10.5061/DRYAD.F8K84
Stange, Madlen
University of Zurich
University of Basel
Sánchez-Villagra, Marcelo R.
University of Zurich
Salzburger, Walter
University of Oslo
University of Basel
Matschiner, Michael
University of Oslo
University of Basel
Data from: Bayesian divergence-time estimation with genome-wide SNP data
of sea catfishes (Ariidae) supports Miocene closure of the Panamanian
isthmus
Dryad
dataset
2018
Teleosts
Ariidae
Fossil record
Dorylinae
SNPs
Miocene
2018-01-25T20:00:38Z
2018-01-25T20:00:38Z
en
https://doi.org/10.1093/sysbio/syy006
132060667 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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
Central American Seaway
Tropical Eastern Pacific
Panamanian Isthmus
Neotropics
Caribbean