Permo-Carboniferous–Cenozoic Lepidoptera Genomic Radiation, Angiosperm-Coupled Ditrysia & Papilionoidea Time-Tree, and COX1 DNA Barcode Resolution vs. Deep-Node Saturation Boundaries

Permo-Carboniferous–Cenozoic Lepidoptera Genomic Radiation, Angiosperm-Coupled Ditrysia & Papilionoidea Time-Tree, and COX1 DNA Barcode Resolution vs. Deep-Node Saturation Boundaries Across 92 NCBI RefSeq and GenBank sequence records spanning 1,078,183 bp (1.08 Mb) —comprising 72 complete mitogenomes (1,053,261 bp), 56 profile-anchored 450 bp (150-codon) in-frame COX1 barcode alignments, 15 nuclear coding orthologs ( EF-1α , CAD , CYP6B1 / CYP6B4 ; 20,330 bp), and 16 fossil calibrations ( B = 500 RuNIE replicates)—we resolve the 298.6 Ma Permo-Carboniferous–Cenozoic radiation of Lepidoptera and map the empirical diagnostic boundary between species-level COX1 DNA barcoding and deep-node phylogenomics. While COX1 resolves sister species below 35 Ma ( Ostrinia nubilalis vs. O. furnacalis d K2P = 0.0045; Bombyx mori vs. B. mandarina d K2P = 0.0181, Ti/Tv = 8.00; Papilio machaon vs. P. xuthus d K2P = 0.0651; 2nd-codon H pos2 = 0.1575 bits vs. 3rd-codon H pos3 = 1.1371 bits), 3rd-codon AT bias (82.90% core AT3, RCFV = 0.2845) and transition saturation (Ti/Tv = 0.41–0.73) collapse unpartitioned trees above 85 Ma—a boundary rescued by nuclear coding orthologs, Dayhoff-6 recoding, and Dual-Pass Blinded screening. A 72-taxon, 1,078,183 bp (1.08 Mb across 92 NCBI RefSeq/GenBank sequence records) Dual-Pass Blinded synthesis uniting complete mitogenomes, 450 bp profile-anchored COX1 barcodes, nuclear EF-1a/CAD/CYP6B1 coding orthologs, and 16 fossil calibrations (B = 500 RuNIE replicates) resolves the 298.6 Ma radiation of Lepidoptera and maps the 0–35 Ma COX1 species barcode window against >85 Ma AT3 saturation. Canonical Preprint URL: https://crvscience.com/labs/preprints/lepidoptera-ditrysia-timetree-cox1-gap-preprint Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs