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    Resolving relationships in an exceedingly young Neotropical orchid lineage using Genotyping-by-sequencing data

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    Authors
    Pérez-Escobar, Oscar Alejandro
    Bogarin, Diego
    Schley, Rowan
    Bateman, Richard M.
    Gerlach, Günter
    Harpke, Dörte
    Brassac, Jonathan
    Fernández-Mazuecos, Mario
    Dodsworth, Steven
    Hagsater, Eric
    Blanco, Mario A.
    Gottschling, Marc
    Blattner, Frank R.
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    Affiliation
    Royal Botanic Gardens Kew
    University of Gothenburg
    Gothenburg Global Biodiversity Centre
    Universidad de Costa Rica
    Botanischer Garten München-Nymphenburg
    Institute of Plant Genetics and Crop Plant Research
    Real Jardín Botánico
    University of Bedfordshire
    Herbarium AMO
    Ludwig-Maximillians University
    Imperial College London
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    Issue Date
    2019-11-14
    Subjects
    phylogenomics
    
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    Abstract
    Poor 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.
    Citation
    Perez-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)
    Publisher
    Elsevier
    Journal
    Molecular Phylogenetics and Evolution
    URI
    http://hdl.handle.net/10547/624068
    DOI
    10.1016/j.ympev.2019.106672
    PubMed ID
    31734454
    Additional Links
    https://www.sciencedirect.com/science/article/pii/S1055790318307139
    Type
    Article
    Language
    en
    ISSN
    1055-7903
    EISSN
    1095-9513
    ae974a485f413a2113503eed53cd6c53
    10.1016/j.ympev.2019.106672
    Scopus Count
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