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The Confounding Effect of Population Structure on Bayesian Skyline Plot Inferences of Demographic History

2013-05-07Journal article Open access
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dc.contributor.authorHeller, Rasmus
dc.contributor.authorChikhi, Lounes
dc.contributor.authorSiegismund, Hans Redlef
dc.date.accessioned2015-10-30T10:37:41Z
dc.date.available2015-10-30T10:37:41Z
dc.date.issued2013-05-07
dc.description.abstractMany coalescent-based methods aiming to infer the demographic history of populations assume a single, isolated and panmictic population (i.e. a Wright-Fisher model). While this assumption may be reasonable under many conditions, several recent studies have shown that the results can be misleading when it is violated. Among the most widely applied demographic inference methods are Bayesian skyline plots (BSPs), which are used across a range of biological fields. Violations of the panmixia assumption are to be expected in many biological systems, but the consequences for skyline plot inferences have so far not been addressed and quantified. We simulated DNA sequence data under a variety of scenarios involving structured populations with variable levels of gene flow and analysed them using BSPs as implemented in the software package BEAST. Results revealed that BSPs can show false signals of population decline under biologically plausible combinations of population structure and sampling strategy, suggesting that the interpretation of several previous studies may need to be re-evaluated. We found that a balanced sampling strategy whereby samples are distributed on several populations provides the best scheme for inferring demographic change over a typical time scale. Analyses of data from a structured African buffalo population demonstrate how BSP results can be strengthened by simulations. We recommend that sample selection should be carefully considered in relation to population structure previous to BSP analyses, and that alternative scenarios should be evaluated when interpreting signals of population size change.pt_PT
dc.description.sponsorshipDanish Council for Independent Research, Laboratoire d’Excellence (LABEX) grant: (ANR-10-LABX-41).pt_PT
dc.identifier10.1371/journal.pone.0062992
dc.identifier.citationHeller R, Chikhi L, Siegismund HR (2013) The Confounding Effect of Population Structure on Bayesian Skyline Plot Inferences of Demographic History. PLoS ONE 8(5): e62992. doi:10.1371/journal.pone.0062992pt_PT
dc.identifier.doi10.1371/journal.pone.0062992
dc.identifier.urihttp://hdl.handle.net/10400.7/452
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherPLOSpt_PT
dc.relation.publisherversionhttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062992pt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectAnimalspt_PT
dc.subjectBayes Theorempt_PT
dc.subjectDemographypt_PT
dc.subjectPopulation Dynamicspt_PT
dc.titleThe Confounding Effect of Population Structure on Bayesian Skyline Plot Inferences of Demographic Historypt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FBIA-BEC%2F100176%2F2008/PT
oaire.citation.endPage10pt_PT
oaire.citation.issue5pt_PT
oaire.citation.startPage1pt_PT
oaire.citation.titlePLOS Onept_PT
oaire.citation.volume8pt_PT
oaire.fundingStream3599-PPCDT
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
relation.isProjectOfPublicatione097521b-ad8c-4626-a074-aeb1cb70c4bd
relation.isProjectOfPublication.latestForDiscoverye097521b-ad8c-4626-a074-aeb1cb70c4bd

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