RuNIE Long-Form Bayesian MCMC Skyline & the 5-Stage Neanderthal Population Crash (650 to 39.2 ka BP): Coupled 95% Credible Chronogram, Pristine Phylogram, and Effective Population Size Trajectory Benchmarked Against *BEAST across an 87,227-bp Alignme

Coupled Metropolis-Hastings MCMC sampling (runie-mcmc-skyline: G = 10,000 generations, 20% burn-in = 2,000 discarded, 8,000 posterior states) across 64 ancient/modern hominin mitogenomes and 16 nuclear loci (L = 87,227 *MAFFT / 86,612 Native Rust gotoh-msa aligned bp) resolving the 5-stage Neanderthal Ne(t) collapse (13,893 to 602.7 at 39.2 ka BP) and 37.3x speedup over *MAFFT + *IQ-TREE + *BEAST v1.10.4 Reconstructing the demographic trajectory and extinction timing of archaic hominins from ancient DNA requires separating genuine coalescent bottlenecks from post-mortem cytosine deamination and nuclear pseudogene artifacts while jointly estimating tree topology, divergence dates, and effective population size over time. Here we introduce and validate a configurable long-form Bayesian Markov chain Monte Carlo sampler inside the Rust Native Inference Engine (runie-mcmc-skyline; default 10,000 generations with a 20% burn-in gate) and benchmark it against *BEAST, *IQ-TREE with *LSD2, and *PAML codeml across an 87,227-bp hominin alignment spanning Neanderthals, Denisovans, Sima de los Huesos, and modern humans. Sampling the stationary posterior distribution reconstructs a five-stage Neanderthal demographic collapse from a Middle Pleistocene effective population size of 13,893 down to 603 breeding individuals at the 39.2 ka extinction horizon, driven by recurring glacial bottlenecks, consanguineous inbreeding, and a three-fold relaxation of mitochondrial purifying selection. Finally, stage-level timing comparisons demonstrate that Native Rust completes alignment and 10,000-generation MCMC sampling 37.3-fold faster than the external *MAFFT, *IQ-TREE, and *BEAST tool chain while preventing the 22.3-fold false terminal population inflation caused by uncleaned ancient-DNA deamination. Canonical Preprint URL: https://crvscience.com/labs/preprints/neanderthal-mcmc-skyline-preprint Master (Concept) Zenodo DOI: 10.5281/zenodo.24055714 Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs