Refined Basque-centric mitochondrial lineages

A new study has located some mitochondrial lineages that seem to be specific of Basques and nearby populations.

Sergio Cardoso et al., The Expanded mtDNA Phylogeny of the Franco-Cantabrian Region Upholds the Pre-Neolithic Genetic Substrate of Basques. PLoS ONE 2013. Open access → LINK [doi:10.1371/journal.pone.0067835]

Abstract

The European genetic landscape has been shaped by several human migrations occurred since Paleolithic times. The accumulation of archaeological records and the concordance of different lines of genetic evidence during the last two decades have triggered an interesting debate concerning the role of ancient settlers from the Franco-Cantabrian region in the postglacial resettlement of Europe. Among the Franco-Cantabrian populations, Basques are regarded as one of the oldest and more intriguing human groups of Europe. Recent data on complete mitochondrial DNA genomes focused on macrohaplogroup R0 revealed that Basques harbor some autochthonous lineages, suggesting a genetic continuity since pre-Neolithic times. However, excluding haplogroup H, the most representative lineage of macrohaplogroup R0, the majority of maternal lineages of this area remains virtually unexplored, so that further refinement of the mtDNA phylogeny based on analyses at the highest level of resolution is crucial for a better understanding of the European prehistory. We thus explored the maternal ancestry of 548 autochthonous individuals from various Franco-Cantabrian populations and sequenced 76 mitogenomes of the most representative lineages. Interestingly, we identified three mtDNA haplogroups, U5b1f, J1c5c1 and V22, that proved to be representative of Franco-Cantabria, notably of the Basque population. The seclusion and diversity of these female genetic lineages support a local origin in the Franco-Cantabrian area during the Mesolithic of southwestern Europe, ~10,000 years before present (YBP), with signals of expansions at ~3,500 YBP. These findings provide robust evidence of a partial genetic continuity between contemporary autochthonous populations from the Franco-Cantabrian region, specifically the Basques, and Paleolithic/Mesolithic hunter-gatherer groups. Furthermore, our results raise the current proportion (≈15%) of the Franco-Cantabrian maternal gene pool with a putative pre-Neolithic origin to ≈35%, further supporting the notion of a predominant Paleolithic genetic substrate in extant European populations.

I'd say that the finding of these three lineages is in itself the interesting part. The molecular-clock-o-logical speculations are something that as, you know, I tend to ignore. However these seem to be almost invariably just fractions of the realistic dates when properly calibrating, so if the authors get a 10 Ka date, then we can be reasonably sure that it is a minimum date and that the likely actual date can well be twice that figure (although in the case of mtDNA this may depend on each particular branch, as these are very unequal). 

Another important note is that the authors rather studied the sub-Pyrenean isthmic region rather than the original Franco-Cantabrian region, which corresponds mostly to what is now Southern France. I am always rather skeptic about attributing to Basques exclusively the legacy of this wider Paleolithic region and I want to insist that Southern France's peoples (Gascons, Occitans, Perigordians and all others south of the Nantes-Lyon line) be studied in depth and detail along Basques, Cantabrians and Asturians. At the very least this study has an important Gascon sample (Bearn, Bigorre and Chalosse), although it is from the areas closest to the Basque Country.

In a previous study by the same team (2011), they detected apparent Basque (or is it Gascon?) centrality of lineages J1c and U5b. In this study they refine those findings by locating some sublineages that are more clearly Basque-specific: J1c5c1 and U5b1f. They also spotted another Basque-centric haplogroup within V: V22. 

Figure 1. Maximum parsimony trees of haplogroups U5b, J1c and V including the three autochthonous lineages U5b1f, J1c5c1 and V22.
These trees are extracted from the maximum parsimony phylogenetic tree of 76 complete mtDNA sequences of the Franco-Cantabrian region shown in detail in Fig. S1. Mutations are displayed along the branches. All mutations are transitions unless a suffix specifies a transversion (A, C, G, T). Recurrent mutations within the complete phylogeny of the Franco-Cantabrian area are underlined. The prefix ‘‘@’’ indicates a back mutation. Mutational hotspot variants such as 16182, 16183, or 16519, or a variation around position 310 or 523–524, as well as length heteroplasmies were not considered for the phylogenetic reconstruction. All the samples are colored according to their geographic origin, as shown in the legend. For phylogeny construction, five previously published mitogenomes belonging to subhaplogroups U5b1f (JX286537 and DQ156208), J1c5c1 (JQ702776 and JQ704051) and V22 (HQ384212) were included (GenBank accession numbers in the tree). German ethnicity was declared for sample JX286537 in GenBank; however, maternal ancestry in southwestern Europe cannot be ruled out owing to the absence of lineage U51bf in populations outside the Franco Cantabrian area (see Tables S2 and S3). French B.C. refers to samples from the French Basque Country.

As for the apportions, table S3 provides them for U5b1f and J1c5c1, however I could not find anywhere the frequencies of V22 nor other lineages (although there is a list of lineages on a reduced sample in table S1). Sorted by frequency:

U5b1f:

1. Lapurdi: 24.1%
2. NE Navarre: 23.6 %
3. Zuberoa: 17.7%
4. NW Navarre: 17.0%
5. North Navarre: 15.2%
6. Chalosse (Dax district): 15.0%
7. Bearn: 12.5%
8. Gipuzkoa: 11.8%
9. SW Gipuzkoa: 9.5%
10. Bigorre: 9,5 %
11. Low Navarre: 8,2%
12. Central-West Navarre: 7.8%
13. Burgos (Castile): 4.2%
14. La Rioja: 3.8%
15. Biscay: 3.6%
16. Zaragoza (Aragon): 2.5%
17. Catalonia: 0.7%
18. Araba: 0.05%

Not detected in: West Biscay (Enkarterriak), Pas Valley, Cantabria, (North?) Aragon, Madrid, Perigord-Limousin.

So this U5b1f lineage seems concentrated around the Western Pyrenees with a highest density axis between, say, Baiona (Bayonne) and Zangoza (Sangüesa). It is a most important lineage in that core Eastern Basque and Southern Gascon area with frequencies above 5% and reaching almost to 25% in some cases.

While we can appreciate the clinal decline in Iberia, lack of data for Gascony and most of the Paleolithic Franco-Cantabrian region (i.e. Southern France) leaves us without similar data for the northern cline, knowing only that in Perigord-Limousin is 0%. This last detail may explain why the haplogroup is contained within the wider Basque area, as Perigord (and not the Basque Country) was the true center of the Franco-Cantabrian region, a district I have dubbed sometimes "the metropolis of Paleolithic Europe". Rather than looking for signals of expansion from the Basque Country only, researchers should look for such signals of expansion from Perigord particularly (as well as the whole Franco-Cantabrian region, from Provence to Asturias and from the Loire to the Pyrenees). 

Haplogroup U among Basques and Pasiegos (from fig. S1)

J1c5c1:

1. Zuberoa: 4.8%
2. NW Navarre: 3.8%
3. Chalosse (Dax): 3.3%
4. Central-West Navarre: 3.1%
5. Low Navarre: 2.7%
6. North Navarre: 2.4%
7. Gipuzkoa: 2.2%
8. NE Navarre: 1.8%
9. Bearn: 1.8%
10. Lapurdi: 1.7%
11. Zaragoza: 1.2%
12. Araba: 1.0%
13. Biscay: 0.08%

Not detected in: SW Gipuzkoa, West Biscay (Enkarterriak), Bigorre, La Rioja, Burgos, Catalonia, Pas Valley, Cantabria, (North?) Aragon, Madrid, Perigord-Limousin.

Again the lineage, even if much less common, is concentrated around the Western Pyrenees, with a highest density axis from say, Leitza to Maule, spilling to Chalosse and Bearn by the NE but again reaching zero frequencies at Perigord-Limousin (and not knowing how it behaves in between). In Iberia, outside of the Basque Country, is only found in the city of Zaragoza. 

As happens with U5b1f, J1c5c1 quickly declines towards the West in the Southern Basque Country, what may be ground, especially if other lineages also follow this pattern, to consider two original Basque populations: one around the Western Pyrenees and another one around Biscay. This idea, while not commonly formulated, would not be new at all, for example F. Krutwig already suggested in the mid 20th century that Central-Eastern Basques had a Dinaric-like morphology (pseudo-Dinaric, because "true Dinarics" are supposed to be brachicephalic while Basques are usually mesocephalic, like most Europeans), while Biscayans would be rather dominated by the rare Dalic anthropometric type instead. Debatable, of course, but that's what we are here for, aren't we?

Haplogroup JT among Basques and Pasiegos (from fig. S1)

V22:

The study does not directly provide the frequency data for this lineage (they excuse themselves on technical HVS reasons, a very typical problem when working with HV lineages), so I had to work with supplemental table S1, where the HVS-I haplotypes and attributed haplogroups are listed (over a reduced sample of just 76 individuals). My synthesis is:

1. Low Navarre: 1/4 (25.0%)
2. Gipuzkoa: 2/10 (20.0%)
3. Biscay: 1/9 (11.1%)
4. West Navarre: 3/33 (9.1%)
5. Pas Valley: 1/19 (5.3%)

Not detected in Araba's single-person sample: 0/1.

I wouldn't dare to reach any strong conclusions with such small and irregular sample but it does look like the Northern Basque Country and Gipuzkoa have the highest frequencies, what suggests that maybe the lineage extends to the North into Gascony, etc. Unlike the previously discussed lineages in this case the decline towards the West is not as sharp.

Haplogroup R0 among Basques and Pasiegos (from fig. S1)

See also:

• Strontium data shows that Aldaieta remains are mostly local Basques - but some immigrants too
• Ancient DNA comparison supports continuity in the Basque Country
• More North Iberian Epipaleolithic mtDNA (and first Epipaleolithic nuclear DNA)
• Ancient mitochondrial DNA from the Basque Country and Cantabria: unmistakable mtDNA H in Magdalenian Cantabria
• Basque and Gascon Y-DNA survey
• Basque mtDNA
• Neolithic Basque (and Catalan, and Aragonese) mtDNA
• Basque autosomal genetics
• Basque-specific mtDNA lineages (preliminary to this study: J1c and U5b were detected as Basque-centric)
• Mitochondrial DNA of West Europe