Algerian Y chromosomes and mtDNA

Algerian Y chromosomes and mtDNA

From the paper:

For the R-M343 subdivision, the Iberian Peninsula reflects a genuine European profile [45] except for the presence of one Sahel R-V88 type. In contrast, all R-M343 detected in W. Saharan-Mauritanian belong to sub-group R-V88, reaching a frequency of 7%, similar to those observed in other Sahel samples [40]. In the Maghreb countries, the frequency of R-V88 drops to around 1%. On the other hand, the presence in this area of representatives of the European sub-groups R-M412, R-S116, R-U152 and R-M529 points to North-South maritime contacts across the Mediterranean

It would be interesting to estimate the depth of common ancestry of the North African "European" Y chromosomes to determine the epoch during which they arrived there, i.e., whether the common ancestry stems from recent historical contacts (Roman Empire, Vandals, etc.) or from the early settlement of both Mediterranean coasts during the arrival of R-M269 into Europe.

A few observations on Y-haplogroup frequencies:

• The ubuquity of haplogroup Q at trace frequencies in most regions except North Africa (only a little in ALG) is interesting and it's high time that someone looked at the relationship between West Eurasian Q-bearers and their much more numerous East Eurasian cousins.
• I find the paucity of Y-haplogroup I in North Africa noteworthy; given its high levels in most of Western Europe, its relative absence might indicate that the people who brought "European" R-M269 into N Africa were not occasional recent migrants, but rather earlier settlers. 
• The relative absence of J2 is expected, given that neither of the two main strata of population ("Berber" and "Arab") may have possessed it initially; it has also not been found in a historical sample from the Canary Islands, whereas its J1 counterpart has.
• The paucity of haplogroup G, which is the European Neolithic lineage par excellence probably argues against the involvement of the people who colonized Europe during the Early Neolithic in similar events on the south shore of the Mediterranean.
• The further study of F chromosomes could also be further attempted, given their possible involvement in the Upper Paleolithic of Eurasia

The authors highlight that 80% of mtDNA is Eurasian vs. 90% of Y chromosomes. This might point to asymmetric gene flow from Sub-Saharan Africa. Alternatively, it might point to some mtDNA that is characterized as non-Eurasian (because it does not belong to the M, N macro-haplogroups) being in fact so. It is a persistent question whether lineages that have a wide frequency differential in two regions do so because of gene flow (from the high- to low-frequency area), or because of other processes.

PLoS ONE 8(2): e56775. doi:10.1371/journal.pone.0056775

Introducing the Algerian Mitochondrial DNA and Y-Chromosome Profiles into the North African Landscape

Asmahan Bekada et al.

North Africa is considered a distinct geographic and ethnic entity within Africa. Although modern humans originated in this Continent, studies of mitochondrial DNA (mtDNA) and Y-chromosome genealogical markers provide evidence that the North African gene pool has been shaped by the back-migration of several Eurasian lineages in Paleolithic and Neolithic times. More recent influences from sub-Saharan Africa and Mediterranean Europe are also evident. The presence of East-West and North-South haplogroup frequency gradients strongly reinforces the genetic complexity of this region. However, this genetic scenario is beset with a notable gap, which is the lack of consistent information for Algeria, the largest country in the Maghreb. To fill this gap, we analyzed a sample of 240 unrelated subjects from a northwest Algeria cosmopolitan population using mtDNA sequences and Y-chromosome biallelic polymorphisms, focusing on the fine dissection of haplogroups E and R, which are the most prevalent in North Africa and Europe respectively. The Eurasian component in Algeria reached 80% for mtDNA and 90% for Y-chromosome. However, within them, the North African genetic component for mtDNA (U6 and M1; 20%) is significantly smaller than the paternal (E-M81 and E-V65; 70%). The unexpected presence of the European-derived Y-chromosome lineages R-M412, R-S116, R-U152 and R-M529 in Algeria and the rest of the Maghreb could be the counterparts of the mtDNA H1, H3 and V subgroups, pointing to direct maritime contacts between the European and North African sides of the western Mediterranean. Female influx of sub-Saharan Africans into Algeria (20%) is also significantly greater than the male (10%). In spite of these sexual asymmetries, the Algerian uniparental profiles faithfully correlate between each other and with the geography.

Link

Disentangling the histories of mtDNA haplogroups M1 and U6

Disentangling the histories of mtDNA haplogroups M1 and U6

mtDNA haplogroups M1 and U6 are often mentioned in terms of Eurasian back-migration in Africa. The former is the only clade of the Asian haplogroup M which occurs in Africa at all; the latter is the only clade of the West Eurasian haplogroup U that does the same. These haplogroups also tend to co-exist in North and East Africa, although they are largely absent in sub-Saharan Africa. Different ideas have been offered for their occurrence, including a "Paleolithic" spread or a more recent one associated with the spread of Afroasiatic languages.

The new paper offers useful new data on this debate. The most important conclusion is that despite their oft-mentioned association, these two haplogroups appear to have distinct histories. One argument for this is their separate geographic distribution:

M1 (on panel A) is much more common in Northeast Africa and the Near East (including the Caucasus), whereas U6 (panel B) is more confined in Africa, and has its stronger peak in NW Africa, being rare in NE Africa.

An interesting aside, is that all the mysterious M1 from the Caucasus belongs to subclade M1a, while the smaller M1b clade tends to co-occur with M1a in other parts of Africa and the Near East. This indicates a founder effect for the origin of Caucasian M1a, but leaves open the issue of the immediate origins of M1. Hopefully it will become possible to place this haplogroup within the broader M phylogeny in the future.

The Bayesian skyline plots also contrast M1 and U6 in terms of their demographic histories:

The authors argue that these histories are inconsistent with either a very early dispersal history with the Dabban industry, as well as a more recent spread with Afroasiatic. From the paper:

The transition from the Middle Palaeolithic to Upper Palaeolithic in North Africa is characterised by the appearance of the “Dabban”, an industry that is restricted to Cyrenaica in northeast Libya and represented at the caves of Hagfet ed Dabba and Haua Fteah [19]. Whilst a techno-typological shift occurred within the Dabban ~33 KYA [19], starker changes in the archaeological record occurred throughout North Africa and Southwest Asia ~23-20 KYA, represented by the widespread appearance of backed bladelet technologies. The appearance of these backed bladelet industries more or less coincides with the timing of the Last Glacial Maximum (LGM) (~23-18 KYA), including: ~21 KYA in Upper Egypt [20]; ~20 KYA at Haua Fteah with the Oranian [21]; the Iberomaurusian expansion in the Jebel Gharbi ~20 KYA [22]; and the first Iberomaurusian at Tamar Hat in Algeria ~20 KYA [23]. The earliest Iberomaurusian sites in Morocco appear to be only slightly younger ~18 KYA [24].

A disassociation of these haplogroups from the UP in North Africa might be consistent with my idea that the UP was in part a cultural revolution that spread not only with people, but often with ideas across a species that already had the "biological machinery" for behavioral modernity and was already established in both Africa and the Near East.

As for the connection to Afroasiatic, the authors detect a linguistic correlation with M1a, which, however, appears too old to have been involved directly in the spread of this language family:

Concerning haplogroup M1 individually, a significant correlation with languages was observed. Furthermore, within M1, it appears that the correlation is mostly due to M1a. However, given the small sample size of M1b, any potential signal correlating with language might not be detectable. Interestingly, M1a has a likely East African origin, but its coalescent age of ~21 KYA still largely predates that of the proto-AA. Maybe a sub-clade of M1a would still give a similar correlation, but there are not sufficient samples to allow splitting M1a into its various sub-clades, and to test for a correlation. Although we found a correlation, limited sample sizes do not allow drawing unambiguous connection between genes and languages. Furthermore, it is also possible that this putative sub-clade of M1 does not testify for the expansion of AA speaking people, but was already present among the people who inhabited the area before the spread of the AA languages.

Personally, I am in favor of an East African origin of Afroasiatic, as this makes sense of various lines of evidence, one of which is the African shift of the "Southwest_Asian" component that is modal in Semitic populations. I envision that M1 was geographically circumscribed in a NE African population after its much earlier arrival from Asia and piggy-backed onto the expansion of Afroasiatic speakers, thus explaining the observed correlation. A good analogy would be with the expansion of, say, haplogroup H in the Americas which piggybacked on the European colonization, even though the coalescence age of H predates the arrival of Europeans in the New World by many millennia.

BMC Evolutionary Biology 2012, 12:234 doi:10.1186/1471-2148-12-234


Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa

Erwan Pennarun et al.

Abstract (provisional)
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.

Link