
Belmont, JW ;
Boudreau, A ;
Leal, SM ;
Hardenbol, P ;
Pasternak, S ;
Wheeler, DA ;
Willis, TD ;
Yu, FL ;
Yang, HM ;
Zeng, CQ ;
Gao, Y ;
Hu, HR ;
Hu, WT ;
Li, CH ;
Lin, W ;
Liu, SQ ;
Pan, H ;
Tang, XL ;
Wang, J ;
Wang, W ;
Yu, J ;
Zhang, B ;
Zhang, QR ;
Zhao, HB ;
Zhao, H ;
Zhou, J ;
Gabriel, SB ;
Barry, R ;
Blumenstiel, B ;
Camargo, A ;
Defelice, M ;
Faggart, M ;
Goyette, M ;
Gupta, S ;
Moore, J ;
Nguyen, H ;
Onofrio, RC ;
Parkin, M ;
Roy, J ;
Stahl, E ;
Winchester, E ;
Ziaugra, L ;
Shen, Y .
NATURE, 2005, 437 (7063) :1299-1320
[7]   Signatures of natural selection in the human genome [J].
Bamshad, M ;
Wooding, SP .
NATURE REVIEWS GENETICS, 2003, 4 (02) :99-111A
[8]   Identifying adaptive genetic divergence among populations from genome scans [J].
Beaumont, MA ;
Balding, DJ .
MOLECULAR ECOLOGY, 2004, 13 (04) :969-980
[9]   Perspective - From genotype to phenotype: Systems biology meets natural variation [J].
Benfey, Philip N. ;
Mitchell-Olds, Thomas .
SCIENCE, 2008, 320 (5875) :495-497
[10]   Genetic signatures of strong recent positive selection at the lactase gene [J].
Bersaglieri, T ;
Sabeti, PC ;
Patterson, N ;
Vanderploeg, T ;
Schaffner, SF ;
Drake, JA ;
Rhodes, M ;
Reich, DE ;
Hirschhorn, JN .
AMERICAN JOURNAL OF HUMAN GENETICS, 2004, 74 (06) :1111-1120