delimitR

delimitR infers species boundaries using process-based demographic models that incorporate lineage divergence and gene flow and is implemented as an R package.

Key Features:

• Process-Based Approach: Considers evolutionary processes including gene flow and secondary contact in addition to divergence for species delimitation.
• Application to Empirical Data: Applied to empirical datasets such as the reticulate taildropper slug Prophysaon andersoni to identify species boundaries influenced by secondary contact.
• Performance Evaluation via Simulations: Simulation studies report near-zero error rates for three-population models with modest numbers of Single Nucleotide Polymorphisms (SNPs) and moderate divergence times.
• Handling Complex Models: Evaluates complex model sets that include divergence, gene flow, and population size changes, yielding moderate error rates (~0.15) with larger SNP datasets (10,000 SNPs) and detecting misclassifications among highly similar models.

Scientific Applications:

• Speciation research: Investigates the roles of lineage divergence, gene flow, and secondary contact in speciation processes.
• Biodiversity studies: Aids delimitation efforts that account for non-allopatric processes affecting species boundaries.
• Evolutionary biology: Provides a framework for testing demographic scenarios that shape genetic differentiation.
• Empirical dataset analysis: Applied across taxa to assess how secondary contact and gene flow contribute to observed patterns of diversity.

Methodology:

Implemented as an R package and evaluated using simulation studies that compare models incorporating lineage divergence, gene flow, secondary contact, and population size changes across SNP datasets of varying sizes and divergence times.