The Genealogy of Sequences Containing Multiple Sites Subject to Strong Selection in a Subdivided Population

Corresponding author: Magnus Nordborg, University of Southern California, SHS 172, 835 W. 37th St., Los Angeles, CA 90089-1340., magnus{at}usc.edu (E-mail)

Communicating editor: W. STEPHAN

A stochastic model for the genealogy of a sample of recombining sequences containing one or more sites subject to selection in a subdivided population is described. Selection is incorporated by dividing the population into allelic classes and then conditioning on the past sizes of these classes. The past allele frequencies at the selected sites are thus treated as parameters rather than as random variables. The purpose of the model is not to investigate the dynamics of selection, but to investigate effects of linkage to the selected sites on the genealogy of the surrounding chromosomal region. This approach is useful for modeling strong selection, when it is natural to parameterize the past allele frequencies at the selected sites. Several models of strong balancing selection are used as examples, and the effects on the pattern of neutral polymorphism in the chromosomal region are discussed. We focus in particular on the statistical power to detect balancing selection when it is present.

This article has been cited by other articles:

				J. F. Storz and J. K. Kelly Effects of Spatially Varying Selection on Nucleotide Diversity and Linkage Disequilibrium: Insights From Deer Mouse Globin Genes Genetics, September 1, 2008; 180(1): 367 - 379. [Abstract] [Full Text] [PDF]

				A. L. Caicedo Geographic diversity cline of R gene homologs in wild populations of Solanum pimpinellifolium (Solanaceae) Am. J. Botany, March 1, 2008; 95(3): 393 - 398. [Abstract] [Full Text] [PDF]

				K. M. Teshima and H. Innan Neofunctionalization of Duplicated Genes Under the Pressure of Gene Conversion Genetics, March 1, 2008; 178(3): 1385 - 1398. [Abstract] [Full Text] [PDF]

				J. F. Storz, M. Baze, J. L. Waite, F. G. Hoffmann, J. C. Opazo, and J. P. Hayes Complex Signatures of Selection and Gene Conversion in the Duplicated Globin Genes of House Mice Genetics, September 1, 2007; 177(1): 481 - 500. [Abstract] [Full Text] [PDF]

				R. M. Clark, G. Schweikert, C. Toomajian, S. Ossowski, G. Zeller, P. Shinn, N. Warthmann, T. T. Hu, G. Fu, D. A. Hinds, et al. Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana Science, July 20, 2007; 317(5836): 338 - 342. [Abstract] [Full Text] [PDF]

				D. A. Moeller, M. I. Tenaillon, and P. Tiffin Population Structure and Its Effects on Patterns of Nucleotide Polymorphism in Teosinte (Zea mays ssp. parviglumis) Genetics, July 1, 2007; 176(3): 1799 - 1809. [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]

				H. Innan Modified Hudson-Kreitman-Aguade Test and Two-Dimensional Evaluation of Neutrality Tests Genetics, July 1, 2006; 173(3): 1725 - 1733. [Abstract] [Full Text] [PDF]

				P. K. Ingvarsson, M. V. Garcia, D. Hall, V. Luquez, and S. Jansson Clinal Variation in phyB2, a Candidate Gene for Day-Length-Induced Growth Cessation and Bud Set, Across a Latitudinal Gradient in European Aspen (Populus tremula) Genetics, March 1, 2006; 172(3): 1845 - 1853. [Abstract] [Full Text] [PDF]

				C. W. Wheat, W. B. Watt, D. D. Pollock, and P. M. Schulte From DNA to Fitness Differences: Sequences and Structures of Adaptive Variants of Colias Phosphoglucose Isomerase (PGI) Mol. Biol. Evol., March 1, 2006; 23(3): 499 - 512. [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]

				C. Wiuf, K. Zhao, H. Innan, and M. Nordborg The Probability and Chromosomal Extent of trans-specific Polymorphism Genetics, December 1, 2004; 168(4): 2363 - 2372. [Abstract] [Full Text] [PDF]

				M. J. Clauss and T. Mitchell-Olds Functional Divergence in Tandemly Duplicated Arabidopsis thaliana Trypsin Inhibitor Genes Genetics, March 1, 2004; 166(3): 1419 - 1436. [Abstract] [Full Text] [PDF]

				D. Charlesworth, C. Bartolome, M. H. Schierup, and B. K. Mable Haplotype Structure of the Stigmatic Self-Incompatibility Gene in Natural Populations of Arabidopsis lyrata Mol. Biol. Evol., November 1, 2003; 20(11): 1741 - 1753. [Abstract] [Full Text] [PDF]

				H. Innan, B. Padhukasahasram, and M. Nordborg The Pattern of Polymorphism on Human Chromosome 21 Genome Res., June 1, 2003; 13(6): 1158 - 1168. [Abstract] [Full Text] [PDF]