Monthly Archives: April 2012
Ancient mitochondrial DNA from the Basque Country and Cantabria: unmistakable mtDNA H in Magdalenian Cantabria
After the first read to the paper my impression was that they had only tested the HVS (both subsectors I and II), leaving some, even if smaller, doubt about the adscription of the Cantabrian Magdalenian lineages to mtDNA H.
But, luckily for truth, Jean Lohizun (see comments) found that the authors, who are partly the same team as Izagirre & De la Rúa 1999 and are using the same methodology up to a point, have actually tested not for coding region SNPs but for a standard list of RFLP markers. However the mention is so cryptic that it is most difficult to find:
In order to classify the mitochondrial variability of the individuals
analyzed in this study, we proceeded to amplify 11 markers, which are
required for defining the 10 Caucasian haplogroups described . The protocol and primers are described in , , . The digestion patterns were verified using a fragment Bioanalyzer (Agilent Technologies).
This seemed to imply that when the authors say “H” they mean -7025a (aka -Alu I) but this marker as such are listed nowhere that we can see easily.
So I squeezed my mind until I concluded that Jean must be correct but a very slight doubt remained, so I emailed the authors, who quickly responded confirming Jean’s keen reading.
Excerpts and translations:
Concepción De la Rúa (corresponding author) said:
Para conocer con más seguridad el haplogrupo, se hicieron además
RFPLs, que es una tecnica que permite evaluar la existencia de
mutaciones puntuales en la region codificante del mtDNA.
Translation: In order to know with greater certainty the haplogroup,
RFLPs were performed, which are a technique that allows for evaluation
of punctual mutations in the coding region of mtDNA.
She added in relation to a previous study of her authorship:
Ambos analisis se realizaron en el paper recien publicado, pero no en
el paper de Izagirre & de la Rúa de 1999, en donde solo se hicieron
Translation: Both analysis [RFLPs and HVS] were made in the recently published
paper but not in that of Izagirre & de la Rúa from 1999, where only
RFLPs were tested for.
Montserrat Hervella (lead author) said:
También, hemos realizado PCR-RFLPs con el fin de determinar los SNPs de la región codificante y así reconfirmar el haplogrupo al que pertenecen cada uno de los haplotipos que hemos obtenido mediante secuenciación. Los enzimas que hemos utilizado aparecen en varias citas bibliográficas en el articulo (17, 20, 42, 63).
La cuestión que nos plantea en torno a la determinación del haplogrupo H, la respuesta es que si hemos usado la enzima Alu I para determinar el SNP en la posición 7025 de la region codificante del ADNmt.
Translation: We have also performed PCR-RLFPs with the purpose of determining the SNPs from the coding region and therefore confirm the haplogroup to which each of the haplotypes obtained by sequenciation belong. The enzimes we used appear in several bibliographic citations in the article (17, 20, 42, 63).
About the question that you ask on the matter of the determination of haplogroup H, the answer is that we have indeed used the enzyme Alu I to determine the SNP in position 7025 of the coding region of mtDNA.
This should dispel any doubt: there was mtDNA H (and H6) in Magdalenian Cantabria.
(End of the edited section)
In any case these are the results as reported by the researchers (and synthesized by me in a single image):
Food for thought (a hypothesis)
As of late, although I have yet to formalize it somehow, I’ve been thinking that a serious possibility is that mtDNA might have spread partly with Dolmenic Megalithism. While there is some apparent Neolithic expansion of H in the Basque area (apparent in this paper and resulting in an almost modern genetic pool), in other parts of Europe this is less obvious, with H showing up but not reaching modern levels just with Neolithic. In fact the loss of other Neolithic lineages like N1a strongly suggests that the populations of Central Europe were largely replaced after the Early Neolithic. Where from? Again from Southwest Europe, I suspect but not in the context that was once believed of Magdalenian expansion, but maybe in the context of Megalithic expansion instead, with origin not in the Franco Cantabrian region but in Portugal.
|Air view of some the acropolis of Zambujal (the roofed area is a modern farm that sits atop)|
The farming way of life originated in the Near East some 11,000 years ago and had reached most of the European continent 5000 years later. However, the impact of the agricultural revolution on demography and patterns of genomic variation in Europe remains unknown. We obtained 249 million base pairs of genomic DNA from ~5000-year-old remains of three hunter-gatherers and one farmer excavated in Scandinavia and find that the farmer is genetically most similar to extant southern Europeans, contrasting sharply to the hunter-gatherers, whose distinct genetic signature is most similar to that of extant northern Europeans. Our results suggest that migration from southern Europe catalyzed the spread of agriculture and that admixture in the wake of this expansion eventually shaped the genomic landscape of modern-day Europe.
|click to enlarge|
We can see that the dominant component of the Megalithic farmer is orange, which is dominant in Sardinia but almost lacks the yellow component dominant in West Asians (and to lesser extent North Caucasus and Italy). The not compared Iberians could be a good match as we can see below.
Update (Jun 8): published in French but it is from the Neolithic, discussed here.
|The Tulum man in situ before the robbery|
|Stone saws from Kostenki|
In my view, the extremely rich archaeological record of the east
European plain clearly supports the two-stage concept of an eastern
Gravettian with occasional leaf point production, followed by a
Gravettian with (Micro)-Gravettes, backed microliths and shouldered
points (Mitoc Malu Galben in the Pruth valley; Molodova 5,
layers VIII and VII; Molodova 1, lower layer; Korman’ 4, layers VII and
VI; Voronovitsa 1, upper layer; and Babin I in the Dnester river basin, Khotylevo 2 in the Desna river basin).
|Reconstructed Kostenki tent/home, one of those not built with mammoth bones|
|From Supplemental Figure 1 – PC analysis|
As you can see in the PCA plot, the inter-population variation is most subtle, almost impossible to discern with so much overlap. The lack of structure repeats for the other components.