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

Citation

Foucher, Fabrice et al. (2021), Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the genus Rosa, Dryad, Dataset, https://doi.org/10.5061/dryad.3xsj3txgw

Abstract

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.

Methods

The methods are described in the manuscript associated with the data.

Funding

Conseil Régional des Pays de la Loire, Award: RFI Objectif Végétal

Ministère de l’Enseignement Supérieur et de la Recherche Scientifique

European Regional Development Fund

Angers Loire Métropole