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

Abstract

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.

Figure 1

Interpolation maps for U6 haplogroup. (A) Map representing the centroids of sampling locations used for the spatial smoothing analyses of haplogroup frequencies (based on HV-I data sets). The resulting frequency maps are shown for U6 (B), U6a (C) and U6bd (D).

Figure 2

BSPs of median effective population size through time for U6 (A) and U5 (B), using the internal calibration of mutation rate. The black line represents the posterior effective population size through time. The blue region is the 95% highest posterior density interval for effective population size at any time point. Effective population size is plotted on a log scale. A generation time of 25 years was assumed.