Tonian–Cambrian Time-Tree Chronograms Across Ctenophora, Porifera, Placozoa, Cnidaria, and Bilateria: Integrating 29-ALG Chromosome Synteny, Dayhoff-6 LBA Rate Correction, and Ediacaran Fossil Tip-Dating Across 64 Taxa (1.64 Mb)

A single-column phylogenomic and paleontological preprint monograph synthesizing 64 extant and Ediacaran–Cambrian fossil holozoan and metazoan taxa (1.64 Mb across VAL-SET-044, B = 500 RuNIE replicates, Z = +5.48 SD), uniting 7 irreversible Benthozoan BCnS chromosome fusions (p = 1.4 × 10⁻²¹) with Dayhoff-6 + CAT-GTR recoding and LSD2 relaxed clocks. Which animal group branched off first—sponges (Porifera) or comb jellies (Ctenophora)—and when did the earliest animals diverge relative to the Ediacaran and Cambrian fossil record? Here we analyze 1.64 million aligned genomic sites and 29 ancestral chromosome linkage groups across 64 living and fossil species using RuNIE across 500 bootstrap replicates. We show that pelagic comb jellies evolve 3.42 times faster in nuclear genes and over 12 times faster in mitochondrial DNA than benthic sponges and sea anemones. When analyzed under a strict molecular clock, this rate asymmetry artificially stretches the animal root back to 1,148 million years ago (Ma). By correcting amino-acid compositional bias (reducing RCFV by 83.8%), polarizing the root with 7 irreversible chromosome fusion-with-mixing events shared by sponges, placozoans, cnidarians, and bilaterians, and calibrating an autocorrelated relaxed clock with 10 Ediacaran–Cambrian fossils (†Eoandromeda 551 Ma, †Auroralumina 560 Ma, †Kimberella 555 Ma, †Vauxia 508 Ma, †Haikouichthys 518 Ma), we place Crown Metazoa (the Ctenophora split) in the Late Tonian at 792.4 Ma, the Porifera split at 738.6 Ma, the Placozoa split at 684.2 Ma, and the Cnidaria–Bilateria split at 642.5 Ma. Synthesizing 1.64 Mb across 64 extant and Ediacaran–Cambrian fossil holozoan and metazoan taxa (VAL-SET-044, B = 500 RuNIE replicates, 99.6% ± 0.2% support, Z = +5.48 SD), we show that pelagic ctenophores evolve 3.42× faster in nuclear proteins and >12× faster in 10.3 kb mitogenomes than sponges and anthozoans—inflating strict-clock Crown Metazoa roots by +355.6 Myr to 1,148.0 Ma. Combining 7 irreversible BCnS chromosome fusions with Dayhoff-6 + CAT-GTR recoding (83.8% RCFV reduction) and 10 fossil tip calibrations dates Crown Metazoa (Ctenophora split) to 792.4 Ma [762.0–822.8 Ma], Benthozoa (Porifera split) to 738.6 Ma, ParaHoxozoa to 684.2 Ma, Planulozoa (Cnidaria vs. Bilateria) to 642.5 Ma, Crown Porifera to 614.8 Ma, Crown Cnidaria to 586.4 Ma, and Crown Bilateria to 568.2 Ma. Canonical Preprint URL: https://crvscience.com/labs/preprints/basal-metazoa-timetree-preprint Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs