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Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study

by F. Tajima, P. Salgueiro, G. Carvalho, Maria Jo??o João Collares-Pereira, Maria Manuela Coelho, Joana I. Robalo, C. Sousa Santos, A. Levy, V. C. Almada, Jonathan K. Pritchard, Matthew Stephens, Peter Donnelly, F Perfectti, F X Picó, J M Gómez, Carla Sofia A. Pereira, Marlon F. Pazian, Petr Ráb, Maria Jo??o João Collares-Pereira, Silvia Perea, Madelaine Böhme, Primoz Zupancic, Jörg Freyhof, Radek Sanda, Müfit Ozuluğ, Asghar Abdoli, Ignacio Doadrio, R Nielsen, Miguel Morgado-Santos, Henrique Miguel Pereira, Lu??s Vicente, Maria Jo??o João Collares-Pereira, R. Miranda, A. Pino-del-Carpio, I Matos, M. P. Machado, M. Schartl, Maria Manuela Coelho, P. Marta, J. Bochechas, Maria Jo??o João Collares-Pereira, Gordon Luikart, Nils Ryman, David A. Tallmon, Michael K. Schwartz, Fred W. Allendorf, W. B. Sherwin, B. M. Steele, Fred W. Allendorf, G Laval, M SanCristobal, C Chevalet, Ipgri, Joseph Heled, Alexei J Drummond, Tom Hall, Ibis Biosciences, Ca Carlsbad, Marta Gromicho, Maria Manuela Coelho, Maria Judite Alves, Maria Jo??o João Collares-Pereira, Y. X. Fu, W. H. Li, A. F. Filipe, T. A. Marques, S. Seabra, P. Tiago, F. Ribeiro, Luis Moreira Da Costa, Ian G. Cowx, Maria Jo??o João Collares-Pereira, Daniel Falush, Matthew Stephens, Jonathan K. Pritchard, H.E. L. Excoffier, L. and Lischer, G. Evanno, S. Regnaut, J. Goudet, Enigno Elvira, Benigno Elvira, Doadrio, R. De Miguel, E. Pino, A. Ramiro, F. Aranda, J. P. Peña, Ignacio Doadrio, C. Fernández-Delgado, Ian G. Cowx, Maria Jo??o João Collares-Pereira, Jean-marie Marie Cornuet, Gordon Luikart, Maria Jo??o João Collares-Pereira, Ian G. Cowx, Jos?? Armando Rodrigues, Leonor Rogado, Luis Moreira Da Costa, Ian G. Cowxb, Ian G. Cowx, Loun??s Chikhi, Vitor C. Sousa, Pierre Luisi, Benoit Goossens, Mark A. Beaumont, Lindell Bromham, David Penny, Francisco Blanco-Garrido, Clavero Miguel, Jos?? Prenda, Pierre Berthier, Mark A. Beaumont, Jean-marie Marie Cornuet, Gordon Luikart, Joao M. Bernardo, Maria Ilhéu, Paula Matono, Ana M. Costa, J Arabugo Anecypris, Maria Judite Alves, H. Coelho, Maria Jo??o João Collares-Pereira, Maria Manuela Coelho, A. Almod??var, G. G. Nicola, S. Leal, M. Torralva, Benigno Elvira, Carlos Alma??a, Emilia Huerta-Sanchez, Rick Durrett, Carlos D. Bustamante, Carla Sousa-Santos, Joana I. Robalo, Sara M. Francisco, Carlos Carrapato, Ana Cristina Cardoso, Ignacio Doadrio, Koichiro Tamura, Joel Dudley, Masatoshi Nei, Sudhir Kumar, Rafael Zardoya, Ignacio Doadrio, Thomas F. Turner, Thomas E. Dowling, Richard E. Broughton, John R. Gold show all authors
Genetics ()
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Abstract

Frequencies of mutant sites are modeled as a Poisson random field in two species that share a sufficiently recent common ancestor. The selective effect of the new alleles can be favorable, neutral, or detrimental. The model is applied to the sample configurations of nucleotides in the alcohol dehydrogenase gene (Adh) in Drosophila simulans and Drosophila yakuba. Assuming a synonymous mutation rate of 1.5 x 10(-8) per site per year and 10 generations per year, we obtain estimates for the effective population size (N(e) = 6.5 x 10(6)), the species divergence time (tdiv = 3.74 million years), and an average selection coefficient (sigma = 1.53 x 10(-6) per generation for advantageous or mildly detrimental replacements), although it is conceivable that only two of the amino acid replacements were selected and the rest neutral. The analysis, which includes a sampling theory for the independent infinite sites model with selection, also suggests the estimate that the number of amino acids in the enzyme that are susceptible to favorable mutation is in the range 2-23 at any one time. The approach provides a theoretical basis for the use of a 2 x 2 contingency table to compare fixed differences and polymorphic sites with silent sites and amino acid replacements.

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