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

Autor: Debray K; Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 42 rue Georges Morel - CS 60057, F-49000 Angers, France., Le Paslier MC; Etude du Polymorphisme des Génomes Végétaux (EPGV), INRA, Université Paris-Saclay, 91000 Evry, France., Bérard A; Etude du Polymorphisme des Génomes Végétaux (EPGV), INRA, Université Paris-Saclay, 91000 Evry, France., Thouroude T; Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 42 rue Georges Morel - CS 60057, F-49000 Angers, France., Michel G; Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 42 rue Georges Morel - CS 60057, F-49000 Angers, France., Marie-Magdelaine J; Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 42 rue Georges Morel - CS 60057, F-49000 Angers, France., Bruneau A; Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke Est, Montréal, QC H1X 2B2, Canada., Foucher F; Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 42 rue Georges Morel - CS 60057, F-49000 Angers, France., Malécot V; Institut Agro, Univ Angers, INRAE, IRHS, SFR QUASAV, 2 Rue André le Notre, F-49000 Angers, France.
Jazyk: angličtina
Zdroj: Systematic biology [Syst Biol] 2022 Apr 19; Vol. 71 (3), pp. 547-569.
DOI: 10.1093/sysbio/syab064
Abstrakt: 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. Among these methods, comparisons of topologies obtained from plastid markers with those from a few nuclear sequences are 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. We successfully recovered robust plastid and nuclear phylogenies and performed in-depth tests for several scenarios of hybridization using a maximum pseudo-likelihood approach on taxon subsets. Our diploid-first approach followed by hybrid and polyploid grafting resolved most of the evolutionary relationships among Rosa subgenera, sections, and selected species. Based on these results, 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. [Amplicon sequencing; interspecific hybridization; polyploid detection; reticulate evolution.].
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Databáze: MEDLINE
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