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

Area of Science:

• Botany
• Evolutionary Biology
• Genomics

Background:

• Resolving phylogenetic relationships in recently diversified plant lineages is challenging due to low molecular variability and phenomena like incomplete lineage sorting (ILS) and hybridization.
• The Neotropical orchid genus Cycnoches presents a species complex with difficult-to-resolve evolutionary relationships using traditional molecular markers.

Purpose of the Study:

• To disentangle the evolutionary relationships within the Cycnoches orchid species complex using a Genotyping-by-sequencing (GBS) approach.
• To investigate the utility of GBS data for reconstructing phylogenies in young, rapidly evolving plant clades.

Main Methods:

• Employed Genotyping-by-sequencing (GBS) to analyze 31 individuals from six Cycnoches taxa.
• Utilized Neighbour-net and coalescent-based analyses on approximately 13,000 GBS loci.
• Performed maximum likelihood (ML) inference on concatenated GBS loci for comparative analysis.

Main Results:

• A robust phylogeny revealed three main clades within Cycnoches, supported by morphological and geographic data.
• Phylogenomic, coalescent, and network-based analyses yielded comparable results.
• Identified that up to 50% of GBS loci may be uninformative, potentially affecting phylogenetic support.

Conclusions:

• The study suggests that six previously recognized Cycnoches entities may represent only three distinct segregates.
• Genotyping-by-sequencing (GBS) is effective for resolving relationships in young, rapidly evolving Neotropical plant clades.
• This work opens new research avenues for understanding species complexes in the orchid family.