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March 29, 2021

Basque against the Romans

Filed under: Basque,Human Genetics — Razib Khan @ 8:56 pm

Genetic origins, singularity, and heterogeneity of Basques:

Basques have historically lived along the Western Pyrenees, in the Franco-Cantabrian region, straddling the current Spanish and French territories. Over the last decades, they have been the focus of intense research due to their singular cultural and biological traits that, with high controversy, placed them as a heterogeneous, isolated, and unique population. Their non-Indo-European language, Euskara, is thought to be a major factor shaping the genetic landscape of the Basques. Yet there is still a lively debate about their history and assumed singularity due to the limitations of previous studies. Here, we analyze genome-wide data of Basque and surrounding groups that do not speak Euskara at a micro-geographical level. A total of ∼629,000 genome-wide variants were analyzed in 1,970 modern and ancient samples, including 190 new individuals from 18 sampling locations in the Basque area. For the first time, local- and wide-scale analyses from genome-wide data have been performed covering the whole Franco-Cantabrian region, combining allele frequency and haplotype-based methods. Our results show a clear differentiation of Basques from the surrounding populations, with the non-Euskara-speaking Franco-Cantabrians located in an intermediate position. Moreover, a sharp genetic heterogeneity within Basques is observed with significant correlation with geography. Finally, the detected Basque differentiation cannot be attributed to an external origin compared to other Iberian and surrounding populations. Instead, we show that such differentiation results from genetic continuity since the Iron Age, characterized by periods of isolation and lack of recent gene flow that might have been reinforced by the language barrier.

The main takeaway seems to be that Basque distinctiveness dates to the Roman period.

September 7, 2012

Across the sea of grass: how Northern Europeans got to be ~10% Northeast Asian

Across the sea of grass: how Northern Europeans got to be ~10% Northeast Asian

The Pith: You’re Asian. Yes, you!

A conclusion to an important paper, Nick Patterson, Priya Moorjani, Yontao Luo, Swapan Mallick, Nadin Rohland, Yiping Zhan, Teri Genschoreck, Teresa Webster, and David Reich:

In particular, we have presented evidence suggesting that the genetic history of Europe from around 5000 B.C. includes:

1. The arrival of Neolithic farmers probably from the Middle East.

2. Nearly complete replacement of the indigenous Mesolithic southern European populations by Neolithic migrants, and admixture between the Neolithic farmers and the indigenous Europeans in the north.

3. Substantial population movement into Spain occurring around the same time as the archaeologically attested Bell-Beaker phenomenon (HARRISON, 1980).

4. Subsequent mating between peoples of neighboring regions, resulting in isolation-by-distance (LAO et al., 2008; NOVEMBRE et al., 2008). This tended to smooth out population structure that existed 4,000 years ago.

Further, the populations of Sardinia and the Basque country today have been substantially less influenced by these events.


It’s in Genetics, Ancient Admixture in Human History. Reading through it I can see why it wasn’t published in Nature or Science: methods are of the essence. The authors review five population genetic statistics of phylogenetic and evolutionary genetic import, before moving onto the novel results. …Across the sea of grass: how Northern Europeans got to be ~10% Northeast Asian

February 25, 2012

Basque maternal heritage & continuity

Filed under: Agriculture,Anthroplogy,Basque — Razib Khan @ 3:02 pm

There’s a new paper in AJHG which caught my eye, The Basque Paradigm: Genetic Evidence of a Maternal Continuity in the Franco-Cantabrian Region since Pre-Neolithic Times (ungated). The first thing you need to know about this paper is that it focuses on only the direct maternal lineage of Basques via the mtDNA. In some ways this is weak tea, since it doesn’t give us a total genome estimate. But there are major upsides to mtDNA and Y. First, because of the lack of recombination it is relatively easy to generate a nice phylogenetic tree using a coalescent model. And second, for mtDNA the molecular clock is considered relatively reliable.

In this specific paper they also expanded the scope of their analysis to the whole mtDNA sequence, instead of just the hypervariable region. Not only did they look at whole sequences, but they also had an enormous sample size. They sequenced over 400 mtDNA genomes from the Basque country and neighboring regions. Haplogroup H peaks in frequency among Basques, and drops off among their neighbors (Gascons, Spaniards, etc.). Because the Basque speak a non-Indo-European language they are usually presumed to be indigenous in relation to their neighbors (or at least more indigenous). Until recently there was a strong presupposition that the Basque were ideal representatives of the pre-Neolithic populations of Western Europe. One common method of analysis would be to use the Basque as a pre-Neolithic “reference,” and simply estimate the impact of a Neolithic demographic wave of advance by using a eastern Mediterranean population as a second “reference” within an admixture framework. But more recent work has muddled the idea that the Basque are the descendants of Paleolithic Europeans. Finally, I suspect we’ll also have to acknowledge complexity in demographic histories. To say that the Basque exhibit continuity with Mesolithic Iberians may not contradict a substantial Neolithic contribution. South Asians for example are one numerous modern group which exhibits sharply divergent affinities if you use Y chromosomes (West Eurasian) or mtDNA (not West Eurasian). Why? The details are prehistorical.

The major takeaway from this paper is that the Basque mtDNA exhibit a pattern of demographic expansion ~4,000 years BP, and ~8,000 years BP. But I think it is important to look at the range of outcomes over their confidence intervals, so I’ve reproduced their second table below:

Table 2. Time Estimates of the Six Autochthonous Haplogroups

HaplogroupNPercentageRhoStandard ErrorAge (in Years)95% Confidence Interval
Coalescence Age
H1j15212.4%1.860.4948452324 − 7408
H1t1348.1%1.940.97505799 – 10176
H2a5a1225.2%1.330.653422118 – 6800
H1av1174.0%1.240.523213567 – 5906
H3c2a143.3%1.270.3732911403 – 5204
H1e1a1122.9%1.230.723187−464 – 6927
Splitting Age
H1j15212.4%2.861.1175141764 – 13470
H1t1348.1%2.941.397730554 – 15227
H2a5a1225.2%2.331.196094−6 – 12434
H1av1174.0%2.241.13585465 – 11860
H3c2a143.3%2.271.075934443 – 11619
H1e1a1122.9%5.232.13140112729 – 26000

For our purposes the splitting age is important, because it shows when the Basque specific H lineages diverged from other European H lineages. Some of the intervals are huge (look at H1e1a1), so I don’t know what to make of it. I’ll leave further comments to those more well versed in the mtDNA literature, but I would like to say that it is important to remember that we don’t know where the demographic events inferred occurred. It may not have been in the trans-Pyrenees region at all.

More later.

Basque maternal heritage & continuity

June 27, 2011

First Farmers Facing the Ocean

First Farmers Facing the Ocean

The image above is adapted from the 2010 paper A Predominantly Neolithic Origin for European Paternal Lineages, and it shows the frequencies of Y chromosomal haplogroup R1b1b2 across Europe. As you can see as you approach the Atlantic the frequency converges upon ~100%. Interestingly the fraction of R1b1b2 is highest among populations such as the Basque and the Welsh. This was taken by some researchers in the late 1990s and early 2000s as evidence that the Welsh adopted a Celtic language, prior to which they spoke a dialect distantly related to Basque. Additionally, the assumption was that the Basques were the ur-Europeans. Descendants of the Paleolithic populations of the continent both biologically and culturally, so that the peculiar aspects of the Basque language were attributed by some to its ancient Stone Age origins.

As indicated by the title the above paper overturned such assumptions, and rather implied that the origin of R1b1b2 haplogroup was in the Near East, and associated with the expansion of Middle Eastern farmers from the eastern Mediterranean toward western Europe ~10,000 years ago. Instead of the high frequency of R1b1b2 being a confident peg for the …

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