Luxmanda: a 3,000 years-old proto-Horner in Tanzania

I knew, more intuitively than rationally, that the Horner (Ethiopian, Somali, Eritrean) type of Afro-Eurasian admixture was very old but no idea it was so much. I knew that West Eurasian Upper Paleolithic had an impact on Africa (LSA) but I did not know it went so deep South nor that it had left such a massive legacy as ancient DNA reveals.

Pontus Skoglund et al. Reconstructing Prehistoric African Population Structure. Cell 2017 (open access). DOI:10.1016/j.cell.2017.08.049

The data analysis speaks volumes by itself:

Figure 1 - Overview of Ancient Genomes and African Population Structure

Figure S2 - Ancient Individuals and African Population Structure

Figure 2 - Ancestral Components in Eastern and Southern Africa

We show bar plots with the proportions inferred for the best model for each target population. We used a model that inferred the ancestry of each target population as 1-source, 2-source, or 3-source mixture of a set of potential source populations.

So much that I don't really know what else to say. Of course this is just a sample of what there is in the paper, read it. I'm sure there will be plenty of comments even if the study was published months ago.

Regarding haploid DNA, I don't see anything outstanding but, as I know there is generally quite a bit of interest, these are screenshots of the ancient lineages found (full data in the supp. materials of the study):

Ancient Y-DNA (screenshot)

Ancient mtDNA (screenshot)

Related: No Iberian in Iberomaurusian.

Correction: I first titled this "a 30,000 years-old...". That was a major error on my part and I apologize for any confusion it may have caused. Thanks to Capra Internetensis for spotting it.

No Iberian in Iberomaurusian

After almost a century of controversy on the matter, it seems that archaeogenetics solved the riddle. Not in the sense I thought it would but it did anyhow.

Marieke van de Loosdrecht et al., Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. Science 2018 (pay per view). DOI:10.1126/science.aar8380 -- See also supplementary materials (free but hard to find). 

Ancient DNA samples from Taforalt (Iberomaurusian or Oranian culture, Upper Paleolithic of North Africa) show no trace of Paleoeuropean ancestry (WHG), however they show strong affinity to West Asians of Palestinian type, showing also some significant amount of African Aboriginal ancestry, probably closer to East African Hadza and Sandawe and ancient Mota than to West African types. The result is something roughly similar to Afars but not quite the same in any case. 

Fig. S8 - Taforalt individuals on the top PCs of present-day African, Near Eastern and South European populations.

Fig. S11 - ADMIXTURE results for a few informative K values.

So the conclusion must thus be that the Eurasian influence in North African Upper Paleolithic (call it Iberomaurusian, Oranian or my personal unorthodox preference: Taforaltian) arrived from West Asia with whichever intermediate stage in Egypt and Cyrenaica, where that influence is quite apparently much older in the archaeological record. This seems contradictory to the chronology of Taforaltian, with Western sites producing older radiocarbon dates but the genetic data seems overwhelming. 

I must say I wish they would have contrasted with older (and available) Paleoeuropean samples than WHG (Epipaleolithic) but I guess that some WHG influence would have shown up if there was some older European influx because the various Paleoeuropean layers are not disconnected. But it is still something someone should test, just in case. 

Haploid DNA

The Taforalt sample was rich in mtDNA U6a, with also one instance of M1b:

All six male samples carried Y-DNA E1b1b, with most of them being well defined as E1b1b1a1-M78 (see table S16 for details).


Related: Luxmanda: a 3,000 years-old proto-Horner in Tanzania.

North African Neolithic was influenced by Europe... and European Chalcolithic by Iberian Neolithic

Or so it seems considering the data of Fregel et al., a study I have in my to-do list for some time and that I don't see cited often or ever at all.

Rosa Fregel et al., Neolithization of North Africa involved the migration of people from both the Levant and Europe. BioRxiv 2017 (pre-pub). DOI:10.1101/191569

The critical piece is probably this selection from Admixture results but which repeats over and over through the study with many more analyzed populations from all West Eurasia and North Africa:

We see how KEB (Morocco Neolithic) is a mix of European Neolithic intermediate between Iberia (purple) and Sardinian (blue) on one side and, on the other, something like Mozabites (not shown in this detail, cream). TOR is a new Neolithic sample from Andalusia.

Another ancient Moroccan sample IAM (pre-Neolithic, not shown here either) is fully cream-colored like mostly are modern Mozabites. 

Interestingly we see for the first time the emergency of a purple-colored component that differentiates Iberian Early Neolithic from the rest (although this does not happen at lower K-values, so they are still related), a component that, in the MNChL (Middle Neolithic and Chalcolithic) period, somehow appears as dominant in Italy (no data for earlier times) and becomes quite dominant in Central Europe. 

This is intriguing to say the least. It must be said that modern Sardinians and Basques (these probably, not labeled) are low in the purple component, although less than other populations, and that somehow the Early Neolithic (blue) component made a comeback:

I do not want to over-interpret all this (autosomal genetics are not an exact science) but, judging on KEB, the purple component is not just a generic southern branch (Cardium Pottery) distinction but something specifically Iberian or Italo-Iberian. The matter needs more research but it is in any case very intriguing that the purple component seems to expand from Iberia or somewhere nearby (France?, Italy?) in the period leading to the Chalcolithic, a most critical one in the formation of the genetics of Europe.

There is a also a little hoard of DNAmt and Y-DNA, with G2a-M201 (in Europe), E1b-L19* (in pre-Neolithic North Africa) and T-M184 (in Neolithic North Africa) in the patrilineal side and quite a bit of varied K1a in the matrilineal one, as well as JT (also in both shores) and U6 and M1 in North Africa.

Worth reading and keeping in mind, no doubt.

Caribbean Taino ancient DNA still alive in admixed populations

Taino Native Americans also had a very high genetic diversity, comparable to other continental large native populations such as Andeans or Amazonians, what speaks of high mobility in the Caribbean islands before European colonization.

The mitochondrial lineage B2 was sequenced, although it is today rare in the region.

Hannes Schroeder et al., Origins and genetic legacies of the Caribbean Taino. PNAS 2018. DOI:10.1073/pnas.1716839115

The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher’s Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.

Fig. 2.

Taino demography. Total estimated length of genomic ROH for the Taino and the Clovis genome (13) and selected Native American and Siberian genomes (15, 31, 32) in a series of length categories. ROH distributions for modern individuals have been condensed into population-level silhouettes (SI Appendix, section 14).

Extensive ancient Iberian mtDNA analysis

A very interesting thesis on Iberian ancient mitochondrial DNA is available (found via Bell Beaker Blogger):

Christina Roth, Once upon a time in the West : paleogenetic analyses on Mesolithic to Early Bronze Age individuals from the Iberian Peninsula. University of Mainz (thesis), 2016. Freely available → LINK

As all theses, it is very extensive, and I can only make some comments here (space and time are always too limited, you know), hoping to grasp the most interesting aspects of it.

First of all Roth finds that Iberian hunter-gatherers (HGW in the paper) were not quite like Central European ones (HGC), at least not in the mtDNA. Instead, in this aspect the Central European hunter-gatherers were closer to Eastern European ones (HGE), as well as to the Pitted Ware late subneolithic population of Gotland.

Iberia-only mtDNA analysis

This will be a recurrent issue along the analysis she makes. But let's focus on Iberia by the moment. Notice that she does not just use her own data but also from many other sources, including some unpublished materials, this makes a bit difficult to follow all the details, so I feel I can only focus on the statistical analysis she makes and which is the core of the thesis.

Annotated by me, because I found the abbreviations quite hard to follow

The general overview is confirmed, with minor variations, in the cluster analysis (which I also took the liberty of annotating, but take my notes for what they are: mere scribbling on the margin in an attempt to better understand the data, nothing else):

Particular care not to take the arrows of my notes too seriously: they are just conceptual, a very loose sequencing of the available data for a very tentative visualization of it. If it helps you, cool, else ignore please.

In any case, it seems clear cluster 2 is more influenced by hunter-gatherer genetics and that, with the data available in this study, we reach the end of the timeline within it in the following regions: Upper Ebro and Basque Country (data up to Late Neolithic but see my own 2013 compilation for a longer period), Southern Iberia (up to Chalcolithic) Southeast and Northeast, this one after originally being in the "more Neolithic" cluster 1 (in fact the author does argue for Catalonia as main "gate" for Neolithic genetics into Iberia on light of the available data, which does not include another important "gate", the SE one, for lack of data for the early period).

Inversely, cluster 1 is more influenced by "farmer" genetics, first detected in the Northeast (Catalonia and nearby areas of Aragon) but then also affecting the Northern Plateau and the West (Central Portugal). This last is very important because it is here where a key civilizational hub, the oldest known civilization of the Atlantic shores, emerged in the Chalcolithic, playing a key role in the wider Megalithic and Bell Beaker phenomena. I have at times speculated that it might be the origin of "modernity" in Western European genetic pools but on light of this data I have to recant, the origin should be elsewhere, probably in/around what is now France (and therefore it's not likely to be directly related to Bell Beaker, except maybe in the islands, but rather to Michelsberg/SOM, Artenacian and such -- always in wait of more data, just a cautious hypothesis). 

Finally the farmer-leaning cluster reaches the Southern Plateau, near Madrid, what suggests a N→S move of the then-forming Cogotas I herder culture, rather than the opposite. 

What we do see is not inconsistent with modern Iberian genetics anyhow: while Central Europe seem to have seen an increase of "hunter-gatherer" genetics along time, in Iberia the main tendency is the opposite: an increase of "farmer" genetics and further dilution of the aboriginal genetic pool. There is however at least one clear exception in the Northeast and that is also consistent with modern Iberian genetics. Some regions (south, southeast and the totally unknown northwest) have only fragmentary sequences here, so unclear, although the final tendency, up to the Bronze Age, is to cluster 2b (i.e. mixed but rather tending to "hunter-gatherer" genetics).

To finish with the Iberia-only bloc, notice that these are the lineages found among early Iberian farmers by region (in color those haplogroups associated to the arrival of Neolithic per the available data):

Notice how the pool in the Northern region is quite modern-like, not yet exactly as it is locally today but it would pass quite unnoticed in a map of Europe.

Iberia and the rest of Europe

What about the pan-European context (with the usual huge blanks in France, Britain, etc.)? Quite interesting as well:

Annotated by Maju on fig. 23 (click to enlarge)

As mentioned before, the Iberian hunter gatherers (HGW) appear clearly distinct from their Central and Eastern cousins in the mtDNA analysis. And with all this Iberian dataset it becomes apparent that there seem to be two "zones of admixture": one for Iberians and another for Central Europeans, the difference being on which aborigines they mix with. 

Notice that it is not possible to differentiate here between local Central European and intrusive Eastern European admixture, as both aboriginal hunter-gatherer populations appear closely related in all analyses (maybe an artifact of the sampling strategy or maybe actually relevant, can't say). 

It also caught my eye that a German site (Blätterhöhle, Westfalia, famed because farmer and hunter-gatherers living side by side were located there some years ago), clusters intensely with Iberian hunter-gatherers and related populations. I have to research more on this matter (which I had ignored so far) but I suspect it may be very relevant, because we could get an even longer chain of early "modern" mtDNA pools, adding this site to Paternabidea (Navarre) and Gurgy (Burgundy), spanning a long stretch of Western Europe, an area quite neglected by archaeogenetics so far, it must be said.

It is also worth mentioning that UC (which I believe stands for Unetice Culture) pulls the "Central European zone of admixture" in the PCA downwards, with a polarity of its own, a polarity that should probably be considered as specifically Indoeuropean. 

The cluster analysis confirms much of what I just said above, not annotated for a change:

We see very clearly here a larger cluster more influenced by "farmer" genetics and a smaller one that includes all pre-Neolithic aborigines, plus two populations already post-Neolithic but clearly identifiable as at least largely aboriginal (PWC and BLA), plus a subcluster of Neolithic Iberians, from the North (NSE and EVN) and the West (CPE). 

The author notices that: Bernburg (BEC) and Funnel Beaker (FBC) samples (...) show almost no significant differences to any Iberian group, except to the Early Neolithic of Northern Spain (NSE) and Chalcolithic of East Spain (ESC). Hard to interpret but worth noticing, no doubt.

And there is a lot more in the thesis but I can only review so much, so take a look and tell me and the World if I'm missing something of relevance or you feel I'm misinterpreting something or whatever.

Reconstructing Sardinian population history

A very interesting pre-pub study, dealing with Sardinian genetics in great sub-national detail but also within the wider European and Mediterranean context, became available in the last weeks. I won't probably be able to make justice to it here, so please take a look yourselves.

Charleston W.K. Chiang et al., Population history of the Sardinian people inferred from whole-genome sequencing. BioRXiv 2016. Open access pre-pub → LINK [doi:10.1101/092148]

Abstract

The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of traits and diseases. The history of the Sardinian population has also been the focus of much research, and in recent ancient DNA (aDNA) studies, Sardinia has provided unique insight into the peopling of Europe and the spread of agriculture. In this study, we analyze whole-genome sequences of 3,514 Sardinians to address hypotheses regarding the founding of Sardinia and its relation to the peopling of Europe, including examining fine-scale substructure, population size history, and signals of admixture. We find the population of the mountainous Gennargentu region shows elevated genetic isolation with higher levels of ancestry associated with mainland Neolithic farmers and depleted ancestry associated with more recent Bronze Age Steppe migrations on the mainland. Notably, the Gennargentu region also has elevated levels of pre-Neolithic hunter-gatherer ancestry and increased affinity to Basque populations. Further, allele sharing with pre-Neolithic and Neolithic mainland populations is larger on the X chromosome compared to the autosome, providing evidence for a sex-biased demographic history in Sardinia. These results give new insight to the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations.

The authors call to some question the extreme simplicity of the three populations model of Lazaridis and subsequent studies. They do not flatly reject it but it seems that the lack of nuance bothers them a lot, as it does to me. This is quite clear when they find once and again Sardinian-Basque lines of relationship without going through Italian, Spaniard or French intermediaries, also when they face the issue of the largest Y-DNA haplogroups in the island, I2a1a (M26, almost exclusively a Sardinian and Pyrenean haplogroup) and R1b1a2 (M269), which are not typically associated with Neolithic farmers, suggesting that there is more to Neolithic settlement than meets the eye in the too simplistic three populations' model. They even seem to consider if Paleolithic peoples from Sardinia itself or maybe some other locations contributed heavily to what they feel is a sex-biased genetic pool.

They do confirm that Sardinians have both strong "Neolithic" (Stuttgart) and "Paleolithic" (Lochsbour) ancestry and no (negative even) "Steppe" (Yamnaya) one, although this last is truer for the most isolated sub-populations than for the more cosmopolitan ones. 

They also estimate that Sardinians have been generally isolated from the rest of Europeans for some 330 generations, what reads as approx. 9900 years, i.e. since the very early Neolithic settlement of the island. We would actually have to reduce that time span a bit but within reason, else it becomes Epipaleolithic in fact, what is most unlikely. Alternatively, as the main comparison is Northern Europe, this date could refer to the branching out of Painted-Linear (continental) and Impressed-Cardium (maritime) Neolithic cultures in the Aegean or the Balcans.

Ancient aboriginal DNA from El Hierro (Canary Islands)

The island of El Hierro (lit. The Iron) is one of the westernmost of the Canary Islands. I have never visited but it seems to be very beautiful, far enough from the Sahara to enjoy a warm yet humid climate. It wasn't far enough to remain uninhabited however and now we get to know something more about its original dwellers, generally known as Guanches (although technically this name only applied to the inhabitants of La Palma originally).

Alejandra C. Ordóñez et al., Genetic studies on the prehispanic population buried in Punta Azul cave (El Hierro, Canary Islands). Journal of Archaeological Science 2016. Pay per view → LINK [doi:10.1016/j.jas.2016.11.004]

Abstract

The aim of this study was to establish the genetic studies of the population from one of the most important known aboriginal funerary spaces of the island of El Hierro (Canary Islands), the Punta Azul cave, which harbors remains of 127 individuals. Sixty-one adult tibiae were examined, 32 left and 29 right. Radiocarbon dating yields an antiquity of 1015–1210 AD. We have obtained an overall success rate of 88.5% for the molecular sexing, and of 90.16% for the uniparental markers. Short tandem repeats (STR) profiles were also possible for 45.9% of the samples. This performance is a consequence of the good conservation of the bones in their archaeological context. The mtDNA composition of the sample is characterized by the complete fixation of the H1-16260 lineage. These results can be explained by a mixture of consecutive founding events, a bottleneck episode at the beginning of the colonization and/or as a consequence of genetic drift. Paternal lineages were also affected by these processes but in a less acute way. These differences lead us to propose social behaviors as an explanation for this difference. The maternal transmission of the lineages, mentioned in ethnohistorical sources of the Archipelago, could be an explanation. These results could be in agreement with endogamous practices, but the autosomal STR results indicate a relative high diversity. These results have allowed us to characterize the Punta Azul cave population and see the way in which geographical isolation, the process of adaptation and specific social behaviors affected the aboriginal population of the Island.

And now the interesting stuff, the findings:

As should be expected, the remote and rather small western island, which is the most direct threat to the security of the USA and the Western World in general because of the danger its volcano may slide into the Ocean and cause a huge tsunami of devastating consequences, something that no nuclear arsenal can do anything against, shows clear indication of very strong genetic drift relative to its relatives of the larger islands, caused either by founder effects and/or endogamous drift. Otherwise it is within the general patterns for the pre-colonial islanders. 

We see a lot of likely mtDNA H and certain Y-DNA R1b1a2. The Canary Islands were settled c. 1000 BCE (11,000 HE) by people arrived from what is now Morocco and the Western Sahara. They seem to retain a somewhat archaic genetic pool, relatively rich in Europe-related genetic elements, not so abundant at all today in Northwest Africa anymore, and by this I mean of course very especially Y-DNA haplogroups I and R1b. While we can still find some R1b in NW Africa, haplogroup I is almost impossible to find nowadays, yet it was present in the Canary Islands prior to European conquest and nearly disappeared afterwards (so it's definitely not a colonial input, accidentally misidentified, not at all). 

See also: Leherensuge: Ancient Guanche Y-DNA.

Iberomaurusian ancient mtDNA

This is an issue that has lingered for a long time in the online anthropology circles. Once upon a time (2005) there was online a presentation in which a good deal of mitochondrial DNA (HVS-I) sequences from the key Iberomaurusian (or Oranian) culture site of Taforalt (North Morocco) were (not too formally) published. Eventually this presentation became almost impossible to find... however now Rym Kefi (the original author if I remember correctly) and colleagues have got back to resurrect that important data set from oblivion, plus sequences from Afalou cave as well.

Rym Kefi et al., On the origin of Iberomaurusians: new data based on ancient mitochondrial DNA and phylogenetic analysis of Afalou and Taforalt populations. Forsenic Sciences Research 2016. Freely available at the time & space of writing this → LINK [doi:10.1080/24701394.2016.1258406]

Abstract

The Western North African population was characterized by the presence of Iberomaurusian civilization at the Epiplaeolithic period (around 20,000 years before present (YBP) to 10,000 YBP). The origin of this population is still not clear: they may come from Europe, Near East, sub-Saharan Africa or they could have evolved in situ in North Africa. With the aim to contribute to a better knowledge of the settlement of North Africa we analysed the mitochondrial DNA extracted from Iberomaurusian skeletons exhumed from the archaeological site of Afalou (AFA) (15,000–11,000 YBP) in Algeria and from the archaeological site of Taforalt (TAF) (23,000–10,800 YBP) in Morocco. Then, we carried out a phylogenetic analysis relating these Iberomaurusians to 61 current Mediterranean populations.

The genetic structure of TAF and AFA specimens contains only North African and Eurasian maternal lineages. These finding demonstrate the presence of these haplotypes in North Africa from at least 20,000 YBP. The very low contribution of a Sub-Saharan African haplotype in the Iberomaurusian samples is confirmed. We also highlighted the existence of genetic flows between Southern and Northern coast of the Mediterranean.

The bulk of the data is this (tables 1 and 2):

Notice that all sequences are "old style", i.e. HVS-I only, and that's why haplogroup assessment is not always 100% certain, with particular emphasis on the "CRS" sequences, which have been proven in some ancient cases to belong not to the modern normal (H1, rarely H2 o other H) but to a very rare modern haplotype within U*, AFAIK only preserved in Asturias but somewhat common in the Magdalenian of South Germany. 

In any case, that they produce 100% safe H1, H6, H14, etc. and, even more surprisingly, J and T2 variants, should make people think about the hidden Paleolithic mtDNA diversity in the wider Mediterranean area. And by this I do not just mean North Africa but also all Southern Europe, including many areas that can't be considered part of the Mediterranean basin, such as most of the crucial Franco-Cantabrian Region, the most densely populated province, by far, of post-LGM Upper Paleolithic Europe, source of several cultural waves (including the Solutrean one, almost certainly at the origin of Iberomaurusian), yet outrageously neglected by research.

Table 5 and other materials in the paper also deal with which modern populations appear closest to the Iberomaurusian ancient mtDNA pool and these are:

1. Tuscans (0.00090)
2. Catalans (0.00134)
3. Galicians (0.00223)
4. Sicilians (0.00377)
5. El Alia (0.00699)
6. Valencian (0.00787)
7. Matmata (0.00788)
8. Slougia (0.00831)
9. Jerba Berbers (0.00934)

Figures in brackets are FST distances, the smaller the closer the match, statistically speaking. Populations in cursive are from Northwest Africa.

That is I'd say quite surprising because we tend to think of those near matches as quite impacted by Neolithic and post-Neolithic inflows, at least judging on other recent research. It seems that the debate on the origin of modern Europeans and North Africans refuses to come to a close, as different aspects of the evidence available may be somewhat contradictory. What do you make up of all this?

See also:

• Leherensuge: 2009 review of mtDNA H studies (some re. North Africa).
• I'd emphasize Sykes et al 2005 on Portuguese Epipaleolithic and Neolithic mtDNA also rich on "CRS" and other H sequences, because it provides another anchor point for the presence of mtDNA H in pre-Neolithic Europe.
• But for North African mtDNA studies Enafaa 2009 is pretty much seminal, showing that SW Europe related haplogroups H1, H3, H4 and H7 are absolutely hegemonic in the region's H.
• MtDNA H in Magdalenian Cantabria
• MtDNA U6 in Aurignacian from Romania
• On South Iberian Solutrean (surely at the origin of Iberomaurusian)
• And in general the Oranian label (alternative name of Iberomaurusian)

UPDATE: single marker inferred lineages (not always the haplogroup is reported correctly):

Down in the comments' section, Capra questions with good sense the certainty of inferred haplogroups. The most clear one is TafV27, claimed to be H6a1a8, which cannot actually be that (would need another HVS-I marker defining H6, which is missing), however this means that it must be HV0 and possibly V, a lineage that appears (per the aDNA literature) in the European Neolithic, already quite towards the West, out of nowhere, and that "nowhere" should not be West Asia, where it has never been sequenced, unlike K. 

I'm therefore reviewing here all the single-marker inferred haplogroups as carefully as possible, please double-check them and report if I seem to be committing any error:

• AF22B - 16126C (reported as JT or H14b1) - JT(xJ,xT) or H14b1 indeed, notice that JT* was probably also one of the lineages described (also by the HVS-I method) for Nerja cave (Solutrean, same time frame), just across Alboran Sea (cf. Fernández-Domínguez 2005). Whether is one or the other or even something else, it's almost certain that the lineage was shared across the sea between Europe and Africa, what just makes total sense for this culture.
• Taf55-IB - 16239T (reported as H1) - I actually get specific H1 variants (H1bf'bg'bh'ch specifically) or H17c. H sublineages in any case, unless it is an extinct or unreported R* lineage, most unlikely.
• TafV27 - 16298C (reported as H6a1a8) - must be HV0, possibly even V, a distributed Euro-African lineage with three hotspots: Kabylia, Catalonia and Lappland. Per Caramelli 2003 and successor studies, this lineage was already present in Italy (Pagilicci cave) in the Gravettian era.
• TafVIII - 16223T (reported as U4a2b) - It cannot be U4 at all because it lacks the HVS-I mutation 16356C. In fact the reverse 16223C mutation defines macro-haplogroup R, and I can't find any other matches within R, so it must be L3(xR), maybe N(xR) but maybe M or other L3. The possibilities are many, for example: N1, N2, N9, N11, etc. within N, a lot of possibilities within M, and also several within L3e'i'k'x(xL3x). The only thing we should be certain here is that it is not R and also not upstream of L3 (that's how good as it gets with HVS-I methodology, really). 
• TafXXV3 - 16126C (reported as H14b1) - as with AF22B, it can be JT(xJ,xT) or H14b1 and again I must emphasize that there is an extremely good chance that this matrilineage had relatives in Iberia (Nerja) within the Solutrean culture.

In case you want to re-check, the best resource is of course PhyloTree.

IMPORTANT CAVEAT: the above update was done assuming they had fully sequenced the HVS-I, which is not that long, but it seems that in many cases (second column of the tables above) they have only sequenced up to the 16317 locus, what makes prediction of haplogroup even harder. That would explain their H6a1a8 prediction, although there's no way they can exclude the much more common HV0 (H6 is unheard of in North Africa). Thanks again to Capra for pointing that out.

Mitochondrial DNA from post-Neolithic Santimamiñe (Basque Country)

Four human remains dated to the Bronze Age were sequenced for mitochondrial DNA in Santimamiñe cave (Kortezubi, Biscay, Basque Country), along with single instances from the Neolithic, Chalcolithic and Roman period.

J.C. López Quintana et al., NUEVOS DATOS SOBRE LA SECUENCIA DE USO SEPULCRAL DE LA CUEVA DE SANTIMAMIÑE (KORTEZUBI, BIZKAIA). Arqueología y Prehistoria del Interior Peninsular (ARPI), 2016. Freely accessible (PDF) → LINK [no DOI]

The mtDNA study is not "brand new" but a synthesis of a previous doctoral thesis and advance publications:

Un primer avance de este estudio fue publicado en la monografía de las campañas de 2004 a 2006 de Santimamiñe (Cardoso et al. 2011), incluyendo el conjunto completo en la Tesis Doctoral de L. Palencia Madrid (Palencia 2015).

So we are talking of relatively old data, that has partly remained within the (sometimes absurdly greedy and anti-social) academic circles until now. The relative antiquity of the DNA study is important when assessing it, because genetic analysis is evolving very fast and, in most cases in the rather closed and under-budgeted Spanish universitary circles, they tend to do things "the old way", so we are almost certainly dealing here with HVS-I sequencing, something that is not explicit in the paper (I'm searching for Leire Palencia's thesis to make sure but no luck until now). 

If I am correct in this (and I should be), then we must understand that it is impossible in many cases to determine the exact haplogroup in the crucial R0 upper tier haplogroup, which includes HV and the extremely common H. Lacking the original HVS-I sequences by the moment, I can't but take the authors labels at face value but I must warn here that where it reads "R0" it is almost certainly H (HV0 or V are easy to recognize with this method, as is R0a) and where it reads "H1" it is probably H1 but not 100% certain. 

For more details see the relevant PhyloTree page, where the HVS-I markers are the last bloc in blue, beginning always with the sequence "16" (the other markers in blue of lower numerical value are HVS-II, more rarely used, and the ones in black are the coding region markers, which are in this case fundamental for proper assignment).

The mtDNA haplogroups (as reported) are:

• Neolithic:
• U5a2a (S2011-M2, c. 5100 BCE)
• Chalcolithic:
•  T2b (S-1, c. 2000 BCE)
• Bronze Age:
• U5b (S2011-M1 c. 1700 BCE) 
• H1 (S2011-M4, c. 1700 BCE)
• R0 (S2011-M6, c. 1500 BCE)
• U3a (S2011-M3 c. 1300 BCE)
• Roman period: 
• R0 (S2011-M5, c. 300 CE)

Interpretation attempts

It's difficult to extract conclusions from them but they should be compared with other sequences from the area, for which I recommend my 2013 synthesis. In general, treat "R0" as meaning "H", even if I chose to use a different color (magenta instead of red) for exactitude. 

In order to aid that analysis, I reproduce here my 2013 graphic:

We cannot compare the single Neolithic and Roman Era individuals but we can compare the Satimamiñe Chalcolithic+Bronze group of five sequences with the peripheral Chalcolithic large dataset of De La Rúa:

1. R*+H (very similar):
1. Peripheral "Basque" Chalcolithic: ~40%
2. Santimamiñe Chalcolithic+Bronze: 40% 
3. Santimamiñe Bronze only: 50%
2. U(xK) (very different):
1. Peripheral "Basque" Chalcolithic: ~15%
2. Santimamiñe Chalcolithic+Bronze: 40%
3. Santimamiñe Bronze only: 50%
3. Other lineages (all them of certain Neolithic immigrant origin, very different too):
1. Peripheral "Basque" Chalcolithic: ~45%
2. Santimamiñe Chalcolithic+Bronze: 20%
3. Santimamiñe Bronze only: 0%

However one of the U(xK) lineages in Santimamiñe is U3, which is also quite certain to be of Neolithic immigrant origin, and one is an important figure when n=5 so we can also see it this way:

1. Paleolithic lineages:
1. Peripheral "Basque" Chalcolithic: ~55%
2. Santimamiñe Chalcolithic+Bronze: 60%
3. Santimamiñe Bronze only: 75%
2. Neolithic lineages:
1. Peripheral "Basque" Chalcolithic:  ~45%
2. Santimamiñe Chalcolithic+Bronze: 40%
3. Santimamiñe Bronze only: 25%

The comparison of #1 with #2 is much more similar. This could be important, because Santimamiñe is not anymore a "peripheral" site, as are those from De La Rúa's dataset, but a rather central one with a extremely long and uninterrupted Paleolithic sequence, dating to Neanderthal-made Chatelperronian culture. It is still a single site with a small number of samples but it does provide a counterpoint that, in one approach could produce similar results. 

But, surprisingly, when we consider a distinct Bronze Age category, comparing not anymore with #2 but with #3 everything changes, suggesting a totally different interpretation of the available dataset, in which, the "Chalcolithic interlude" (if real at all, more data is needed) would be reversed quickly with the onset of the Bronze Age. 

I am sorry but I cannot lean for either interpretation: the data is just not extensive enough to allow for conclusions. I am tempted to support the continuity hypothesis, allowing only for lesser changes to happen, and keep the Chalcolithic dataset under a big question mark, but the question mark is admittedly a bit smaller now: something in terms demographic may have happened in the Chalcolithic period and may have been reversed in the Bronze Age. But "may" is not "for sure", we need more data points.

Feel free to discuss in good mood, as always.

Thanks for the heads up to Jean Lohizun (again).

Paleolithic European mtDNA lineage U5b2c1 in Carthaginian man

Quickies

Elizabeth A. Matisoo-Smith et al. A European Mitochondrial Haplotype Identified in Ancient Phoenician Remains from Carthage, North Africa. PLoS ONE 2016. Open access → LINK [doi:10.1371/journal.pone.0155046]

Abstract

While Phoenician culture and trade networks had a significant impact on Western civilizations, we know little about the Phoenicians themselves. In 1994, a Punic burial crypt was discovered on Byrsa Hill, near the entry to the National Museum of Carthage in Tunisia. Inside this crypt were the remains of a young man along with a range of burial goods, all dating to the late 6th century BCE. Here we describe the complete mitochondrial genome recovered from the Young Man of Byrsa and identify that he carried a rare European haplogroup, likely linking his maternal ancestry to Phoenician influenced locations somewhere on the North Mediterranean coast, the islands of the Mediterranean or the Iberian Peninsula. This result not only provides the first direct ancient DNA evidence of a Phoenician individual but the earliest evidence of a European mitochondrial haplogroup, U5b2c1, in North Africa.

The lineage is the same one as La Braña 1, an Epipaleolithic man buried in a cave at the mountains NE of León. Its presence on a Carthaginian from the 6th century BCE almost certainly indicates that he had native Iberian maternal ancestry, that his family had arrived to Carthage from Gadir (modern Cádiz) or some of the other Phoenician colonies of Andalusia. The location of his burial at the acropolis and the wealth of the burial goods indicate that he belonged to the highest social elite of the still incipient Carthaginian empire. He has been nicknamed "Ariche" (the loved one) and his face reconstructed as you can see in this blog.

Thanks to Jamel of Lapurdi for the reference an a nice related discussion.

Mitochondrial DNA of ancient Tocharians

Quickies

It seems there is still something to learn about the ancient Tocharian mummies of Uyghuristan:

Chunxiang Li et al., Analysis of ancient human mitochondrial DNA from the Xiaohe cemetery: insights into prehistoric population movements in the Tarim Basin, China. BMC Genetics 2016. Open access → LINK [doi:10.1186/s12863-015-0237-5]

Abstract

Background

The Tarim Basin in western China, known for its amazingly well-preserved mummies, has been for thousands of years an important crossroad between the eastern and western parts of Eurasia. Despite its key position in communications and migration, and highly diverse peoples, languages and cultures, its prehistory is poorly understood. To shed light on the origin of the populations of the Tarim Basin, we analysed mitochondrial DNA polymorphisms in human skeletal remains excavated from the Xiaohe cemetery, used by the local community between 4000 and 3500 years before present, and possibly representing some of the earliest settlers.

Results

Xiaohe people carried a wide variety of maternal lineages, including West Eurasian lineages H, K, U5, U7, U2e, T, R*, East Eurasian lineages B, C4, C5, D, G2a and Indian lineage M5.

Conclusion

Our results indicate that the people of the Tarim Basin had a diverse maternal ancestry, with origins in Europe, central/eastern Siberia and southern/western Asia. These findings, together with information on the cultural context of the Xiaohe cemetery, can be used to test contrasting hypotheses of route of settlement into the Tarim Basin.

Neolithic DNA from Southern Anatolia

I know, I know: I'm decaying into a total procrastinator. I don't have any excuse other than I don't feel like blogging as of late: neither on anthropology nor on politics. I rather feel like learning new stuff and playing, rather than writing and I lack of the structured environment to force myself to do otherwise than what I feel like most of the time. Being of compulsive temperament only worsens things.

I also know that this is not the proper way to start an article. Yes, I know. Do I even care?

So getting to mention now some of the stuff that I have not discussed in these last months and is definitely worth posting about. First of all this key study on more easterly Anatolian early farmers than those seen so far.

Intriguingly they are notoriously similar to those sequenced farther West (see here), what seems to support the model of Anatolian origin of European Neolithic peoples, largely ancestral to modern Europeans. However even Western Anatolian early farmers show already some extra admixture with the Paleoeuropean "WHG" component relative to their Southern Anatolian precursors. So, as the authors suggest, admixture between immigrant farmers and native foragers was a gradual and continuous process beginning in Asia Minor itself.

Gülşah Merve Kılınç, Ayça Omrak, Füsun Özer et al., The Demographic Development of the First Farmers in Anatolia. Current Biology 2016. Open access → LINK [doi:10.1016/j.cub.2016.07.057]

Summary

The archaeological documentation of the development of sedentary farming societies in Anatolia is not yet mirrored by a genetic understanding of the human populations involved, in contrast to the spread of farming in Europe [ 1–3 ]. Sedentary farming communities emerged in parts of the Fertile Crescent during the tenth millennium and early ninth millennium calibrated (cal) BC and had appeared in central Anatolia by 8300 cal BC [ 4 ]. Farming spread into west Anatolia by the early seventh millennium cal BC and quasi-synchronously into Europe, although the timing and process of this movement remain unclear. Using genome sequence data that we generated from nine central Anatolian Neolithic individuals, we studied the transition period from early Aceramic (Pre-Pottery) to the later Pottery Neolithic, when farming expanded west of the Fertile Crescent. We find that genetic diversity in the earliest farmers was conspicuously low, on a par with European foraging groups. With the advent of the Pottery Neolithic, genetic variation within societies reached levels later found in early European farmers. Our results confirm that the earliest Neolithic central Anatolians belonged to the same gene pool as the first Neolithic migrants spreading into Europe. Further, genetic affinities between later Anatolian farmers and fourth to third millennium BC Chalcolithic south Europeans suggest an additional wave of Anatolian migrants, after the initial Neolithic spread but before the Yamnaya-related migrations. We propose that the earliest farming societies demographically resembled foragers and that only after regional gene flow and rising heterogeneity did the farming population expansions into Europe occur.

Autosomal DNA

Maybe the most informative graph is this one (fig. 2):

Genetic Structure and Diversity of Central Anatolian Neolithic Populations
(A) PCA on contemporary west Eurasian populations onto which a total of 85 ancient individuals are projected from this study and previous studies. See Table S1 for number of SNPs per individual. Neighboring modern populations and ancient Anatolian populations are shown encircled. Modern population names are in italics.
Etc. (not so interested here in B, C and D, legend too long, check in the original paper)
Click to expand

It is interesting that, in spite of the Anatolian origin of this ancient ancestral population, they do not tend so much to modern Anatolian Turks but rather to Levant populations like Cypriots (closest ones), Lebanese, Palestinians, etc.

This is probably because, even if early Neolithic peoples of the Levant were not quite like them (see here again) they had become almost like them before the Bronze Age because of regional admixture, which I understand was mostly (but not only) north-to-south flow.

Notice that the Boncuklu (Bon) people had very low genetic diversity and they seem to be a dead end rather than directly ancestral. Instead, the Tepecik-Çiftilik (Tep) population seems a good proxy for the ancestors of Neolithic peoples of Western Anatolia and Europe. 

When we think about South Anatolia Neolithic, we usually think first and foremost about the famous Çatalhöyük site. Well, this ancient settlement is in the area of Boncuklu (to the West, both are near Konya) rather than that of Tepecik-Çiftilik (to the East, near Niğde), so it is quite possible that it is another demographic dead end, related but not directly ancestral to mainline European Neolithic. 

Personally I still think they could well have migrated at least partly by boat, along the southern Turkish coast but, until new data comes, I may need to alter my hypothesis of the ultimate origin being in the Northern Levant (Syria, Lebanon, Cyprus even) rather than Anatolia. These people of Tepecik-Çiftilik were, if not direct ancestors at least very closely related to the actual source population, which may well have lived closer to the coast in any case.

Mitochondrial DNA

The newly sequenced South Anatolian farmers had some of the lineages that were later present in Hungary's and Germany's "Danubian Neolithic", notably the now rare N1a1a1, found in 4/9 samples in this study. Also present were K1a (3/9, incl. one K1a12a), U3 (1/9) and N1a1b (1/9).

So it is time to dismiss the hypothesis that claimed N1a1a1 as a European aboriginal lineage: it came with the immigrant farmers and now there can be no doubt about it.

Neolithic DNA from Greece and NW Anatolia and their influence on Europe

This is a most interesting study that brings to us potentially key information on the expansion of European Neolithic and the formation of modern European peoples.

Zuzana Hofmanová, Susanne Kreutzer et al., Early farmers from across Europe directly descended from Neolithic Aegeans. PNAS 2016. Open access → LINK [doi:10.1073/pnas.1523951113]

Abstract

Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.

Uniparental DNA

One of the most important findings is that the two Epipaleolithic samples from Theopetra yielded mtDNA K1c, being the first time in which haplogroup K has been detected in pre-Neolithic Europe. Sadly enough these two individuals could not be sequenced for full genome. 

The other five individuals are all Neolithic (three early, two late) and did provide much more information.

• Rev5 (c. 6300 BCE): mtDNA X2b
• Bar31 (c. 6300 BCE): mtDNA X2m, Y-DNA G2a2b
• Bar8 (c. 6100 BCE): mtDNA K1a2
• Pal7 (c. 4400 BCE): mtDNA J1c1
• Klei10 (c. 4100 BCE): mtDNA K1a2, Y-DNA G2a2a1b (same as Ötzi's)

I color coded their abbreviated names according to the usage in the study's many maps, for easier reference: green shades are for Greece (Western Macedonia), red shades for Turkey (Bursa district). It is also very convenient to get straight their real geography because many of the map-styled graphs are not precise at all about that:

Fig. 1.

North Aegean archaeological sites investigated in Turkey and Greece.

Autosomal DNA affinities

This is probably the most interesting part. There is a lot about it in the supplementary information appendix but I find that the really central issue is how they relate to each other (or not) and to other ancient and modern Europeans. I reorganized figs S21 and S22 to better visualize this:

Ancient samples compared to each other and other ancient samples ("inferred proportions of ancestry")

Ancient samples compared to modern Europeans ("inferred proportions of ancestry")

So what do we see here? First of all that the strongest contribution of known Aegean Neolithic peoples on mainline European Neolithic is from Bar31, which is from NW Anatolia, and not from Greece. Bar8 is a less important contributor but may have impacted particularly around the Alps (Stuttgart-LBK, modern North Italians).

This goes against most archaeology-based interpretations, which rather strongly suggest a Thessalian and West Macedonian origin of the Balcanic and, therefore, other European branches of the mainline Neolithic of Aegean roots, and do instead support some sort of cultural barrier near the European reaches of the Marmara Sea. Of course we lack exhaustive sampling of Greek Neolithic so far, so it might be still possible that other populations from Thessaly or Epirus could have been more important. However the lack of Anatolian-like influence on the Western Macedonian Neolithic until c. 4100 BCE, makes it quite unlikely.

So it seems that, once again, new archaeogenetic information forces us to rethink the interpretative theories based on other data.

However we do see a strong influence of Greek Neolithic and particularly the oldest sample, Rev5, in SW Europe, very especially among Basques, who seem to have only very minor Anatolian Neolithic ancestry, unlike everyone else relevant here. This impact is also apparent in Sardinia and to some extent North Italy (but overshadowed in these two cases by the one from Anatolia, particularly Bar31).

There are also similar analyses for other four ancient samples (Lochsbour, Stuttgart, Hungary Neolithic and Hungary Bronze) but they don't provide truly new information, so I'm skipping them here. As I said before, there's a hoard of analyses in the SI appendix, enjoy yourselves browsing through them and feel free to note in the comments anything you believe important.

A synthesis of the various "inferred proportions of ancestry" analyses is anyhow shown in fig. 3:

Fig. 3. (click to expand)

Inferred mixture coefficients when forming each modern (small pies) and ancient (large pies, enclosed by borders matching key at left) group as a mixture of the modern-day Yoruba from Africa and the ancient samples shown in the key at left.

The fractions may be misleading however, especially for the ancients. For example: Lochsbour (a total outlier among the ancients in this study) appears best correlated with Pal7 but in fig. S24 it is clear that does no correlate with any Neolithic sample at any significant level. But in general terms it can give a good idea of where does ancestry, particularly for modern samples, come from.

Note: elsewhere someone was being a crybaby about the Polish sample (may well be an error) or the Kalmyk sample (who are obviously most related to East Asians, not used here) but those are minor issues.

Of course there's a lot more to learn from the remains of the ancients. Let's keep up the good work.

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 access → LINK [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.