Data from: Sex-biased dispersal obscures species boundaries in integrative species delimitation approaches

Accurate delimitation of species is crucial for a stable taxonomy, which
provides the foundation for the study of evolutionary biology, ecology and
essentially all biological disciplines. Several approaches towards
impartial and repeatable taxonomic practices are available but all
existing methods have potentially unacceptable shortcomings. In
particular, problems can arise when the underlying model assumptions are
violated, for instance in the presence of reduced gene flow. This is
observed in the context of sex-biased dispersal, which is a common but
underappreciated feature in many groups of organisms. Previously,
simulations have indicated that sex-biased dispersal may lead to erroneous
estimations of the true species numbers. However, this phenomenon has
never been examined using empirical data. We evaluate the bias introduced
by extreme female philopatry on a range of de novo (GMYC, PTP, ABGD,
statistical parsimony, trinomial distribution of triplets model [tr2]) and
validation (STACEY, iBPP) approaches to species delimitation in the scarab
beetle genus Pachypus. Since female philopatry exhibited in this genus in
particular can affect mitochondrial gene flow, we compared the results
from analyses of single loci, mitochondrial loci, nuclear loci and
combined data, as well as the performance of morphometric data as a
secondary data source in a fully integrative Bayesian framework. Large
overestimation of species numbers was observed across all analyses of
combined and mitochondrial DNA datasets, suggesting specimens from nearly
every sampling location as separate species. The use of nuclear data
resulted in more reasonable estimations of species boundaries, which were
largely supported by morphometrics of linear measurements, while geometric
morphometrics of body outlines resulted in stronger splitting. Simulations
of population divergence with migration, corresponding to the biology of
Pachypus, showed that female philopatry strongly increases reciprocal
monophyly of mitochondrial markers and may substantially contribute to
over-splitting in species delimitation. Robust results recovered using
nuclear DNA and morphological data nevertheless enabled us to reach novel
conclusions about species boundaries in Pachypus. Our findings suggest
that mitochondrial DNA will be less suited to species delimitation in many
cases, in particular in the presence of sex-biased dispersal.