DOI: 10.5061/dryad.f8k84
title: Data from: Bayesian divergence-time estimation with genome-wide SNP data of sea catfishes (Ariidae) supports Miocene closure of the Panamanian isthmus

description: The closure of the Isthmus of Panama has long been considered to be one of
 the best defined biogeographic calibration points for molecular
 divergence-time estimation. However, geological and biological evidence
 has recently cast doubt on the presumed timing of the initial isthmus
 closure around 3 Ma but has instead suggested the existence of temporary
 land bridges as early as the Middle or Late Miocene. The biological
 evidence supporting these earlier land bridges was based either on only
 few molecular markers or on concatenation of genome-wide sequence data, an
 approach that is known to result in potentially misleading branch lengths
 and divergence times, which could compromise the reliability of this
 evidence. To allow divergence-time estimation with genomic data using the
 more appropriate multi-species coalescent model, we here develop a new
 method combining the SNP-based Bayesian species-tree inference of the
 software SNAPP with a molecular clock model that can be calibrated with
 fossil or biogeographic constraints. We validate our approach with
 simulations and use our method to reanalyze genomic data of Neotropical
 army ants (Dorylinae) that previously supported divergence times of
 Central and South American populations before the isthmus closure around 3
 Ma. Our reanalysis with the multi-species coalescent model shifts all of
 these divergence times to ages younger than 3 Ma, suggesting that the
 older estimates supporting the earlier existence of temporary land bridges
 were artifacts resulting at least partially from the use of concatenation.
 We then apply our method to a new RAD-sequencing data set of Neotropical
 sea catfishes (Ariidae) and calibrate their species tree with extensive
 information from the fossil record. We identify a series of divergences
 between groups of Caribbean and Pacific sea catfishes around 10 Ma,
 indicating that processes related to the emergence of the isthmus led to
 vicariant speciation already in the Late Miocene, millions of years before
 the final isthmus closure.
description: ariidae.xmlSNAPP input file in XML format for analyses of Neotropical sea catfish SNP data with the multi-species coalescent model.eciton.xmlSNAPP input file in XML format for analyses of Neotropical army ant SNP data with the multi-species coalescent model.eciton_concatenated.xmlBEAST input file in XML format for analyses of Neotropical army ant SNP data based on concatenation.ariidae.treesCombined posterior tree distribution of SNAPP analyses of Neotropical sea catfish SNP data with the multi-species coalescent model.eciton.treesCombined posterior tree distribution of SNAPP analyses of Neotropical army ant SNP data with the multi-species coalescent model.eciton_concatenated.treesCombined posterior tree distribution of BEAST analyses of Neotropical army ant SNP data based on concatenation.ariidae.logCombined posterior parameter distributions of SNAPP analyses of Neotropical sea catfish SNP data with the multi-species coalescent model.eciton.logCombined posterior parameter distributions of SNAPP analyses of Neotropical army ant SNP data with the multi-species coalescent model.eciton_concatenated.logCombined posterior parameter distributions of BEAST analyses of Neotropical army ant SNP data based on concatenation.ariidae.treMaximum-clade-credibility summary tree of SNAPP analyses of Neotropical sea catfish SNP data with the multi-species coalescent model.eciton.treMaximum-clade-credibility summary tree of SNAPP analyses of Neotropical army ant SNP data with the multi-species coalescent model.eciton_concatenated.treMaximum-clade-credibility summary tree of BEAST analyses of Neotropical army ant SNP data based on concatenation.Supplementary MaterialSupplementary Texts S1-S2, Supplementary Figures S1-S7, Supplementary Tables S1-S7, and Supplementary References.supplementary_material.pdf