Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and...

Area of Science:

• Evolutionary biology
• Genetics
• Biodiversity science

Background:

• DNA barcoding studies utilize single-locus data for evolutionary diversity surveys.
• Species delimitation is crucial for biodiversity assessments, particularly with environmental DNA.
• The Generalized Mixed Yule Coalescent (GMYC) method is a common tool for species delimitation using gene trees.

Purpose of the Study:

• To present detailed reformulations and a thorough evaluation of the GMYC method.
• To assess the robustness of GMYC under various biological scenarios and model departures.
• To compare the performance of single-threshold versus multiple-threshold GMYC versions.

Main Methods:

• Reconstruction of gene trees from single-locus DNA barcoding data.
• Application of the Generalized Mixed Yule Coalescent (GMYC) method for species delimitation.
• Extensive simulations evaluating GMYC performance under diverse population and divergence scenarios.

Main Results:

• GMYC accuracy is primarily influenced by the ratio of mean population size to divergence times.
• Deviations from model assumptions, like varying population sizes or growth, have minor impacts.
• Likelihood-derived support measures reliably indicate GMYC performance.
• The single-threshold GMYC model consistently outperformed the multiple-threshold version in simulations.

Conclusions:

• The GMYC method is a robust tool for species delimitation with single-locus data.
• Understanding the interplay between population size and divergence is key for accurate delimitation.
• The single-threshold GMYC model is recommended for its superior performance in simulated datasets.