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

  • Oscar Alejandro Pérez-Escobar(corresponding author)
    ,
  • Diego Bogarín
    ,
  • Rowan Schley
    ,
  • Richard M. Bateman
    ,
  • Günter Gerlach
    ,
  • Dörte Harpke
*Corresponding author for this work
  • University of Gothenburg
    ,
  • Royal Botanic Gardens, Kew
    ,
  • University of Costa Rica
    ,
  • Imperial College London
    ,
  • Botanischer Garten München-Nymphenburg
    ,
  • Leibniz Institute of Plant Genetics and Crop Plant Research
Research Output:
Contribution to journal
Article
 Peer-review

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.

Publication Information

Output type

Research Output:
Contribution to journal
Article
 Peer-review

Original language

English

Article number

106672

Journal (Volume, Issue Number)

Molecular Phylogenetics and Evolution (Volume 144)

Publication milestones

  • Accepted/In press - 05/11/2019
  • Published - 14/11/2019

Publication status

Published - 14/11/2019

ISSN

1055-7903

Publication IDs

  • handle.net: 10547/624068
  • Scopus: 85076489129
  • PubMed: 31734454

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