Data from: Understanding species boundaries that arise from complex histories: Gene flow across the speciation continuum in the spotted whiptail lizards

Gene flow between diverging lineages challenges the resolution of species
boundaries and the understanding of evolutionary history in recent
radiations. Here, we integrate phylogenetic and coalescent tools to
resolve reticulate patterns of diversification and use a perspective
focused on evolutionary mechanisms to distinguish interspecific and
intraspecific taxonomic variation. We use this approach to resolve the
systematics for one of the most intensively studied but difficult to
understand groups of reptiles: the spotted whiptail lizards of the genus
Aspidoscelis (A. gularis complex). Whiptails contain the largest number of
unisexual species known within any vertebrate group and the spotted
whiptail complex has played a key role in the generation of this diversity
through hybrid speciation. Understanding lineage boundaries and the
evolutionary history of divergence and reticulation within this group is
therefore key to understanding the generation of unisexual diversity in
whiptails. Despite this importance, long-standing confusion about their
systematics has impeded understanding of which gonochoristic species have
contributed to the formation of unisexual lineages. Using reduced
representation genomic data, we resolve patterns of divergence and gene
flow within the spotted whiptails and clarify patterns of hybrid
speciation. We find evidence that biogeographically structured ecological
and environmental variation has been important in morphological and
genetic diversification, as well as the maintenance of species boundaries
in this system. Our study elucidates how gene flow among lineages and the
continuous nature of speciation can bias the practice of species
delimitation and lead taxonomists operating under different frameworks to
different conclusions (here we propose that a two species arrangement best
reflects our current understanding). In doing so, this study provides
conceptual and methodological insights into approaches to resolving
diversification patterns and species boundaries in rapid radiations with
complex histories, as well as long-standing taxonomic challenges in the
field of systematic biology.