Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the genus Rosa
| Autor: | Tatiana Thouroude, Valéry Malécot, Kevin Debray, Aurélie Bérard, Anne Bruneau, Fabrice Foucher, Marie-Christine Le Paslier, Jordan Marie-Magdelaine, Gilles Michel |
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| Přispěvatelé: | Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universiteit Gent = Ghent University [Belgium] (UGENT), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université du Québec à Montréal = University of Québec in Montréal (UQAM) |
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0106 biological sciences
Nuclear gene interspecific hybridization Biology Rosa 010603 evolutionary biology 01 natural sciences Polyploidy 03 medical and health sciences polyploid detection Polyploid Phylogenomics Genetics Taxonomic rank Phylogeny Ecology Evolution Behavior and Systematics 030304 developmental biology Likelihood Functions 0303 health sciences reticulate evolution Phylogenetic tree amplicon sequencing fungi food and beverages Reticulate evolution [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding Taxon Evolutionary biology Hybridization Genetic Subgenus |
| Zdroj: | Systematic Biology Systematic Biology, Oxford University Press (OUP), 2021, pp.syab064. ⟨10.1093/sysbio/syab064⟩ |
| ISSN: | 1063-5157 1076-836X |
| DOI: | 10.1093/sysbio/syab064⟩ |
| Popis: | 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.] |
| Databáze: | OpenAIRE |
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