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dc.contributor.authorJónás, Ágnes
dc.contributor.authorTaus, Thomas
dc.contributor.authorKosiol, Carolin
dc.contributor.authorSchlötterer, Christian
dc.contributor.authorFutschik, Andreas
dc.date.accessioned2017-02-08T12:30:14Z
dc.date.available2017-02-08T12:30:14Z
dc.date.issued2016-10-11
dc.identifier.citationJónás , Á , Taus , T , Kosiol , C , Schlötterer , C & Futschik , A 2016 , ' Estimating the effective population size from temporal allele frequency changes in experimental evolution ' , Genetics , vol. 204 , no. 2 , pp. 723-735 . https://doi.org/10.1534/genetics.116.191197en
dc.identifier.issn0016-6731
dc.identifier.otherPURE: 249097930
dc.identifier.otherPURE UUID: f4e0bc45-1102-4199-bbe9-46d7a7671069
dc.identifier.otherPubMed: 27542959
dc.identifier.otherPubMedCentral: PMC5068858
dc.identifier.otherScopus: 84991501359
dc.identifier.urihttp://hdl.handle.net/10023/10250
dc.descriptionA.J. and T.T. are members of the Vienna Graduate School of Population Genetics, which is funded by the Austrian Science Fund (FWF, W1225). C.S. is also supported by the European Research Council grant ”ArchAdapt,” and T.T. is a recipient of a Doctoral Fellowship (DOC) of the Austrian Academy of Sciences.en
dc.description.abstractThe effective population size (Ne) is a major factor determining allele frequency changes in natural and experimental populations. Temporal methods provide a powerful and simple approach to estimate short-term Ne. They use allele frequency shifts between temporal samples to calculate the standardized variance, which is directly related to Ne. Here we focus on experimental evolution studies that often rely on repeated sequencing of samples in pools (Pool-seq). Pool-seq is cost-effective and often outperforms individual-based sequencing in estimating allele frequencies, but it is associated with atypical sampling properties: Additional to sampling individuals, sequencing DNA in pools leads to a second round of sampling, which increases the variance of allele frequency estimates. We propose a new estimator of Ne, which relies on allele frequency changes in temporal data and corrects for the variance in both sampling steps. In simulations, we obtain accurate Ne estimates, as long as the drift variance is not too small compared to the sampling and sequencing variance. In addition to genome-wide Ne estimates, we extend our method using a recursive partitioning approach to estimate Ne locally along the chromosome. Since the type I error is controlled, our method permits the identification of genomic regions that differ significantly in their Ne estimates. We present an application to Pool-seq data from experimental evolution with Drosophila and provide recommendations for whole-genome data. The estimator is computationally efficient and available as an R package at https://github.com/ThomasTaus/Nest.
dc.format.extent13
dc.language.isoeng
dc.relation.ispartofGeneticsen
dc.rightsCopyright © 2016 Jónás et al. Available freely online through the author-supported open access option. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.subjectEffective population sizeen
dc.subjectGenetic driften
dc.subjectPool-seqen
dc.subjectExperimental evolutionen
dc.subjectQH301 Biologyen
dc.subjectQH426 Geneticsen
dc.subjectNDASen
dc.subject.lccQH301en
dc.subject.lccQH426en
dc.titleEstimating the effective population size from temporal allele frequency changes in experimental evolutionen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews.School of Biologyen
dc.contributor.institutionUniversity of St Andrews.Centre for Biological Diversityen
dc.identifier.doihttps://doi.org/10.1534/genetics.116.191197
dc.description.statusPeer revieweden


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