Intraspecific differentiation of <i>Allium canadense</i> var. <i>canadense</i> (Amaryllidaceae) across the North American Coastal Plain

Polyploidy increases genetic variation in plants, leading to adaptations allowing expansion into novel habitats and increased genetic differentiation among populations isolated by barriers to dispersal. Allium canadense var. canadense is a polyploid taxon distributed within the North American Coastal Plain (NACP) biodiversity hotspot. It is the only one of six varieties in a species complex of wild onions native to North America that exhibits bulbils responsible for vegetative reproduction, which may lead to low levels of genetic variation within populations. Despite its threatened/endangered status in the northeast United States and noxious weed listing in Arkansas, USA, little is known about intraspecific differentiation among populations which may be impacted by riverine barriers or seasonal latitudinal gradients. We used sequences of one nuclear (ITS) and two chloroplast (trnL-F and rpl32-trnL) DNA regions generated from eight populations in the NACP and one population in Kansas, USA to examine genetic diversity and population structure of A. canadense var. canadense. A total of 12 ITS ribosomal and 10 chloroplast DNA haplotypes were identified. Phylogenetic analyses indicated two major lineages which corresponded to the genealogical relationships identified in the population structure analyses. Significant genetic subdivision among populations was detected across all populations by analysis of molecular variance. Overall, geographic structuring is apparent among populations of A. canadense var. canadense and populations showed moderate levels of gene diversity. These findings are indicative of the complex nature of polyploids and their contribution to genetic diversity among populations with mating systems that might otherwise have no phylogeographic structure.