April 02, 2009

Internal variation within mtDNA macro-haplogroup R0

PLoS ONE doi:10.1371/journal.pone.0005112

New Population and Phylogenetic Features of the Internal Variation within Mitochondrial DNA Macro-Haplogroup R0

Vanesa Álvarez-Iglesias et al.



R0 embraces the most common mitochondrial DNA (mtDNA) lineage in West Eurasia, namely, haplogroup H (~40%). R0 sub-lineages are badly defined in the control region and therefore, the analysis of diagnostic coding region polymorphisms is needed in order to gain resolution in population and medical studies.

Methodology/Principal Findings

We sequenced the first hypervariable segment (HVS-I) of 518 individuals from different North Iberian regions. The mtDNAs belonging to R0 (~57%) were further genotyped for a set of 71 coding region SNPs characterizing major and minor branches of R0. We found that the North Iberian Peninsula shows moderate levels of population stratification; for instance, haplogroup V reaches the highest frequency in Cantabria (north-central Iberia), but lower in Galicia (northwest Iberia) and Catalonia (northeast Iberia). When compared to other European and Middle East populations, haplogroups H1, H3 and H5a show frequency peaks in the Franco-Cantabrian region, declining from West towards the East and South Europe. In addition, we have characterized, by way of complete genome sequencing, a new autochthonous clade of haplogroup H in the Basque country, named H2a5. Its coalescence age, 15.6±8 thousand years ago (kya), dates to the period immediately after the Last Glacial Maximum (LGM).


In contrast to other H lineages that experienced re-expansion outside the Franco-Cantabrian refuge after the LGM (e.g. H1 and H3), H2a5 most likely remained confined to this area till present days.



Maju said...

Interesting, thanks.

While the abstract mentions the age estimate of c. 11,000 BP for the major H subclades, it is now known that H2-CRS has been found in early Gravettian Italy dated c. 28,000 BP [doi: 10.1371/journal.pone.0002700] and that H (no subclades specified) was already dominant in Epipaleolithic Portugal c. 8,000 BP (not V though that only appears in Neolithic samples).

An interesting piece of info is the fig. 3 map series. In it H* (underived?) is found mostly in mainland Europe, between France and Turkey, with offshots in the Caucasus area. H1 and H3 show a western distribution, H4 and H6a an Iberian one, while H2a and H11 show instead a rather Eastern European pattern. H8 is Central Asian mostly, while H5a and H7 show scattered patterns. There is no single H subclade with a West Asian core apparently, what to me suggests that haplogroup H as a whole expanded from Europe, regardless of the secondary Magdalenian expansion of H1 and H3. A likely scenario for H expansion is Gravettian culture.

Complementary info for North Africa can be found in Enafaa et al., 2009 (found at Mathilda's blog). It is nteresting that the two most common H subclades in North Africa are precisely H1 (42% of all H) and H3 (13%), the former clearly dominant along the Atlantic facade and the latter more concentrated in the Mediterranean one. Neither one can be linked to a West Asian source and another recent paper determined that they were a subset of Iberian variability, in Tunisia at least. Other somewhat relevant subclades in North Africa are H4 (5%, concentratd among Berbers) and H7 (also 5% concentrated in Tunisia and Mauritania). These two clades could have West Asian or European origins (unclear). Overall H ammounts to some 25% of North African mtDNA (224/880), being highest among Berbers (Mor, Tun) and lowest in Mauritania.

Unless Iberian-derived H in North Africa arrived there with Megalithism (i.e. very late in Chalcolithic times), there is only one moment where it could have spread: the Iberomaurusian genesis, possibly derived from Southern Iberian Gravetto-Solutrean. This would date to c. 20,000 BP and would makes sense with a Gravettian origin and spread of H.

Ponto said...

I have already stated that the age finding of the CRS in bones from Italy supposedly from a Cro Magnoid human estimated age 28 kya is probably contamination from the people who dug those bones out of the cave floor or the osteologists who examined the bones or museum employees. The CRS is found mostly in Eastern Europe and is Middle Eastern in origin. I accept the age estimates of haplogroups as done in most reputable genetic studies.

MtDNA haplogroup U is very old, 60 kya, but that does not mean it was in Europe at that time. Middle Eastern people could have brought the haplogroup or subclades of it to Europe only 15 kya.

Studies of ancient remains has shown time and again that we modern European people are not representatives of our ancestors. Our haplogroup frequencies are not theirs, not are they the same. Even the Iceman Otzi had a mtDNA group K which has not been found in any living European, it is extinct. So mtDNA haplogroup V has not been found in some old remains from Iberia. Not a surprise is it? By the way, I am haplogroup V. I am also Y haplogroup J1, and I don't match with any non Europeans, my genetic cousin is American of Italian origin, and my closest matches otherwise are in the North of Portugal near Galicia. Haplogroup frequencies in Eurasia today as just part of the story of human movements in that region not the whole story. And remember there were Paleolithic humans in the Middle East long before they were in Europe, and their descendants still live there.

Maju said...

Re. "contamination" of the sample:

The fragmentised remains (tibia, skulls, jaw and maxilla) of a Cro-Magnon individual, named Paglicci 23, were excavated by F.M in 2003 from the Paglicci cave, Southern Italy. Radiocarbon tests dated the layer to 28.100 (+/−350) years ago [24]. Because of its fragmentary nature, the sample was neither restored nor studied from the morpho-anatomical point of view. Therefore, no contamination could possibly be introduced at these stages by direct handling and washing. The remains were deposited in the storage room at controlled temperature in the Department of Archaeology, University of Pisa. In 2005 three splinters, a piece of tibia (Figure 1) and two pieces of skull, were moved to the ancient DNA laboratory at the University of Florence. In the course of the whole process, from excavation of the remains to genetic typing, only seven persons had any contacts with the sample, namely six of us (F.M, S.V, A.M., E.Pi., M.L., and D.C.) and Carles Lalueza-Fox (hereafter: C.L.) who replicated the sequence at the University Pompeu Fabra, Barcelona.

Have you even read the relevant paper? It details very well how the sample could not be contaminated and how the analysis showed it was not contaminated.

MtDNA haplogroup U is very old, 60 kya...

Haplogroup U is separated from the R node by exactly 3 SNPs, while haplogroup R0 (pre-HV) is separated by 2 SNPs and HV by 3 (one more). Hence, R0 is likely to be somewhat older than U, and HV of about the same age as U. That assuming there's anything like the "molecular clock".

H is derived (from the R node) by 5 SNPs, while the main European U subclades are derived by 6 SNPS (U3,4,8,9 and U6) and 7 SNPs (U5 and U7). Hence European U would be if anything somewhat younger than H.

This would alone perfectly explain why H is dominant, especially in the West. Because H (that shows a mainland European core apparently) can perfectly be Aurignacian (what fits well with the starlike boom), while U would have either gone with it in smaller ammounts or participated in later expansions (like Gravettian, more relevant towards the East - this would apply particularly to U5).

I have always been flippant that U was claimed to be Aurignacian and H presumed Gravettian because their distribution is exactly the opposite as would be expected with such chronology. But if H is Aurignacian and at least U5 more strictly associated with Gravettian, everything makes sense. And, counting SNPs, U5 is younger than H.

Studies of ancient remains has shown time and again that we modern European people are not representatives of our ancestors.

Which studies? I have read some on not so ancient remains (i.e. Medieval basically) and the results are not really different. The apportions vary somewhat (as with any two samples) but the general picture is the same, even if some authors have written down the opposite conclusions in spite of the data for reasons that I cannot understand (except ideological bias).

I have also mentioned above a case of Epipaleolithic and Neolithic aDNA in which the overall pattern is of continuity even if, surely because of Zilhao's presence among the authors (he holds strong opinions against demic continuity and is a very opinionated person for what I know), the conclussions went against the evidence of the raw data: claiming discontinuty where anybody could see mostly continuity.

So I ask you and everyone to read the raw data and not so much only the conclussions, which are often biased.

Even the Iceman Otzi had a mtDNA group K which has not been found in any living European, it is extinct.

Even if it is (of what you cannot be totally sure), it means nothing. It's anecdotic data.

So mtDNA haplogroup V has not been found in some old remains from Iberia. Not a surprise is it?

It has not been found in pre-Neolithic Portuguese but was found in early Neolithic ones. That and the presence of some N* or R* in the Paleolithic sample was all the difference. H and U (but not K, J, T, I, X or W) were there all the time in about the same hegemonic apportions. I read continuity with minor changes, Chandler, Sykes and Zilhao claim radical discontinuty instead (what makes absolutely no sense to me). V anyhow could perfectly have arrived from Catalunya for what I know (assuming it was foreign at all).

Maju said...

And FYI, Galicia and Northern Portugal were surely one of the last provinces of all Europe ever colonized by H. sapiens. There is absolutely no evidence of the presence of AMHs in that region until deep in Neolithic times, almost Megalithic.

The only exception is a small coastal area near Asturias that experienced some Epipaleolithic colonisation. Before that, the western border of Humankind in Northern Iberia was in the middle of Asturias - and that applies to all the Upper Paleolithic.

That means that Galicians and Northern Portuguese have with all likehood many more Neolithic and post-Neolithic founder effects than any other Atlantic European people. In fact they are pretty much unusual.

Ponto said...

Maju mate, I am a geneticist, molecular biologist. I am telling you it is near to impossible to sterilise ancient bones found covered in organic material that has been handled by humans and other animals prior to or after being found. Unless you absolutely destroy the bone by irradiating it or chemically treating it to smithereens, then there would be no dna left at all.

Those Italian geneticists could have had all their hairs shaved off, their outer skin abraded off, covered themselves in the most effective chemicals to prevent dna contamination and wrapped themselves up like the parcels Italian style and all their efforts to prevent contamination or remove the previous contamination of those bones from Apuglia would be futile. All they could hope to do would be to stop further contamination.

Those Dago scientists are having us on. Its all pure BS finding mtDNA CRS in ancient bones.

Those bloke at Athroscape keeps quoting the "discovery" of the CRS in those bones which incidentally has never been verified by other scientists. I wonder why? Such an earth shattering discovery in Paleolithic remains even if near to the Mesolithic is something you need to verify. You should look up fraud and hoaxes in science. It is a big list, and Italians do not have the best of reputations.

Maju said...

Hmmm. I understand your concerns but many others seem to think that there is very good chance of DNA contamination not penetrating the bones (all samples are from the interior, of course).

Also at least some of these studies used double testing by separate labs (I recall perfectly this was the case with Paglicci 23). And it's become customary to register the haplotypes of all people related to the remains and discard any possible contaminated sample.

These methods have also been tested successfully with Neanderthals, for example, yielding always totally different sequences than anybody alive. Some H. sapiens remains, like the famous Ötzi yielded totally unheard of sequences.

They seem reasonably safe to me.

And, by the way, FYI, I've been told that Anthroscape is dead. Have not attempted to confirm, of course.