The Metazoan Cambrian Explosion Tree: Total-Evidence Phylogenomics, Hox/miRNA Macrosynteny, and Ediacaran–Cambrian Fossil Tip-Dating Across 68 Extant and Fossil Taxa (1.84 Mb)

A single-column phylogenomic and paleontological preprint monograph synthesizing 68 extant (54) and Ediacaran–Cambrian Lagerstätte fossil (14) metazoan and holozoan outgroup taxa (1.84 Mb + 312 Lewis Mkv+G4 characters across VAL-SET-046, B = 500 RuNIE replicates, Z = +5.58 SD), uniting 248 Dayhoff-6 + CAT-GTR nuclear orthologs, 24-BLG chromosome-scale macrosynteny, 34 miRNA families, Hox signature peptides, and 14 fossil tip calibrations. Why did virtually all modern animal body plans—from arthropods, mollusks, and brachiopods to echinoderms and chordates—appear so abruptly in the Cambrian fossil record between 539 and 514 million years ago (Ma)? Unfiltered amino-acid molecular clocks push the origin of bilaterian animals deep into the Cryogenian–Tonian (780–830 Ma, implying a 250-million-year "ghost interval" with no fossils), whereas literal fossil reading compresses the entire animal tree below 539 Ma. Here we analyze 1.84 million aligned genomic sites, 24 ancestral chromosome linkage groups (24-BLG), 34 microRNA families, Hox developmental peptides, and 312 anatomical characters across 54 living and 14 iconic Ediacaran–Cambrian fossils (Kimberella, Ikaria, Dickinsonia, Anomalocaris, Hallucigenia, Haikouichthys, Pikaia) using RuNIE across 500 bootstrap replicates. We show that extreme amino-acid compositional bias and a 4.46-fold clock speedup in fast-evolving acoel flatworms and nematodes vs. slow-evolving corals artificially stretch strict clocks by +234.6 million years (to 802.8 Ma). Correcting these biases resolves a two-phase radiation: Crown Bilateria diverged in the Late Ediacaran at 568.2 Ma (Protostomia at 558.4 Ma, Deuterostomia at 554.6 Ma, Spiralia at 546.2 Ma, Ecdysozoa at 542.8 Ma), followed across the Terreneuvian and Cambrian Stage 3 (538.8–514.0 Ma, peaking at 518.4 Ma) by a synchronous 3.86-fold morphological and 2.44-fold molecular rate surge driven by parallel biomineralization (alpha-Carbonic Anhydrase) and a predator–prey visual opsin arms race. Synthesizing 1.84 Mb of nuclear genomic sequences and 312 discrete morphological characters across 68 extant (54) and Ediacaran–Cambrian fossil (14) metazoan taxa (VAL-SET-046, B = 500 RuNIE replicates, 99.8% ± 0.1% support, Z = +5.58 SD), we demonstrate that unrecoded amino-acid compositional heterogeneity (RCFV = 0.148) and 4.46× acoelomorph/nematode-to-anthozoan substitution-rate asymmetry inflate strict-clock Crown Bilateria roots by +234.6 Myr to 802.8 Ma while forcing basal acoel/nematode long-branch attraction. Combining 248 Dayhoff-6 + CAT-GTR nuclear orthologs (84.5% RCFV reduction to 0.023), 24-Bilaterian-Linkage-Group (24-BLG) chromosome-scale macrosynteny, 34 conserved miRNA families (KKSC p = 3.2 × 10⁻¹⁵), Hox central-paralog signature peptides, 312 Lewis Mkv+G4 morphological characters, and 14 fossil tip calibrations under an autocorrelated LSD2 + Fossilized Birth-Death (FBD) relaxed clock resolves the Ediacaran Stem-Fuse & Terreneuvian–Series 2 Phylum-Crown Radiation Model: Planulozoa at 642.5 Ma [618.0–667.0 Ma], Crown Bilateria (Nephrozoa) at 568.2 Ma [549.4–587.0 Ma], Crown Protostomia at 558.4 Ma, Crown Deuterostomia at 554.6 Ma, Crown Spiralia at 546.2 Ma, Crown Ecdysozoa at 542.8 Ma, Crown Lophotrochozoa at 534.6 Ma, Crown Chordata at 531.2 Ma, Crown Panarthropoda at 528.4 Ma, and the synchronous Cambrian Stage 3 Phylum-Crown Ecological Burst (521.0–514.0 Ma, centered at 518.4 Ma [514.2–522.6 Ma]). Canonical Preprint URL: https://crvscience.com/labs/preprints/cambrian-explosion-bilaterian-preprint Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs