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Late Pleistocene and Early Holocene Archeological Sites and Hunter-Gatherer mtDNA Haplogroups

(A) Pre-LGM dispersal of non-African populations, carrying both M and N lineages (hgs R, U, U5, and U2′3′4′7′8′9 belong to the N clade, distinct from the M clade).

(B) Post-LGM re-expansion in Europe while ice sheets retracted.

(C) Late Glacial shift in mtDNA hg frequency.

(D) Holocene hunter-gatherer mtDNA, mainly belonging to hg U5.


How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [1, 2]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [3, 4, 5]; and (2) multiple dispersal, i.e., additional earlier population expansions that may have contributed to the genetic diversity of some present-day humans outside of Africa [6, 7, 8, 9]. Many variants of these models focus largely on Asia and Australasia, neglecting human dispersal into Europe, thus explaining only a subset of the entire colonization process outside of Africa [3, 4, 5, 8, 9].


The genetic diversity of the first modern humans who spread into Europe during the Late Pleistocene and the impact of subsequent climatic events on their demography are largely unknown. Here we analyze 55 complete human mitochondrial genomes (mtDNAs) of hunter-gatherers spanning ∼35,000 years of European prehistory. We unexpectedly find mtDNA lineage M in individuals prior to the Last Glacial Maximum (LGM). This lineage is absent in contemporary Europeans, although it is found at high frequency in modern Asians, Australasians, and Native Americans. Dating the most recent common ancestor of each of the modern non-African mtDNA clades reveals their single, late, and rapid dispersal less than 55,000 years ago. Demographic modeling not only indicates an LGM genetic bottleneck, but also provides surprising evidence of a major population turnover in Europe around 14,500 years ago during the Late Glacial, a period of climatic instability at the end of the Pleistocene.


Results and Discussion

Genetic studies of human mitochondrial DNA (mtDNA) show that all present-day non-Africans belong to two basal mtDNA haplogroups (hgs), M and N [10]. The time to the most recent common ancestor (TMRCA) of each of these two clades has been estimated independently at around 50,000 years ago (50 ka) (95% confidence interval [CI], 53–46 ka) and 59 ka (95% CI, 64–54 ka), respectively [11]. However, whereas present-day Asians, Australasians, and Native Americans carry both M and N mtDNA hgs, modern individuals with European ancestry lack almost completely lineages of the M clade [12]. The different spatial distributions and TMRCA estimates of these two ancestral clades have been interpreted as evidence of an early spread of modern humans carrying hg M into Asia, perhaps via a southern route, followed by a later non-African diffusion of the N clade, perhaps via a northern route [7]. However, an alternative model proposes a rapid and single dispersal across Eurasia, with Asia being reached first, whereas Western Eurasia would have been settled only after a hiatus, during which hg M was lost [4].

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