New paper on mtDNA U6

With focus on chronology and what I think it is a quite interesting analysis of this matter: they calibrate on archaeological grounds, with several anchor points, what is a clear advance in comparison with the "chopper industry" methods used so far.

Luisa Pereira et al., Population expansion in the North African Late Pleistocene signalled by mitochondrial DNA haplogroup U6. BMC Evolutionary Biology 2010. Open access.

Frequency of U6: A - sample sites, B - U6 C - U6a, D- U6b

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.

An intriguing element is that the chronology of the exclusively Canarian (Guanche) lineage U6b1 seems quite older than the (sketchy) evidence for colonization of the islands, suggesting that either this colonization was older than we know from archaeology or that the lineage coalesced first in mainland North Africa, where it has vanished since then (or is yet to be found). This paper suggests 4.8 Ka (2800 BCE) while the archaeological record only reaches to the 6th century BCE.

The chronology for a greater expansion c. 20 Ka ago is consistent with the main Upper Paleolithic culture of the area, the Oranian (or Iberomaurusian) culture, which has oldest dates in the NW of the region and, as I have argued elsewhere, is also responsible for the expansion of haplogroups H and V, which surely joined the genetic pool of North Africans because of Iberian influence (Graveto-Solutrean).

This is not however the estimated age of U6 overall, which is estimated in 33.5 Ka, roughly consistent with previous estimates (34-36 Ka).

The authors reject the theory of Maca-Meyer by which U6a would have expanded from East Africa (the Nile) westwards:

The case for the postulated “U6a1” movement from East Africa back to the Maghreb advanced by Maca-Meyer et al. [20] is not favoured by our inferredphylogeny, as the 16189 transition does not identify non-monophyletic groups. Indeed, the only sub-clade which seems to have a preferred distribution in East Africa (three individuals from Ethiopia) falls within U6a2, with only coding-region diagnostic mutations at positions 6359 and 11204 (dating to 13.4 ± 4.0 ka).

An interesting paragraph, which I'd like to discuss is the following one (from the conclusions section):

The recently revised archaeological dates for the Aterian industry of North Africa emphasize that the makers of this industry do not appear to have left any imprint in the maternal lineages of present-day North Africans. The oldest arrivals amongst extant mtDNAs appear to be the U6 and M1 lineages, which date to 36.6 (24.9; 48.8) and 25.4 (17.9; 33.1) ka respectively [31]. As with U5 in Europe [11], the arrival time could be older in each case, since the haplogroups appear likely to have arisen within the southern Mediterranean region from haplogroup U and M ancestors, making dating the arrival time very imprecise. Nevertheless, the estimates seem to match best the appearance of the Upper Palaeolithic Dabban industry in Cyrenaïca, as suggested before [15,23].

I do agree that the antecessor of U6 (and maybe also M1) arrived in North Africa most likely with the Dabban industry and that the chronology estimates confirm that (roughly). However I disagree when they claim that Aterian industry left no genetic legacy. This claim is unfounded because they ignore the L(xM,N) lineages which make up some 25% of North African mtDNA and at least in many cases must be from a time frame older than the Dabban industry, as I discussed in my old blog.

Another substantial disagreement I have is when they claim that:

Aside from U6, North Africa was also the recipient of European, Near Eastern and sub-Saharan African lineages most of which most likely arrived in the Holocene. Haplogroups H1, H3 and V expanded in Iberia in the Lateglacial/postglacial [11,58-61], and evidently spread into North Africa from Iberia across the Gibraltar Straits, most likely in the early Holocene [62-65].

This comes from a calibration error, arbitrarily deciding that H1, H3, V and others (H4, H7) as having expanded only after the Last Glacial Maximum. In turn this stems from a fundamental misunderstanding of what archaeologically makes sense: that the only moment of clear contact between SW Europe and North Africa is at the genesis of Oranian culture, which shows clear influence from the peculiar Iberian Gravetto-Solutrean complex (and in turn Iberian Gravetto-Solutrean later shows influence from North African fashions, notably the back-tipped arrow or spear points). While there is lesser connection between Iberia and some scattered coastal spots of North Africa in the early Holocene (Neolithic) with the Cardium Pottery culture this cannot justify almost 30% of the North African mtDNA. There is a more important later "Iberian" influence in North Africa with the Megalithism, however it is hard to explain why these very late hypothetical colonists contributed so much in the maternal genetic pool and so little in the paternal one, not to mention that non-Megalithic Guanches (Canary Island natives) also show more (fossil) Y-DNA R1b and I (17%) than modern mainland North Africans (discussed here).

The reality of this situation will be better understood when DNA chronologists accept that the timeline of mtDNA H (and V) is older than usually accepted and comparable to that of U, if not even older. In any case my calibration point for these lineages (H1, H3, H4, H7 and V) is precisely the unique trans-Mediterranean connection episode that happened almost without doubt at the genesis of Oranian culture. It is the only safe calibration point, what means that these lineages were formed and consolidated in SW Europe prior to that expansion into North Africa, so they must be at least of Gravettian time-frame (which is c. 22 Ka for Mediterranean Iberia), because Solutrean proper had a very limited presence in this area (two nearby caves in Valencia), even if it gradually modified the strong Gravettian substrate (and was modified by it).