Diversification across a dynamic Holarctic: Beringian ancestry and declining speciation in arvicoline rodents

This repository contains the data, input files, R scripts, and analytical outputs associated with a study of diversification dynamics and historical biogeography in arvicoline rodents (Arvicolinae). The archived materials support analyses investigating temporal and environmental patterns of diversification, ancestral geographic ranges, dispersal history, diversification-rate heterogeneity, and potential episodic changes in diversification through time. The repository includes five major analytical components. BAMM was used to evaluate diversification-rate heterogeneity across the arvicoline phylogeny and within Microtini. BioGeoBEARS was used to reconstruct ancestral geographic ranges using both time-stratified and non-time-stratified models, with associated biogeographic stochastic mapping (BSM) used to characterize the frequency and timing of biogeographic events. RPANDA was used to compare constant, time-dependent, and environment-dependent diversification models incorporating environmental variables including stable oxygen isotopes (δ¹⁸O), atmospheric CO₂, and sea level. TESS/CoMET analyses were used to evaluate Bayesian birth-death models, episodic diversification dynamics, and potential mass-extinction processes. Files are organized by analytical framework and include the phylogenetic and geographic inputs, environmental datasets, analysis scripts, saved R objects, model-comparison results, and selected figures and outputs necessary to document and reproduce the analyses. The archive is intended to provide a transparent and reproducible record of the computational analyses reported in the associated study.