June 6, 2016

MtDNA U6 in Aurignacian Europe

The U6 haplogroup of Pestera Muierii is officially confirmed. 

Extra-officially, it also seems confirmed mtDNA H in Magdalenian El Mirón, another of the haplogroup challenged (without any reasoning) by Fu et al. In this last case, my sources suggest that Fu surely tested a bone belonging to a different individual, because the heap of bones could well include several people and the bones tested by Hervella (a tooth) and Fu (a femur) were different.

Anyhow, to the matter at hand:

Montserrat Hervella et al. The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa. Nature 2016. Open accessLINK [doi:10.1038/srep25501]

Abstract

After the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Peştera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and Neandertals. We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans. The derived U6 haplotypes are predominantly found in present-day North-Western African populations. Concomitantly, those found in Europe have been attributed to recent gene-flow from North Africa. The presence of the basal haplogroup U6* in South East Europe (Romania) at 35 ky BP confirms a Eurasian origin of the U6 mitochondrial lineage. Consequently, we propose that the PM1 lineage is an offshoot to South East Europe that can be traced to the Early Upper Paleolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified, until the emergence of the present-day U6 African lineages.


The interesting part is that today U6 is pretty much constrained to Northwest Africa and parts of Iberia and it has usually been considered until now as a North African haplogroup, even if of Eurasian derivation. 

Fig. 2 - (A) Phylogenetic analysis and temporal estimates for lineages including the Peştera Muierii-1 (PM1) from the mitochondrial tree. (B) Location of the Peştera Muierii cave and surface map based on current frequencies of U6 lineages30; the European borders map was generated in ArcMap 10.1 (ESRI, http://www.esri.com) by modifying the World Borders Dataset (http://www.thematicmapping.org/downloads/world_borders.php), which is licensed under the Attribution-ShareAlike 3.0 Unported license. The license terms can be found on the following link: http://creativecommons.org/licenses/by-sa/3.0/ (This map was created by A.A.).

Another interesting bit is that U6(xU6a'b'd,U6c), U6* for short, is not known to exist today anymore. So it is reasonable to speculate about the "ancestral" position of Muierii in the lineage, regardless of whether Muierii-2 was a true ancestor or just a more or less distant relative of the real ancestor of modern day U6 carriers. 

Complementary information is to be found Secher et al. (2014), which refined the knowledge of the U6 mitochondrial haplogroup, unveiling that the key basal (and rare) U6c sublineage is not only found in Morocco (as known earlier) but also in Europe. Specifically U6c, which hangs directly from the U6 root node, is found in: Hispanic America (5.7% of all U6 carriers), Spain (2.2%), Canada (12.5%), NW Europe (16.7%), Morocco (4.5%), Algeria (10%) and Tunisia (5.9%). It is missing in Brazil, Western, Central and East Africa, Romani ("Gypsies"), Jews, Azores, Madeira, Canary and Cape Verde Islands, Portugal, Central and Eastern Mediterranean, West Sahara, Mauritania and USA (African-Americans,  European-Americans and Hispanics).






Figure 1
Surface maps, based on HVI frequencies (in o/oo), for total U6 (U6), total U6a (Tot U6a), U6a without 16189 (U6a), U6a with 16189 (U6a-189), U6b'd, U6c, U6b and U6d.

While the exact pattern of U6 expansion is not clear except for Africa (with a Moroccan origin surely), Sacher et al. believe that at least this part is related to the Iberomaurusian (aka Oranian) culture, which seems primarily an offshoot of Iberian Solutrean, also with origin in North Morocco (Taforalt) and European-like human looks (Cromagnoid).

Another complementary reference is Carmela L. Hernández et al. (2015):

An inspection of the U6 phylogenetic tree (S1 Dataset) showed that it is not easy to infer whether Iberia or North Africa bear more basal lineages. (...) The U6c (9.9 ky [5.0–15.0]) and U6d (12.0 ky [6.9–17.3]) are present in Iberia, Europe and North Africa at low frequencies.

While she seems to support a North African origin, the data is in fact somewhat contradictory:

Fig 5. Founder analysis for mtDNA U6 haplogroup. The plots show probabilistic distributions of U6 founder clusters for HVS-I sequences (A) and complete genomes (B) across migration times scanned at 200-year intervals from 0 to 60 ky.

Fig 7. Bayesian Skyline Plot (BSP) analysis of entire mtDNA U6 sequences.
Temporal changes of the effective population size, Ne in sub-Saharan Africa (brown color), North Africa (green color), and Iberian Peninsula (red color) are depicted. Solid lines represent the median values for the log10 of Ne on the Y-axis within each analyzed geographic region. The 95% HPD (highest posterior density) interval is shown for the three distributions (dashed lines).
Notice that the "LGM" label is very wrong: it should be around 21.000 years ago!

Usually U6 genetic history is envisioned as a migration from southwest Asia through North Africa [50]. This hypothesis is based on the general origin of haplogroup U sub-clades in Southwest Asia, which is also the center of the geographical distribution of U sub-clades: Europe, India, Central Asia, East Africa and North Africa. Two possible scenarios for the first U6 haplotype (bearing mutations 3348 and 16172) can be advanced: i) these mutations aroused in the founder region but did not leave any genetic legacy in current human populations there; ii) they originated probably somewhere in North Africa, after the arrival of the U6 founder haplotype. Within North Africa U6 is only significantly frequent at its western edge (as well as in South-western Europe). More importantly, all the most basal branches are virtually restricted to that region (U6b, U6c and U6d), what could indicate its western origin. Nevertheless, it cannot be excluded the major sub-clade U6a, which shows a richness of sub-clades in Northwest Africa [29] although a few of derivative branches also include sequences from East African and the Middle Eastern populations (e.g. U6a2).

Her conclusions (insisting on an African origin and first arrival via Egypt) are not something I can share at this stage of the research but her data is clearly very interesting and, combined with the rest, useful in discerning the possible route of primeval U6 to the Gibraltar Strait area, where it found no doubt its niche for consolidated expansion. 

After the Muierii finding the question is open: did primeval U6 arrive to North Africa via Iberia, being pruned in Europe afterwards just because of genetic drift and the sizable impact of Paleolithic migrations in low density areas? I cannot be 100% sure but I would say it is a very likely conclusion based not just on Muierii but also on the rather high basal diversity of U6 in Iberia (and surprisingly NW Europe!) and also on the archaeological data that makes almost necessary to root the first Upper Paleolithic of NW Africa (the Iberomaurusian) in the Iberian Solutrean.


(Special thanks to Jean Lohizun again).


Update (Jun 17):

The Hernández 2015 paper also mentions that  U6a1 appears to be of European and specifically Portuguese origin:

Our U6 tree built from mitogenomes shows that U6a1 is predominantly European because it contains a significant number of sequences of Mediterranean individuals mainly from the northwestern shore with a leading Iberian contribution (21 of the 29 European samples) and has an ancestral node in Portugal (accession number HQ651694).

Thanks to Geog M. for highlighting this important detail.

9 comments:

  1. Portugal have basal U6 lineages as well. The Hérnandez (2015) paper speaks about a modern sample.

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    1. All of them? Particularly the rare basal lineage U6c, AFAIK only known in Morocco and Andalusia? I only see a table on Andalusians and then the large sup. material of 2000+ sequences that I don't feel like downloading and searching right now -- when you can tell me that directly.

      In any case it would not make much difference, right?

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  2. All of them? No, the one that is implied directly on the study (U6a1).

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    Replies
    1. That's not an U6 "basal" branch by definition, as it is at least two nodes downstream. U6, as the paper reminds us has two basal branches: the rare U6c one and the much more common U6a'b'd, which in turn splits into U6b'd and U6a, where U6a1 hangs from.

      This you say (which by the way, was already in the update of the entry, dated June 17th, I just realized) is potentially important re. the origins of U6a1, which older studies suggested that had coalesced in NE Africa and back-migrated to the West later on but not directly regarding U6 as a whole.

      Also it is not correct that Hernández et al. 2015 were only focused on U6a1, on the contrary: their study covered all U6 in Iberia (focus on Andalusia) but also M1 and L(xM,N).

      What is most important for the debate on the origin of U6 is the presence of the very rare (and basal!) U6c in Andalusia on terms fully parallel to those of Morocco. This gives some credency on its own (in addition to the already know presence of all other U6 basal or cuasi-basal derivatives, just as in Morocco and nowhere else) to the hypothesis of an ancient Europe→Africa U6 migration rather than one of some basal U* directly from East Asia all the way to Morocco (without any archaeology we know of that might back it: the early Aurignacian-like Upper Paleolithic of NE Africa reaches to Cyrenaica but does not go further West, while Aterian, a "mode 3" tech, seems to persist to rather late dates instead). Hernández et al. finally dismiss the European origin hypothesis as rather unlikely but, with the discovery of U6 in Aurignacian Romania, the situation changes radically.

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    2. I didn´t said that they focused only on the U6a1, please... I was just saying that they mentioned it. And I used also the original quote directly from the source.
      And like it´s mentioned it has an ancestral node in Portugal. Not very surprising since you can find plenty of ancient mtDNA there as well, not just old U6.

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    3. Though it may not be that basal, I honestly personally doubt that more basal types are absent (having in mind what was already found there).Further genetic data should detect it. But that´s just my opinion, it doesn´t matter, by now.
      So I agree with you, what´s more interesting now is that reinforces the Paleolithic connection between the 2 sides of the Gibraltar strait.

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    4. "I didn´t said that they focused only on the U6a1"...

      OK, sorry, I misunderstood you quite clearly.

      "Though it may not be that basal, I honestly personally doubt that more basal types are absent (having in mind what was already found there)."

      Maybe, after all it is just a survey and rare lineages are hard to find that way. It may be interesting to mention here that there were two U6(xU6a), plus one U6a, sampled in Asturias in a key 2012 paper, what looks like sizable diversity for a place where U6 is not so common, a 1.7% per another study of that same year. Asturias is one of those places where Y-DNA E1b is rather common (second haplogroup after R1b and tied with... F*!!!) and also mtDNA U is common and diverse (the only U* with CRS haplotype I've ever read about among moderns was from Asturias, it's from an older study though). They also have instances of rather rare African haplogroups like M1 (two variants), L1b, L2a, L3x (clearly North African IMO), L3f, etc. No idea how to read all this but clearly there has been some interaction with North Africa and it's probably quite old in many instances, as Asturians seem to retain some of those Paleolithic genetics in spite of also carrying "Neolithic" admixture.

      "... what´s more interesting now is that reinforces the Paleolithic connection between the 2 sides of the Gibraltar strait".

      Absolutely. It's difficult to be sure what is from what date without enough good quality archaeogenetic data but there must be something that is very very old, also because of archaeology (we know nowadays that the North African Upper Paleolithic, known as Iberomaurusian or Oranian, MUST have Iberian Solutrean roots and very likely implied some backflow. See also: http://forwhattheywereweare.blogspot.com/2015/09/detailed-analysis-of-south-iberian.html

      Delete

    5. Yes, Asturians are also interesting on that regard.

      Thanks for the extra info!

      You wrote: «Absolutely. It's difficult to be sure what is from what date without enough good quality archaeogenetic data but there must be something that is very very old, also because of archaeology (we know nowadays that the North African Upper Paleolithic, known as Iberomaurusian or Oranian, MUST have Iberian Solutrean roots and very likely implied some backflow. See also: http://forwhattheywereweare.blogspot.com/2015/09/detailed-analysis-of-south-iberian.html

      Thanks again, I´ll have a good look later on.

      Delete
  3. «...and has an ancestral node in Portugal (accession number HQ651694).»

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