Neotropical Orchid Phylogenetic Data for Cophylogenetic Analysis

Phylogenetic data from a study investigating evolutionary conflict between chloroplast and nuclear genomes in Neotropical Catasetinae orchids. The dataset includes sequence data used to infer phylogenetic relationships and detect outlier associations using PACo and ParaFit methods. It was authored by Oscar Alejandro Pérez-Escobar and published in 2020.

Use Cases

• Test PACo and ParaFit cophylogenetic methods on chloroplast and nuclear sequence data to detect outlier operational terminal units.
• Analyze topological incongruence between organellar and nuclear phylogenies within Catasetum, Cycnoches, and Mormodes genera.
• Assess the impact of using patristic distance matrices versus unit branch length trees on outlier detection performance.
• Investigate evolutionary processes like chloroplast capture and hybridization using linked pairs of operational terminal units from conflicting gene trees.

Strengths

• Data is derived from a focused phylogenetic study on Neotropical Catasetinae orchids, a group known for hybridization.
• Includes a provided R pipeline for executing PACo and ParaFit analyses and visualizing outlier associations.
• Published under a CC0 1.0 public domain license, permitting unrestricted reuse.

Limitations

• Specific data volume (rows, columns, file size) and file formats are not provided in the metadata.
• The dataset's utility is specialized for cophylogenetic methods testing and may require phylogenetic expertise to use effectively.
• Data is from 2020 and may not reflect the most recent phylogenetic research or software versions.

Provenance

Source

Dryad digital repository.

Collection Method

Phylogenetic relationships inferred from multilocus organellar and nuclear DNA sequence data.

Freshness

Last updated 2020-06-24.

Geography

Neotropical region, focusing on Catasetinae orchids.