Data from: The spectre of too many species

Recent simulation studies examining the performance of Bayesian species
delimitation as implemented in the BPP program have suggested that BPP may
detect population splits but not species divergences and that it tends to
over-split when data of many loci are analyzed. Here we confirm these
results and provide the mathematical justifications. We point out that the
distinction between population and species splits made in the protracted
speciation model has no influence on the generation of gene trees and
sequence data, which explains why no method can use such data to
distinguish between population splits and speciation. We suggest that the
protracted speciation model is unrealistic as its mechanism for assigning
species status assumes instantaneous speciation, contradicting prevailing
taxonomic practice. We confirm the suggestion, based on simulation, that
in the case of speciation with gene flow, Bayesian model selection as
implemented in BPP tends to detect population splits when the amount of
data (the number of loci) increases. We discuss the use of a recently
proposed empirical genealogical divergence index (gdi) for species
delimitation and illustrate that parameter estimates produced by a full
likelihood analysis as implemented in BPP provide much more reliable
inference under the gdi than the approximate method PHRAPL. We distinguish
between Bayesian model selection and parameter estimation, and suggest
that the model selection approach is useful for identifying sympatric
cryptic species while the parameter estimation approach may be used to
implement empirical criteria for determining species status among
allopatric populations.