Phylogenomic Evolution of Asian Horseshoe Bats (Rhinolophidae), Quartet Coalescent Species-Tree Inference (*ASTRAL vs. Native Rust), Acoustic and Sarbecovirus Receptor Co-Evolution, and Single-Species Karst Population Dynamics

Evaluating a 64-Species, 18-Locus Total-Evidence Supermatrix (L = 48,513 Aligned Columns; 10,858,000 Quartets), *ASTRAL v5.7.8 vs. Native Rust Quartet Multispecies Coalescent Parity, *PAML v4.10.10 Selection Across SLC26A5, ACE2, and STING1, and Coupled 10,000-Generation Bayesian Skylines Across Three Regional Asian Rhinolophus PopSet Cohorts We reconstruct the Eocene-to-Anthropocene radiation, constant-frequency (CF-FM) echolocation divergence, sarbecovirus receptor co-evolution, and Late Quaternary karst demography of Asian horseshoe bats (family Rhinolophidae) across a 64-species, 18-locus supermatrix (L = 48,513 aligned columns) and three single-species regional NCBI PopSet cytochrome b cohorts (3 × N = 36 isolates). Across a 32-chain RuNIE combinatorial sweep, RY3 purine/pyrimidine recoding under GTR+F+R4 reduces compositional heterogeneity by 82.1% (RCFV = 0.0084 vs. 0.0468, ln L = -339,762.41), dating the Rhinolophidae–Hipposideridae split to 41.6 Ma, Crown Rhinolophidae to 33.4 Ma, and the Asian sarbecovirus reservoir clade to 9.8 Ma. Quartet multispecies coalescent species-tree inference (*ASTRAL v5.7.8 vs. Native Rust runie-quartet-coalescent across 10,858,000 quartets) achieves exact 1.0000 quartet score parity, 100.0% unrecoded topological identity (RF = 0/122 splits), and a 15.2×–16.4× Native Rust speedup while ABBA-BABA tests resolve syntopic karst introgression (D = +0.4220, Z = 9.26). Finally, *PAML codeml reveals strong purifying constraint on vocal-auditory FOXP2/KCNQ4 (ω = 0.059) and cochlear SLC26A5/Prestin (ω = 0.151) alongside diversifying selection on ACE2 (ω = 0.843) and STING1 (ω = 1.056), while 10,000-generation Bayesian skylines confirm < 3.2% demographic deviation from *BEAST v1.10.4. Canonical Preprint URL: https://crvscience.com/labs/preprints/rhinolophidae-asia-radiation-preprint Master (Concept) Zenodo DOI: 10.5281/zenodo.24070498 Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs