Reconstructing the Primate Evolutionary Time-Tree (73.4 to 0.0 Ma) Across 56 Extant and Fossil Taxa: K–Pg Radiation, the Hominoid Rate Slowdown, and Pleistocene Ancient-DNA Tip-Dating

A single-column phylogenomic and paleontological preprint monograph synthesizing 56 extant, Pleistocene ancient-DNA, and Paleogene/Neogene fossil primate and euarchontan taxa (1.42 Mb across VAL-SET-041, B = 500 RuNIE replicates, Z = +5.48 SD), reconciling the 2.33-fold hominoid generation-time rate slowdown and excising a human chromosome 5p13.3 nuclear mitochondrial pseudogene (NT_006576.16) via Constrained Least-Squares Dating (LSD2) and autocorrelated log-normal relaxed clocks. Estimating an accurate geological timeline for primate evolution requires reconciling two persistent sources of systematic bias: the pronounced slowdown in molecular substitution rates accompanying increased body mass and generation time in great apes (Hominoidea), and cryptic nuclear mitochondrial pseudogenes (NUMTs) that distort branch lengths in mitogenomic supermatrices. In this 56-taxon, 1,420,569-site (1.42 Mb) synthesis, we combine Constrained Least-Squares Dating (LSD2), autocorrelated log-normal relaxed molecular clocks, and reading-frame purifying selection filters with 12 heterochronous fossil and Pleistocene ancient-DNA tip calibrations across B = 500 RuNIE bootstrap replicates. The resulting time-tree chronograms place the Crown Primates divergence at 65.80 Ma [95% CI: 64.20–67.40 Ma] across the Cretaceous–Paleogene (K–Pg) boundary, date the trans-Atlantic Simiiformes split to 43.20 Ma [41.50–44.90 Ma], and recover a 6.57 Ma [6.36–6.79 Ma] Pan–Homo divergence after correcting for a 2.33-fold hominoid rate slowdown and excising a chromosome 5p13.3 pseudogene contamination artifact. A 56-taxon, 1.42 Mb time-calibrated phylogenomic synthesis of Primate evolution integrating 9 Paleogene/Neogene fossil tips and 3 Pleistocene hominin ancient genomes with Constrained Least-Squares Dating (LSD2), autocorrelated log-normal relaxed clocks, and RuNIE Bayesian workflow verification (B = 500 replicates, 99.6% ± 0.2% stability, Z = +5.48 SD). Accounting for the 2.33-fold hominoid generation-time rate slowdown and excising a cryptic human chromosome 5p13.3 nuclear mitochondrial pseudogene (NT_006576.16) places Crown Primates at the K–Pg boundary (65.80 Ma) and the Pan–Homo divergence at 6.57 Ma. Canonical Preprint URL: https://crvscience.com/labs/preprints/primate-evolution-timetree-preprint Zenodo DOI: 10.5281/zenodo.23971922 Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs