Phylogenomic Evolution of Ecosystem Function and Coalescent Population Dynamics Across Six Families of Beetles (Coleoptera) Under FreeRate and Bayesian Skyline Models

32-chain RuNIE phylogenomic and functional selection analysis across 64 species and 16 loci (L = 37,741 aligned columns; Carabidae, Scarabaeidae, Coccinellidae, Cerambycidae, Chrysomelidae, and Curculionidae) coupled with 10,000-generation (20% burn-in) Bayesian coalescent skyline reconstructions across three independent PopSets (Dendroctonus ponderosae, Harmonia axyridis, and Pterostichus melanarius) benchmarked against *MAFFT, *IQ-TREE/*LSD2, *PAML codeml, and *BEAST v1.10.4 The hyperdiverse radiation of beetles (Order Coleoptera) across terrestrial ecosystems was propelled by key physiological and enzymatic innovations—from cursorial predation and pygidial chemical defense in Adephaga (Carabidae) and hindgut microbial fermentation in Scarabaeiformia (Scarabaeidae) to cryptonephridic Malpighian tubule water conservation in Cucujiformia (Coccinellidae) and horizontally transferred plant cell wall degrading enzymes (GH5, GH28, and GH45) in Phytophaga (Cerambycidae, Chrysomelidae, and Curculionidae). Here we execute a 32-chain RuNIE phylogenomic and functional selection analysis across a 16-locus, 64-species supermatrix (L = 37,741 aligned columns with 15,440 parsimony-informative sites) coupled with independent 10,000-generation (20% burn-in) Bayesian coalescent skyline reconstructions across three localized population datasets benchmarking Native Rust against *MAFFT, *IQ-TREE with *LSD2, *PAML codeml, and *BEAST. Our dated chronogram and codon selection models anchor Crown Coleoptera at 295.0 Ma, Cucujiformia cryptonephridic water conservation at 224.8 Ma, and the Phytophaga cell-wall enzyme radiation at 174.0 Ma, revealing strong purifying constraint on GH28 pectinases (omega = 0.2251) alongside diversifying selection on CYP6 detoxification monooxygenases (omega = 1.0657). Across the three localized PopSet skyline cohorts, we resolve an 11.1-fold Anthropocene drought and winter-warming outbreak expansion in the mountain pine beetle Dendroctonus ponderosae (Ne = 184,439 to 2,052,657), an 88.1% biocontrol founder bottleneck followed by a 37.4-fold invasive bridgehead explosion in Harmonia axyridis (Ne = 62,937 to 2,351,789), and an 83.0% agrochemical intensification crash followed by beetle-bank corridor recovery in the epigean predator Pterostichus melanarius, while demonstrating that *MAFFT progressive alignment consumes 80.1% of external pipeline runtime compared to a 21.0-fold end-to-end speedup in Native Rust. Canonical Preprint URL: https://crvscience.com/labs/preprints/coleoptera-ecosystem-function-preprint Master (Concept) Zenodo DOI: 10.5281/zenodo.24058171 Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs