November 10, 2010

More ancient mtDNA from a peripheral Danubian population

Wolfang Haak's team is again providing interested, yet unclearly representative, ancient mtDNA data from the Elbe region:


[doi:10.1371/journal.pbio.1000536]


Caution foreward

Before I proceed discussing the findings, which are interesting, I must warn of two caveats:

One concerns the use by Haaks et al. of only the HVS-I fragment of the mtDNA, which in many cases is inconclusive for haplogroup identification. In this sense, Bramanti made a much better job in 2009 by checking also the control region for more clearly defining mutations which in some cases were decisive in clarifying haplogroup adscription. I had hoped this example of carefulness would set precedent, but seems not.

The other is the concentration of the new and old samples in a very small area of the Middle Elbe, which is totally unrepresentative of the wider Danubian Neolithic. This was a major issue in the previous research (2005) and is aggravated by the new data coming only from Derenburg. I would highly commend trying to get more samples from further south, specially Hungary, Austria, Moravia and the Rhine basin, where the bulk of Danubian Neolithic (LBK) existed. Alternatively I'd commend to compare the Elbe group and the other Danubians separately, in order to discern if there are more or less important differences, as there is a very serious risk of the Elbe group being not really representative for the whole Danubian Neolithic peoples.

On the positive side, I applaud publishing this new paper as open access and I rather like the comparison with modern populations they made.


The data

The new 22 Derenburg mtDNA samples, which make 27 after adding the five ones from the previous study, include three individuals each (13.64%) from each of the following haplogroups: H, HV, J, T, N1a and K. Additionally two individuals (9.09%) belong to W, while one is V and another U5a (4.55% each).

Y-DNA was successfully sequenced from three individuals, which make now the oldest Y-DNA sequences anywhere in the World. They are two F(xG,H,J,I,K) and one G2a3, very much marginal in the modern Y-DNA pools, confirming the outlier nature of these farmers and their likely low impact on modern Europeans, even in Central Europe itself.


Comparisons and analysis

Most interesting are the PCA analysis (fig. 2) and the genetic distances with modern populations, expressed on a map in fig. 3.

PCA (fig.2) annotated by me
The most obvious conclusion is that Danubians, specially the hyper-mega-super-ultra-oversampled Elbe group, are total outliers in the context of all modern populations, throwing downhill the hypothesis of Neolithic replacement even for the Central European case.

The most similar populations are Highland West Asians (Anatolia-Caucasus) by PC1 and some Central Europeans and French by PC2.

It is also notable that an also quite suspicious "hunter-gatherer" aDNA pool (mostly from the Baltic area and in many cases actually peripheral Neolithic), labeled HG and dominated by U5 and U4 haplogroups, is much closer to modern Europeans than the LBK peoples. However their best modern match are Mordvins (MOR), suggesting these may represent best the ancient NE European pre-Neolithic pool, at least mtDNA-wise.

Fig. 3 distances of all LBK samples (A) and Derenburg (B) to modern populations

Warning update (Nov13): it is not the least clear how these maps come from the raw data. I can't find any way in which Anatolia-Caucasus become closer than other regions.

Here it is interesting that the greatest affinities of Danubians are with Anatolia and Picardie, while they have low affinity with Northeasternmost Europeans (Finnic peoples) and then with Ibero-Aquitanians, Welsh-Cornish, Baltics (incl. Belarus), as well as Bosnians. They also have low affinity to the peoples of Arabia and Palestine.

The Derenburg sample looks most akin to modern Iranic peoples such as Kurds, retaining to some extent the Picardie connection as well.

This is overall strongly suggestive of a genuine founder effect in at least some Danubian farmer populations coming ultimately from the Taurus-Zagros area, rather than the Balcans or Hungary.

However their extremely low influence in modern populations still needs of a good explanation.

It is notable that the lineages that best define the position of Danubians in the PCA are N1a, X, W and K. I was already quite persuaded that X and W, as well as the rare N1a, were of Neolithic arrival in Europe, but I was unsure about K. This seems to confirm, I understand, that K, the best-surviving Danubian-specific haplogroup, is of Neolithic origin and dispersal. 

Haplogroup K has in general low frequencies nowadays (c. 6%) but is more concentrated in some scattered regions:

mtDNA K frequency, from Geneamusings

The other relative success history is T, possibly T2. T is widely distributed but T2 shows an star-like structure sign of a sudden expansion, possibly in Neolithic times. K subclades also show sign of sudden expansion, in my opinion, about the same recent period.

As for the other Danubian or Neolithic haplogroups, W is thinly distributed, being most common in Northern Pakistan, finally N1a is also very rare, with largest frequencies among Peninsular Arabians, some Croatian islands, mountain Ruthenians and Volga populations.

For N1a specifically, please notice that renowned geneticist M. Palanichamy concluded that LBK's N1a variant is a native European clade, not a West Asian one.

The other lineages found are more normal among modern populations: HV(xH,V) suggests West Asia as does X. Instead H, V and U5a are most common and probably original from Europe.


For further references in aDNA, visit Jean Manco's excellent page. See also my (not yet updated) map series on European ancient mtDNA.


Important update (Nov 11): 

Eurologist in the comments section makes what seems to be an excellent point: Haak and colleagues have, somewhat arbitrarily, divided the haplotypes in "informative", "non-informative" and "unique" (table S4), on what they found their conclusions and the map of affinities posted above (fig. 3).

The unique clades are those that have no matches, fair enough, but the non-informative ones are the ones that have lots of matches. This is problematic to say the least, because they are happily excluding 59.5% of all matching haplotypes.

So they build the affinities map only on 40.5% of all matching sequences and this is surely not acceptable. Specially when Anatolia, Zagros and Caucasus happen to achieve only a poor 19.8% match overall, while several European regions reach well above 30%.

[Note: had to modify what follows because it contained errors].

When we ignore this arbitrary distinction, the best matching region is Wales+Ireland at 39.8%, followed by:
  • >35%: Scandinavia
  • 30-35%: Scotland, North-Central England, Portugal, Basques/North Spain, rest of Spain, N. France, mainland Italy, Italian islands, central Germany, South Germany/Austria/Switzerland, Poland and Volga Finns. 
  • 25-30%: Iceland, Shetland, other Scottish Islands, West/East England Finnland/Karelia, Low Germany, Baltic countries, South Russia Ukrainie, Belarus, Czech/Slovakia, Croatia/Slovenia, HungariyRomania and  Balkans (minus Greeks).
  • 20-25%: North Russia, Volga Turks, Greece and Morocco.
  • 15-20%: all West Asia and Caucasus samples. 
So is it the other way around to what Haak et al. claim? Probably the answer is complex rather than simple, as the founder LBK peoples must have been themselves. But it is clear that there are good reasons to think that aboriginal European lineages were already part of the Danubian Neolithic at its very foundations.

Best regional matches by ancient LBK lineage (red: "non-informative", green: "informative"):
  • J (069-126) (n=4): Wales/Ireland (30/500)
  • H (311) (n=4): Volga Finns (24/500)
  • H (CRS) (n=4): Italian islands (112/500)
  • H (093) (n=1): W/E England and Scottish islands (7/500 each)
  • V (298) (n=2): Basques/North Spanish (32/500)
  • T2 (126-294-296-304) (n=3): Baltic countries (19/500)
  • T (126-294-296) (n=1): Central Germany and Caucasus (10/500 each)
  • T (126-294-304) (n=1): Cezch/Slovaks (7/500)
  • W (223-292) (n=1): Finland/Karelia (28/500)
  • K (093-224-311) (n=2): Caucasus (10/500)
  • K (224-311) (n=2): Iceland (30/500)
  • K (224-249-311) (n=2): North Russia (1/500)
  • W (093-223-292) (n=2): Baltic countries and Anatolia (1/500 each)
  • T2 (093-126-294-296-304) (n=1): Arabs/Cypriots (2/500)
  • T2 (126-147-294-296-297-304) (n=1): Scotland (3/500)
  • T (126-189-294-296) (n=1): Croatia/Slovenia (4/500)
  • T (126-292-294-296) (n=1): Czechs/Slovaks (3/500)
  • U5a (093-256-270) (n=1): Iran (3/500)
  • N1a (147-172-223-248-355) (n=1): Czech/Slovaks (1/500)
  • N1a (147A-172-223-248-320-355) (n=2): Iran (2/500)
  • N1a (092-129-147-154-172-223-248-320-355) (n=1): Central/North England, Scandinavia and South Russia (1/500 each)
Additionally there are other four lineages (2 N1a, 1 H and 1 U3) with no known modern matches ("unique").


Update (Nov 12):

Eurologist notices the following, comparing with Palanichamy's paper (mentioned above):

Here are some more matches or close relations when comparing to the data listed in Palanichamy:

"informative":
--------------
N1a (147A-172-223-248-320-355 (n=2): Iran (2/500): also a match each in France and US of European descent

"unique":
---------
N1a (086-147-172-223-248-320-355) - exact match with Portugal, and 1 Austria and 4 Switzerland very close

N1a (129-147-154-172-223-248-320-
355) is relatively close to
(92-129-147A-154-172-223-248-320-355) - Italy, Norway, Germany, Russia



30 comments:

  1. "two F(xG,H,J,I,K) and one G2a3"

    I believe that it was one F and two G2a3.

    ReplyDelete
  2. On the merits, I think that your skepticism of this mtDNA sample being unrepresentative of LBK is unwarranted, because there is reasonable good evidence from other lines of evidence (for example, physical anthropology) that the LBK was quite unified demographically and that the expansion happened in a fairly compact period of time. And, if there was a difference between the core LBK and the peripheral LBK, one would expect the opposite of what is seen - a diluted Near Eastern signal with more U4/U5, and not a very strong one.

    A three person, non-independent, Y-DNA sample, of course, is so small that sampling error makes it very hard to say much of anything definitive about the population as a whole from it, other than that those two hgs were present at that time and place in the early Danubian Neolithic.

    But, it is notable that there was no R1a. In contrast, every one of a couple of dozen Kurgan men from ca. 1800 BCE to 100 BCE just to the North of the Tarim Basin was R1a. It is also notable that F* and G2a3 are phylogenically close to each other and basal relative to more phylogenically distant Y-DNA hgs I, J, T and R. Could these hgs have arrived in a later wave of migration, either Indo-European or earlier?

    This is particularly striking because one of the most plausible for the ethnogenesis of the Indo-Europeans is that LBK men and non-LBK women in the North Pontic plains formed a hybrid Sredny Stog community. How does a Central Asian, ethnically European population end up all R1a by 1800 BCE, if the men who provide much of the male DNA pool for the population lack it?

    ReplyDelete
  3. Let me start with what I commented @ Dienekes:

    Generally speaking, I am quite disappointed with Haak's analysis.

    (i) Logic: there is no reason to assume the currently available mesolithic data apply to the pre-neolithic Danubian. If anything, evidence indicates that Europe was not homogeneous. The middle Danubian had 8,000 years of opportunity after LGM of easy contact with people along the Black Sea. So just based on that, one would assume the pre-neolithic middle Danubian to show some proximity to Anatolia and to the Southern Caucasus.

    (ii) Analysis: they declare those haplogroups that are widely distributed in the NW (but much less so in the SE) as uninformative, and those with more significant local occurrence (incidentally more so in the SE) as informative. Then they claim the ratio between these two is pertinent*. Clearly this ratio just by construct hugely favors the SE. (*) the "uninformative" far outnumber the "informative" - so the percentage of "informative" to total is in practicality the ratio I mention).


    On the flip side, the weird N1a, thought to be so significant, has almost no match SE of Hungary (2 in Iran versus 9 in Hungary and NW of there). And, Iran is high because it matches three U5a - not exactly your typical, expected neolithic line! The other high scorers in the SE are mostly T and T2.

    I stick by my interpretation that LBK started essentially with a local middle-Danubian population, just very slightly modified by agriculturalist newcomers from Anatolia. That also matches the finding that a large 16% of lineages found are unique to LBK.

    As to the y-DNA findings, they are weird but also support the idea that the local population was somewhat unique. It is still compatible with the idea that R1b in the west is pre-LGM.

    --

    Also, as Dienekes points out, the F* they found could be some I (or precursor thereof) - which could of course again be local, same as G2a3 - absolutely no need to invoke migration from Anatolia.

    Again, what defines the Danubians here does not make them neolithic nor does it necessarily show any connection to Anatolia. In fact, by direct comparison of the haplogroups (rather than the extremely biased mathematical construct used) it largely shows no such connection unless Anatolia was completely different 7,000 years ago. The latter is certainly a possibility (and likely e.g. true of y-DNA J and E, for example) - but if it is true, we cannot use extant distributions at all to make a case for the Danubian coming from there (because then we have no idea what there was, in Anatolia).

    ReplyDelete
  4. I forgot to mention R1a as another haplogroup that was perhaps at a much lower occurrence in Anatolia 7,000 years ago, and of course most of the Mongolian haplotypes.

    At any rate, to be honest, I think the entire Haak paper is one huge logical fallacy.

    Let's turn the argument around and assume I am correct, and LBK largely originated from a local Danubian population.

    (i) This would explain it's by all standards very weird makeup that doesn't really match anything today - it was just completely arbitrary from what happened to be there, locally, in the presumably quite inhomogeneous (wider) Balkans, on top of a (known to be) inhomogeneous Europe, and then randomly exaggerated by the sudden explosion and drift.

    (ii) This would also make it much easier to explain extant populations. LBK's makeup was then by definition different from its surroundings (close to its core - it could have been more similar at the edge) and different from Anatolia. When LBK fell apart due to climate change and/or diseases (including animals and plants), people from the fringe and surrounding regions - some hunter-gatherers, some herders, some farmers - would have exploited the vacuum. And these people could have brought in the R1b from the SW, the R1a from the East, and the much higher H, U4, and U5 of today.

    Perhaps there was continuity after all - just not for most of the LBK farmers and for some of the hunter-gatherers it replaced. We really can't tell, at this point.

    ReplyDelete
  5. Also see this recent paper by Palanichamy et al.

    http://www.biomedcentral.com/content/pdf/1471-2148-10-304.pdf

    which comes to the conclusion that much (if not all) of the so important and characteristic LBK N1a is of local European origin.

    ReplyDelete
  6. @Andrew:

    "I believe that it was one F and two G2a3".

    That is all in table 1 and is very clear: two F* and one G2a3. So no idea where you get that "belief" from.

    "I think that your skepticism of this mtDNA sample being unrepresentative of LBK is unwarranted"...

    It's a matter of degree probably. For me it is clear that this a most peripheral group and therefore some caution is certainly warranted. I'm not saying that there was not a demic expansion but that the apportion of haplogroups may be somewhat different because of some founder effect at the Elbe. For instance the Rhine group (from Haak 2005, n=10) shows up as: 4 T, 2 K, 2 H, 1 N1a and 1 U*. This is clearly a different apportion.

    The other samples are Austria (1/1 H) and NE Hungary (1/1 N1a) - this is not really LBK, btw, but a related group. So I think some clades like HV* and N1a are over-represented in the Elbe group. These are precisely haplogroups that are quite rare in modern populations, unlike somewhat more common T and K.

    Still the Rhine group is also part of the Western group of LBK, and there is some serious chance that the situation may be even more different in Austria, Moravia, West Hungary, which was the true core of LBK and the group that was stable for longer (Lengyel, Baden...)

    So I do think my caution is warranted at least to some extent and that samples from the core Danubian area (at the Danube) would clarify the matter a lot.

    "one would expect the opposite of what is seen - a diluted Near Eastern signal with more U4/U5, and not a very strong one".

    U4 has never been detected in South Germany aDNA. U4 was surely all the time restricted to NE Europe.

    U5 and U* have been found in Swabian late Magdalenian/Epipaleolithic but they are a relatively isolated sample in a huge blank area, with H showing up the closest (in South Tyrol).

    Even considering that the demic replacement in most of Central Europe is likely (but then why modern populations are not like LBK samples?), the German sites are not the most representative of the whole phenomenon. Oddly enough the best representative is one isolated H from Austria (but being alone says nothing clear). In all the core Danubian area we have only that single H sample (and the related N1a from NE Hungarian Eastern Linear Pottery, which is a different, albeit related, culture).

    "But, it is notable that there was no R1a. In contrast, every one of a couple of dozen Kurgan men from ca. 1800 BCE to 100 BCE just to the North of the Tarim Basin was R1a".

    You don't need to go as far as to Tarim Basin, please! In the Elbe basin, the Kurgan site of Eulau (2600 BCE) is also all R1a1 (2/2). However G2a persisted in Frankish Bavaria much later, so it did not totally go extinct overall.

    Something we have to consider for Chalcolithic and later periods is that the lower castes/classes may not have been buried properly and that these IE/Kurgan burials may represent only the elite.

    ReplyDelete
  7. @Eurologist: you make some good points, specially regarding N1a. I'm going to add the Palanychamy paper's link to the main article (I had read it but then forgot).

    However:

    "as Dienekes points out, the F* they found could be some I (or precursor thereof)"

    Extremely unlikely, as I should be evolved and re-evolved by that time (I2a was surely involved at that time in Cardium Pottery, as shown by the Sardinian and SW European presence of a derived clade). IMO it may be the most rare F4, so far only found in the Netherlands (per Karafet 2008). Of course we cannot discard IJK* or IJ* but these lineages, AFAIK, are unattested for in living people.

    "I think the entire Haak paper is one huge logical fallacy".

    I have made an independent analysis of their data because I can't agree with some of their conclusions (specially their happy assumption that all pre-LBK was mtDNA U) but I'm not that extreme either. Essentially we lack of good references for pre-Neolithic mtDNA in Central Europe overall (only the Swabian ones are relevant so far) and we also lack of good references for LBK out of the Western group.

    As you say we have no direct information of Anatolian or other non-European Neolithic/Paleolithic mtDNA but I do think that those populations have been reasonably stable along time, as have been others in Europe - only North-Central Europe seems to have experienced clear changes (though probably that also happened in East and North Europe as well).

    However the connection with modern "Anatolian" peoples is still not really strong, just somewhat stronger than others.

    ReplyDelete
  8. "However the connection with modern "Anatolian" peoples is still not really strong, just somewhat stronger than others."

    Have you looked closely at the excel sheet data? Maybe I am misinterpreting something, so I would like your opinion. To me, their separation into "uninformative" and "informative" clades is completely arbitrary and biased - but the main conclusions of the paper are based on that.

    They are artificially raising the signal level by exploiting the fact that H (CRS) is much lower in the SE, and then deviding by that number.

    If, on the other hand, you look at the particular haplogroups, a connection to Anatolia and surroundings pretty much vanishes - not just for N1a.

    Yes, the results show that a smallish group from the Danube area likely made up some/much of the LBK, rather than local people - but it does not show these people themselves originated from Anatolia. And as you point out, we don't know yet what happened in time and space with sufficient resolution.

    One idea I had is that perhaps, the initial "sweep" was very fast, just making use of the best and sunniest Loess sites, leaving huge gaps (the majority area, in fact) in which mesolithic people remained. Later, local hunter-gatherers could have been integrated - perhaps first the males, as workers. There is at least one statistical study in Belgium that shows an extended time of cohabitation.

    Of course, the above model requires that the HG males decided to only marry H-women, they must have been the prettiest ;)

    ...in other words, likely, a lot of different things happened to arrive at today's distribution of haplogroups.

    ReplyDelete
  9. "Have you looked closely at the excel sheet data?"

    I had not till now (table S4) and you certainly do have a point or even are absolutely correct.

    The highest match percentage overall is Scandinavians (36%), other matches above 30% are (from left to right) Spaniards, North French, Italians, Middle Germans, Southern Germans/Austrian/Swiss, Polish and Volga Finns.

    Turks/Kurds/Armenians and Caucasus are under 20%!!! Being the worst match except for other West Asians. Even Moroccans are a better raw match.

    That's a most important insight and I will at least write an update on that. Thanks a lot.

    "To me, their separation into "uninformative" and "informative" clades is completely arbitrary and biased - but the main conclusions of the paper are based on that".

    My problem is that I seldom care about the conclusions but the data. However I did not look at the "small print", only at the haplogroups.

    Their reasoning seems to be that, as clades as CRS are so common, they lack any informative value. But this is no doubt an arbitrary decision that needs qualification: it cannot be taken at face value.

    "One idea I had is that perhaps, the initial "sweep" was very fast, just making use of the best and sunniest Loess sites, leaving huge gaps (the majority area, in fact) in which mesolithic people remained. Later, local hunter-gatherers could have been integrated - perhaps first the males, as workers. There is at least one statistical study in Belgium that shows an extended time of cohabitation".

    That's an excellent hypothesis. I know the Belgian (and North French) case, where LBK cohabited for long with other small Neolithic cultures, surely the product of partial cultural diffusion. Also, there is an important Cardium Pottery related culture in South Germany and NE France, called La Hoguette, whose interaction with LBK is not well understood. As we know Cardial/Epicardial is mostly a native phenomenon, rather than the product of immigration - and that must be specially the case so far north.

    Maybe we'd get better info from later sites, when regionalized LBK became mainstream, instead of looking only at early sites.

    "Of course, the above model requires that the HG males decided to only marry H-women, they must have been the prettiest ;)"

    You doubt it? Those ugly N1a-s had nothing to do in the Neolithic beauty contests :p

    Actually, if H represents the pre-farming substrate, as I think is the case (specially H1-CRS), then we have already a clear case of absorption of pre-Neolithic (European aboriginal) people into LBK since the beginning (Austrian 1/1 H sample), which is what I always suspected anyhow. This may have been further exaggerated as time passed, maybe in part via migrations (Megalithism, Funnelbeaker, even Kurgans), reabsorbing the LBK peoples, something was clearly completed by the time of Urnfields, when Elbe basin samples are already "normal" (fully modern).

    I'll write an update now with this issue and probably will address this matter in greater depth later on (I'm debilitated by a tooth problem, which has been putting me in deep pain the last two days or so - thankfully inflammation has finally stopped the pain tonight and I have dentist this evening).

    ReplyDelete
  10. Oh, man! What a cheat! LOL.

    I am impressed now I have worked a bit with that spreadsheet. How could dare to divide rare matches by overall match? That makes that the less overall match the better (provided there's some meaningful rare, aka "informative", matching value).

    It's a total abuse of trust. I can't believe they thought they'd get away with this!

    Great eye, Eurologist, you made my day! :)

    ReplyDelete
  11. And by the way, erratum to my earlier comment: I said:

    "The highest match percentage overall is Scandinavians (36%)"

    Actually it's Welsh/Irish (39.8%), the left area populations got hidden while working on that and I did not notice.

    ReplyDelete
  12. I don't have time now to publish anything else but just a quick comment here for discussion: what you must do is exactly the opposite of what Haak did: multiply instead of divide.

    So I did. The best actual matches are:

    1. Central/North English: v=820
    2. Croatians/Slovenians: v=740
    3. Czech/Slovaks: v=720
    4. Scandianvians: v=540
    5. Iranians: v=498
    6. Austrians/Swiss/S. Germans: v=492
    7. Scottish: v=486

    etc.

    Anatolia and Caucasus have values of only 291, ranking quite midling. Of course, all populations with zero values, still have zero values, as this depends on rare ('informative') lineages matching.

    However this includes North French, so maybe Haak did not cheat after all. What did he do then? Can you explain me? Why do North French show high values when they share no rare lineages and are not outstanding on common ones? Which is the equation involved?

    I'm puzzled now. :?

    ReplyDelete
  13. As Maju said, great observation eurologist. You also said that Iran's greater matching was due mainly to some U5 haplogroups, right? Which of course has some ironic implications.

    There are 8 N1a from Haak 2005, Haak 2010, and the recent ancient mtdna study of France. All 8 belong to lineages (per Palanichamy 2010) that today are centered in Europe. Out of some 6 modern N1a samples from Anatolia and the Middle East, not even one belongs to any of these lineages. So N1a, the most important haplogroup in these Neolithic samples, indicates population continuity, if we go by Haak's own method of determining this by looking at which modern regions have the best matches with the ancient mtdna haplotypes.

    ReplyDelete
  14. Maju, is this ancient mtdna study of Iberia the one you noted some time ago which had found their mtdna to be similar to modern Iberian mtdna?

    Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe

    Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe (Sampietro, 2007)

    ReplyDelete
  15. @aargiedude

    The two most notable points in Sampietro are the conclusion

    "We propose here a dual model of Neolithic spread: acculturation in Central Europe and demic diffusion in southern Europe."

    And this observation:

    "The only previous aDNA analysis on 25000-year-old European remains (Caramelli et al. 2003) yielded two mtDNA sequences from the pre-HV and N haplogroups that seem compatible with both models."

    Caramelli D, et al. Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans. Proc. Natl Acad. Sci. USA. 2003;100:6593–6597. doi:10.1073/pnas.1130343100 [PMC free article] [PubMed]

    The implication from this point in Caramelli, is that perhaps the N1a and U5a in Haak should be should both be viewed as paleolithic introgression into an early farmer community (perhaps a founder community in the source area in the Balkans) that failed to thrive either because of continued influx in later times of more purely farmer populations (continuing the overall trend of declining hunter-gatherer proportions), or perhaps because they were at some disadvantage in the community as farmer families thrived demographically relative to introgressed hunter-gatherers (e.g., perhaps the hunter-gatherer descendants were lactose intolerant and were strongly selected against when food was scarce, or perhaps farmers had immunity to livestock related diseases that had not yet culled hunter-gatherer descendants from the early farming community).

    A selection hypothesis didn't make any sense with N1a as a Neolithic mtDNA hg, but makes quite a bit of sense relative to demographic replacement by yet another wave with N1a as a Paleolithic mtDNA hg. It is easy to imagine the combined selective effect of lactose intolerance and farm related disease immunity having a 150-1 magnitude given the comparable effects of European diseases in the New World and other first contact situations, and the undeniable evidence of very strong transition from lactose intolerance to lactose tolerance to the point of fixation in Europe.

    It is very hard to see why LBK "did not have a strong impact on the genetic population structure of the modern European female lineages" otherwise. No area that was LBK ever reverted to hunting-gathering, and farming produces much higher population densities than hunting-gathering. So, by all rights there should be an intense founders effect. Maybe there was, but maybe the impact was of LBK lineages (xPaleolithic lineages).

    Also, this could explain the elevation of H later. Imagine that almost all local descendants of hunter-gatherers (who would probably have been distinguishable ethnically on sight), die off in a plague or because they can't drink milk in a food shortage. How are you going to replace them? You are going to go back to the homeland and try to recruit ladies from their to become wives for newly widowed men, not try to recruit women from the neighboring wilds.

    There is partial demic replacement, then, but it takes a few hundred more years to become nearly complete through selection.

    Presumably surviving N1a represents someone who had non-matriline ancestors who had the protective traits before some event made them selective.

    ReplyDelete
  16. Maju,

    Here are some more matches or close relations when comparing to the data listed in Palanichamy:

    "informative":
    --------------
    N1a (147A-172-223-248-320-355 (n=2): Iran (2/500): also a match each in France and US of European descent

    "unique":
    ---------
    N1a (086-147-172-223-248-320-355) - exact match with Portugal, and 1 Austria and 4 Switzerland very close

    N1a (129-147-154-172-223-248-320-355) is relatively close to
    (92-129-147A-154-172-223-248-320-355) - Italy, Norway, Germany, Russia

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  17. @Argiedude: Sampietro's paper does not deal with Paleolithic peoples. The one I probably mentioned is this one, by Chandler, Sykes and Zilhao.

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  18. Also, Argie, in general all Iberian aDNA studies fall within modern range. But Chandler 2005 is the only one that deals with Epipaleolithic peoples.

    Oddly enough several of these papers conclude "discontinuity" but that is not sustainable on the data they actually manage. For example, Chandler argues that the minor vanishing of the "other" clade and appearance of similarly minor V in the Neolithic is "evidence" of lack of continuity. But all the rest is yelling continuity, so they are forcing the data to their own preconceptions in a way that is not acceptable.

    Maybe more famous is the paper of Izagirre and de la Rúa on ancient Basque mtDNA. Again, in spite of some reasonable coincidence with modern Basques, they throw all the weight onto the lack of V. However mtDNA V is low in the areas they studied, and is only relatively high among Gipuzkoans, a region they did not study for mtDNA.

    And anyhow, these two papers at best would suggest Neolithic flows involving mtDNA V, not all the people, as they claim happily.

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  19. @Andrew:

    "The two most notable points in Sampietro are the conclusion

    "We propose here a dual model of Neolithic spread: acculturation in Central Europe and demic diffusion in southern Europe.""

    LOL, how deeply ingrained some misconceptions are. It'd be the other way around if anything, right? That's why I never read the conclusions and only focus on the raw data: because a lot of papers conclude the opposite of what the data says.

    "perhaps the N1a and U5a in Haak should be should both be viewed as paleolithic introgression into an early farmer community"...

    Notice that the U5a found in LBK farmers only has matches in Iran.

    "No area that was LBK ever reverted to hunting-gathering"...

    Sure. But they "reverted" to Megalithism, to Funnelbeaker and finally to IE Kurgan cultures. By c. 2400 BCE there was not more Danubian culture in Europe: what the Indoeuropeans did not take, the Basques did (Artenac culture).

    One major problem we have is that LBK influences should be more persistant in the South, specially in the mid-Danubian plain and nearby mountain areas. But Haak and company are all the time looking at the very margins of the Danubian cultural area: Poland, North Germany... which was never really important (never... before the Indoeuropeans made it their Western home base).

    In fact, when you look at the overall markers, the Nordalpine, Sudcarpathian and Northern Dinaric areas all appear more akin to LBK genetics.

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  20. @Eurologist:

    Alright, thanks. I'll copy-paste that as an update (with due attribution).

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  21. It is notable that all of the N1a in the new data comes from females, as does all the T and U and that sample.

    In the hunter-gatherer data set, recall that all of the non-U mtDNA came from the Ostorf Funnel Beaker community in Northern Germany which was all post-3200 BCE (the youngest part of the sample). In that sample, three of the four non-U mtDNA types (K, T2e, and T2e) came from men, and 1 came from a sex unidentified sample (J). The study notes that the non-U mtDNA haplotypes could be from admixture with Neolithic populations. The only female sample from Ostorf was U5. The T2e type from Ostorf was from different sublineages from the old LBK sample and is found today in Iceland, Scottish West Islands, and the "SW Fringe of Europe."

    The old LBK data doesn't identify gender so it is not possible to determine if the gender pattern in the new sample and the old one are the same. It does note that six N1a individuals produced 5 N1a subtypes - the Easternmost from a Central Asian branch, two types (three samples) from European branches previously observed, and two from unobserved ancesteral nodes of the European branch.

    The mtDNA/Y-DNA pairs in the new data were:
    HV/F*
    K/F*
    W/G2a3

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  22. "Sure. But they "reverted" to Megalithism, to Funnelbeaker and finally to IE Kurgan cultures. By c. 2400 BCE there was not more Danubian culture in Europe: what the Indoeuropeans did not take, the Basques did (Artenac culture)."

    U4/U5 are currently about 8%-10% in Central Europe and more than 20% in NE European Uralic peoples. These are the only definitively attested post-LGM, pre-LBK hunter-gather mtDNA types in Northern Europe. So, in the areas that the LBK data come from, there has been 90% replacement of pre-LBK hunter-gatherer populations by subsequent waves originating from the South.

    It is implausible that a culture that showed continuity for thousands of years in the area which continued to use the agriculture that they brought would be diminished by 99% in a new demographic wave while leaving a 8%-10% hunter-gatherer remnant. There is no evidence that any of the subsequent demographic waves were complete enough to wipe out almost all traces of N1a.

    N1a certainly does seem to arrived in this location with the LBK, and given the substantial geographic dispersal of the N1a finds (800 km), the diversity of N1a types present (suggesting that there is no one single recent ancestor of all of them in a founder population) and the spead of LBK expansion, N1a must have been reasonably common in the Danubian founder LBK population.

    It is quite plausible, in contrast, that people in the original LBK group with longer farmer lineages had traits that allowed them to survive while people with shorter farmer lineages didn't and were reduced by disease or inability to get enough nutrition, etc.

    And, the fact that all of the N1a in the new sample involved females, is suggestive of recent admixture (presumably with non-farmer peoples of Southeastern Europe), even if it doesn't definitely establish it because the sample size is small.

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  23. "U4/U5 are currently about 8%-10% in Central Europe and more than 20% in NE European Uralic peoples. These are the only definitively attested post-LGM, pre-LBK hunter-gather mtDNA types in Northern Europe".

    Maybe but that is more, I believe, than the apportion of N1a, K, T and W together, which are the only clear LBK clades. So they seem to have left more of a legacy than the early farmers.

    Unless... we are focusing too much in the Baltic area, because of sampling bias.

    (And notice the ironic U5a rare sublineage that only matches Iranians)

    I have three issues:

    1. Which was the real hunter-gatherer mtDNA pool in the Danube area (and in general)?

    2. LBK peoples seem to have make a limited impact in modern populations.

    3. Excess sampling in the Baltic region for all relevant periods. What does Kunda Culture say about, for example, Belgium? Nothing at all. A lot of the so-called "hunter-gatherers" in that area have pottery, of the Ukranian type, (and probably pigs and some cereals) and are not correctly classified as pre-Neolithic but are much better understood as Neolithic, even if peripheral and "regressive".

    "So, in the areas that the LBK data come from, there has been 90% replacement of pre-LBK hunter-gatherer populations by subsequent waves originating from the South".

    And of the LBK farmers themselves, it seems to me, a they are too low in H and most modern clades.

    But we do not know clearly where those waves originated. All data from Denmark/South Sweden does not match the U5/U4 paradigm and we know almost nothing about West Europe (Iberia apart), where most people lived in the Paleolithic.

    "It is implausible that a culture that showed continuity for thousands of years in the area which continued to use the agriculture that they brought would be diminished by 99% in a new demographic wave while leaving a 8%-10% hunter-gatherer remnant".

    Yes, it's implausible, but that's what we see (even if to lesser extent than 99%). However all this data is from earliest LBK. Soon later, there was regionalization and then intense divisions and recycling.

    For example, Western Danubians were split into Michelsberg culture (North, possibly with Funnelbeaker influence) and epi-Rössen in the South (more conservative but also influenced by Megalithism, as happened with the non-Danubian cultures of Low Germany and Scandinavia). I think they fought each other, what favored IE penetration.

    ...

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  24. ...

    "There is no evidence that any of the subsequent demographic waves were complete enough to wipe out almost all traces of N1a".

    Yah, but what can I say: it happened somehow. It is as mysterious as the decrease of mtDNA I (curiously a relative of N1a) in Denmark in the Middle Ages.

    "N1a must have been reasonably common in the Danubian founder LBK population".

    Yes, same for K, T and W.

    "It is quite plausible, in contrast, that people in the original LBK group with longer farmer lineages had traits that allowed them to survive while people with shorter farmer lineages didn't and were reduced by disease or inability to get enough nutrition, etc".

    Not necessarily because there was a population decrease after the early population growth. Danubians penetrated Central Europe in the warmest of all periods ever, even warmer than today. Then they may not have been able to face the climatic restrictions, while other peoples may, for instance Megalithic peoples with a sea-oriented economy.

    In LBK the population grew by x10 and then divided by 5, so in the end it only grew by x2 from the original forager base. All this happened in 1500 years and it does not seem like the population levels ever regained the LBK ranges, the closest thing is the early IE period (Globular Amphorae, Baalberge in Poland some time earlier), 2000-2500 years later, but then there was another demographic dump again.

    Maybe these demographics ups and downs help to explain the matter? Probably they were much more radical in North Europe than in the South (though we do not have data for the South) because the climate is less hospitable. However Megalithic Denmark and Britain seem to have withstood in better shape (fishing/trading economy again?)

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  25. By the way, I am right now reviewing the Euro-Med aDNA data (my map series has become a bit obsolete), using Jean Manco's site for reference, and I just noticed that Bramanti'08 has a sample of LBK from Moravia, which does not have N1a.

    This is important because it illustrates that core LBK may have lacked that clade. The reported lineages are (one each): H, K, T2 and J1c. If we exclude the Elbe group, there's only one N1a in all the LBK area and it belongs to the Rhine group. There's also no W. Overall, even if not modern (low H, high T and K), it makes LBK aDNA make more sense.

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  26. I personally think this is all a hoax
    I think someone is trying to play a big joke on Europeans, with eastern ideology.

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  27. I believe the data is valid but conclusions may and are probably biased.

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  28. Maju, I think you and eurologist should get together, both of you are the only one's so far who can make lots of sense on this whole situation.
    You two guys are brilliant.
    Andrew lost his credibility when he commented on dienekes' page, saying something in the matter of " this might be the reason for blue eyes in Europe" or something to that fashion, so to him and others this is what is all about. Andrew blue eyes must of came into Europe through mtDNA not Ydna, as we can still see it in Europe today harboring mostly in "females".

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  29. Well, thanks. But I do not think anyone "loses his credibility" by just having his/her own opinion, right or wrong. That borders an ad-hominem attack and, sincerely, I'd strongly prefer that discussions are about content rather than people. There can always be exceptions, like when we lose our temper or someone really deserves a scolding, but exceptions are not rules.

    So let's respect each other, ok?

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  30. Your right, I apologize sincerely.

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