An ABC Method for Estimating the Rate and Distribution of Effects of Beneficial Mutations

Moura de Sousa, J. A.; Campos, P. R. A.; Gordo, I.

Publication

An ABC Method for Estimating the Rate and Distribution of Effects of Beneficial Mutations

2013-03-23Journal article

dc.contributor.author	Moura de Sousa, J. A.
dc.contributor.author	Campos, P. R. A.
dc.contributor.author	Gordo, I.
dc.date.accessioned	2015-11-03T17:34:57Z
dc.date.available	2015-11-03T17:34:57Z
dc.date.issued	2013-03-23
dc.description.abstract	Determining the distribution of adaptive mutations available to natural selection is a difficult task. These are rare events and most of them are lost by chance. Some theoretical works propose that the distribution of newly arising beneficial mutations should be close to exponential. Empirical data are scarce and do not always support an exponential distribution. Analysis of the dynamics of adaptation in asexual populations of microorganisms has revealed that these can be summarized by two effective parameters, the effective mutation rate, Ue, and the effective selection coefficient of a beneficial mutation, Se. Here, we show that these effective parameters will not always reflect the rate and mean effect of beneficial mutations, especially when the distribution of arising mutations has high variance, and the mutation rate is high. We propose a method to estimate the distribution of arising beneficial mutations, which is motivated by a common experimental setup. The method, which we call One Biallelic Marker Approximate Bayesian Computation, makes use of experimental data consisting of periodic measures of neutral marker frequencies and mean population fitness. Using simulations, we find that this method allows the discrimination of the shape of the distribution of arising mutations and that it provides reasonable estimates of their rates and mean effects in ranges of the parameter space that may be of biological relevance.	pt_PT
dc.description.sponsorship	Fundação Calouste Gulbenkian, FCT, LAO/ITQB, Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco (FACEPE), program PRONEX/MCT-CNPq-FACEPE.	pt_PT
dc.identifier	10.1093/gbe/evt045
dc.identifier.citation	Jorge A. Moura de Sousa, Paulo R.A. Campos, and Isabel Gordo An ABC Method for Estimating the Rate and Distribution of Effects of Beneficial Mutations Genome Biol Evol (2013) Vol. 5 794-806 first published online March 29, 2013 doi:10.1093/gbe/evt045	pt_PT
dc.identifier.doi	10.1093/gbe/evt045
dc.identifier.uri	http://hdl.handle.net/10400.7/464
dc.language.iso	eng	pt_PT
dc.peerreviewed	yes	pt_PT
dc.publisher	Oxford University Press	pt_PT
dc.relation	Microbial adaptation within ecosystems
dc.relation.publisherversion	http://gbe.oxfordjournals.org/content/5/5/794.long	pt_PT
dc.rights.uri	http://creativecommons.org/licenses/by-nc/4.0/	pt_PT
dc.subject	Models, Genetic	pt_PT
dc.subject	Mutation	pt_PT
dc.subject	Probability	pt_PT
dc.subject	Mutation Rate	pt_PT
dc.title	An ABC Method for Estimating the Rate and Distribution of Effects of Beneficial Mutations	pt_PT
dc.type	journal article
dspace.entity.type	Publication
oaire.awardTitle	Microbial adaptation within ecosystems
oaire.awardURI	info:eu-repo/grantAgreement/EC/FP7/260421/EU
oaire.citation.endPage	806	pt_PT
oaire.citation.issue	5	pt_PT
oaire.citation.startPage	794	pt_PT
oaire.citation.title	Genome Biology and Evolution	pt_PT
oaire.citation.volume	5	pt_PT
oaire.fundingStream	FP7
project.funder.identifier	http://doi.org/10.13039/501100008530
project.funder.name	European Commission
rcaap.rights	openAccess	pt_PT
rcaap.type	article	pt_PT
relation.isProjectOfPublication	1f01df05-f8af-4e76-8dec-0fc6237b41fd
relation.isProjectOfPublication.latestForDiscovery	1f01df05-f8af-4e76-8dec-0fc6237b41fd