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

Reticulation, caused by hybridization and allopolyploidization, is
considered an important and frequent phenomenon in the evolution of
numerous plant lineages. Although both processes represent important
driving forces of evolution, they are mostly ignored in phylogenetic
studies involving a large number of species. Indeed only a scattering of
methods exists to recover a comprehensive reticulated evolutionary history
for a broad taxon sampling. Plastid markers, sometimes combined with a few
nuclear sequences, are therefore favored, even though they restrict
in-depth studies of hybridization and polyploidization. The genus Rosa
encompasses c. 150 species widely distributed throughout the northern
hemisphere and represents a challenging taxonomic group in which
hybridization and polyploidization are prominent. Our main objective was
to develop a general framework that would take patterns of reticulation
into account in the study of the phylogenetic relationships among Rosa
species. Using amplicon sequencing we targeted allele variation in the
nuclear genome as well as haploid sequences in the chloroplast genome. A
stepwise diploids-first approach was developed to reconstruct the
reticulate evolutionary history of the genus Rosa. We successfully
recovered robust plastid and nuclear phylogenies and performed in-depth
tests for several scenarios of hybridization. Using this strategy, we were
able to resolve most of the evolutionary relationships among Rosa
subgenera, sections, and selected species, and we provide new directions
for a future revision of the infrageneric classification in Rosa. The
stepwise strategy proposed here can be used to reconstruct the
phylogenetic relationships of other challenging taxonomic groups with
large numbers of hybrid and polyploid taxa.