Genomic analysis of Isoetes appalachiana species complex

Allopolyploidy is an important driver of diversification and a key contributor to genetic novelty across the tree of life. However, many studies have questioned the importance of extant polyploid lineages, suggesting that the vast majority may constitute evolutionary "dead-ends." Furthermore, recurrent formation of polyploid lineages and subsequent gene flow can complicate taxonomic circumscription and hinder conservation of members of hybrid and polyploid species complexes. There are few taxa that exemplify this two-edged contribution like the lycophyte genus Isoetes. Isoetes, also known as quillworts, are notable for their frequent hybridization and an exceptionally high number of polyploid species. Isoetes appalachiana is an allotetraploid that is broadly distributed throughout the eastern United States along with its diploid progenitors I. valida and I. engelmannii. As such this species complex provides an excellent opportunity to investigate the processes that underpin the formation and proliferation of allopolyploid lineages. Here we utilize ddRADseq and whole chloroplast sequencing to unravel the demographic and evolutionary history of hybridization in this widespread polyploid species complex.