November 29, 2012

Asturian internal genetic barriers for both uniparental markers (revised)

¡Bumped because of correction and updates that markedly change the original!


Formal correction (Nov 29):

All what I said about not testing for G2a seems incorrect because one individual with this lineage was reported in the Oviedo district. This leaves 21 F(xG2a,K) individuals (15 of them from the Avilés district, making 20% of the local gene pool) in the mystery zone. They could still be other G subclades (but rare in Iberia or elsewhere in Europe), H (but normally thought as restricted to Roma People in Europe) or F* (F-other). 

Some rare F clades have been reported in Europe before but never in such large numbers, I believe. Sadly the authors mention for comparison old (2004-06) studies of the Caucasus, etc. which appear not to have tested for G, leading me to think (with the help of awfully presented, or rather hidden, raw data) that they had not tested for G2a. 

The seem to have done it after all. Thanks for noticing to Jean.

Follows original entry and update (bottom) with haplogroup frequencies (based on the work of Jean Lohizun, who sorted up the raw lists into something you can at least count).

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Original entry (Nov 28):



This new paper on the genetics of Asturias (Iberia) seems to be of limited interest because the authors only appear interested in statistical inference, instead of properly reporting basic data as primary social service of their publicly paid research effort. They also seem dead set into not testing for well known Iberian lineages like Y-DNA G2a (or even G, never mind discerning subclades of E) something that was already obvious in their previous attempt with mtDNA, and seem oblivious to some of the most important work on the population (haploid) genetics of the Iberian Peninsula such as Adams 2008.

Still it may be of interest for data miners but be warned that all the haplogroup data is only available as long unsorted PDF lists in the supplemental material (mtDNA list download, Y-DNA list download).

Antonio F. Pardiñas et al., Assessing the Genetic Influence of Ancient Sociopolitical Structure: Micro-differentiation Patterns in the Population of Asturias (Northern Spain). PLoS ONE 2012. Open access → LINK [doi:10.1371/journal.pone.0050206]

Maybe the only highlight of the study is that the authors infer some genetic barriers within Asturias, especially segregated seem to be the coastal district of Avilés (3) and the mountain miner districts so-called Southern Oviedo and Caudal (5, 9), also including the Narcea (2) district for matrilineages (mtDNA). Meanwhile the largely Galician-speaking Eastern district of Eo-Navia (1) appears segregated only for patrilineages (Y-DNA). 

Figure 2. Map of Asturias showing the SAMOVA group division coupled with the inferred barriers to gene flow.
Panels show results for the mtDNA data (A) and NRY data (B). Thin lines indicate division in the SAMOVA analysis but no actual barrier inference, while inferred barriers between groups are shown by strong lines. Bootstrap value for each of the barriers is shown next to it and only those with values equal or higher than 70 are shown.

The authors find hard to understand the genetic distinctiveness of Avilés district and talk wildly about "basal F" (probably G2a but why did not you test for that?!) Haplogroup G is relatively rare in Asturias but common for example in Portugal or Ibiza, being surely an indicator of Neolithic-derived settlement (found in ancient DNA from Occitan and Catalan Cardium Pottery sites and is also the lineage of the famous Alpine mummy Ötzi, probably also of Cardial ancestry). However, as you may know, no Cardium pottery is known so far to the North or West, so it may indicate a post-Neolithic resettlement of some sort. 

The paper also provides some PC analysis in relation to Europe but fails to explain properly which are each of the various Asturian "groups" (which seem to correspond to clusters by thin lines in the map above - maybe digging in the supp. material... but worth it?)

Figure 3. PCA plot of mtDNA haplogroups of Asturias and other regions of Iberia, the British Isles and Mainland Europe.

Figure 4. PCA plot of NRY haplogroups of Asturias and other regions of Iberia, the British Isles and Mainland Europe.

En fin: a confusing paper that could have been much better or at least user-friendly with some little extra effort and better focus. Still worth mentioning, I guess. 

See also: Asturian mtDNA (on a previous paper by the same team) and category: Iberia


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Update (Nov 29): haplogroup count

Based on lists made by Jean Lohizun.

Y-DNA:
  • E: 22
  • F*: 21
  • G2a: 1
  • I: 5
  • J: 12
  • K*: 9
  • R*: 8
  • R1b1a2: 106

Mitochondrial DNA:
  • HV*: 2
    • HV0*: 9
      • V: 5
    • (within HV4):
      • HV4a*: 5 
        • HV4a1a: 3
      • HV4b: 2
    • HV6: 1
    • HV12b: 13
    • H*: 12
      • H1*: 1
        • H1a*: 1
          • H1a3: 4
        • H1b: 1
        • H1c*: 6
          • H1c3: 3
        • H1f: 2
        • H1h: 4
        • H1j: 3
        • H1x: 1
      • H2a2*: 50
        • H2a2b: 4
          • H2a2b1: 9
        • H2a5b: 1
      • (within H3d):
        • H3d: 6
        • H3f: 6
        • H3g: 12
        • H3h: 3
      • H5: 13
      • H6*: 10
        • H6a1a1a: 1
      • H7a1: 1
      • H9a: 1
      • H10a1: 4
      • H15: 3
      • H20: 1
  • JT*: 1
    • (within J):
      • J1*: 1
        • J1b1a1: 7
        • J1c*: 4
          • J1c1: 5
          • J1c2: 12
      • (within J2):
        • J2a1a: 1
        • J2a2: 1
        • J2b1a: 5
    • T*: 3
      • T1: 1
        • T1a: 9
          • T1a2a: 1
      • T2*: 2
        • T2b*: 16
          • T2b3*: 2
            • T2b3a: 1
        • T2c*: 2
          • T2c1b: 1
        • T2e*: 2
          • T2e1: 4
  • (within U):
    • U1a2: 1
    • U4*: 2
      • U4a1*:2
        • U4a1d: 3
      • U4a3: 1
      • U4b3: 1
    • (within U5):
      • U5a1*: 4
        • U5a1a1: 1
        • U5a1b1*: 1
          • U5a1b1e: 1
      • U5a2: 2 
      • U5b*: 1
        • U5b1b1*: 1
          • U5b1b1e: 1
        • U5b1d: 5
        • U5b1f: 2
        • U5b1g: 1
        • U5b2a1a: 1
        • U5b2a1b: 1
    • U6*: 2
      • U6a:1
    • (within U8):
      • U8a: 1
      • K*: 1
        • K1*: 1
          • K1a*: 2
            • K1a1: 1
            • K1a3a: 3
            • K1a4c: 6
            • K1b1a2: 2
        • K2*: 1
          • K2a: 1
  • R9*: 1
    • R9b2: 1
  • (within N1):
    • I*: 1
      • I1a1: 1
      • I2a: 1
    • N1b: 1
    • N1e'l*: 1
  • W*: 1
    • W1: 1
  • (within X2):
    • X2b: 1
    • X2d: 1
  • (within M):
    • D4k: 1
    • M1*: 1
      • M1b1a: 1
  • (within L3(xM,N)):
    • L3f1b4a: 5
    • L3x: 1
  • L2a: 1
  • L1b: 1

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