HST femur yields Neanderthal mtDNA basal to all known Neanderthal lineages. HST mtDNA splits from other Neanderthals 270,000 years ago (316–219 ka). This sets lower bound for African mtDNA introgression into Neanderthals before 270 ka. Early Neanderthals like Sima de los Huesos had Denisovan-like mtDNA replaced by African lineage. Complete mtDNA replacement feasible with minimal introgression over 300 ka if Ne <5,000. Neanderthal mtDNA diversity doubled including HST, exceeding prior estimates. HST pairwise distance to other Neanderthals averages 104 nucleotides, upper range of modern human diversity. Neanderthal effective population size declined through Middle to Late Pleistocene. Late Neanderthal population expanded before extinction. HST dated molecularly to 124 ka (183–62 ka), consistent with forested MIS 5 environment. Valdegoba Neanderthal shares mutations with HST branch, persisting to 48 ka. African introgression reconciles nDNA and mtDNA phylogeny discrepancies. Alternative: HST and Altai lineages arrived independently from Africa before 160 ka. Modern human admixture detected in Altai Neanderthal (0.1–2.1%) post-divergence from other Neanderthals. HST collagen isotopes indicate forested habitat unlike late Neanderthals. Neanderthal-Denisovan split after modern human divergence 765–550 ka. Neanderthal-modern human mtDNA divergence 413 ka (468–360 ka).