Data from: Bayesian divergence-time estimation with genome-wide SNP data of sea catfishes (Ariidae) supports Miocene closure of the Panamanian isthmus

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.