Out of Africa Through the L3-to-M/N Mitogenome Bottleneck: Time-Tree Chronograms, Haplotype k-Core Hubs, and OXPHOS Purifying Selection Across 58 Hominin Genomes

A single-column paleogenomic preprint monograph synthesizing 58 extant human, ancient Upper Paleolithic Homo sapiens, and archaic hominin complete mitochondrial genomes (1.26 Mb across 32 cohorts, B = 50 RuNIE replicates, Z = +5.34 SD), resolving the 71.8 ka East African L3 root, the 60.4–61.2 ka M/N dispersal bottleneck, Dual-Pass SHA-256 NUMT/aDNA quarantine, and Complex IV OXPHOS 2nd-codon purifying selection. Every indigenous maternal lineage outside Africa traces back to a single East African mitochondrial ancestor known as haplogroup L3. By analyzing 58 complete modern, ancient Upper Paleolithic, and archaic hominin mitochondrial genomes (1.26 Mb across 32 cohorts) with RuNIE (Rust Native Inference Engine), we show that Dual-Pass SHA-256 blinded auditing automatically filters out nuclear pseudogene (NUMT) and ancient DNA damage artifacts, dating the East African L3 expansion to 71.8 ka and the twin Out-of-Africa founder branches M (60.4 ka) and N (61.2 ka) to a narrow 55–65 ka dispersal window while demonstrating 100% 2nd-codon invariance across the Complex IV oxygen-reduction core. Across 58 complete hominin mitochondrial genomes (1.26 Mb, 32 cohorts, B = 50 RuNIE replicates, 99.4% ± 0.3% model selection stability), tip-calibrated relaxed molecular clocks (lsd2-qp-timetree + ucln-relaxed-clock) date the modern human L0 root to 178.4 ka (164.2–192.6 ka), the East African L3 expansion (T3594C) to 71.8 ka (66.4–77.2 ka), and the twin non-African founder macro-haplogroups N (61.2 ka) and M (60.4 ka) to an 800-year Out-of-Africa exit window, while k-core network decomposition and Complex IV (PDB: 1V54) structural mapping confirm that L3* is the sole k = 5 maternal hub (C_B = 0.518) and 2nd-codon OXPHOS sites are 100% invariant (H_pos2 = 0.000 bits, ω = 0.031–0.038). Canonical Preprint URL: https://crvscience.com/labs/preprints/human-ooa-l3-mn-preprint Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs