Mezmaiskaya 3 is female Neanderthal from early Eastern Micoquian layer 3. Her mtDNA clusters closest with Mezmaiskaya 1 and Stajnia S5000. These early Neanderthals genetically distant from later European Neanderthals. Population turnover replaced early branches by late NL clade 47-39 ka. Proposed Neanderthal mtDNA haplogroups: NA ancestral, NE early, NM middle Europe-specific, NL late. Mezmaiskaya 3 dated 96.7 kya by mtDNA clock. Shows first mtDNA heteroplasmy in Neanderthal at position 8839. Nuclear data confirms closer to Chagyrskaya 8 (17%) and Vindija (13%) than Altai Neanderthal. NM haplogroup limited to Europe, absent in Asia. Early NA1 clade European, replaced by Asian-derived NA2 descendants. Late Neanderthals spread from Altai to Europe. Fixed Neanderthal 827G variant pathogenic for deafness in humans. NA2 clade shows adaptive selection in ATP6 and ND1 genes. No severe deleterious mtDNA variants explain Neanderthal disappearances. Eastern Micoquian Neanderthals NM2-specific in Caucasus. Replacement began late MIS 5 in northwest Europe, spread to Caucasus by MIS 3.