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Monthly Archives: April 2012

For those only reading the RSS: Magdalenian mtDNA H in Cantabria confirmed by RFLP testing

Just a short heads up mostly for RSS-only readers to an important update/edit of one of today’s entries:
… on Hervella et al., 2012 (oa).
The key element of novelty is that the authors themselves have confirmed to me by email that they did test for RFLP markers, specifically Alu I in the case of mtDNA H. 
Therefore, against all rumors and confusion, we finally have unmistakable confirmation of the presence of mtDNA H (and H6) in Magdalenian Europe, specifically in Cantabria. It is not any Neolithic arrival to Europe and the studies (not peer-reviewed) of Chandler 2005 and Kéfif 2005, both reporting high mtDNA H in pre-Neolithic Portugal and Morocco can now be seen with a bit more credibility, with less systematic doubts.
For more details read the edited section in the relevant entry.  
Thanks again to the authors for the quick clarification.
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Ancient mitochondrial DNA from the Basque Country and Cantabria: unmistakable mtDNA H in Magdalenian Cantabria

This seems a very important paper because, if everything is correct, it is the first peer-reviewed publication to establish conclusively that mitochondrial haplogroup H, the most common matrilineage of Europe today, existed in Paleolithic populations in Europe, specifically in Cantabria, Spain.
There have been previous reports of such important presence of mtDNA H in the area, notably Chandler 2005 (on Epipaleolithic and Neolithic Portuguese) and Kéfi 2005 (on Upper Paleolithic Moroccans). However both studies were informal for some reason, what has been used by some to grasp for straws in their claim of this lineage having arrived to Europe (and North Africa) only after Neolithic and oversimplify the Paleolithic genetic pool of Europe to almost only variants of haplogroup U (never mind that U is such a large, ancient and widespread haplogroup that saying “U” is almost like saying nothing).


Edited section: the authors did test for RFLPs, the haplogroup assignation is as good as it can be.

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 [63]. The protocol and primers are described in [17], [20], [42]. 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
RFPLs.


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):
Notice that the dots are not really precise in their geographic locator role (I may try creating a better map later).

Instead of using numerals I repeated the name of the reported haplogroup with the intention of giving a more visually intuitive impression (without going through the process of creating charts). 
The results for Paternabidea (tested for coding region markers) were discussed in November. They basically seem to establish that modern Basques are almost identical to Neolithic Basques.
But what about Paleolithic ones? The results of this one study rather suggest that a little bit of both: on the side of continuity, the same U5 sequence is reported for Erraila (Magdalenian) and Marizulo (Neolithic) but, on the side of change, all Paleolithic Basque sequences (n=2) are U5 lineages, while U5 today is a much less important matrilineage. 
It may well be argued that this result is a fluke, a coincidence, but it is consistent with what we see in Epipaleolithic Central and North Europe (mostly U5 with some U4, Bramanti 2009), suggesting that, while the model of recolonization of much of Europe from the Franco-Cantabrian region may well be correct, the story does not end there at all.
On the other side we see that the dominant lineage today among Basques and Western Europeans in general, haplogroup H, was already present in Magdalenian times in Cantabria, what is consistent with it being found in Epipaleolithic Portugal and Oranian Morocco and really puts to rest the hypothesis that promoted that it had arrived from West Asia with Neolithic colonists (something argued as a matter of fact but without any clear evidence). 

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. 

This is just a draft hypothesis that I have mentioned before only in private discussions or at best in the comments section somewhere, and certainly it would need more research. My main argument is that before these results for Cantabria, the only pre-Neolithic location where the data clearly suggested very high levels of mtDNA H (near 75%) was Portugal (Chandler 2005) and Portugal played a major role in Neolithic and Chalcolithic Western Europe. As I said above, ancient Portuguese apparently developed the Dolmenic Megalithic pehnomenon (culture, religion…), later they developed some of the earliest Western European civilizations, since the Third millennium BCE, specially Zambujal (also at Wikipedia), which were central elements of this long-lasting Megalithic culture and later of the Bell Beaker phenomenon as well.
And we need very high levels of mtDNA H in a colonizer population to changed the genetic landscape from c. 20% H into c. 45% H, we need something like a 70-80% H ancestral population unless replacement was total, what I think unlikely. 
What happened to that overwhelmingly H population of Portugal (assuming that the hypothesis is correct)? They were probably colonized in due time, possibly in the Bronze Age (the mysterious archaeological “horizons” that replace urban life in much of Southern Portugal in that period with their strange crab-shaped elite tombs, vaguely resembling Mycenaean circular walled ones)  and/or in the period of Celtic invasions from inland Iberia later in the Iron Age (Hallstat periphery).
It’s just a tentative hypothesis so far but one that I believe I must state for your consideration.

Air view of some the acropolis of Zambujal (the roofed area is a modern farm that sits atop)

 

Swedish Neolithic autosomal comparisons

In brief: it suggests Iberian-like and Russian-like origins for two different Neolithic populations of Scandinavia.

Abstract

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. 

I don’t have access to the paper as such but the substance seems to be, as so often, in the supplementary materials, which are freely available (direct PDF link). 

The study analyzes the autosomal genetic signature of four prehistoric Swedes from the Neolithic period. Three are from Götland and belong to the regressive (neo-hunter, forest Neolithic) Neolithic culture of Pitted Ware, which has its roots probably in the Neolithic of Eastern Europe (Dniepr-Don culture). While they have been used as proxy for Paleolithic peoples, the comparison is not really valid: they were probably recent immigrants from Eastern Europe (or admixed with the Paleolithic locals maybe) with a Neolithic background although, because of the peculiarities of the Baltic frontier, they were not much into farming (it seems), although they did keep pigs. 
At the right, meet what is left from one of them, known as Ajvide 70. We can see some of the characteristic burial traits common in Pitted Ware culture but also in their apparent ancestors from Dniepr-Don culture (farmers): burial in extended position with ochre (visible at the legs in this case). 
The fourth one is from South-Western Sweden, near Göteborg and is consistently described as “farmer”. This individual belonged to the Megalithic cultural phenomenon (or more properly Dolmenic Megalithism, as there are some megalithic structures that may not be related or only tangentially so) that began in SW Iberia c. 5000 BCE and which is characterized by collective (clannic?) burial in dolmens, where the older burials were pulled aside to make room for the new ones. They also buried their people in extended position although the use of ochre is less common. 
Dolmenic Megalithism extended since the fourth millennium (at least a thousand years after it was conceived in SW Iberia) through much of Atlantic Europe, being these settlements of Southern Sweden in their further North-Eastern reach (together with Denmark and much of Low Germany). Later, after the loss of those areas to the Indoeuropeans of Kurgan cultural background (Corded Ware) the phenomenon would also expand into the West and even Central Mediterranean (North Africa, Italy)… but that’s another story.
Both burial traditions stand in contrast with those of the Neolithic cultural arrivals from the Balcans (and possibly earlier from West Asia), the Balcano-Danubian tradition and the Cardium Pottery one of most European Mediterranean areas, which practiced burial in flexed or fetal position. 
So let me emphasize my point: both groups studied here are Neolithic but both belong to cultures which are not exactly what we could describe as “core Neolithic” but rather cultures that appear to have at least partial roots in Paleolithic Europe: one from the East and the other from the Southwest and later all the West. 
Interestingly the autosomal genetics of these two groups are consistent with what I just outlined: the Pitted Ware people resemble Eastern Europeans, while the Megalithic farmer clusters best with Iberians and other SW Europeans.
Visually (all from the supplemental materials):
Cluster analysis (K=4):

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.
Two of the three Pitted Ware individuals cluster best with Russians, while the third does instead with some Finnish maybe. 
The main difference with modern populations in general is that the yellow (West Asian) component is residual, exactly as happens among modern Basques, Sardinians and Finns, which may have been rather isolated all this time. 
Several Principal Component analyses:

Judge yourselves because these comparisons are never 100% conclusive, but my impressions is that the Megalithic farmer (red) clusters mostly with Iberians, except in the last graph where it does with the British-CEU sample.
The Pitted Ware samples (cyan or sky blue) are less precise (they are three after all) but where Eastern European samples other than Finnish are available for comparison, they tend to cluster with them (or between them and Sweden and Finland). In the last panel, where Swedes have been oversampled and non-Finnic Eastern Europeans removed, Ire8 and Ajv52 cluster withing modern Northern Swedes, while Ajv70 is anomalous. 
So I do not think that the conclusions publicited in the press release (which are probably also those of the paper) can be taken at face value but rather with a good pinch of salt: the factual data seems to suggest that the genetics of these prehistoric people are quite related to that of modern Europeans from Scandinavia, Eastern and Western Europe. The comparison cannot be expected to produce identical individuals because, no matter how hard we might try or how much we may owe them in a sense, we are not our ancestors.
 

Ancient DNA from Santimamiñe (Biscay): not yet published but on the way

Researchers from the University of the Basque Country (UPV-EHU) have already sequenced but not yet published, it seems, mitochondrial DNA from the Paleolithic inhabitants of Santimamiñe, a cave with a lengthy sequence from the Gravettian (and earlier Mousterian and Chatelperronian but these are supposed to be Neanderthals) to the Iron Age. 
The cave is located not far from Gernika, in the municipality of Kortezubi and hosts some rock art of bisons, horses and bears, all located in a small hidden corner that I had the luck to visit as a kid (now it’s not accessible to the general public for preservation reasons).
At the moment of writing this, I am not very sure to which period the human remains belong. Publications usually emphasize the techno-cultural and artistic aspects and unless a skull would have been found, what is not the case, there is little emphasis on human remains. However nowadays, with the advent of genetics, they get a new significance as, at least potentially, links to modern and other prehistoric people can be established or discarded, producing potentially valuable information for the understanding of Prehistory. 
On May 6th the research team is heading to the area to collect samples from maternally-rooted locals, in order to compare with the already decoded but not yet published ancient DNA sequence. 
I can’t way to read the results, you can imagine. But even more because one of my ancestral lineages, the patrilineal one, is from a nearby village: Ibarrangelua.
I just hope that they have done the testing properly and not just sequenced the control region (HVS), which is often more confusing than revealing. 
Source[es]: Deia (found via Pileta).

Update (Jun 8): published in French but it is from the Neolithic, discussed here.

 

Key remains of American Prehistory stolen

The Tulum man in situ before the robbery
The skeleton known as Tulum man, found in a cenote (flooded underground chasm) in Quintana Roo, Mexico, and which was not yet retrieved from site by archaeologists, has gone missing. 
The Tulum man was dated to at least 10,000 years ago and therefore was one of the key pieces in the reconstruction of the Prehistory of America.
The managers of the research project, dependent of the National Institute of Anthropology and History (INAH) have denounced having been repeatedly the victim of thieves. That in spite of having kept a policy of strict discretion about the exact location of the findings. 
Requests of help have been distributed among divers because such a heist would have needed the participation of several of them.
Source: Milenio[es].
 

A qualified opinion on the Eastern Gravettian

The always interesting Aggersbach’s Paleolithic Blog offers today an entry pondering the Eastern Gravettian and the so-called Willendorf-Kostenki complex. You probably want to read it in full but in any case I appreciate a pondered opinion on these matters, which may help us to understand better the overall process of the European Upper Paleolithic. 

Stone saws from Kostenki

My pick is:


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).

Also mentioned, as the best approximation to a non-existing online paper in English about the Willendorf-Kostenki complex is an article at another fabulous and veteran site: Don’s Maps, from which I’m borrowing some illustrations to complement this entry.

Reconstructed Kostenki tent/home, one of those not built with mammoth bones
 

Cis-regulatory variability has almost no geographic structure

That is what a new paper has found:
Cis-regulatory elements are key pieces of the overall codification of the genome. The main finding of this paper is that they show almost no geographic structure, that virtually all variation in these key elements is inter-individual and not among populations.

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.