pSTDistanceR

pSTDistanceR computes probabilistic distances between species tree models under the multispecies coalescent (MSC) framework to compare species tree hypotheses using gene tree probability and site-pattern distributions, including network-based MSC extensions that accommodate hybridization.

Key Features:

• Probabilistic Distance Measures: Computes distances between species tree models by comparing gene tree topology probabilities and site-pattern probability distributions rather than only topology or branch-length metrics.
• Multispecies Coalescent Models: Implements MSC parameterizations of the discrete probability distribution of gene trees conditioned on species tree topology and divergence times (in coalescent units).
• Network-Based Extensions: Supports network-based MSC models to represent hybridization and reticulate histories among taxa when computing model distances.
• Simulation and Empirical Application: Applied to simulated datasets and empirical species tree estimates to evaluate and demonstrate distance behavior.

Scientific Applications:

• Phylogenomic Inference: Enables probabilistic comparison of competing species tree hypotheses in phylogenomic analyses.
• Population Genomics: Accommodates gene tree heterogeneity and hybridization for analyses of complex population structure and reticulate evolution.
• Model Comparison: Facilitates rigorous post hoc comparisons of species tree and network models under the MSC framework.

Methodology:

Extends the theory of Garba et al. (2018) to species tree models by computing probabilistic distances based on gene tree topology and site-pattern probability distributions conditioned on a given species tree, and includes network-based MSC models to allow hybridization.