delimtools: an R package for species delimitation

Area of Science:

• Ecology and Evolutionary Biology
• Bioinformatics
• Computational Biology

Background:

• Single-locus species delimitation methods using DNA barcoding are crucial for biodiversity inventories and integrative taxonomy.
• Existing methods (e.g., ABGD, ASAP, GMYC, mPTP) produce idiosyncratic outputs, hindering integration and comparison.
• A need exists for a standardized platform to manage and analyze diverse species delimitation outputs.

Purpose of the Study:

• To introduce delimtools, an R package designed to standardize and scale species delimitation analyses.
• To provide a unified platform for pre-processing, analyzing, and visualizing DNA barcoding data for species delimitation.

Main Methods:

• The delimtools R package facilitates data pre-processing, cleaning, and formatting.
• It collapses and summarizes haplotype information.
• The package executes, parses, and merges outputs from various species delimitation programs, tabulating and visualizing results on phylogenetic trees.

Main Results:

• delimtools offers a comprehensive solution for managing and integrating outputs from multiple species delimitation methods.
• The package enables efficient data handling, analysis execution, and result visualization.
• It standardizes the workflow for species delimitation, improving scalability and repeatability.

Conclusions:

• The delimtools R package provides a powerful, open-source platform for advancing species delimitation research.
• It addresses the challenge of integrating diverse software outputs, promoting consistency in biodiversity assessments.
• This tool facilitates large-scale biodiversity inventories and integrative taxonomy by standardizing analyses.