SPEDE-sampler

SPEDE-sampler evaluates methodological and sampling influences on Generalized Mixed Yule Coalescent (GMYC) species delimitation using BEAST-derived phylogenies.

Key Features:

• Assessment of Methodological Choices: Evaluates effects of BEAST and GMYC parameters, including prior configurations, threshold models (single vs. multiple), and clock models, on GMYC outcomes.
• Sampling Effects Analysis: Analyzes how variation in sample size and the presence or absence of singletons influences GMYC species delimitations.
• Comparison with Predefined Groupings: Compares GMYC delineations to predefined groupings such as morphospecies or ecotypes and computes percentage match scores to identify discrepancies.
• Identification of Taxonomic Overestimations: Records instances where GMYC merging indicates that traditional taxonomy may overestimate or misrepresent species counts.
• Empirical Data Application: Applies the above analyses to four worked empirical examples to illustrate how methodological choices affect GMYC results.

Scientific Applications:

• Taxonomy and species discovery: Supports evaluation of species delimitations and detection of potential cryptic species or taxonomic inconsistencies.
• Biodiversity and genetic diversity assessment: Assesses how methodological and sampling decisions influence estimates of species richness and genetic structure.
• Evolutionary biology and species boundaries: Informs interpretation of species boundaries and geographical substructuring derived from GMYC analyses.

Methodology:

Uses BEAST-derived output phylogenies to test effects of varying BEAST and GMYC parameters (priors, single vs. multiple threshold models, clock models), examines sampling variation including sample size and singletons, compares GMYC clusters to predefined groupings (morphospecies, ecotypes) and computes percentage match scores, and records cases where GMYC merges indicate potential taxonomic overestimation; applied to four empirical datasets as worked examples.