Molecular methods for differentiating Phragmites australis subspecies and identification of hybrid stands in the Upper Midwestern United States

Premise In North America, Phragmites australis (common reed) has drawn a great deal of research attention. Non‐native P. australis subsp. australis is a noxious weed that has locally displaced native P. australis subsp. americanus in some areas. Although morphological features can distinguish the two subspecies, molecular tools often are required to confirm identifications. Additionally, the existence of natural intrasubspecific hybrids presents novel management challenges. Hybrid Phragmites is difficult to detect, and it has become standard practice to apply molecular tools to survey for hybrids. Methods We applied several molecular techniques—microsatellite, DArTseq (a type of genotyping‐by‐sequencing), restriction fragment length polymorphism (PCR‐RFLP), and next‐generation sequencing—to characterize P. australis at the landscape scale in Minnesota and Wisconsin and to search for hybrids. Results We obtained molecular data for Phragmites plants sampled from 341 stands, ultimately characterizing 98 stands as native and 236 as non‐native. Plants from two adjacent stands in Washington County, Minnesota, were confirmed to be hybrids. Discussion These are the first confirmed hybrids from the Upper Midwest/western Great Lakes region. We also discuss the relative cost and effectiveness of the various molecular methods and offer recommendations for future studies.