Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Filters applied. Clear all
. 2011 Dec 1;2:85.
doi: 10.3389/fgene.2011.00085. eCollection 2011.

On Detecting Selective Sweeps Using Single Genomes

Free PMC article

On Detecting Selective Sweeps Using Single Genomes

Priyanka Sinha et al. Front Genet. .
Free PMC article


Identifying the genetic basis of human adaptation has remained a central focal point of modern population genetics. One major area of interest has been the use of polymorphism data to detect so-called "footprints" of selective sweeps - patterns produced as a beneficial mutation arises and rapidly fixes in the population. Based on numerous simulation studies and power analyses, the necessary sample size for achieving appreciable power has been shown to vary from a few individuals to a few dozen, depending on the test statistic. And yet, the sequencing of multiple copies of a single region, or of multiple genomes as is now often the case, incurs considerable cost. Enard et al. (2010) have recently proposed a method to identify patterns of selective sweeps using a single genome - and apply this approach to human and non-human primates (chimpanzee, orangutan, and macaque). They employ essentially a modification of the Hudson, Kreitman, and Aguade test - using heterozygous single nucleotide polymorphisms from single individuals, and divergence data from two closely related species (human-chimpanzee, human-orangutan, and human-macaque). Given the potential importance of this finding, we here investigate the properties of this statistic. We demonstrate through simulation that this approach is neither robust to demography nor background selection; nor is it robust to variable recombination rates.

Keywords: adaptation; demography; selective sweeps; statistical inference.


Figure 1
Figure 1
K value for region containing varying recombination rates (θ = 0.00094).

Similar articles

See all similar articles

Cited by 2 articles


    1. Begun D. J., Aquadro C. F. (1992). Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356, 519–52010.1038/356519a0 - DOI - PubMed
    1. Broman K. W., Murray J. C., Sheffield V. C., White R. L., Weber J. L. (1998). Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am. J. Hum. Genet. 63, 861–86910.1086/302112 - DOI - PMC - PubMed
    1. Carlson C. S., Thomas D. J., Eberle M. A., Swanson J. E., Livingston R. J., Rieder M. J., Nickerson D. A. (2005). Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res. 15, 1553–156510.1101/gr.4326505 - DOI - PMC - PubMed
    1. Enard D., Depaulis F., Roest Crollius H. (2010). Humans and non-human primate genomes share hotspots of positive selection. PLoS Genet. 6, e1000840.10.1371/journal.pgen.1000840 - DOI - PMC - PubMed
    1. Frazer K. A., Ballinger D. G., Cox D. R., Hinds D. A., Stuve L. L., Gibbs R. A., Belmont J. W., Boudreau A., Hardenbol P., Leal S. M., Pasternak S., Wheeler D. A., Willis T. D., Yu F., Yang H., Zeng C., Gao Y., Hu H., Hu W., Li C., Lin W., Liu S., Pan H., Tang X., Wang J., Wang W., Yu J., Zhang B., Zhang Q., Zhao H., Zhao H., Zhou J., Gabriel S. B., Barry R., Blumenstiel B., Camargo A., Defelice M., Faggart M., Goyette M., Gupta S., Moore J., Nguyen H., Onofrio R. C., Parkin M., Roy J., Stahl E., Winchester E., Ziaugra L., Altshuler D., Shen Y., Yao Z., Huang W., Chu X., He Y., Jin L., Liu Y., Shen Y., Sun W., Wang H., Wang Y., Wang Y., Xiong X., Xu L., Waye M. M., Tsui S. K., Xue H., Wong J. T., Galver L. M., Fan J. B., Gunderson K., Murray S. S., Oliphant A. R., Chee M. S., Montpetit A., Chagnon F., Ferretti V., Leboeuf M., Olivier J. F., Phillips M. S., Roumy S., Sallée C., Verner A., Hudson T. J., Kwok P. Y., Cai D., Koboldt D. C., Miller R. D., Pawlikowska L., Taillon-Miller P., Xiao M., Tsui L. C., Mak W., Song Y. Q., Tam P. K., Nakamura Y., Kawaguchi T., Kitamoto T., Morizono T., Nagashima A., Ohnishi Y., Sekine A., Tanaka T., Tsunoda T., Deloukas P., Bird C. P., Delgado M., Dermitzakis E. T., Gwilliam R., Hunt S., Morrison J., Powell D., Stranger B. E., Whittaker P., Bentley D. R., Daly M. J., de Bakker P. I., Barrett J., Chretien Y. R., Maller J., McCarroll S., Patterson N., Pe’er I., Price A., Purcell S., Richter D. J., Sabeti P., Saxena R., Schaffner S. F., Sham P. C., Varilly P., Altshuler D., Stein L. D., Krishnan L., Smith A. V., Tello-Ruiz M. K., Thorisson G. A., Chakravarti A., Chen P. E., Cutler D. J., Kashuk C. S., Lin S., Abecasis G. R., Guan W., Li Y., Munro H. M., Qin Z. S., Thomas D. J., McVean G., Auton A., Bottolo L., Cardin N., Eyheramendy S., Freeman C., Marchini J., Myers S., Spencer C., Stephens M., Donnelly P., Cardon L. R., Clarke G., Evans D. M., Morris A. P., Weir B. S., Tsunoda T., Mullikin J. C., Sherry S. T., Feolo M., Skol A., Zhang H., Zeng C., Zhao H., Matsuda I., Fukushima Y., Macer D. R., Suda E., Rotimi C. N., Adebamowo C. A., Ajayi I., Aniagwu T., Marshall P. A., Nkwodimmah C., Royal C. D., Leppert M. F., Dixon M., Peiffer A., Qiu R., Kent A., Kato K., Niikawa N., Adewole I. F., Knoppers B. M., Foster M. W., Clayton E. W., Watkin J., Gibbs R. A., Belmont J. W., Muzny D., Nazareth L., Sodergren E., Weinstock G. M., Wheeler D. A., Yakub I., Gabriel S. B., Onofrio R. C., Richter D. J., Ziaugra L., Birren B. W., Daly M. J., Altshuler D., Wilson R. K., Fulton L. L., Rogers J., Burton J., Carter N. P., Clee C. M., Griffiths M., Jones M. C., McLay K., Plumb R. W., Ross M. T., Sims S. K., Willey D. L., Chen Z., Han H., Kang L., Godbout M., Wallenburg J. C., L’Archevêque P., Bellemare G., Saeki K., Wang H., An D., Fu H., Li Q., Wang Z., Wang R., Holden A. L., Brooks L. D., McEwen J. E., Guyer M. S., Wang V. O., Peterson J. L., Shi M., Spiegel J., Sung L. M., Zacharia L. F., Collins F. S., Kennedy K., Jamieson R., Stewart J. (2007). A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851–86110.1038/nature06258 - DOI - PMC - PubMed

LinkOut - more resources