Considerable effort has been devoted to detecting genes that are under natural selection, and hundreds of such genes have been identified in previous studies. Here, we present a method for extending these studies by inferring parameters, such as selection coefficients and the time when a selected variant arose. Of particular interest is the question whether the selective pressure was already present when the selected variant was first introduced into a population. In this case, the variant would be selected right after it originated in the population, a process we call selection from a <italic>de novo</italic> mutation. We contrast this with selection from standing variation, where the selected variant predates the selective pressure. We present a method to distinguish these two scenarios, test its accuracy, and apply it to seven human genes. We find three genes, ADH1B, EDAR, and LCT, that were presumably selected from a de novo mutation and two other genes, ASPM and PSCA, which we infer to be under selection from standing variation.
%0 Journal Article
%1 peter2012distinguishing
%A Peter, Benjamin M.
%A Huerta-Sanchez, Emilia
%A Nielsen, Rasmus
%D 2012
%I Public Library of Science
%J PLoS Genet
%K age_of_allele approximate_bayesian_computation methods selective_sweep standing_variation
%N 10
%P e1003011
%R 10.1371/journal.pgen.1003011
%T Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation
%U http://dx.doi.org/10.1371%2Fjournal.pgen.1003011
%V 8
%X Considerable effort has been devoted to detecting genes that are under natural selection, and hundreds of such genes have been identified in previous studies. Here, we present a method for extending these studies by inferring parameters, such as selection coefficients and the time when a selected variant arose. Of particular interest is the question whether the selective pressure was already present when the selected variant was first introduced into a population. In this case, the variant would be selected right after it originated in the population, a process we call selection from a <italic>de novo</italic> mutation. We contrast this with selection from standing variation, where the selected variant predates the selective pressure. We present a method to distinguish these two scenarios, test its accuracy, and apply it to seven human genes. We find three genes, ADH1B, EDAR, and LCT, that were presumably selected from a de novo mutation and two other genes, ASPM and PSCA, which we infer to be under selection from standing variation.
@article{peter2012distinguishing,
abstract = {Considerable effort has been devoted to detecting genes that are under natural selection, and hundreds of such genes have been identified in previous studies. Here, we present a method for extending these studies by inferring parameters, such as selection coefficients and the time when a selected variant arose. Of particular interest is the question whether the selective pressure was already present when the selected variant was first introduced into a population. In this case, the variant would be selected right after it originated in the population, a process we call selection from a <italic>de novo</italic> mutation. We contrast this with selection from standing variation, where the selected variant predates the selective pressure. We present a method to distinguish these two scenarios, test its accuracy, and apply it to seven human genes. We find three genes, ADH1B, EDAR, and LCT, that were presumably selected from a de novo mutation and two other genes, ASPM and PSCA, which we infer to be under selection from standing variation.},
added-at = {2013-01-18T23:31:59.000+0100},
author = {Peter, Benjamin M. and Huerta-Sanchez, Emilia and Nielsen, Rasmus},
biburl = {https://www.bibsonomy.org/bibtex/2fa320783ee2e13efda16a47602f3edd3/peter.ralph},
doi = {10.1371/journal.pgen.1003011},
interhash = {c849d2265745804f8bd1bb909f2fb187},
intrahash = {fa320783ee2e13efda16a47602f3edd3},
journal = {PLoS Genet},
keywords = {age_of_allele approximate_bayesian_computation methods selective_sweep standing_variation},
month = {10},
number = 10,
pages = {e1003011},
publisher = {Public Library of Science},
timestamp = {2013-01-29T19:22:24.000+0100},
title = {Distinguishing between Selective Sweeps from Standing Variation and from a {\it De Novo} Mutation},
url = {http://dx.doi.org/10.1371%2Fjournal.pgen.1003011},
volume = 8,
year = 2012
}