Phylogenomics Reveals Deep Divergences and Cryptic Species Within a Rare Sand‐Dwelling Milkweed, Asclepias tomentosa Elliott

Integrative taxonomy incorporates multiple data types to delineate and describe species and discovers hidden biodiversity (i.e. , ‘cryptic’ species) previously undetected when relying solely on morphology. Phylogenomic data, when combined with morphological and ecological data, have revealed many cryptic species in animal and plant taxa with large geographic ranges and disjunct distributions. In the present study, we examined the genetic structure of the rare 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 F ST , and a Bayesian species delimitation model, we uncovered three well‐separated genetic lineages, 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.