Data from: Model-based species delimitation: are coalescent species reproductively isolated?

A large and growing fraction of systematists define species as
independently evolving lineages that may be recognized by analyzing the
population genetic history of alleles sampled from individuals belonging
to those species. This has motivated the development of increasingly
sophisticated statistical models rooted in the multispecies coalescent
process. Specifically, these models allow for simultaneous estimation of
the number of species present in a sample of individuals and the
phylogenetic history of those species using only DNA sequence data from
independent loci. These methods hold extraordinary promise for increasing
the efficiency of species discovery, but require extensive validation to
ensure that they are accurate and precise. Whether the species identified
by these methods correspond to the species that would be recognized by
alternative species recognition criteria (such as measurements of
reproductive isolation) is currently an open question, and a subject of
vigorous debate. Here we perform an empirical test of these methods by
making use of a classic model system in the history of speciation
research, flies of the genus Drosophila. Specifically, we use the uniquely
comprehensive data on reproductive isolation that is available for this
system, along with DNA sequence data, to ask whether Drosophila species
inferred under the multispecies coalescent model correspond to those
recognized by many decades of speciation research. We found that
coalescent based and reproductive isolation based methods of inferring
species boundaries are concordant for 77% of the species pairs. We explore
and discuss potential explanations for these discrepancies. We also found
that the amount of prezygotic isolation between two species is a strong
predictor of the posterior probability of species boundaries based on DNA
sequence data, regardless of whether the species pairs are sympatrically
or allopatrically distributed.