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dc.contributor.authorPérez-Escobar, Oscar Alejandro
dc.contributor.authorBogarin, Diego
dc.contributor.authorSchley, Rowan
dc.contributor.authorBateman, Richard M.
dc.contributor.authorGerlach, Günter
dc.contributor.authorHarpke, Dörte
dc.contributor.authorBrassac, Jonathan
dc.contributor.authorFernández-Mazuecos, Mario
dc.contributor.authorDodsworth, Steven
dc.contributor.authorHagsater, Eric
dc.contributor.authorBlanco, Mario A.
dc.contributor.authorGottschling, Marc
dc.contributor.authorBlattner, Frank R.
dc.date.accessioned2020-06-22T11:59:17Z
dc.date.available2020-06-22T11:59:17Z
dc.date.issued2019-11-14
dc.identifier.citationPerez-Escobar OA, Bogarin D, Schley R, Bateman RM, Gerlach G, Harpke D, Brassac J, Fernandez-Mazuecos M, Dodsworth S, Hagsater E, Blanco MA, Gottschling M, Blattner FR (2020) 'Resolving relationships in an exceedingly young Neotropical orchid lineage using Genotyping-by-sequencing data', Molecular Phylogenetics and Evolution, 144 (106672)en_US
dc.identifier.issn1055-7903
dc.identifier.pmid31734454
dc.identifier.doi10.1016/j.ympev.2019.106672
dc.identifier.urihttp://hdl.handle.net/10547/624068
dc.description.abstractPoor morphological and molecular differentiation in recently diversified lineages is a widespread phenomenon in plants. Phylogenetic relationships within such species complexes are often difficult to resolve because of the low variability in traditional molecular loci. Furthermore, biological phenomena responsible for topological incongruence such as Incomplete Lineage Sorting (ILS) and hybridisation complicate the resolution of phylogenetic relationships among closely related taxa. In this study, we employ a Genotyping-by-sequencing (GBS) approach to disentangle evolutionary relationships within a species complex belonging to the Neotropical orchid genus Cycnoches. This complex includes seven taxa distributed through Central America and the Colombian Chocó, and is nested within a clade estimated to have first diversified in the early Quaternary. Previous phylogenies inferred from few loci failed to provide support for internal relationships within the complex. Our Neighbour-net and coalescent-based analyses inferred from ca. 13,000 GBS loci obtained from 31 individuals belonging to six of the seven traditionally accepted Cycnoches taxa provided a robust phylogeny for this group. The genus Cycnoches includes three main clades that are further supported by morphological traits and geographic distributions. Similarly, a topology reconstructed through maximum likelihood (ML) inference of concatenated GBS loci produced results that are comparable with those reconstructed through coalescence and network-based methods. Our comparative phylogenetic informativeness analyses suggest that the low support evident in the ML phylogeny might be attributed to the abundance of uninformative GBS loci, which can account for up to 50% of the total number of loci recovered. The phylogenomic framework provided here, as well as morphological evidence and geographical patterns, suggest that the six entities previously thought to be different species or subspecies might actually represent only three distinct segregates. We further discuss the limited phylogenetic informativeness found in our GBS approach and its utility to disentangle relationships within recent and rapidly evolving species complexes. Our study is the first to demonstrate the utility of GBS data to reconstruct relationships within young (~2 Ma) Neotropical plant clades, opening new avenues for studies of species complexes that populate the species-rich orchid family.en_US
dc.language.isoenen_US
dc.publisherElsevieren_US
dc.relation.urlhttps://www.sciencedirect.com/science/article/pii/S1055790318307139en_US
dc.rightsGreen - can archive pre-print and post-print or publisher's version/PDF
dc.subjectphylogenomicsen_US
dc.titleResolving relationships in an exceedingly young Neotropical orchid lineage using Genotyping-by-sequencing dataen_US
dc.typeArticleen_US
dc.identifier.eissn1095-9513
dc.contributor.departmentRoyal Botanic Gardens Kewen_US
dc.contributor.departmentUniversity of Gothenburgen_US
dc.contributor.departmentGothenburg Global Biodiversity Centreen_US
dc.contributor.departmentUniversidad de Costa Ricaen_US
dc.contributor.departmentBotanischer Garten München-Nymphenburgen_US
dc.contributor.departmentInstitute of Plant Genetics and Crop Plant Researchen_US
dc.contributor.departmentReal Jardín Botánicoen_US
dc.contributor.departmentUniversity of Bedfordshireen_US
dc.contributor.departmentHerbarium AMOen_US
dc.contributor.departmentLudwig-Maximillians Universityen_US
dc.contributor.departmentImperial College Londonen_US
dc.identifier.journalMolecular Phylogenetics and Evolutionen_US
dc.date.updated2020-06-22T11:49:57Z
dc.description.noteover 3 months from publication


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