Interpretation of Variation Across Marker Loci as Evidence of Selection

Corresponding author: Renaud Vitalis, Laboratoire Génétique et Environnement, C.C. 065, Institut des Sciences de l'Évolution de Montpellier, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France., vitalis{at}isem.univ-montp2.fr (E-mail)

Communicating editor: J. HEY

Population structure and history have similar effects on the genetic diversity at all neutral loci. However, some marker loci may also have been strongly influenced by natural selection. Selection shapes genetic diversity in a locus-specific manner. If we could identify those loci that have responded to selection during the divergence of populations, then we may obtain better estimates of the parameters of population history by excluding these loci. Previous attempts were made to identify outlier loci from the distribution of sample statistics under neutral models of population structure and history. Unfortunately these methods depend on assumptions about population structure and history that usually cannot be verified. In this article, we define new population-specific parameters of population divergence and construct sample statistics that are estimators of these parameters. We then use the joint distribution of these estimators to identify outlier loci that may be subject to selection. We found that outlier loci are easier to recognize when this joint distribution is conditioned on the total number of allelic states represented in the pooled sample at each locus. This is so because the conditional distribution is less sensitive to the values of nuisance parameters.

This article has been cited by other articles:

				M. Foll and O. Gaggiotti A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective Genetics, October 1, 2008; 180(2): 977 - 993. [Abstract] [Full Text] [PDF]

				H. Innan and Y. Kim Detecting Local Adaptation Using the Joint Sampling of Polymorphism Data in the Parental and Derived Populations Genetics, July 1, 2008; 179(3): 1713 - 1720. [Abstract] [Full Text] [PDF]

				A. Caballero, H. Quesada, and E. Rolan-Alvarez Impact of Amplified Fragment Length Polymorphism Size Homoplasy on the Estimation of Population Genetic Diversity and the Detection of Selective Loci Genetics, May 1, 2008; 179(1): 539 - 554. [Abstract] [Full Text] [PDF]

				Y. Tsumura, T. Kado, T. Takahashi, N. Tani, T. Ujino-Ihara, and H. Iwata Genome Scan to Detect Genetic Structure and Adaptive Genes of Natural Populations of Cryptomeria japonica Genetics, August 1, 2007; 176(4): 2393 - 2403. [Abstract] [Full Text] [PDF]

				N. C. Kane and L. H. Rieseberg Selective Sweeps Reveal Candidate Genes for Adaptation to Drought and Salt Tolerance in Common Sunflower, Helianthus annuus Genetics, April 1, 2007; 175(4): 1823 - 1834. [Abstract] [Full Text] [PDF]

				L. Pariset, I. Cappuccio, P. Ajmone-Marsan, M. Bruford, S. Dunner, O. Cortes, G. Erhardt, E.-M. Prinzenberg, K. Gutscher, S. Joost, et al. Characterization of 37 Breed-Specific Single-Nucleotide Polymorphisms in Sheep J. Hered., September 1, 2006; 97(5): 531 - 534. [Abstract] [Full Text] [PDF]

				L. Camus-Kulandaivelu, J.-B. Veyrieras, D. Madur, V. Combes, M. Fourmann, S. Barraud, P. Dubreuil, B. Gouesnard, D. Manicacci, and A. Charcosset Maize Adaptation to Temperate Climate: Relationship Between Population Structure and Polymorphism in the Dwarf8 Gene Genetics, April 1, 2006; 172(4): 2449 - 2463. [Abstract] [Full Text] [PDF]

				A. Bonin, P. Taberlet, C. Miaud, and F. Pompanon Explorative Genome Scan to Detect Candidate Loci for Adaptation Along a Gradient of Altitude in the Common Frog (Rana temporaria) Mol. Biol. Evol., April 1, 2006; 23(4): 773 - 783. [Abstract] [Full Text] [PDF]

				J. M. Burke, S. J. Knapp, and L. H. Rieseberg Genetic Consequences of Selection During the Evolution of Cultivated Sunflower Genetics, December 1, 2005; 171(4): 1933 - 1940. [Abstract] [Full Text] [PDF]

				M.A Toro and A Caballero Characterization and conservation of genetic diversity in subdivided populations Phil Trans R Soc B, July 29, 2005; 360(1459): 1367 - 1378. [Abstract] [Full Text] [PDF]

				A. Vasemagi, J. Nilsson, and C. R. Primmer Expressed Sequence Tag-Linked Microsatellites as a Source of Gene-Associated Polymorphisms for Detecting Signatures of Divergent Selection in Atlantic Salmon (Salmo salar L.) Mol. Biol. Evol., April 1, 2005; 22(4): 1067 - 1076. [Abstract] [Full Text] [PDF]

				I. Goldringer and T. Bataillon On the Distribution of Temporal Variations in Allele Frequency: Consequences for the Estimation of Effective Population Size and the Detection of Loci Undergoing Selection Genetics, September 1, 2004; 168(1): 563 - 568. [Abstract] [Full Text] [PDF]

				R. Vitalis, K. Dawson, P. Boursot, and K. Belkhir DetSel 1.0: A Computer Program to Detect Markers Responding to Selection J. Hered., September 1, 2003; 94(5): 429 - 431. [Abstract] [Full Text] [PDF]

				M. Kayser, S. Brauer, and M. Stoneking A Genome Scan to Detect Candidate Regions Influenced by Local Natural Selection in Human Populations Mol. Biol. Evol., June 1, 2003; 20(6): 893 - 900. [Abstract] [Full Text] [PDF]

				J. M. Akey, G. Zhang, K. Zhang, L. Jin, and M. D. Shriver Interrogating a High-Density SNP Map for Signatures of Natural Selection Genome Res., December 1, 2002; 12(12): 1805 - 1814. [Abstract] [Full Text] [PDF]

				J. F. Storz, M. A. Beaumont, and S. C. Alberts Genetic Evidence for Long-Term Population Decline in a Savannah-Dwelling Primate: Inferences from a Hierarchical Bayesian Model Mol. Biol. Evol., November 1, 2002; 19(11): 1981 - 1990. [Abstract] [Full Text] [PDF]

				C. Schlotterer A Microsatellite-Based Multilocus Screen for the Identification of Local Selective Sweeps Genetics, February 1, 2002; 160(2): 753 - 763. [Abstract] [Full Text] [PDF]