Unravelling complex evolutionary histories by a multidisciplinary approach : the case of the common moonwort ferns

Abstract

Ferns are a highly diverse group of land plant present in almost every continent and most climates. Even though ferns diverged from the seed plants about 360-430 million years ago, most extant ferns originated from recent Cenozoic radiation events. Recently diverged groups often consist of species exhibiting subtle morphological differences with frequent naturally occurring hybrids, resulting in a poorly understanding of these groups’ diversity The rapid decline of biodiversity emphasizes the need to characterize the species’ richness of such groups to further identify potential threats and define conservation measures. The thesis presented here focused on the understanding of the common moonwort ferns complex evolutionary history by a multidisciplinary approach. The Botrychium lunaria group (common moonwort) is a species complex of the Ophioglossaceae family. One of the main limitations of the studies of fern evolutionary histories, including for the B. lunaria group, is the availability of nuclear genomic resources. The paucity of such genome-wide datasets is mostly due to the complexity and the size of fern genomes. A recent breakthrough came with the 1KP project which led to the sequencing 1,000 plant transcriptomes. With the motivation of providing genomic tools for Botrychium ferns, we applied a similar transcriptomic approach as the 1KP project. We showed that transcriptome-wide dataset was a powerful tool to resolve population structure and investigate ploidy level. The newly established transcriptome is also a precious resource for defining single-copy markers for phylogenetic studies. Then, we assessed the B. lunaria group diversity on a global scale and investigated the role of climatic and ecological factors in the speciation process. We recovered ten well-defined monophyletic clades corresponding to eleven species-level clades. Three clades were not previously identified and need to be considered in future research. The diversification of the group coincides with the Pleistocene climatic oscillations. We also identified indications for soil preferences among species. Finally, we examined the morphological features of the uncharacterized species and subspecies-level clade. We described four new species from Eurasia, two exhibiting a large distribution range and one being restricted to the Himalayas. This thesis improves our understanding of the genetic, morphological, and ecological diversity in the B. lunaria group. Also, the genomic resources we developed open doors to study reticulate evolution and population differentiation in this and related groups.