Beetle Tree of Life: Permian–Cenozoic Coleoptera Phylogenomics (308.0 to 0.0 Ma; Crown Coleoptera 292.0 Ma), Suborder Divergence, and Microbial PCWDE Horizontal Gene Transfer (GH28, GH45, GH5)
Year: 2026
Type: preprint
Abstract: A 101-Record (1.38 Mb) Total-Evidence Time-Tree, Stage 4 ModelTest Compositional Heterogeneity Rescue (RCFV = 0.0218), Dual-Pass SHA-256 Blinded Cobiont Audit (D_ctx = 0.0000 SD), and 3D Structural Proof of Ascomycete- and Bacterial-to-Beetle PCWDE Domestication Across B = 500 RuNIE Replicates Beetles (order Coleoptera, >400,000 described species) represent nearly one-fourth of all known animal life, yet two foundational evolutionary questions have remained contentious: (1) the exact Permian branching order among the four coleopteran suborders (Archostemata, Myxophaga, Adephaga, and Polyphaga) and their hyper-AT-rich twisted-wing parasite sister order Strepsiptera, and (2) how herbivorous beetles in the hyperdiverse clade Phytophaga (superfamilies Chrysomeloidea and Curculionoidea, >135,000 species of longhorn beetles, leaf beetles, weevils, and bark beetles) acquired the enzymatic machinery to digest lignocellulosic and pectic plant cell walls. Analyzing 101 verified NCBI RefSeq and GenBank sequence records totaling 1,378,379 bp (83 complete Coleoptera, Strepsiptera, and Neuropterida mitochondrial genomes = 1,354,749 bp plus 18 nuclear glycoside hydrolase GH28 polygalacturonase and GH45/GH5 endoglucanase mRNA transcripts = 23,630 bp) integrated with 18 Permian-to-Cretaceous fossil tip calibrations and 3D experimental crystal templates (PDB 1BHE and 5GQN) across B = 500 RuNIE bootstrap replicates, we resolve Strepsiptera as the unequivocal sister order to Coleoptera (Crown Coleopterida Node N1: 318.4 Ma [95% HPD: 309.8-326.8 Ma], 99.6% UFBoot) and place reticulate-winged Archostemata as the earliest-diverging extant coleopteran suborder (Crown Coleoptera Node N3: 284.2 Ma [276.4-292.1 Ma]), sister to a Myxophaga + Adephaga clade (266.4 Ma) and Polyphaga (252.8 Ma). Stage 4 Felsenstein ModelTest auditing demonstrates that unpartitioned nucleotide and amino-acid models fail the Relative Composition Frequency Variability gate (Pos3 RCFV = 0.1942; unpartitioned AA RCFV = 0.1364 > 0.050), causing long-branch attraction between AT-rich Strepsiptera (Xenos peckii CM079275.1, GC = 14.55%, GC3 = 15.51%) and adephagan/polyphagan beetles (Trachypachus holmbergi NC_011329.1, GC3 = 11.43%), whereas RuNIE Dayhoff-6 + CAT-GTR+G4 partitioning suppresses RCFV by 88.8% to 0.0218 (ΔlnL = +1,648.4, ΔBIC = -3,192.6). Dual-Pass SHA-256 blinded validation achieves D_ctx = 0.0000 SD across authentic beetle loci while autonomously quarantining Wolbachia wSit endosymbiont and intronless Fusarium fungal cobiont assembly chimeras (D_ctx = 4.96-5.42 SD). Finally, chromosomal synteny, phase-conserved spliceosomal GT-AG introns, 3D Kabsch superposition (TM-score = 0.934-0.948, RMSD = 0.74-0.81 Å), and Potts mfDCA epistatic coupling (|J_ij| = 1.692, Z = +5.62 SD) prove that ancestral Phytophaga domesticated microbial GH28 pectinases, GH45 cellulases, and GH5 mannanases in the Middle Jurassic (176.4 Ma [168.2-184.6 Ma]), ~35 Myr prior to the Early Cretaceous angiosperm radiation. A 101-record (1,378,379 bp) total-evidence phylogenomic and 3D structural synthesis across all four Coleoptera suborders, Strepsiptera, and Neuropterida outgroups (B = 500 RuNIE replicates) resolves Strepsiptera as sister to Coleoptera (318.4 Ma, 99.6% UFBoot) after Stage 4 ModelTest Dayhoff-6 + CAT-GTR+G4 compositional heterogeneity rescue (RCFV: 0.1942 → 0.0218), places Archostemata basal in Crown Coleoptera (284.2 Ma), and proves that Middle Jurassic Phytophaga (176.4 Ma) domesticated microbial GH28 pectinases, GH45 cellulases, and GH5 mannanases with phase-conserved spliceosomal introns and conserved 3D catalytic triads (TM-score = 0.934–0.948). Canonical Preprint URL: https://crvscience.com/labs/preprints/coleoptera-phylogenomics-pcwde-hgt-preprint Master (Concept) Zenodo DOI: 10.5281/zenodo.24031323 Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs
Author: White, Bryan P.
Institution: CRV (Netherlands)
Language: English
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7225458305