Monday, May 19, 2014

The story of mtDNA haplogroup U6

A new paper on the history of the mtDNA haplogroup U6 uses new detailed data of U6 subclades, the location of modern individuals with this mtDNA haplogroup, and ancient DNA data to trace the origins of the current distribution of this genotype.

The paper is Bernard Secher, et al., "The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents", BMC Evolutionary Biology; 2014,14:109 doi:10.1186/1471-2148-14-109.

I summarize the paper's conclusions in detail below.

Arrival In Africa

The mtDNA U6 clade is one of several clades of mtDNA U that expanded out of Central Asia and corresponds archaeologically to the intrusive Levantine Aurignacian around 35 kya.  Parallel haplogroup U5 gaves rise to the Aurignacian in Europe and U2 to a contemporaneous expansion into India. "This period coincides with the Early Upper Paleolithic (EUP) period, prior to the Last Glacial Maximum, but cold and dry enough to force a North African coastal route."  

The authors note that mtDNA clade M1 back migrated to Africa at about the same time, but was probably not a fellow traveler with U6 for very long as it has a very different geographic distribution focused around Northeast Africa and East Africa.  There are several Y-DNA clades that could plausibly have been fellow travelers of U6, but their mutation rate estimated ages are so much younger than the mtDNA clade ages that later male dominated migration and replacement seems to be a better fit for these correlations.

Expansion Within Africa

U6a expanded in Northwest Africa about 9,000 years after the Levatine Aurignacian after a gradual diffusion across the North Africa coast where it expanded from Morocco ca. 26 kya and is associated archaeologically and anthropologically with the Iberomaurusian culture in the  Maghreb.
Others have pointed to the Dabban industry in North Africa and its supposed source in the Levant, the Ahmarian, as the archaeological footprints of U6 coming back to Africa. However, we disagree for several reasons: firstly, they most probably evolved in situ from previous cultures, not being intrusive in their respective areas; second, their chronologies are out of phase with U6 and third, Dabban is a local industry in Cyrenaica not showing the whole coastal expansion of U6. In addition, recent archaeological evidence, based on securely dated layers, also points to the Maghreb as the place with the oldest implantation of the Iberomaurusian culture, which is coincidental with the U6 radiation from this region proposed in this and previous studies. 
The U6a2 branch expanded from Ethiopia around 20kya, corresponding with a maximal period of aridity in North Africa.  This was probably not due to "a return to East Africa across the Sahara."  Instead:
The most probable scenario is that small human groups scattered at a low density throughout the territory, retreated in bad times to more hospitable areas such as the Moroccan Atlas Mountains and the Ethiopian Highlands.
Some investigators have proposed that U6 bearing people left Africa via the Levant ca. 40 kya.  The authors of this paper disagree.
[T]he proposed movement out of Africa through the Levantine corridor around 40 kya did not occur or has no maternal continuity to the present day. This is because: first, in that period the Eurasian haplogroups M and N had already evolved and spread at continental level in Eurasia, and, second, there is no evidence of any L-derived clade outside Africa with a similar coalescence age to that proposed movement. Under this perspective, the late Pleistocene human skull from Hofmeyr, South Africa, considered as a sub-Saharan African predecessor of the Upper Paleolithic Eurasians, should be better considered as the southernmost vestige of the Homo sapiens return to Africa.  
The rest of the human movements inside Africa, such as the Saharan occupation in the humid period by Eastern and Northern immigrations, or the retreat to sub-Saharan African southwards and to the Maghreb northwards in the desiccation period, or even the colonization of the Canary Islands, all faithfully reflect the scenarios deduced from the archaeological and anthropological information. 
The paper catalogs radiations of U6a branches with the Maghreb including two lineages that may spread to Iberia ca. 20 kya (U6a1, U6a1b).  There are no expansions from 17 kya to 13 kya, likely reflecting the lingering effects of the LGM's slow retreat.  There are multiple subsequent clade expansions whose timing largely correspond to inferred population growth and climate trends.
After that, the climate shifted to a humid period in Africa and population growth was reinitiated. In Ethiopia, periodical bursts at around 13 kya (U6a2a1), 9 kya (U6a2b, U6a2a1a) and 6 kya (U6a2a1b) are detectable. 
Basic clusters like U6b, U6c and U6d also emerged within a window between 13 to 10 kya. 
U6b lineages spread from the Maghreb, through the Sahel, to West Africa and the Canary Islands (U6b1a), and are also present from the Sudan to Arabia, but not detected in Ethiopia. 
In contrast, U6c and U6d are more localized in the Maghreb. 
Further spreads of secondary U6a branches are also apparent, going southwards to Sahel countries and reaching West Africa (U6a5a). 
Autochthonous clusters in sub-Saharan Africa first appeared at around 7 kya (U6a5b), coinciding with a period of gradual desiccation that would have obliged pastoralists to abandon many desert areas. Consequently, no more U6 lineages in the Sahel are detected, while later expansions continued in West Africa (U6a3f, U6a3c, and U6b3) and the Maghreb with an additional spread to the Mediterranean shores of Europe involving U6b2, U6a3e, U6a1b and U6a3b1. . . . using only African sequences . . . 
The subdivision of HVI sequences into geographic components shows that the Maghreb component is dominant over all of North Africa, reaching 45.7% even in Arabia. Frequencies drop in Central and West Africa, suggesting a southward spread, and it is absent in East Africa where all haplotypes belong to the Ethiopian U6a2 cluster. This East African lineage is also the most prevalent in Central and West Africa, pointing to a westward expansion through the Sahel corridor. In North Africa it is second in frequency except in Algeria where it is dominant (55%) . . . . U6a2 may have reached the region through the Sahara, by maritime contacts from the Levant or, most probably both. 
U6c is confirmed to be a Maghreb lineage restricted to the Mediterranean area. 
U6b has the most widespread geographic range. . . . its present-day western and eastern areas must have been connected sometime in the past, perhaps through the Sahara during the Holocene Humid Period.

The Canary Islands.

The Canary Islands, 100km from Western Sahara was first "inhabited by indigenous people, today collectively known as Guanches. On the basis of anthropological, archaeological and linguistic grounds,
close affinities with the North African Berbers were soon identified. Molecular analyses have confirmed these affinities. Later studies of indigenous remnants confirmed that these lineages were in the Canaries before the European colonization. . . . it is broadly accepted that the most ancient human settlement on the Canaries was not earlier than 2.5 kya."

Multiple U6 clades as well as H1 clades were present in the founding population of the Canary Island.  The aboriginal samples has as much mtDNA diversity as the current population and aborigine ancient DNA included both "basic and derived U6b1a and U6c1 haplotypes."  U6c1 and U6b1 probably arrived in separate waves of premediated maritime colonization of the islands (not a sporadic male contact) with origins in the Mediterranean in Roman or Arab times.  Both clades originate in the Maghred of North Africa.

"Curiously, one U6b1 lineage has been sporadically detected in a Lebanese mtDNA survey that might bring speculation about a Levantine origin for the U6b1 cluster. However, a more or less recent immigration of this lineage from the Canary Islands seems more convincing explanation." I am inclined to see this as a possible Phoenician, Roman or Arabian back migration to the Levant with a Mediterranean sailor possibly bringing a Guanche wife back with him to a Lebanese home.

In general, haplogroup U6 has very low frequencies in Europe. It is more frequent in the Mediterranean countries, mainly in those with longer histories of Moorish influence since medieval times, such as Portugal (2.5%), Spain (1.1%) or Sicily (0.4%). In fact, there is a significant longitudinal gradient in Mediterranean Europe, with frequencies decreasing eastwards (r = −0.87; p = 0.008) that run parallel to that found in North Africa (r = −0.97; p <0.001). Congruently, the presence of U6 in the Iberian Peninsula has been attributed to the historic Moorish expansion. However, without denying this historic gene flow, others have also suggested prehistoric inputs from North Africa.  
Actually, the U6 phylogeny and the phylogeography of its lineages are better explained admitting both prehistoric and historic influences in Europe.
Two Iberian lineages of U6a1 expand ca. 18.6 kya.  U6a1a expands in Europe ca. 13.1 kya. "There are also two sequences of Mediterranean European origin that directly emerged from the ancestral node of the East African cluster U6a2a (19.8 kya)."

Later expansions into Europe involve waves of Maritime contacts with North Africa and from Eastern areas to the Maghreb from Neolithic to Chalcolithic (U6a3a1, U6a7a1, U6a7a2, and U6c1) to 14 European lineages that coalesce in historic times.
Some may be associated with the Roman conquest of Britain (U6d1a), the diaspora of Sephardic Jews (U6a7a1b), or the European colonization of the Americas (U6a1a1a2, U6a7a1a, U6a7a2a1, U6b1a). Roughly, 35 European lineages have prehistoric spreads and 50 sequences historic spreads. In all cases they are involved with clear North African counterparts. 
We also know something about clades that are not European specific that are found in Europe.
The largest U6 Maghreb component in Europe is found in Portugal (69.9%), then in Spain (50.0%) and Italy (53.0%), and decreases sharply in the Eastern Mediterranean (25.0%). No U6b representatives have been detected in Italy, although it is present in Iberia to the west and in the Near East to the east. 
Regarding the Canarian motif, 33% and 50% of the U6b haplotypes found respectively in mainland Portugal and Spain belong to the Canary Islands autochthonous U6b1a subgroup. Curiously, it has not been detected in the Portuguese island of Azores and Madeira or in Cape Verde either. 
U6c is confirmed as a low-frequency Mediterranean haplogroup. All four identified U6 HVI components have representatives in Atlantic Europe. This Maghreb component could have arrived through Atlantic Copper or Bronze age networks, leaving the presence of U6c to Punic or more probably, Roman colonization. 
On the other hand, the East African component in Europe has its peak in eastern Mediterranean area (62.5%) and gradually diminishes westward toward Italy (46.0%), Spain (28.3%) and mainland Portugal (20.0%). . . .  
[A]rchaeological comparisons of the different prehistoric cultures that evolved on both shores of the Mediterranean Sea point to the conclusion that each region had its own technological traditions, despite some parallel developments. This finding weakens the hypothesis of important demic or cultural interchanges, at least until the beginning of the Neolithic when prehistoric seafaring started in the Mediterranean Sea. Indeed, the rapid spread of the Neolithic Cardial Culture, or the presence of the Megalithic culture on both sides of the Mediterranean during the Chalcolithic period, would suffice to explain the presence in Europe of U6 lineages with coalescence ages since Neolithic times onwards. 
A couple of U6a lineages may have been part of a larger Mesolithic expansion to the North and South from a Franco-Cantabrian refugia as the climate after the LGM eased, although an absence of archaeological or ancient DNA evidence makes this mere conjecture.
[A]t least two U6 lineages, U6a1a and U6a5, both with European coalescences around 13 kya . . . . These would coincide with climatic improvement during the Late Glacial period. . . . several European mtDNA lineages, with similar coalescence ages, such as V, U5b1, H1 and H3, have been proposed as maternal footprints in North Africa of a hypothetical southward human spread after the Last Glacial period, from the Franco-Cantabrian refuge.
Jews and Gypsies

The presence of U6 in Sephardic Jews and some Gypsy populations is about what would be expected given the known histories of local admixture of these groups in the historic era.

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