Phylogenomic Evolution of the North American Rodent Radiation, Zoonotic Reservoir Competence, and Coalescent Population Dynamics Across Sciuromorpha, Castorimorpha, and Myomorpha Under FreeRate and Bayesian Skyline Models
Year: 2026
Type: preprint
Abstract: 32-chain RuNIE phylogenomic and functional selection analysis across 64 species and 18 loci (L = 26,700 aligned columns; Lagomorpha outgroups, Sciuromorpha, Castorimorpha, Dipodoidea, invasive Muridae, and New World Cricetidae: Arvicolinae, Neotominae, and Sigmodontinae) coupled with 10,000-generation (20% burn-in) single-species Bayesian coalescent skyline reconstructions across three North American PopSets (Peromyscus maniculatus, Sigmodon hispidus, and Urocitellus parryii; 3 × N = 36 = 108 conspecific isolates) benchmarked against *MAFFT, *IQ-TREE/*LSD2, *PAML codeml, and *BEAST v1.10.4 The continental radiation of rodents (Order Rodentia) across North America via Paleogene Beringian corridors, Miocene grassland expansions, and Great American Biotic Interchange exchanges—coupled with the Anthropocene introduction of Old World commensal murids—established both the foundational small-mammal trophic guilds of Nearctic ecosystems and the primary sylvatic reservoirs for North America's major rodent-borne zoonoses. Here we execute a 32-chain RuNIE phylogenomic and functional selection analysis across an 18-locus, 64-species Glires supermatrix (L = 26,700 aligned columns with 7,979 parsimony-informative sites and 8,803 distinct site patterns) paired with independent 10,000-generation (20% burn-in) single-species Bayesian coalescent skyline reconstructions across three conspecific North American population datasets (3 × N = 36 = 108 isolates) benchmarking Native Rust against *MAFFT v7.526, *IQ-TREE v2.4.0 with *LSD2 v2.4.4, *PAML v4.10.10 codeml, and *BEAST v1.10.4. Our fossil-calibrated chronogram anchors the Glires root (Lagomorpha vs. Rodentia) at 65.2 Ma, Crown Rodentia at 56.8 Ma, the Sciuromorpha–Castorimorpha split at 36.4 Ma, Myodonta (Dipodoidea vs. Muroidea) at 46.5 Ma, the Muridae–Cricetidae divergence at 24.8 Ma, Crown Cricetidae at 18.6 Ma, and the New World Neotominae–Sigmodontinae split at 13.4 Ma. Codon selection modeling (*PAML codeml) reveals strong purifying constraint on the Sin Nombre hantavirus endothelial receptor ITGB3 beta-3 integrin (omega = 0.5319), intermediate selective constraint on the high-altitude and fossorial hypoxia axis EPAS1/HBB (omega = 0.0343) and rodenticide-detoxification locus VKORC1/CYP2C (omega = 0.2572), and diversifying positive selection on bacterial pattern-recognition receptors TLR2/TLR4 (omega = 0.2631) and the New World Arenavirus receptor TFRC transferrin receptor 1 apical domain (omega = 0.1453). Across the three single-species PopSet skyline cohorts, we resolve post-glacial forest/oak-mast expansion and contemporary ENSO Sin Nombre hantavirus / Lyme disease amplification in the North American deer mouse (Peromyscus maniculatus, N = 36, Ne = 433,194 to 653,847; *BEAST = 667,970), northward agricultural grassland expansion and Black Creek Canal / Tamiami viral irruptions in the hispid cotton rat (Sigmodon hispidus, N = 36, Ne = 1,534,254 to 1,753,302; *BEAST = 1,808,005), and post-LGM Beringian steppe-tundra recolonization and high-latitude permafrost-thaw dynamics in the Arctic ground squirrel (Urocitellus parryii, N = 36, Ne = 707,606 to 1,687,680; *BEAST = 1,740,336), while demonstrating that Native Rust achieves a 42.9-fold end-to-end speedup (13.88 s vs. 595.24 s Hybrid and 1861.52 s full External UFBoot). Canonical Preprint URL: https://crvscience.com/labs/preprints/rodent-north-america-radiation-preprint Master (Concept) Zenodo DOI: 10.5281/zenodo.24066499 Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs
Author: White, Bryan P.
Institution: CRV (Netherlands)
Language: English
Subfield: Paleontology
Field: Earth and Planetary Sciences
Domain: Physical Sciences
Open Access status: green
OpenAlex ID: W7225644209
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