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Resolving relationships in an exceedingly young Neotropical orchid lineage using Genotyping-by-sequencing data
- Source :
- Digital.CSIC. Repositorio Institucional del CSIC, instname, Molecular Phylogenetics and Evolution144, Kérwá, Universidad de Costa Rica, instacron:UCR
- Publication Year :
- 2020
- Publisher :
- Academic Press, 2020.
-
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 UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Agroalimentarias::Jardín Botánico Lankester (JBL)
- Subjects :
- 0106 biological sciences
0301 basic medicine
Species complex
American tropics
DNA, Plant
Genotype
Genotyping Techniques
Phylogenetic incongruence
Subspecies
Biology
010603 evolutionary biology
01 natural sciences
Coalescent theory
03 medical and health sciences
Phylogenetics
Phylogenomics
Genetics
Orchidaceae
Clade
Molecular Biology
Phylogeny
Ecology, Evolution, Behavior and Systematics
High-throughput sequencing
Phylogenetic tree
Central America
Sequence Analysis, DNA
Biological Evolution
Phylogeography
030104 developmental biology
Taxon
Evolutionary biology
Hybridization, Genetic
Rapid diversification
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- Digital.CSIC. Repositorio Institucional del CSIC, instname, Molecular Phylogenetics and Evolution144, Kérwá, Universidad de Costa Rica, instacron:UCR
- Accession number :
- edsair.doi.dedup.....b25930b994dad74a17a856d85ed97a52