Pancrustacea-to-Hexapoda Tree of Life (538.4 to 0.0 Ma): A 3-Way RuNIE Pipeline Comparison (100% Native Rust vs. 100% External Binaries vs. Unconstrained Hybrid Optimal ln L) Resolving Remipedia Sisterhood, Epipodite-to-Wing Homology, and Terrestrial

Controlled 32-chain, 3-way RuNIE pipeline benchmark (100% Native Rust vs. 100% External Reference Binaries vs. Unconstrained Hybrid Optimal ln L) across all 122 downloaded full-length NCBI sequences totaling 1,527,591 bp (1.53 Mb: 100 Panarthropoda mitogenomes = 1,459,606 bp aligned to 69,911 bp in *MAFFT / 180,536 bp in Native Gotoh + 22 nuclear functional loci = 67,985 bp aligned to 10,642 bp) and 16 fossil calibrations Controlled 32-chain, 3-way RuNIE pipeline comparison across all 122 downloaded full-length NCBI records totaling 1,527,591 bp (1.53 Mb: 100 complete mitogenomes = 1,459,606 bp + 22 nuclear functional orthologs = 67,985 bp) demonstrates that on the full-length 69,911 bp *MAFFT mitogenome alignment (+ 10,642 bp nuclear = 80,553 bp), Unconstrained Hybrid RuNIE (ln L = −1,080,085.18 nats on -te [BIC = 2,162,479.44, 1,020.73 s] / −1,070,186.29 nats unconstrained [793.66 s]) beats 100% External Binaries on the exact same unrecoded 69,911 bp alignment (ln L = −1,232,483.61 nats on -te / −1,223,120.89 nats unconstrained, 910.95 s) by +152,398.43 nats, while 100% Native Rust (pancrustacea_3way.exe) aligns all 100 full-length mitogenomes (180,536 bp) in 1.29 s (557.8× faster MSA than *MAFFT 717.77 s) and finishes the full pipeline in 344.61 s (2.96× faster than Hybrid; ln L = −1,471,910.53 nats), uniting Remipedia + Hexapoda (Labiocarida; 478.6 Ma, 100% support) and dating Crown Hexapoda to 442.4 Ma. Canonical Preprint URL: https://crvscience.com/labs/preprints/pancrustacea-hexapoda-3way-preprint Master (Concept) Zenodo DOI: 10.5281/zenodo.24045575 Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs