Strategies for improving approximate Bayesian computation tests for synchronous diversification

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dc.contributor.authorOvercast, Isaac
dc.contributor.authorBagley, Justin C. [UNESP]
dc.contributor.authorHickerson, Michael J.
dc.contributor.institutionCUNY City Coll
dc.contributor.institutionCUNY
dc.contributor.institutionUniversidade de Brasília (UnB)
dc.contributor.institutionUniversidade Estadual Paulista (Unesp)
dc.date.accessioned2018-11-26T17:40:21Z
dc.date.available2018-11-26T17:40:21Z
dc.date.issued2017-08-24
dc.description.abstractBackground: Estimating the variability in isolation times across co-distributed taxon pairs that may have experienced the same allopatric isolating mechanism is a core goal of comparative phylogeography. The use of hierarchical Approximate Bayesian Computation (ABC) and coalescent models to infer temporal dynamics of lineage co-diversification has been a contentious topic in recent years. Key issues that remain unresolved include the choice of an appropriate prior on the number of co-divergence events (psi), as well as the optimal strategies for data summarization. Methods: Through simulation-based cross validation we explore the impact of the strategy for sorting summary statistics and the choice of prior on psi on the estimation of co-divergence variability. We also introduce a new setting (beta) that can potentially improve estimation of psi by enforcing a minimal temporal difference between pulses of co-divergence. We apply this new method to three empirical datasets: one dataset each of co-distributed taxon pairs of Panamanian frogs and freshwater fishes, and a large set of Neotropical butterfly sister-taxon pairs. Results: We demonstrate that the choice of prior on. has little impact on inference, but that sorting summary statistics yields substantially more reliable estimates of co-divergence variability despite violations of assumptions about exchangeability. We find the implementation of beta improves estimation of psi, with improvement being most dramatic given larger numbers of taxon pairs. We find equivocal support for synchronous co-divergence for both of the Panamanian groups, but we find considerable support for asynchronous divergence among the Neotropical butterflies. Conclusions: Our simulation experiments demonstrate that using sorted summary statistics results in improved estimates of the variability in divergence times, whereas the choice of hyperprior on psi has negligible effect. Additionally, we demonstrate that estimating the number of pulses of co-divergence across co-distributed taxon-pairs is improved by applying a flexible buffering regime over divergence times. This improves the correlation between. and the true variability in isolation times and allows for more meaningful interpretation of this hyperparameter. This will allow for more accurate identification of the number of temporally distinct pulses of co-divergence that generated the diversification pattern of a given regional assemblage of sister-taxon-pairs.en
dc.description.affiliationCUNY City Coll, Dept Biol, New York, NY 10031 USA
dc.description.affiliationCUNY, Grad Ctr, New York, NY 10016 USA
dc.description.affiliationUniv Brasilia, Dept Zool, BR-70910900 Brasilia, DF, Brazil
dc.description.affiliationUniv Estadual Paulista, IBiLCE, Dept Zool & Bot, BR-15054000 Sao Jose Do Rio Preto, SP, Brazil
dc.description.affiliationUnespUniv Estadual Paulista, IBiLCE, Dept Zool & Bot, BR-15054000 Sao Jose Do Rio Preto, SP, Brazil
dc.description.sponsorshipFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
dc.description.sponsorshipNASA
dc.description.sponsorshipNational Science Foundation
dc.description.sponsorshipConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
dc.description.sponsorshipBrigham Young University Fulton Supercomputing Lab
dc.description.sponsorshipIdFAPESP: 2013/50297-0
dc.description.sponsorshipIdNASA: DOB 1343578
dc.description.sponsorshipIdNational Science Foundation: DEB-1253710
dc.description.sponsorshipIdNational Science Foundation: CNS-0958379
dc.description.sponsorshipIdNational Science Foundation: CNS-0855217
dc.description.sponsorshipIdCNPq: 314724/2014-1
dc.format.extent11
dc.identifierhttp://dx.doi.org/10.1186/s12862-017-1052-6
dc.identifier.citationBmc Evolutionary Biology. London: Biomed Central Ltd, v. 17, 11 p., 2017.
dc.identifier.doi10.1186/s12862-017-1052-6
dc.identifier.fileWOS000408465100001.pdf
dc.identifier.issn1471-2148
dc.identifier.urihttp://hdl.handle.net/11449/163162
dc.identifier.wosWOS:000408465100001
dc.language.isoeng
dc.publisherBiomed Central Ltd
dc.relation.ispartofBmc Evolutionary Biology
dc.relation.ispartofsjr1,656
dc.rights.accessRightsAcesso aberto
dc.sourceWeb of Science
dc.subjectApproximate Bayesian computation (ABC)
dc.subjectComparative phylogeography
dc.subjectDivergence times
dc.subjectSynchronous diversification
dc.titleStrategies for improving approximate Bayesian computation tests for synchronous diversificationen
dc.typeArtigo
dcterms.rightsHolderBiomed Central Ltd
unesp.author.orcid0000-0001-8614-6892[1]

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