Data from: The species versus subspecies conundrum: quantitative delimitation from integrating multiple data types within a single Bayesian approach in Hercules beetles

With the recent attention and focus on quantitative methods for species
delimitation, an overlooked but equally important issue regards what has
actually been delimited. This study investigates the apparent
arbitrariness of some taxonomic distinctions, and in particular how
species and subspecies are assigned. Specifically, we use a recently
developed Bayesian model-based approach to show that in the Hercules
beetles (genus Dynastes) there is no statistical difference in the
probability that putative taxa represent different species, irrespective
of whether they were given species or subspecies designations. By
considering multiple data types, as opposed to relying exclusively on
genetic data alone, we also show that both previously recognized species
and subspecies represent a variety of points along the speciation spectrum
(i.e., previously recognized species are not systematically further along
the continuum than subspecies). For example, based on evolutionary models
of divergence, some taxa are statistically distinguishable on more than
one axis of differentiation (e.g., along both phenotypic and genetic
dimensions), whereas other taxa can only be delimited statistically from a
single data type. Because both phenotypic and genetic data are analyzed in
a common Bayesian framework, our study provides a framework for
investigating whether disagreements in species boundaries among data types
reflect (i) actual discordance with the actual history of lineage
splitting, or instead (ii) differences among data types in the amount of
time required for differentiation to become apparent among the delimited
taxa. We discuss what the answers to these questions imply about what
characters are used to delimit species, as well as the diverse processes
involved in the origin and maintenance of species boundaries. With this in
mind, we then reflect more generally on how quantitative methods for
species delimitation are used to assign taxonomic status.