Estimating the Time Since the Fixation of a Beneficial Allele

Corresponding author: Molly Przeworski, Deutscher Platz 6, 04103 Leipzig, Germany., przewors{at}eva.mpg.de (E-mail)

Communicating editor: N. TAKAHATA

The fixation of a beneficial allele in a population leaves a well-characterized signature in patterns of nucleotide variation at linked sites. This signature can be used to estimate the time since fixation from patterns of polymorphism in extant individuals. I introduce a method to assess the support in polymorphism data for a recent episode of directional positive selection and to estimate the time since fixation. I summarize the polymorphism data by three statistics that carry information about levels of diversity, the allele frequency spectrum, and the extent of allelic associations. Simulations are then used to obtain a sample from the posterior distribution of the time since fixation, conditional on the observed summaries. I test the performance of the approach on simulated data and apply it to the gene tb1 in maize. The data support the recent fixation of a favored allele, consistent with what is known about the importance of tb1 in the domestication process of maize.

This article has been cited by other articles:

				L.-M. Chevin and F. Hospital Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation Genetics, November 1, 2008; 180(3): 1645 - 1660. [Abstract] [Full Text] [PDF]

				L. Camus-Kulandaivelu, L.-M. Chevin, C. Tollon-Cordet, A. Charcosset, D. Manicacci, and M. I. Tenaillon Patterns of Molecular Evolution Associated With Two Selective Sweeps in the Tb1-Dwarf8 Region in Maize Genetics, October 1, 2008; 180(2): 1107 - 1121. [Abstract] [Full Text] [PDF]

				L.-M. Chevin, S. Billiard, and F. Hospital Hitchhiking Both Ways: Effect of Two Interfering Selective Sweeps on Linked Neutral Variation Genetics, September 1, 2008; 180(1): 301 - 316. [Abstract] [Full Text] [PDF]

				S. Beisswanger and W. Stephan Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila PNAS, April 8, 2008; 105(14): 5447 - 5452. [Abstract] [Full Text] [PDF]

				C. Becquet and M. Przeworski A new approach to estimate parameters of speciation models with application to apes Genome Res., October 1, 2007; 17(10): 1505 - 1519. [Abstract] [Full Text] [PDF]

				J. de Meaux, A. Pop, and T. Mitchell-Olds Cis-regulatory Evolution of Chalcone-Synthase Expression in the Genus Arabidopsis Genetics, December 1, 2006; 174(4): 2181 - 2202. [Abstract] [Full Text] [PDF]

				P. Fearnhead Perfect Simulation From Nonneutral Population Genetic Models: Variable Population Size and Population Subdivision Genetics, November 1, 2006; 174(3): 1397 - 1406. [Abstract] [Full Text] [PDF]

				K. M. Teshima, G. Coop, and M. Przeworski How reliable are empirical genomic scans for selective sweeps? Genome Res., June 1, 2006; 16(6): 702 - 712. [Abstract] [Full Text] [PDF]

				K. Thornton and P. Andolfatto Approximate Bayesian Inference Reveals Evidence for a Recent, Severe Bottleneck in a Netherlands Population of Drosophila melanogaster Genetics, March 1, 2006; 172(3): 1607 - 1619. [Abstract] [Full Text] [PDF]

				Y. Kim Allele Frequency Distribution Under Recurrent Selective Sweeps Genetics, March 1, 2006; 172(3): 1967 - 1978. [Abstract] [Full Text] [PDF]

				J. E. Pool, V. B. DuMont, J. L. Mueller, and C. F. Aquadro A Scan of Molecular Variation Leads to the Narrow Localization of a Selective Sweep Affecting Both Afrotropical and Cosmopolitan Populations of Drosophila melanogaster Genetics, February 1, 2006; 172(2): 1093 - 1105. [Abstract] [Full Text] [PDF]

				J. P. Pollinger, C. D. Bustamante, A. Fledel-Alon, S. Schmutz, M. M. Gray, and R. K. Wayne Selective sweep mapping of genes with large phenotypic effects Genome Res., December 1, 2005; 15(12): 1809 - 1819. [Abstract] [Full Text] [PDF]

				K. Thornton Recombination and the Properties of Tajima's D in the Context of Approximate-Likelihood Calculation Genetics, December 1, 2005; 171(4): 2143 - 2148. [Abstract] [Full Text] [PDF]

				R. Nielsen, S. Williamson, Y. Kim, M. J. Hubisz, A. G. Clark, and C. Bustamante Genomic scans for selective sweeps using SNP data Genome Res., November 1, 2005; 15(11): 1566 - 1575. [Abstract] [Full Text] [PDF]

				V. B. DuMont and C. F. Aquadro Multiple Signatures of Positive Selection Downstream of Notch on the X Chromosome in Drosophila melanogaster Genetics, October 1, 2005; 171(2): 639 - 653. [Abstract] [Full Text] [PDF]

				H. Li and W. Stephan Maximum-Likelihood Methods for Detecting Recent Positive Selection and Localizing the Selected Site in the Genome Genetics, September 1, 2005; 171(1): 377 - 384. [Abstract] [Full Text] [PDF]

				P. R. Haddrill, K. R. Thornton, B. Charlesworth, and P. Andolfatto Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations Genome Res., June 1, 2005; 15(6): 790 - 799. [Abstract] [Full Text] [PDF]

				S. I. Wright and B. S. Gaut Molecular Population Genetics and the Search for Adaptive Evolution in Plants Mol. Biol. Evol., March 1, 2005; 22(3): 506 - 519. [Abstract] [Full Text] [PDF]

				P. Tiffin, R. Hacker, and B. S. Gaut Population Genetic Evidence for Rapid Changes in Intraspecific Diversity and Allelic Cycling of a Specialist Defense Gene in Zea Genetics, September 1, 2004; 168(1): 425 - 434. [Abstract] [Full Text] [PDF]

				Y. Kim and R. Nielsen Linkage Disequilibrium as a Signature of Selective Sweeps Genetics, July 1, 2004; 167(3): 1513 - 1524. [Abstract] [Full Text] [PDF]