Population expansion in the North African Late Pleistocene signalled by mitochondrial DNA haplogroup U6

Background: The archaeology of North Africa remains enigmatic, with questions of population continuity versus
discontinuity taking centre-stage. Debates have focused on population transitions between the bearers of the
Middle Palaeolithic Aterian industry and the later Upper Palaeolithic populations of the Maghreb, as well as
between the late Pleistocene and Holocene.
Results: Improved resolution of the mitochondrial DNA (mtDNA) haplogroup U6 phylogeny, by the screening of
39 new complete sequences, has enabled us to infer a signal of moderate population expansion using Bayesian
coalescent methods. To ascertain the time for this expansion, we applied both a mutation rate accounting for
purifying selection and one with an internal calibration based on four approximate archaeological dates: the
settlement of the Canary Islands, the settlement of Sardinia and its internal population re-expansion, and the split
between haplogroups U5 and U6 around the time of the first modern human settlement of the Near East.
Conclusions: A Bayesian skyline plot placed the main expansion in the time frame of the Late Pleistocene, around
20 ka, and spatial smoothing techniques suggested that the most probable geographic region for this
demographic event was to the west of North Africa. A comparison with U6’s European sister clade, U5, revealed a
stronger population expansion at around this time in Europe. Also in contrast with U5, a weak signal of a recent
population expansion in the last 5,000 years was observed in North Africa, pointing to a moderate impact of the
late Neolithic on the local population size of the southern Mediterranean coast.