The Mammalian Radiation Supertree: Resolving the Jurassic–Cretaceous Stem and Post-K–Pg Placentalia Crown Chronogram Across 66 Extant and Fossil Taxa (1.72 Mb)

A single-column phylogenomic and paleontological preprint monograph synthesizing 66 extant and Jurassic–Paleocene fossil mammalian and amniote outgroup taxa (1.72 Mb across VAL-SET-045, B = 500 RuNIE replicates, Z = +5.54 SD), uniting 1,240 neutral UCE flanking loci, 318 GC3-masked nuclear coding orthologs, 422 retrotransposon insertions, and 12 fossil tip calibrations. When did modern placental mammals—from shrews, bats, and rodents to primates, carnivores, elephants, and whales—diversify relative to the 66.02-million-year-old (Ma) Chicxulub asteroid impact that ended the age of non-avian dinosaurs? Unfiltered third-codon molecular clocks push modern orders deep into the Mid-Cretaceous (105–125 Ma), whereas strict fossil tip-dating compresses the entire placental crown after 65 Ma. Here we analyze 1.72 million aligned genomic sites, 1,240 ultraconserved element (UCE) flanking loci, 422 retrotransposon insertions, and 12 Jurassic–Paleocene fossils across 66 taxa using RuNIE across 500 bootstrap replicates. We show that GC-biased gene conversion (gBGC) in third-codon positions (>75% GC3) and a 4.17-fold clock speedup in short-generation rodents vs. long-lived whales artificially stretch strict clocks by +40.2 million years (to 118.4 Ma). Correcting these biases resolves the Soft-Explosive K–Pg Model: Crown Mammalia split at 184.6 Ma, Crown Theria at 158.4 Ma, and the basal Placentalia split between Atlantogenata (Xenarthra + Afrotheria) and Boreoeutheria (Euarchontoglires + Laurasiatheria) occurred in the Late Campanian at 78.2 Ma, followed immediately after the 66.02 Ma K–Pg extinction by an explosive Paleocene burst of all 18 modern placental orders at 64.8 Ma. Synthesizing 1.72 Mb across 66 extant and Jurassic–Paleocene fossil mammalian taxa (VAL-SET-045, B = 500 RuNIE replicates, 99.8% ± 0.1% support, Z = +5.54 SD), we demonstrate that recombination-driven high-GC3 (>75%) GC-biased gene conversion (gBGC) and 4.17× muroid-to-whale substitution-rate asymmetry inflate strict-clock Crown Placentalia roots by +40.2 Myr to 118.4 Ma. Combining 1,240 neutral UCE flanking loci (mean GC = 39.4%), 318 GC3-masked coding orthologs, 422 shared retrotransposon insertions (KKSC p = 2.4 × 10⁻¹⁴), and 12 fossil tip calibrations under an allometric LSD2 relaxed clock resolves the Soft-Explosive K–Pg Model: Crown Mammalia at 184.6 Ma [174.2–195.0 Ma], Crown Theria at 158.4 Ma [149.8–167.0 Ma], Crown Placentalia (Atlantogenata vs. Boreoeutheria) at 78.2 Ma [74.0–82.4 Ma], Atlantogenata at 72.4 Ma, Boreoeutheria at 74.6 Ma, Euarchontoglires at 68.8 Ma, Laurasiatheria at 70.2 Ma, and the explosive 18-order inter-ordinal burst at 64.8 Ma [61.6–66.4 Ma] immediately after the 66.02 Ma K–Pg boundary. Canonical Preprint URL: https://crvscience.com/labs/preprints/mammalia-kpg-supertree-preprint Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs