From Jurassic Paravian Theropods to the K–Pg Neoaves Radiation: Time-Tree Chronograms (246.5 to 0.0 Ma) Across 62 Dinosaurian and Avian Taxa

A single-column phylogenomic and paleontological preprint monograph synthesizing 62 extant, Holocene ancient-DNA, and Mesozoic/Paleogene fossil archosaurian, theropod, and avian taxa (1.54 Mb across VAL-SET-042, B = 500 RuNIE replicates, Z = +5.62 SD), resolving the Avian "Rocks vs. Clocks" discrepancy via Constrained Least-Squares Dating (LSD2), autocorrelated relaxed clocks, and microchromosomal GC3/NUMT filtering. For over two decades, avian macroevolution has been divided by a 35-to-45-million-year discrepancy between strict molecular clocks—which place the radiation of modern birds (Neoaves) deep in the Early Cretaceous (100–115 Ma)—and the paleontological record, where crown neoavian fossils appear abruptly after the 66.0 Ma Cretaceous–Paleogene (K–Pg) boundary. Here we synthesize 1,540,000 aligned sites (1.54 Mb) across 62 extant, Holocene ancient-DNA, and Mesozoic/Paleogene fossil archosaurian and avian taxa using RuNIE (Rust Native Inference Engine), Constrained Least-Squares Dating (LSD2), autocorrelated log-normal relaxed clocks, and dual-pass blinded compositional filtering across B = 500 bootstrap replicates. Excising GC3-saturated microchromosomal coding exons (GC3 = 86.4%) and a chromosome 2 nuclear mitochondrial pseudogene (NC_052533.1) while modeling the 2.84-fold post-Chicxulub substitution-rate surge places Paraves at 162.50 Ma, Crown Aves at 89.40 Ma, and Crown Neoaves at 66.80 Ma [95% CI: 65.40–68.20 Ma]—bringing genomic time-trees into direct quantitative concordance with the fossil record. A 62-taxon, 1.54 Mb time-calibrated phylogenomic synthesis from Crown Archosauria (246.5 Ma) and Jurassic Paraves (†Anchiornis 160 Ma, †Archaeopteryx 150 Ma) to Crown Aves (89.4 Ma) and Neoaves (66.8 Ma) evaluated across B = 500 RuNIE bootstrap replicates (99.4% ± 0.3% stability, Z = +5.62 SD). Filtering GC3-saturated microchromosomal exons (GC3 = 86.4%) and a Gallus chromosome 2 NUMT (NC_052533.1) while modeling the 2.84-fold K–Pg substitution-rate spike reconciles molecular clocks with the Maastrichtian–Paleocene fossil record (†Asteriornis 66.7 Ma, †Vegavis 66.5 Ma, †Waimanu 61.0 Ma). Canonical Preprint URL: https://crvscience.com/labs/preprints/theropoda-crown-aves-preprint Zenodo DOI: 10.5281/zenodo.23971261 Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs