Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the genus Rosa

Reticulate evolutions caused by hybridization and allopolyploidization occur frequently in evolutionary biology, especially in plants. Although they represent important driving forces for evolution, they are generally ignored in phylogenetic studies involving a large number of species because only few methods exist to recover a comprehensive reticulated evolutionary history on such broad sampling. Plastid markers, sometimes combined with few nuclear sequences, are therefore favored, despite they restrict in-depth studies of hybridization and polyploidization. The genus Rosa encompasses about 150 species well-distributed throughout the northern hemisphere and represents a challenging taxonomic group where hybridization and polyploidization are prominent. Our main objective was to develop a framework able to take patterns of reticulation into account in the study of the phylogenetic relationships of Rosa species. We therefore targeted allele variations in the nuclear genome as well as haploid sequences in the chloroplast genome using amplicon sequencing.Then, we developed a stepwise diploids-first approach to reconstruct the reticulate evolutionary history of the genus Rosa. We successfully recovered robust plastid and nuclear phylogenies and we performed in-depth studies of several scenarios of hybridization. Using this strategy, we were able to address most of the evolutionary relationships between Rosa sections, subgenera and selected species, and we gave new directions for a future revision of the infrageneric classification in the genus Rosa. The stepwise strategy that we developed can be used to reconstruct the phylogenetic relationships in other challenging taxonomic groups that encompass a large number of hybrid and polyploid taxa.