Phylogenomics support a Cenozoic rediversification of the “living fossil” Isoetes

The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that ancient losses of Isoetes diversity did not prevent rediversification of small, highly-specialized descendants despite competition from flowering plants. Extant Isoetes appear as “living fossils” due to morphological stasis, but they are not the last remnants of a previously dominant group, instead representing the recent success of a group pre-adapted to environments that spread during the last 60 million years.