September 30, 2009

Some mtDNA links between Europe and Asia

I was planning on writing up a more complete narrative for this post, but I don't think the evidence is -as of yet- strong enough to support very strong speculation. I will simply say that the recent results of Bramanti et al. for a U-dominated older mtDNA stratum in Central/North-eastern Europe can be reasonably extended to cover both North-western Europe and northern Eurasia up to Lake Baikal, the prehistoric limit between Caucasoids and Mongoloids.

This boreal zone of U dominance contrasts with that of the Neolithic and Bronze Age inhabitants, where the familiar mix of ten or so main Caucasoid haplogroups makes its appearance, in various proportions and in various degrees of admixture at the eastern end of its expansion. The eastern Caucasoids were probably derived from both (i) West Asia via the spread of the Neolithic economy to the east wherever it could be ecologically supported, (ii) in the more northern parts, from migrations across the steppe from Central and Eastern Europe.

More ancient DNA research is needed to establish (i) how complete was the U dominance in the pre-Neolithic northern zone, and (ii) when, and where did the other Caucasoid haplogroups break into it.

Anyway, here is the post as it stands:

Ricaut et al. (2004) discovered the presence of mtDNA haplogroup N1a (16147A, 16172C, 16223T, 16248T, and 16355T) in an Iron Age Scytho-Siberian skeleton from the Altai, reporting the presence of haplogroup N1a among Iranians and upper caste Havik Brahmins from India.

The same sequence was detected in a Neolithic Central European (DER1) of the Linearbandkeramik (LBK) culture, with reported modern matches in Egypt and Armenia. The following haplogroups were detected in the Neolithic LBK gene pool: H*, N1a, K, HV, T2, V, J, W, U3.

A later study by Gokcumen et al. (2008) discovered the presence of N1a in modern Kazakhs from the Altai:
The haplotypic variation within the seven N1a samples was relatively high (Table 2), with these haplotypes belonging to both the European and Central Asian branches of this haplogroup, as recently defined by Haak et al. (2005). Thus, the source of N1a haplotypes in Altaian Kazakhs was unclear, although they seemed to have originated west of this part of Central Asia (Gokcumen et al., 2007).
Haplogroup N1a was found to be a genuine signature of the Central European Neolithic by contrasting its high representation in the LBK with the overwhelming presence of haplogroup U (and especially U5 and U4) mtDNA among the Paleolithic and Mesolithic populations of the region.

A separate Neolithic Funnel Beaker (TRB) sample from Scandinavia (Malmström et al. 2009) included only three individuals belonging to haplogroups H, J, and T. Obviously, a sample of 3 is insufficient, but the absence of haplogroup U in it parallels that of the LBK. By contrast, the contemporaneous Mesolithic Pitted Ware culture, represented by 19 samples had single instances of J, and T (which may be due to admixture with the TRB), a single instance of haplogroup V, one of the few ones thought to be European in origin, and a gene pool that was apparently dominated by haplogroups U4 and U5. The picture emerging from the northmost European hunter-gatherers is one of a restricted set of haplogroups where U subclades were dominant (about 3/4).

N1a was also detected in medieval high-status Hungarians:
Commoners show a predominance of mtDNA haplotypes and haplogroups (H, R, T), common in west Eurasia, while high-status individuals, presumably conquering Hungarians, show a more heterogeneous haplogroup distribution, with haplogroups (N1a, X) which are present at very low frequencies in modern worldwide populations and are absent in recent Hungarian and Sekler populations.
While, as we saw, N1a was frequent among Neolithic Central Europeans, its absence in Hungarian commoners suggests that it was re-introduced -in the high status individuals- from Asia.

Interestingly, there has been European and Asian mtDNA evidence that allows us to have a good idea of the mtDNA landscape on which N1a-bearing people migrated from west to east:

The pre-farming foragers of Europe were dominated by mtDNA haplogroup U. The easternmost sample in the aforementioned study was from Samara, in European Russia and consisted of a U5a, and a U5a1 sample. How far to the west and east did the U-dominated population of pre-Neolithic northern Caucasoids extend?

Neolithic Siberians from Lake Baikal, the eastermost anthropologically attested limit of prehistoric Caucasoid populations had only U5a as a Western Caucasoid element in a population dominated by Eastern Eurasian mtDNA. Similarly, the Lokomotiv Siberian burials from Lake Baikal only had U5a in an other Mongoloid mtDNA gene pool. Yu Hong, a Sogdian in China (1,400 years ago) also belonged to haplogroup U5.

U5a was not limited to the territory of Central Europe to China in ancient times. It was the haplogroup of Cheddar Man, a Paleolithic Briton, and U5a1 or U5a1a has also been detected in a Mycenaean from Bronze Age Greece. Interestingly, U5a1 seems to have decreased in frequency in Britain from the 4th c. to the present.

Is it possible that negative selection is affecting mtDNA frequencies in Europe? U-haplogroup turns up in many ancient DNA samples, but the discovery that it was absent (or non-detectible) in Neolithic farmers raises the possibility that its reduced frequency may be due to demography, i.e., the overwhelming of Paleolithic foragers by Neolithic (and later) intruders.

We know that in the Bronze and subsequent ages, Siberians from Krasnoyarsk belonged to a rich assortment of Caucasoid haplogroups. It seems that newcomers from the West joined the U-dominated earliest settlers:
Twenty samples were found to belong to west Eurasian haplogroups (U2, U4,
U5a1, T1, T3, T4, H5a, H6, HV, K, and I
), whereas the 6 remaining samples were attributed to east Eurasian haplogroups (Z, G2a, C, F1b and N9a).
At the other end of the Eurasiatic steppe, in the Bronze Age site of Eulau in Germany, the gene pool was also quite different from that of the Paleolithic inhabitants, with haplogroups K1b, U5b, I, H, X2, K1a2 detected.

Haplogroup X2 represents another link between the west and Siberia according to Reidla et al. (2003):
Overall, it appears that the populations of the Near East, the Caucasus, and Mediterranean Europe harbor subhaplogroup X2 at higher frequencies than those of northern and northeastern Europe (P less than .05) and that X2 is rare in Eastern European as well as Central Asian, Siberian, and Indian populations and is virtually absent in the Finno-Ugric and Turkic-speaking people of the Volga-Ural region. [...] the few Altaian (Derenko et al. 2001) and Siberian haplogroup X lineages are not related to the Native American cluster, and they are more likely explained by recent gene flow from Europe or from West Asia.
The Tubalar, Altaic speakers from the northeastern Altai showed a mixed Caucasoid-Mongoloid mtDNA gene pool, with the western component consisting of haplogroups H8, U4b, U5a1, and X2e:
Specifically, northeastern Altai appears to be a good candidate for the ancestral homeland of the haplogroup U4b, which is apparently ancient European. For some haplogroups, such as X2e, the relatively recent arrival to the Altai region is more likely.
Derenko et al. (2002) discovered a rich assortment of Caucasoid haplogroups in several populations from the Altai, including all aforementioned ones (H, HV1, J*, J1, J1b1, T1, T4, U1a, U2, U3, U4, U5a1, I, X and N1a):
The applied approach permitted identification of 60% of mtDNA types the majority of which had southern Caucasoid origin. Less than 10% of mtDNA types were of eastern European origin.
Derenko et al. (2003) also studied several populations from South Siberia where the Caucasoid component was much diminished (17%) with the following haplogroups present: H, U, J, T, I, N1a, X.

47 comments:

terryt said...

"Is it possible that negative selection is affecting mtDNA frequencies in Europe?"

I think the most likely explanation is your subsequent comment, 'its reduced frequency may be due to demography, i.e., the overwhelming of Paleolithic foragers by Neolithic (and later) intruders'. In fact the same idea may be sufficient to explain the lack of Neanderthal haplogroups in modern humans. Only in that case it was the Paleolithic foragers that did the overwhelming.

eurologist said...

The pre-farming foragers of Europe were dominated by mtDNA haplogroup U

That is likely a bit of a generalization. It may only apply to the extreme north and the northeast. U, or some of its subclades, may have entered later than other groups, too: in addition to the recent discussion here about other refuges, there is still some speculation that access to Europe from the rich eastern plains beyond the two great lakes was almost impossible due to melt water, for millennia after LGM.

But once travel was possible, and just before advent of agriculture, there would have been much more resources and a much larger population than in the forested and animal-scarce European north. If these people also brought advanced fresh water fishing and sea-mammal hunting techniques with them, they could have had an advantage (in addition to numbers) over fishing people from the northern Atlantic cost.

just passing by said...

I personally don't the Cheddar Man was U5a, despite what ISOGG shows on its website. That is the old classification that has long since been revised. The Cheddar Man looks to be U5b instead.

Maju said...

That is likely a bit of a generalization.

It is. There seems to be an area south and east of the Baltic where this was the case but that's all we can say. Dienekes is again conveniently ignoring the Portuguese Epipaleolithic data (5 H, 2 U, 2 exotic: N1a?), which contradicts his idea.

So fare the aDNA of pre-Neolithic Europe says:

- Portugal (Epipaleolithic): mostly H, some U, some other. Roughly the same for Neolithics later.
- Mainland North/NE Europe by the Baltic (Epipaleolithic): mostly U5 and U4. Same for Pitted Ware emigrants into Scandinavia later.
- Italy (Gravettian): surely 2 R0/HV (one of them H?) and one N1

I agree we do need more and more varied data but concluding what Dienekes does is putting the cart before the horses. What I see is apparently: U5/U4 dominant by the NE and H dominant by the SW. Who knows what the rest were?

Dienekes said...

That is likely a bit of a generalization. It may only apply to the extreme north and the northeast.

I think that Cheddar Man in the northwest and the Neolithic Siberian data which I cite make the case that the U-dominated zone stretched from the Atlantic to Asia, and was not, in fact, limited to the region studied by the two most recent papers on Central Europe/Scandinavia.

pconroy said...

Here's a great resource on Ancient DNA, by Jean Manco:

http://www.buildinghistory.org/distantpast/ancientdna.shtml

pconroy said...

Here's some great maps of the possible spread of R1b, R1a in Europe and Asia:

Origins, age, spread and ethnic association of European haplogroups and subclades:
http://www.eupedia.com/europe/origins_haplogroups_europe.shtml

Maps of Neolithic and Bronze Age migrations in Europe and the Near East:
http://www.eupedia.com/europe/neolithic_europe_map.shtml

It suggests that R1b first arose in the Maykop culture, and spread from there - which seems about right.

pconroy said...

The Maykop Culture might have spoken an IE language, which they spread first to Central, then Western Europe.

This would probably satisfy Dienekes's requirement that IE's spread had to be via a demic expansion of farmers?!

Annie Mouse said...

Leaving aside other stuff for now...

H6 is wrongly identifyied as Western European in the paper. At this point in time it is considered Altaian along with H8. Although that may change.

Annie Mouse said...

"There has been an idea that most modern European are descended from farmers that came in from the Middle East about 10,000 years ago, reaching Britain about 6,000 years ago," Sykes told British Broadcasting Corp. radio. "This kind of evidence shows that is probably not true, and that modern Britons are in fact descended from the earlier inhabitants like Cheddar Man who existed on hunting and gathering and who were not farmers."

Annie Mouse said...

"The genetic material showed without doubt that Targett is a direct descendant through his mother's line of the skeleton known as Cheddar Man, which was found in 1903 in caves in Cheddar Gorge in southwest England."

Maju said...

I think that Cheddar Man in the northwest and the Neolithic Siberian data which I cite make the case that the U-dominated zone stretched from the Atlantic to Asia...

Cheddar man is a good point. It's just a single sample but does seem to ratify your impression for Britain. True. I also realized after I wrote that that 5 of the German samples are from Swabia, which is pretty much to the SW.

The "Neolithic" (Bronze Age?) data from Siberia does not seem to be truly meaningful in this context: it could well be "intrusive", carried by Indoeuropean migrants. From memory, there are older samples with dominant mtDNA F (oriental) in the area.

Maju said...

PConroy: the first link you provided seems a quite valuable reference resource. Not 100% perfect but quite good. Eupedia is... well... "ideological".

Annie:

H6 is wrongly identifyied as Western European in the paper. At this point in time it is considered Altaian along with H8. Although that may change.

Per Álvarez-Iglesias 2009, H6a is most common in SW Europe, with other pockets of "high" density in the North Caucasus and around Slovenia. Maybe H6b has a different distribution but it seems to be a really minor clade (no branches). However, per the latest PhyloTree, it seems to be related (by an HVS mutation: a weak link) to H8, which has indeed an oriental distribution (though has also pockets of high density in Central Europe and Syria).

Annie Mouse said...

@Maju

In that paper she is just looking at Europe.

What Alvarez-Iglesias does not mention is the 33% H6 in the Chuvash of Russia, or the fact that H6 is still today the dominant H subclade in Central Asia (>20% of H).

http://www.genebase.com/doc/mtdnaHaplogroup_H_Subclade_Table.pdf

H6 seems to have headed East into Central Asia when her sisters and aunts followed the mammoth West into Europe (Gravettian).

Sometime (IMO) in the Bronze/Iron age this haplogroup did a U-turn and headed west into Europe, probably in relatively large numbers (the fact that it is visible at all says that). Any one of the Steppe invaders could have carried it.

IMO one arm migrated through north Europe to Czechoslovackia (probably the Huns or maybe the Mongols, as I dont think the Alars brought their women). There is no data on H6 in Hungary yet.

A second arm travelled south into Dagestan, Syria and the Arabian Peninsula (>15%). This may have been Scythian (included female warriors).

H6 also seems to have been mysteriously teleported (shipped maybe)to Ireland which has been reported to have the highest levels in Europe (almost 10% of H). The British Isles are not in the Álvarez-Iglesias paper for some reason.

The Irish H6 is probably connected to the NorthWestern Spanish H6 (mostly the H6 was found in Galicia, which had about 5% of H).

Annie Mouse said...

I should mention that most of the Arabian H6 is H6b.

Annie Mouse said...

Before someone bites me...

Yes I know the Mongols, Alans and Huns are not Bronze/Iron age. Careless word use on my part.

Polak said...

Anne, if you really think the Mongols carried mtDNA H6 into Europe, then I have to strike you off at once as a serious participant in this debate.

mtDNA H is, of course, one way or another, a far echo of the west in Asia.

"The mtDNA distribution profile in the heart of Central Asia suggests a direct link between this area and Western Eurasia that could be explained by ancient migrations or by more recent historical events, such as Genghis Khan’s conquering efforts and trade or cultural exchanges along the Silk Route. To discriminate between these two possible scenarios, we are now analyzing a subset of these samples at the highest possible level of resolution - that of complete mtDNA sequences - focusing particularly on those H mtDNAs that seem to be the most informative considering their control-region haplotypes. Our preliminary data seems to be in favor of rather ancient genetic inputs from the West in shaping the peculiar mtDNA gene pool of Inner Asia’s present-day populations."

http://www.ashg.org/cgi-bin/2009/ashg09s?abst=mtDNA%20H&sort=ptimes&sbutton=Detail&absno=21466&sid=656312

Annie Mouse said...

Well Polak that really is not fair.

That paper is not even going to be published until next month and YOU are the only one with acccess to the data

If you look at my earlier post I said:

"At this point in time it is considered Altaian along with H8. Although that may change."

I use the published science to draw my conclusions. Not psychic powers. Every scientific body in the world is saying the H6 is Central Asian at this point in time, not just me. Based on what we currently know.

If you really want to have a serious discussion I challenge you to give us access to the data now.

Otherwise I can only assume that you are just taking the opportunity for a little personal self-gratification.

Dienekes said...

The "Neolithic" (Bronze Age?) data from Siberia does not seem to be truly meaningful in this context: it could well be "intrusive", carried by Indoeuropean migrants. From memory, there are older samples with dominant mtDNA F (oriental) in the area.

The R1a1-bearing Krasnoarsk Siberians are not U-dominated.

Maju said...

Annie: I don't know how can you make a link between Scythians and Iberia and Ireland in any case. The closest thing to Scythians in West Europe was the Alans (presumably related to modern day Ossetians, who in turn would be related to ancient Scythians or Cimmerians maybe) and they just passed by. Any truly Scythian input should be much more evident in Central and Eastern Europe, where Scythians actually existed once upon a time.

I don't have an "H6 theory" but I guess that it just spread together with other H (however that happened) and the various core areas we see now are just local founder effects.

Annie Mouse said...

@Maju

I am having difficulty seeing how H6 got all the way to Ireland from Central Asia myself.

Although strangely enough Irish oral History (documented in a 12th century book, The Book of Invasions) claims that Ireland was founded by waves of Scythians, via Western Spain.

The problem with H6 is the coalescent dates put it 30-45k years old and it seems to have skipped the loss of diversity and the more recent expansion that the rest of H had. This is according to published data. But accessing the raw data for this has been harder to achieve, I will admit.

Also H6 is virtually absent from most of Europe. Not what you would expect if H6 expanded out of Spain (or Ireland).

Maju said...

I am highly skeptic about the mythical references to Scythians and even to the much closer Spain in Irish mythology. Scythians were a semi-mythical long gone ethnicity with extremely broad geographical correlations (virtually all the steppes from Hungary to Pakistan) by the time such traditions were compiled and there is rather low evidence of any colonization from Iberia as well (though you can always think of Megalithic diffusion, I guess).

However if, as these recent aDNA studies seem to suggest, H as whole expanded partly through the Neolithic diffusion process, it is not any nonsense that some H6 ended up in the farthest reaches of West and Eastern Europe respectively, just by mere chance. Considering the overall spread of H as a whole and that of H6, it'd seem that both rode on the same wave or waves, whichever these were.

However the whole H spread issue is now even murkier than was before. I was not long ago arguing for a Paleolithic Central European origin of H based on the high clade diversity and geographical centrality of the area, but the lack of any H in all the Paleolithic samples strongly suggests it was not the case, even if the evidence for the, maybe crucial, Middle Danube region is weak in either direction.

Guess that we can just wait for more aDNA studies solving the blanks of the Middle Danube and the Balcans, which should be most important together with West Asia. Until then we can just wonder.

King said...

Distribution of mtdna U (U5*, U4*) is allmost the same as ydna N1c*. Post-LGM recolonisation of Northern Eurasia ?

Maju said...

Sorry to reopen this discussion but I've been working hard on this matter of ancient European mtDNA the last week and today I have finally found what seems the evidence for a more widespread presence of mtDNA in Paleolithic Southern Europe (at least) than just Portugal and Morocco.

An individual from Villabruna (Trentino-South Tirol, Northern Italy) had that haplogroup c. 14,000 years ago, per Di Benedetto 2000.

Thanks to Jean Manco (in whose site I found that and many other references) and to PConroy for pointing me there.

Dienekes said...

>> An individual from Villabruna (Trentino-South Tirol, Northern Italy) had that haplogroup c. 14,000 years ago, per Di Benedetto 2000.

From the paper:

All the neolithic sequences have been observed in contemporary Europeans, suggesting
genealogical continuity between the neolithic and present-day European mtDNA gene pool. The mtDNA
sequence from a 14 000 year-old specimen was not observed in any contemporary Europeans, raising the
possibility of a lack of continuity between the mesolithic and present-day European gene pools.

Maju said...

I know. But it's still H, what implies that mtDNA haplogroup H existed in Europe in the Late Upper Paleolithic beyond the Portuguese samples (on which you cast doubt) and beyond the Moroccan samples (that you considered "irrelevant", though IMO they are very relevant when you consider the whole picture) and beyond the unclear samples of Paglicci 23 and Sunghir.

It is also interesting because it is quite close geographically to the Swabian samples (though sure, some 14,000 years ago the Alps were an absolute impassable frozen barrier). It is also close to the possible source of Danubian Neolithic H (and other haplogroups) that I tentatively suggested that was in the Middle Danube or maybe the Balcans (and not in West Asia) and because H again shows up in the Neolithic of the area (three samples: 1 H, 1 T and 1 K, this last one Ötzi), precisely when these lineages were showing up in Germany as well.

It suggests that, the same that you think (maybe with some reason) that haplogroup U (U5 and U4 specially) was dominant in Central/North Paleolithic Europe, haplogroup H could well have been dominant in the southern half of the continent.

It is an important piece in the aDNA puzzle of Europe, though of course, I also wish we'd have many more.

Dienekes said...

I know. But it's still H

No it's not. The paper uses outdated (1996) phylogeny. There is no reason to assume that the observed sequence from Villabruna belongs to haplogroup H. I will not repeat my argument on why haplogroup inferences based on present-day frequencies of control region polymorphisms in different backgrounds are suspect; suffice to say that for the Villabruna sequence where not even present-day frequency data are in existence, such inferences are doubly suspect. The sequence is ascribed to haplogroup H only on the basis of the absence of diagnostic CR polymorphisms frequent in Torroni et al. (1996).

Maju said...

Ok, you may have a point, however I cannot share your scepticism, which I know is only founded on MCH beliefs ultimately.

Btw, I found that all the Haak's N1a individuals, had, besides of the N1a and N1a1 markers, the 16223-T marker, which is not listed at PhyloTree as defining any N1 clade and that has also been ignored by Haak himself at fig. 2 (the phylogenetic tree). Do you have any explanation for this?

Maju said...

BTW, I have just noticed that the sequence 16356C that Malmström uses to identify U4 can be subjected to the same critique (it could be H1b for example, as I can't find 16260T listed anywhere - there are other candidates but much less likely: M42a, C1a).

Gioiello said...

I think that we must thank once more Argiedude, who has demonstrated on “Genealogy-Dna” that the paper of Di Benedetto (Mitochondrial DNA sequences in prehistoric human remains from the Alps), but which has as a mentor one of the most ferocious Italian against Italians (Barbujani/Farfugliani) and who tries to demonstrate with his master Cavalli Sforza that Europeans come from Middle East and not from Paleolithic or Mesolithic European, is false.
The Paleolithic sample from Villabruna has the mutation 16270T, that defines U5 (don’t forget that U5b3 was born in Italy during Mesolithic and expanded everywhere, also to Middle East). Then it is false to assert that there isn’t connection between Paleolithic Europeans and today ones.

Gioiello said...

As Ian Logan has reconstructed, the mtDNA of Villabruna has:
C16262T
C16270T
and is H1.
There is in mitosearch a mtDNA from Germany with these mutations, plus T16519C not tested on the Villabruna sample.
Then H1 is in Italy from at least 14,000 years.

argiedude said...

The Villabruna sample from 14,000 years ago with 16261, 16274 is closest to J1, but it's not close at all (the study identified it as H). Only 3% of J1 samples have both 16261 and 16274. In mitosearch I found 22 J samples that had both 16261 and 16274, out of 2,000 total. I found absolutely zero non-J samples with that combination, out of 20,000 total samples. But the real problem is that J1 almost always includes 16069 and 16126, which Villabruna does not. I'd say it's more interesting wether or not the sample is U4/U5, instead of H.

The Mezzocorona sample from 6,000 years ago with 16126, 16292, 16294 is most likely T3, with a very slim chance of T2. T3 is found at around 0.5% in north & south Europe, Anatolia, Caucasus, and the Middle East. The study identified it as T.

The Borgo Nuovo sample from 6,000 years ago with no mutations (CRS) is of course most likely H.

Regarding Dienekes' observation that the CRS has been corrected and this study was using the older version, you can see in the link below that the corrections that were made were mostly in the coding region, a couple in the HVRII, and none in the HVRI.

http://www.mitomap.org/CambridgeReanalysis.htm

The 14,000 year old Villabruna sample had 6 errors, and one of them was 16270T, the mutation that identifies U5. The Mezzocorona had 0 errors. The Borgo Nuovo had 1 error, and it was 16270T again.

From the study of Etruscan mtdna:

"The Etruscan sequences show substitutions at sites (069, 126, 223, 270, and 356) known to be prone to recurrent mutation or postmortem damage (Gilbert et al. 2003)."

And notice that another mutation prone to damage is 16356, which is typical of U4 (and H1b).

The mutations of the 14,000 year old Villabruna sample were obtained in 2 of 3 analysis, while the mutations of the Mezzocorona sample were obtained in 4 of 4 and 6 of 6 analysis. The Villabruna analysis that failed to identify 16261 and 16274 is the one that produced the false positive for 16270. I wonder if the analysis of Villabruna were conducted all over again from scratch, perhaps this time it would've been identified as U5?


......................

Gioiello, I think what happened is a slight mix-up when preparing the pdf, but that the results as initially described by Di Benedetto (16261 and 16274) are correct. The reason the 16261 and 16274 mutations don't line up correctly with the 16270T mutation is because one of these 2 sheets of raw data was unwittingly shifted one base to the left/right when preparing the pdf.

Also, since 16270T was found once in 3 analysis, while the other 2 were found in 2 of 3 analysis, it's more likely the sample has 16261 and 16274, but not 16270T. Still, it's kind of shaky. Like I said above, perhaps if they ran this test all over again from scratch, the results would be U5.

argiedude said...
This comment has been removed by the author.
argiedude said...

I just noticed something in my previous post.

"The Etruscan sequences show substitutions at sites (069, 126, 223, 270, and 356) known to be prone to recurrent mutation or postmortem damage (Gilbert et al. 2003)."

Two of the mutations listed as prone to damage are 069 and 126. Those are the 2 mutations I noted in my previous comment were missing from the 14,000 year old Villabruna sample to confirm its membership in J1. Villabruna has 16261 and 16274, which are found together in 22 J samples and in 0 non-J samples. But it's lack of mutations 16069 and 16126 was a serious problem for considering it a J. The quote above informs us that 16069 and 16126 are amongst the mutations most prone to degradation, so their absence in Villabruna might have a valid explanation and the sample could well be a J, after all.

And again, because of the implications, I think it's more interesting that Villabruna isn't a U4/U5, instead of wether or not it's an H.

Maju said...

Gioello: I don't get what you mean.

1. You claim that the Villabruna sequence has the 16270T mutation but that is not what the paper says. It says: 16261T, 16274A.

2. Then you "explain" that Ian Logan has "reconstructed" that sequence as 16270T (16261T, I presume), what, to say the least, I find quite shocking and in need of a good explanation. But it seems that he still thinks it's H (another explanation needed probably).

If nothing else, you should think in your "dumb" (or possibly uninformed) readers when you write, thanks. :)

Maju said...

Argiedude:

The Borgo Nuovo sample from 6,000 years ago with no mutations (CRS) is of course most likely H.

As you know, I tend to agree with that because nowadays CRS HVS-I is almost only found in H1 samples (there are others but are very rare, including U). But in Bramanti's sequences, there is one, Hohler Fels [49 Ib1 66], that is defined as U* by the coding region's polymorphisms: CRS; 1721C 7028Y 12372A 14766T 14793A.

I remember to have seen somewhere listed a modern U (U*?) with CRS haplotype from Asturias.

The Paglicci study also provided one case that was CRS and probably HV(xH).

However I'd think it odd that most of the unclear aDNA CRS sequences would not be H (or rather H1 - AFAIK CRS haplotype is very rare in other H haplogroups, probably limited to H2a2). What is clear is that HVS sequencing alone gives inconclusive results and the way to go in order not to waste such precious research attempts on very valuable and rare material is to try to test coding region polymorphisms.

...

On being (potentially) J. It's an interesting speculation. In your opinion, could it be the rare JT(xJ,T) that seems only to exist in North Africa (where it seems pretty old) and Italy? If necessarily J, what subclade would you suggest? J2b maybe?

Gioiello said...

This is what Logan wrote on “Genealogy-DNA”:

And this gives:
> > C16262T
> > C16270T
> > A16275A !
> >
> > Oh dear!

Now Argiedude makes other observations and I take note of it.
It is 4 o’clock in the night. To-morrow morning I must go to work (I am a teacher in the High School). In the afternoon and Sunday I’ll examine again the matter.

argiedude said...

As you know, I tend to agree with that because nowadays CRS HVS-I is almost only found in H1 samples (there are others but are very rare, including U). But in Bramanti's sequences, there is one, Hohler Fels [49 Ib1 66], that is defined as U* by the coding region's polymorphisms: CRS; 1721C 7028Y 12372A 14766T 14793A.

That's very, very interesting. CRS in what range of HVS-I?

I remember to have seen somewhere listed a modern U (U*?) with CRS haplotype from Asturias.

Found it:

"Y Chromosome and Mitochondrial DNA Characterization of Pasiegos, a Human Isolate from Cantabria (Spain)" (Maca-Meyer, 2003)

2 samples of U* - CRS (one from Cantabrians, one from Pasiegos).
8 samples of U* - not-CRS (from Cantabrians, Lebaniegos, and Pasiegos).

So we have 20% CRS in U*.

In Alvarez-Iglesias (2009), he found 5 U* (Cataluña and Galicia), and none were CRS.

So combining Maca-Meyer and Alvarez-Iglesias (btw, what's up with the double names?), we have 13% CRS in U*. But 3 of the 5 Alvarez U* samples have 270 (aka U5), and 2 of these actually have 192-270 (U5a). That looks really bad. And a 4th has 192-311. 192 is typical of U5, but it's extremely rare that U5 will be missing 270, so I guess we can presume it's U*. So I'd say we really have 12 Iberian U*, and 2 are CRS, so 17% of U* is CRS.

For comparison, in mitosearch, after discarding some 20 samples that really belonged to U8, I ended up with 60 U* samples, of which only 1 was CRS. But excluding the volatile mutation 16519, since all these studies typically use an HVS-I range between 16000 and 16400, the number of U* CRS increases to 5 or 6, resulting in 10% of U* being CRS.

In Richards (2000), using a very restricted HVS-I range (16090 to 16365), he found that 8 of 39 U* were CRS, or 21%. [Note that I adjusted his numbers a bit because I discarded obvious U8 samples and I reduced 9 Iberian U*-CRS to just 1 because they were most probably a case of local genetic drift.]

So it all fits rather well. Richards' somewhat higher percentage of CRS is due to his much more limited HVS-I range. Taking that into account, and discarding the volatile mutation 16519, it seems that U* is about 10% to 15% CRS.

I'm suddenly very interested in U* and CRS, thanks to your pointing out to me that one of the hunter-gatherer studies (U4/U5) found a U*-CRS. That's very, very interesting... revealing, actually...

the way to go in order not to waste such precious research attempts on very valuable and rare material is to try to test coding region polymorphisms.

You know, it creeps me out when I read some of these studies. Are they going around pulverising all these priceless fossils into dust? Do they have to destroy an entire tooth for an mtdna test?

On being (potentially) J. It's an interesting speculation. In your opinion, could it be the rare JT(xJ,T) that seems only to exist in North Africa (where it seems pretty old) and Italy? If necessarily J, what subclade would you suggest? J2b maybe?

I've been trying to find info on JT(xJ,T) but I can't. Exactly in what studies was it found? Do you know any HVS-I data about them?

The 261-274 combination makes J1b the best bet. But every J sub-haplogroup has its problems. In the case of J1b, aside from the fact that it's missing 069-126 (a problem with any J group), it's also missing 145 and 222, which are near universal in J1b. Like I said in my first post, it's closest to J1, but it's not close at all.

Maju said...

That's very, very interesting. CRS in what range of HVS-I? -

No idea. The supplementary material just lists its HVS-I haplotype as CRS.

Found it:

"Y Chromosome and Mitochondrial DNA Characterization of Pasiegos, a Human Isolate from Cantabria (Spain)" (Maca-Meyer, 2003)
.

I think it may be that one, though I only recall one individual, not two. But whatever.

...it seems that U* is about 10% to 15% CRS.

I take your word on that.

You know, it creeps me out when I read some of these studies. Are they going around pulverising all these priceless fossils into dust? Do they have to destroy an entire tooth for an mtdna test? -

I wouldn't mind so much if the test results were unambiguous but testing only the HVS-I it seems we only get more confusion.

I've been trying to find info on JT(xJ,T) but I can't. Exactly in what studies was it found? Do you know any HVS-I data about them? -

I think my only reference on this is Kèfi's paper on Taforalt aDNA (in French). Though there should be others because he's only mentioning that fact after he found 3 or 4 likely JT in the remains.

His sequences for Taforalt JT are: 16126C-16355T, 16126C-16304C and 16126 C. Plus another one tagged as JT or U6 with the sequence: 16126C-16172C-16174T.

He correctly describes his many CRS individuals as "H or U" but in North Africa, if it's not U6 it's most likely that it's not U. CRS in modern North African samples (other studies) was invariably classified as H1, as far as I have seen.

Maju said...

Wait. Actually Kèfi says:

De plus, tous les haplogroupes observés chez
Taforalt sont retrouvés chez cette population actuelle, même
l'haplogroupe J/T. Ce dernier, rarement représenté dans les
populations actuelles, est absent dans les populations nord
africaines à l'exception de la population berbère du Nord
du Maroc (1,6%)


So, even if Kèfi is implying JT(xJ,T) most probably, it's not clear enough. I must have known this issue of JT* as North African/Italian from some other paper and surely browsing at Mathilda's blog (specialized in North African DNA and prehistory) we should be able to find it. I'm sorry I can't recall that one right now. I'll tell you as soon as I find it.

Maju said...

Found it at Mathilda's partial transcription of Kèfis paper:

In modern Human population, JT is presents only in:

1,6% Berbers from the North of Morocco
1,8% of Sicilians,
1,6% of Italians
.

However, when I search for the keyword "JT" in the French original, I cannot find that paragraph. I believe that Mathilda copied it from an English version of the paper (a power point presentation I think, I have seen it myself) and later changed the link to the original in French because it went broken.

Can't say much more.

Maju said...

Ok, this is the link to the PP presentation: http://www.pasteur.fr/~tekaia/BCGA/TALKS/Rym_Kefi.ppt. Browse to slide number 27.

The presentation is signed by Dr. Rym Kèfi, so guess that's what he actually means. Obviously he's not talking of J or T but of JT(xJ,T).

Ponto said...

Cheddar Man is Paleolithic? A long bow to draw. The Holocene started 10 kya and ushered in the Neolithic age. It is splitting hairs to make Cheddar Man whose remains are about 9 ky old a Paleolithic Man. Sure he may have used stone tools, so did Neolithic age people. He lived in a cave, so did the first farmers. What is the difference? Cheddar Man was found in England on the backside and backward end of Europe. Cheddar Man is more correctly a Mesolithic European yet untouched by Neolithic farming way of life which took off in England some time after he died.

The problem with genetics is that people have the habit of running off like rabid dogs frothing at the mouth by the slightest, insignificant detail. Ten thousand years back in European history is nothing, certainly not any connection to real Paleolithic humans living in Europe who mostly were Neanderthals not modern humans like Cheddar Man. Even the infamous Cro Magnon, Old Man, found under a rock shelf in France predates Cheddar by nearly 20 ky. Don't make mountains out of molehills, and don't listen to dickheads like Sykes. Just because the Brits are backward in taking up ideas like farming, the backwardness towards ideas has come with them into today, and have some mtDNA found now in Europe is really quite unspectacular.

What did Cheddar Man tell us? The his version of mtDNA U existed at the time of his birth and maybe a century before (he had a mother!), nothing more.

In Europe the Neolithic transition from a Mesolithic life style took some thousands of years, and happened is a saltatory manner. Even today in Europe there are humans who live an essential Mesolithic lifestyle, hunting/fishing and gathering and prefer it.

Maju said...

I think it's very unfair what you say, Ponto. While the data we get from Cheddar man is not too informative, a good deal of the pre-Neolithic DNA data we're enjoying is in fact Epipaleolithic.

Many Prehistorians make a difference between Epipaleolithic (what we had in Europe) and Mesolithic (what happened in certain areas of West Asia): one being a mere extended Paleolithic after the Ice Age and the other being effectively transitional toward that invention that is farming and herding. There was no native advancement in that direction in Europe in the Epipaleolithic and the knowledge of agriculture and animal husbandry (and also that of high seas sailing that so much power gave to us later on) came to us from, ultimately, West Asia.

Now, if it came with the farmers in the pack or was mostly the knowledge, the seeds and the animals what arrived is what we are discussing here. But there is no doubt that the ultimate source of this important transformation was outside of Europe, in West Asia.

It's impossible to know if Europeans would have developed some sort of Neolithic on their own without that inspiration (it happened in other places, like America) but what is sure is that in fact all the Neolithic "science" came from the other side of the Bosporus. There was no Paleolithic-Neolithic transition in Europe: what we had was the arrival from outside of farmers whose ways we copied - or (not my opinion, at least for most cases) who replaced the natives thanks to their many extra calories per hectare.

Yossarian said...

I learned a while back, after being tested for 37 markers by familytreedna.com that I was of
R1b1 Haplogroup for my DNA and U6b
Haplogroup for my mtDNA. I am fully aware of the ancestral origins of my family. What I would like to ask is:
Do these LETTERS representing the various Haplogroups stand for something- like a place/region, or where they arbitrarily assigned a long time ago? If they do stand for something, I was wondering what the R and the U stand for. Thanks.

Maju said...

Yossarian:

They are arbitrary letters, mere nomenclature. Of course it's sorted so (normally) the R and the U mean they are related with other Rs and other Us... but, specially in mtDNA this is not always the case.

U6b is a NW African/Iberian matrilineage. Ultimately with North African origins, after the U higher level lineage split within the migration from South Asia into West Eurasia some 50 Ka ago probably.

R1b or R1b1 is a very common West Eurasian, Central Asian and Central-East African lineage, depending on the sublineage. It's rare in East Europe though. Like mtDNA, it probably branched out from West Asia long ago.

Thom said...

Can anyone share the difference with my U5b1b1c , meaning the 1c at the end might denote in an overall perspective. I am learning.
Thanks








"Thou that wouldst enjoy thy beloved, and feel the rest of his gospel, and walk in that path which leads thereto, wait to learn of the Spirit.
Know what it is that is to walk in the path of life, and indeed is alone capable of walking therein. It is that which groans, and which mourns; that which is begotten of God in thee. The path of life is for the seed of life. The true knowledge of the way, with the walking in the way, is reserved for God's child, for God's traveller. Therefore keep in the regeneration, keep in the birth; be no more than God made thee. Give over thine own willing; give over thine own running; give over thine own desiring to know, or to be any thing, and sink down to the seed which God sows in the heart; and let that grow in thee, and be in thee, and breathe in thee, and act in thee, and thou shalt find by sweet experience, that the Lord knows that, and loves and owns that, and will lead it to the inheritance of life, which is his portion. And as thou takest up the cross to thyself, and sufferest that to overspread and become a yoke over thee, thou shalt become renewed, and enjoy life, and everlasting inheritance in that.
Watch against the selfish wisdom, in every step of thy growth, and in every spiritual motion, that *that* come not between thee and thy life; that that deceive thee not with a likeness, a shadow, making it appear more pleasing to the eye than the substance. Every step of thy way it will be laying baits for thee; and it is easy for deceit to enter thee at any time, and for that wisdom to get up in thee under an appearance of spiritual wisdom, unless the Lord tenderly and powerfully preserve thee: and if it prevail, it will lead thee from the path of true wisdom; it will cozen thee with a false faith, instead of the true faith; with false praying instead of the breathings of the true child; with diligence and zeal in thy false way, instead of the true zeal and diligence; yea, it will hurry thee on in the path of error, shutting that eye in thee, which should see, and hardening thy heart against thy bosom friend.
Let nothing judge in thee, concerning thine own heart, or concerning others, or concerning any way or truth of God, but only the begotten of God in the heart. Let the light in which thou art begotten to God, and which shines upon his begotten, be the only judge in thee, and then thou canst not err in judgment. Be not hasty, be not forward in judgment; keep back to the life, still waiting for the appearance and openings of the life. A few steps, fetched in the life and power of God, are much safer and sweeter than a hasty progress in the hasty, forward spirit. "
My Ancestral Grandfather Issac Pennington wrote this in 1663