Phylogenomics reveals deep divergences and cryptic species within a sand dwelling milkweed, Asclepias tomentosa Elliott

Integrative taxonomy is the use of multiple data types to delineate and describe species and may uncover hidden biodiversity (i.e. closely-related cryptic species) previously undetected using morphology alone. Phylogenomic data have revealed many cryptic species in animal and plant taxa with large geographic ranges and disjunct distributions, especially when integrated with other data types, such as morphology and ecology. In the present study, we examined the genetic structuring within the nominal milkweed species, Asclepias tomentosa Elliott, found in the southeastern USA, with disjunct sets of populations occurring in Texas, Florida and the Carolinas. Using multiple analyses, including a phylogenomic tree, population structure analysis, principal component analysis of SNP data, calculations of FST, and a Bayesian species delimitation model, we uncovered three well-separated groupings of populations, each corresponding to the major geographic areas. Populations from Texas were most deeply separated from the rest and were differentiated in every analysis, including previously unrecognized morphological characters. Herein, we describe these Texas populations as a new species, Asclepias tonkawae sp. nov. and discuss the conservation implications of this discovery.