Homoploid hybrids, allopolyploids, and high ploidy levels characterize the evolutionary history of a western North American quillwort (Isoëtes) complex.

Abstract Polyploidy and hybridization are important processes in seed-free plant evolution. However, a major gap lies in our understanding of how these processes affect the evolutionary history of high-ploidy systems. The heterosporous lycophyte genus Isoetes is a lineage with many putative hybrids and high-level polyploid taxa (ranging from tetraploid to dodecaploid). Here, we use a complex of western North American Isoetes, to understand the role of hybridization and high-level polyploidy in generating and maintaining novel diversity. To uncover these processes, we use restriction-site associated DNA sequencing (RADseq), multiple alleles of a single low-copy nuclear marker, whole plastomes, cytology (genome size estimates and chromosome counts), and reproductive status (fertile or sterile). With this dataset, we show that hybridization occurs easily between species in this complex and is bidirectional between identical, but not different, cytotypes. Furthermore, we show that fertile allopolyploids appear to have formed repeatedly from sterile homoploid and interploid hybrids. We propose that low prezygotic reproductive barriers and a high frequency of whole-genome duplication allow for high-level polyploid systems to generate novel lineages, and that these mechanisms may be important in shaping extant Isoetes diversity.