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Abstract Background A Southwest Asian origin and dispersal to North Africa in the Early Upper Palaeolithic era has been inferred in previous studies for mtDNA haplogroups M1 and U6. Both haplogroups have been proposed to show similar geographic patterns and shared demographic histories. Results We report here 24 M1 and 33 U6 new complete mtDNA sequences that allow us to refine the existing phylogeny of these haplogroups. The resulting phylogenetic information was used to genotype a further 131 M1 and 91 U6 samples to determine the geographic spread of their sub-clades. No southwest Asian specific clades for M1 or U6 were discovered. U6 and M1 frequencies in North Africa, the Middle East and Europe do not follow similar patterns, and their sub-clade divisions do not appear to be compatible with their shared history reaching back to the Early Upper Palaeolithic. The Bayesian Skyline Plots testify to non-overlapping phases of expansion, and the haplogroups’ phylogenies suggest that there are U6 sub-clades that expanded earlier than those in M1. Some M1 and U6 sub-clades could be linked with certain events. For example, U6a1 and M1b, with their coalescent ages of ~20,000–22,000 years ago and earliest inferred expansion in northwest Africa, could coincide with the flourishing of the Iberomaurusian industry, whilst U6b and M1b1 appeared at the time of the Capsian culture. Conclusions Our high-resolution phylogenetic dissection of both haplogroups and coalescent time assessments suggest that the extant main branching pattern of both haplogroups arose and diversified in the mid-later Upper Palaeolithic, with some sub-clades concomitantly with the expansion of the Iberomaurusian industry. Carriers of these maternal lineages have been later absorbed into and diversified further during the spread of Afro-Asiatic languages in North and East Africa.

Abstract: Understanding the timing, conditions, and characteristics of the Middle to Later Stone Age (MSA/LSA) transition in North Africa is critical for debates regarding the evolution and past population dynamics of Homo sapiens, especially their dispersals within, out of, and back into, Africa. As with many cultural transitions during the Palaeolithic, our understanding is based predominantly on archaeological and paleoenvironmental records preserved within a small number of deep cave sediment sequences. To use such sequences as chronological cornerstones we must develop a robust understanding of the formation processes that created them. This paper utilizes geoarchaeological analyses (field observations, sediment micromorphology, bulk sedimentology) to examine site formation processes and stratigraphic integrity during the MSA/LSA at the Haua Fteah cave, Libya, one of North Africa's longest cultural sequences. The depositional processes identified vary in mode and energy, from eolian deposition/reworking to mass colluvial mudflows. These changing processes impact greatly on the interpretation of the paleoenvironmental and archaeological records, not least in identifying potential colluvial sediment deposition and reworking in layers identified as containing the MSA/LSA transition. This study highlights the importance of developing geoarchaeological analyses of cultural sequences to fully unravel the limitations and potential of their contained archaeological and paleoenvironmental records. [ABSTRACT FROM AUTHOR]