High genomic diversity maintained by populations of Carex scirpoidea subsp. convoluta, a paraphyletic Great Lakes ecotype

Abstract

Range-limited endemic taxa are threatened by loss of genomic diversity, which can lead to extirpation and extinction. The imperiled and narrowly distributed edaphic endemic Carex scirpoidea subsp. convoluta (Cyperaceae), which is primarily limited to alvar soils on the northern shores of Lake Huron in North America, exhibits such risk. In contrast, the conspecific C. scirpoidea subsp. scirpoidea is widely distributed across a vast geographical range and occupies various arctic and alpine habitat types. Using ddRADseq, population genomic analyses of 11 North American populations of C. scirpoidea including five subsp. convoluta populations revealed similar-to-higher levels of genomic diversity in the latter compared to its more widely distributed conspecific subsp. scirpoidea. Dioecy and a nearly obligate outcrossing mode of reproduction have likely contributed to the maintenance of genomic diversity in subsp. convoluta, preventing inbreeding depression, and contributing to the evolutionary potential of populations of this taxon. Phylogenomic and Bayesian analyses of ddRADseq data revealed that subsp. convoluta is paraphyletic with Eastern North American subsp. scirpoidea populations, suggesting that it best be considered a locally adapted ecotype. Furthermore, Eastern North America populations of both taxa arose from populations that likely occupied periglacial refugia south of the Laurentide Ice Sheet, where they no longer occur. Herein, we identify conservation units among the sampled Eastern North American C. scirpoidea populations to aid management efforts, which we suggest should include habitat protection and replanting for habitat restoration purposes.