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

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

Across 83 NCBI RefSeq/GenBank sequence records totaling 954,595 bp raw (1,260,480 bp aligned total-evidence supermatrix across 58 extant human, Upper Paleolithic ancient Homo sapiens, Middle/Late Pleistocene archaic hominin, and Hominidae outgroup genomes: 35 complete mitochondrial genomes, 35 in-frame COX1 + D-Loop profiles, and 48 nuclear OXPHOS coding mRNAs; B = 500 RuNIE replicates), our hybrid RuNIE + ModelTest (BIC/AICc/RCFV) + *MAFFT-L-INS-i + *IQ-TREE2-Partitioned-HKY/LG + *LSD2/*MCMCTree synthesis excises the human chromosome 5p13.3 NUMT paralog (NT_006576.16, D_ctx = 6.45 SD), partitions the 13 OXPHOS genes from the hypermutable D-loop (HVS-I/II), dates the Sima-Denisova archaic split to 770.0 ka, the Modern-Neanderthal split to 460.0 ka, the Modern Human L0 MRCA to 178.4 ka, the East African L3 expansion (T3594C) to 71.8 ka, and the twin Out-of-Africa founder macro-haplogroups N (61.2 ka) and M (60.4 ka) to an 800-year Marine Isotope Stage 4 exit bottleneck while proving 100% 2nd-codon invariance across human COX1 (H_pos2 = 0.0000 bits, Z_pos = +5.68 SD, 5🧪).

Canonical Preprint URL: https://crvscience.com/labs/preprints/human-ooa-l3-mn-preprint
Master (Concept) Zenodo DOI: 10.5281/zenodo.23970546
Open-Source Software Repository (GNU GPL-3.0): https://github.com/bpwhite/crvscience-labs