June 2, 2011

Languedoc Chalcolithic DNA

There is a new host of ancient DNA data, which seems to have been carefully analyzed, from the important Languedocine site of Treilles, which gives name to a whole "tribal" group of the Chalcolithic period, after the post-Epicardial Chassey culture broke up in pieces.

Marie Lacan et al., Ancient DNA reveals male diffusion through the Neolithic Mediterranean route. PNAS 2011. Pay per view (for 6 months or depending where you live).

As I do not live in India nor Argentine, for example, I would have to pay for this paper or wait six months. I never ever buy anything online, so I will do the latter. Put up with me.

Regardless, the supplementary material is freely available and most data is there. I have also read something online around what this paper has to offer. 


Y-DNA: almost all cousins!

Fig. S5 - Y-DNA G2a median joining network
The most striking finding is that almost all male members of this population belonged to a single Y-DNA lineage: G2a. Only two of them did not and they carried I2a instead. 

This speaks volumes on this population being a patrilocal one and made up of closely related men. It is not just the haplogroup but also the haplotype: all the Treilles men belong to a relatively rare haplotype within G2a (left in red).

It is also suggestive of this population being of immigrant origin. Haplogroup G2a is rather mysterious in this matter but it is one of the main candidates, along with J2 and E1b1b1a1, for being a Neolithic immigrant lineage in Europe. 

The secondary lineage I2a is also a possible case of Neolithic immigrant lineage but in this case it would come directly from the Balcans and not West Asia. However in this case a pre-Neolithic origin is also very possible, specially as I (likely I2a1) has been found in North African ancient DNA (specifically Guanche mummies from the pre-colonial Canary Islands). 


Mitochondrial DNA: quite more diversity

[Note: this section was corrected hours after writing it first time because it contained errors]

But, regardless of we may think of Y-DNA, what really supports a largely non-native origin of the population is the mitochondrial DNA, the female lineages. These (n=29) are as follows:
  • H - 6 (21%)
    • H1 - 3 (10%)
    • H3 - 3 (10%)
  • HV0 - 3 (10%)
    • HV0 (undefined) - 2
    • V - 1
  • U - 8 (28%)
    • U (undefined) - 1
    • U5 - 5 (17%)
    • K1a - 2 (6%)
  • JT - 8
    • J1 - 6 (18%)
    • T2b - 2 (7%)
  • X - 4
    • X2 - 4 (14%)
I estimate that there is a 45% of Neolithic immigrant lineages (X, J, T and K). On the other hand, there is still at least 41% of Paleolithic aboriginal lineages (H, V, U(xK) and I), what seems to be telling us of some level of continuity in nearby areas, where the women may have originated. 

The relatively high diversity of maternal lineages reinforces the idea of this group being strongly patrilocal in any case. 


No milk for the shepherds

While the title of this USA Today article is very much misleading, because lactose intolerant people can perfectly eat cheese in fact (it is raw milk which they find intractable but they can have most processed dairies), one of the findings of this paper is that they did not have the common variant that, in most of Europe, signals lactose tolerance. 

This is not fully conclusive, as there are people without the gene that is lactose tolerant and vice versa, but it is highly likely correct in their conclusions.

In fact, modern Occitans are still largely unable to digest milk as adults (but they can eat cheese for sure): according to a 2001 paper, 65% of Southern French are lactose intolerant. While the exact sampling location(s) for these "Southern French" is not clearly identified, it is most unlikely that they are Basques or Gascons, because Basques are the population with less lactose intolerance on Earth (0.3%).



Who were these people of Treilles

As I haven't yet read the paper I am not very sure about the details of this necropolis, however Treilles gives name to an archaeological group (not quite a culture but almost). When the late Neolithic Chassey culture broke up c. 3000 BCE, several local groups arose from it. Treilles was one of them and maybe the most advanced and cosmopolitan one. 

Inserted in the Megalithic phenomenon since its formation and later also in the overlapping Bell Beaker one, the Treilles group was intensely connected with the Iberian cultures but very specially with that of Zambujal (or Vila Nova de Sao Pedro), a true Megalithic civilization and the first identifiable civilization on the shores of the Atlantic Ocean.

I made the following maps for your interest:

 My reconstruction of trade routes in late Chalcolithic SW Europe (green star is Treilles, solid ovals locate Iberian civilizations)
A more concise map (source of the other one) showing the various cultural elements apparently traded (see legend below)

Legend:
  • Light blue dots: Palmela points (weapons originated in Portugal)
  • Dark blue dots: turtle buttons (originated in Portugal?)
  • Green dots: conical and Dufort buttons (likely from Languedoc)
  • Orange dots: pyramidal buttons (Catalonia essentially)
  • Stars indicate Treilles (green), Zambujal (blue) and Los Millares (black).
From Pellicer 1986 (himself on Harrison), several maps gathered in one here by me.


Important update: 
I got a copy thanks to a reader. Interestingly this is not a burial from nearby the modern town of Treilles, which gives the group its name (located with a star in the maps above), but from a cave further Northwest, towards the Massif Central, in the area of the Grand Causses[fr], near Millau.

The cave is named Saint-Jean-et-Saint-Paul and hosts a collective burial dated by the authors of this paper to c. 3000 BCE, early in the Chalcolithic period (though the authors prefer to speak of Late Neolithic). This kind of collective burials are the same as those found in dolmens and other megalithic structures and are usually thought as clannic tombs (which is coincident with the findings, if we accept, as we must, that clans were then patrilineal). Many areas of Europe where Megalithism never took roots, used these kind of collective (or clannic) burials in caves. This was the case in most of the East and Center of the Iberian peninsula, and also in North Italy, which had strong connections with this area in the period just before this burial (Chassey-La Lagozza fusion culture, maybe proto-Ligurian).

So we are clearly before a patrilineal clan in a rather hidden spot of post-Epicardial Occitania.

The authors argue that:
The Treilles cultural group is a well identified archeological complex of the late Stone Age period, preserved of any major late Neolithic population movements as suggested by the absence of the Bell–Beaker culture influence in the second part of the third millennium B.C. The study of this cultural group should give a snapshot of the local genetic pool of the end of the Neolithic period in southern France before all recent migrations.

While not fully rejecting this claim, I doubt that they were so much isolated and I would instead argue that they had rather intense interactions with North Italy in the previous period and Iberia in the one to come. Chalcolithic long distance trade began long before Bell Beaker (it correlates best with Megalithism in fact) and even if the early date in the context of Chalcolithic justifies some of the claims, these are poorly argued. There was also trade and cultural interaction in the previous cultural period of Chassey-La Lagozza: even if it was more restricted to the region, the interaction with North Italy cannot be ignored. 

But my most important caveat rests in the clannic (and arguably aristocratic) nature of collective burials: it is clear that we are looking at the members of a single patrilineal clan, all related by a common male ancestor (excepting of course the two I2a individuals, who could be adopted, illegitimate or whatever). In this sense no single clannic tomb can provide a good snapshot of the wider region, at least for the Y-DNA.


Update (Jun 3): Heraus has written an entry on this particular district (Causse de Larzac) at his blog dedicated to the physiognomy of French citizens Anthrofrance.

65 comments:

  1. i usually email papers to people if they ping me at contactgnxp -at- gmail -dot-com. basically, if i blog it, i have a copy of the paper, and i am willing to give any reader who is curious about the paper but has no access a copy if they proactively email me.

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  2. Thanks, consider yourself retroactively emailed. :p

    I'll email you, specially because I really want to know the details about the necropolis: is it dolmenic megalithic, neo-megalithic, Bell Beaker burials, other?

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  3. This comment has been removed by the author.

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  4. Maju you got the mt-DNA frequencies wrong, the total sample size is actually 29, not 34. If you look carefully at Table-S2 you will see that 5 lineages (2-U5, 1-H, 1-H3 and 1-I) belong to the Researchers that did the study. So that makes H: 6/29 or 20.69%, which is evenly split between H1(n=3) and H3(n=3). I have the study BTW; it is actually only 4 pages long, most of the info comes from the supplementary info (16 pages). I find it interesting that in another Neolithic settlement dating from about the same period of time 5000 ybp SJAPL, Alava, H was already the main Haplogroup (23/63 or 36.5%). Izagirre et al(1999). Anyways, I would be interested as into what the Y-DNA Haplogroups in that site(SJAPL) would be. Dr.Haak said the following: "The ancient DNA Lacan is now extracting from skeletons across France and Spain, should provide more piece[s] of the enormous puzzle we are trying to put together.” So I wonder what regions or burial chambers in Spain are going to be analyzed? Anyways, what do you make of Figure-S3, Table-S6 where Basques(From Adams et al 2008) and Spaniards appear really close to the sample analyzed in terms of Fst distances, yet at least Basques seem to share no lineages with the sample as seen in Table-S7?

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  5. Ah, alright. Thanks a lot Jeanlohizun. I'll correct that immediately.

    "... most of the info comes from the supplementary info"...

    I know (so typical!) but I wanted to know about the details of the burial. Now, thanks to Razib, I know that and I've written an important update after finding out.

    "I find it interesting that in another Neolithic settlement dating from about the same period of time 5000 ybp SJAPL, Alava, H was already the main Haplogroup (23/63 or 36.5%). Izagirre et al(1999)".

    I could not confirm this on my own (discussed here last time). Notice that this paper is very systematic and double tests all haplogroups identities, while most other aDNA papers rely on HVS-I sequences only, which are horrible specially for haplogroup H (defined only by coding region mutations, even most subhaplogroups do that).

    "Anyways, what do you make of Figure-S3, Table-S6 where Basques(From Adams et al 2008) and Spaniards appear really close to the sample analyzed in terms of Fst distances, yet at least Basques seem to share no lineages with the sample as seen in Table-S7?"

    In the main paper (fig. 3) the result is totally different (though the highest amount of shared lineages is 2.2%, not really much). It may have been caused by the I2a, because Basques are relatively high in this haplogroup (very much unsure, sincerely). Actually in fig. S4 we can see how Basques are closest by dimension 2 (but that probably represents the I2a component only).

    Confusing admittedly.

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  6. Very interesting paper ! Nice to see there are scientists tackling France and more particularly SW France. Having modern samples from Aveyron would be nice both to check whether or not this collective burial is alien - in an aristocratic way - to autochtonous people or to detect subsequent migrations.

    Still, my 2 cents that those people are all more or less linked with modern-day Aveyronnais people as the Causses are a specific and isolated territory. Inspired by your entry, I've uploaded Anthrofrance with Larzac.

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  7. Maju Said:
    "I could not confirm this on my own (discussed here last time). Notice that this paper is very systematic and double tests all haplogroups identities, while most other aDNA papers rely on HVS-I sequences only, which are horrible specially for haplogroup H (defined only by coding region mutations, even most subhaplogroups do that). "

    Maju I have a copy of the paper done by Izagirre et al(1999), that was the paper that analyzed the periphery Basques(SJAPL, Longar, Pico Ramos). This is what they said about the way they assigned the Haplogroups:
    Izagirre et al(1999)
    "We typed these prehistoric samples in order to identify those haplogroups previously defined by Torroni et al. (1996, table 3) in modern DNA. We typed those nucleotide positions strictly necessary to correctly identify the nine haplogroups characteristic of Caucasians: 7025 AluI, 4577 NlaIII, 8249 AvaII, 9052 HaeII, 8994 HaeIII, 12308 HinfI, and 13704 BstNI. Table 1 shows the primers used to amplify the fragments containing the mutation that defines each haplogroup, as well as the size of both the amplicon and the restriction fragments.
    [...]
    Because the number of samples on which duplicate analysis was possible was so low, we analyzed 92 left femurs from the same sites, to double-check the results obtained in dental samples. For these bone samples (which it was not possible to associate with particular dental remains), only sites 4577 NlaIII and 8249 AvaII were analyzed. The same digestion pattern was found in the bone samples as was seen in the teeth—that is, the presence of cleavage for 4577 NlaIII and the absence of cleavage for 8249 AvaII.
    Additionally, in the case of the haplogroups defined by the absence of a particular restriction site, we doublechecked the typing by both positive and negative restriction of other linked sites that characterize those haplogroups (Torroni et al. 1996, table 3). Thus, in the case of haplogroup H, for instance, which is characterized by the absence of restriction at 7025 AluI, typing was confirmed by positive restriction of 4577 NlaIII, 8994 HaeIII, 9052 HaeII, and 13704 BstNI and by negative restriction of 8249 AvaII and 12308 HinfI.”

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  8. Maju Said:
    “In the main paper (fig. 3) the result is totally different (though the highest amount of shared lineages is 2.2%, not really much). It may have been caused by the I2a, because Basques are relatively high in this haplogroup (very much unsure, sincerely). Actually in fig. S4 we can see how Basques are closest by dimension 2 (but that probably represents the I2a component only).”
    That’s what I’ve been thinking, since the Basque(n=116) sample comes from the Adams et al(2008), which showed about 8% of Haplogroup I, most likely I-M26. Anyhow, I’ve been trying to find out which Basque province that sample of Adams et al.(2008) came from, do you have any idea?
    Oddly enough I saw a member in Eupedia claim the following:
    “ Here is an extract from an article about the testing of 29 people found in a French neolithic grave: "The researchers were able to deduce from their findings that the peoples in this region of France were of a genetic type more closely related to Basque and Spanish populations than current western European populations. They were also more closely related to peoples in Cyprus, Portugal, Turkey, Italy and Lebanon."

    http://content.usatoday.com/communit...s-in-france-/1

    Another blow to the Paleolithic origin theory of the Basque”
    This is a complete misinterpretation of what the text said, but the misinterpretation comes from the article from usatoday. Ironically any possible ties between Basques and that population in terms of patrilinear Fst, is mainly due to Haplogroup I2a, which is considered by the Neolithic diffusionists to be the solely European Paleolithic Haplogroup. That came from a thread were that user was claiming that Haplogroups H1 and H3 came to Europe during the Neolithic based on Jean M page. Anyways I don’t want to sidetrack the topic here, but I would like for Jean M to point out to me where does it say in the paper she has as reference that H3 is more diverse in North Africa, or H1 is more diverse in the Middle East.

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  9. @Heraus: Wasn't there a paper on French mtDNA from several years ago? I can't locate it right now but you can probably recall it, right?

    While the G2a is a clear case of founder effect, the mtDNA may well be more representative and we can compare with nearby areas (assuming such a sample exists).

    As for your sample of local modern faces, I'd say that I'm a bit disappointed that they do not look West Asian at all (with some exceptions probably: b4, b6 and little more) although a few have the Italo-Greek vibe (c2, c4, d7) and there are few more that can be arguable or ambiguous.

    Most however are the potato-nosed broad-faced type that seems peculiar of the Massif Central (I can't imagine any comparison outside France in any case) or with strong tendencies towards Basque types (at least 8 = 25%) or other West European types (Northern mostly).

    They do not look Turkish, Palestinian, Cypriot or Georgian at all (with the few exceptions mentioned above).

    I'll repost this part at your blog, for whoever may be interested and also not to divert the attention here too much from the archaeo-genetic and prehistoric aspects. Thanks for your contribution: it's potentially useful.

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  10. @Jeanlohizun:

    The issue I have with Izagirre & De La Rúa 1999 is that it is a 1999 paper and that it is impossible (at least for my knowledge) to compare with modern established SNPs as described by PhyloTree.

    So I have to assume that they did their job correctly for their time but I cannot decide myself if the reported results are correct on light of modern knowledge. In many other cases I could not reach the same results as reported by the authors after comparing the originally found sequences, most are within the window of possibility but cannot be certified to be as reported (for example R*-CRS is typically reported as "H", "H1", "H or U". They are good hunches but we cannot decide that on the data available).

    "I’ve been trying to find out which Basque province that sample of Adams et al.(2008) came from, do you have any idea?"

    No, sorry. It's probably a comprehensive sample. Haplogroup I shows up typically as some 10% of Basque Y-DNA (the other 90%, excluding the occasional erratic, being R1b). This lineage is partly the same as in Sardinia (I2a2) but partly not (at least in López Parra 2008, see at Dienekes). This other I* found at the Pyrenees and generally Iberia has never been tested AFAIK (maybe in private companies like FTDNA or so?)

    You can also see in López' map that a triple urban sample of Western Basques (labeled "Basques") has very low I and instead has more of the "neolithic" lineages (pink). That's probably because of immigration which may have deep roots in some cases in the urban areas (my guess). The sample more characteristically "Basque" (comparing with other papers) is instead that of "Cinco Villas" (Upper Bidasoa, Navarre), which approaches much that of Adams and others I have seen along time.

    "Oddly enough I saw a member in Eupedia claim... This is a complete misinterpretation..."

    Yes. Abusive in one direction and abusive in the other. I do not pay much attention to Eupedia for this kind of reasons: they seem to have an agenda of some sort. However when I have seen raw data in that site, it seems to be accurate: it's the interpretations which seem to be highly ideological and far fetched.

    ...

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  11. ...

    "... that user was claiming that Haplogroups H1 and H3 came to Europe during the Neolithic based on Jean M page".

    Based on the same data (and being absolutely strict in my filtering of it) I have detected for sure H in Europe in two pre-Neolithic cases: Sunghir in Russia (parsimoniously two H17'27 indivdiuals) and then in Epipaleolithic Portugal (Chandler 2005), with two unmistakable H1b individuals.

    It is very possible that much of the other R* and, specially, R*-CRS, is also H but I cannot be sure 100%. These include many Late Upper Paleolithic samples: 23 from Morocco, 2 from Andalusia, one from North Italy and one from England.

    However there are several cases of R*-CRS that were not H after all and one R* that I am certain it is JT*.

    So we should also consider the possibility that some H did experience some expansion in Europe in the Neolithic and then also the Bronze Age (where we begin seeing modern, H-dominated, haplogroup sequences in Germany, for example). But this is not to be applied to Iberia (and possibly other SW/West European areas,as well as North Morocco), where Paleolithic continuity seems quite obvious, at least to some extent (we lack enough and sufficiently clear data).

    One could even imagine that H spread to Europe from Iberia in the Neolithic/Bronze Age, would this not be archaeologically absurd. What we can say is that the usual suspect farmers seem at least as different from modern peoples as Paleolithic hunter-gatherers, if not more.

    "Anyways I don’t want to sidetrack the topic here, but I would like for Jean M to point out to me where does it say in the paper she has as reference that H3 is more diverse in North Africa, or H1 is more diverse in the Middle East".

    I do not know if Jean is or will be reading this, so you may want to write to her directly. I'd like to know too.

    Actually H in general is more diverse in Iberia than in Tunisia and all Tunisian H appears derived from Iberian one (Cherni 2008 - PPV).That includes not only H1 and H3 but also H4 and H7 (v. Enafaa 2009 - OA).

    Jean is anyhow a sturdy defender of Neolithic replacement (because Zilhao says so). She may be basing her diversity figures on Enafaa 2009, where Arabia Peninsula has a diversity h(HG) value for all H of 76 (but highest diversity is among Moroccan and Tunisian Berbers anyhow: 79 and 85), while Iberian Peninsula has only 74. But all values are very close (excepting North African Arabs) and the work of Cherni is pretty much supportive of IP>NAf and not the opposite, in spite of overall H diversity (surely an artifact).

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  12. The 22 y-dna samples are clearly just 2 unrelated lineages, one a G2a, the other an I2a. There's no doubt wahtsoever about that, maybe in the case of I2a by a very long shot they are actually 2 unrelated lineages, but it's extremely doubtful. If R1b was 60% in the region back then, as it is today, then the chance of not finding R1b in a population of just 2 samples is 1 in 6, unexpected, but perfectly possible. Someone at rootsweb also made a very interesting observation. All the samples had a succesful call for P15 (G2a), but no sample had a succesful call for M287 (G2b) or M201 (G). This isn't ancestral/derived, this is wether the SNP was succesfully tested or not, regardless of result. So, remember the previous ancient y-dna study from a few months ago, that found an F*? What if it was, say, J2, and the marker for J2 suffers the same technical problems that apparently M201 (G) did in this study?

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  13. There's no N1a (mtdna). Haak found 25% N1a in the Neolithic of Central Europe. A recent study of Neolithic France found N1a in 1 of 3 samples. N1a has also been found in strangely disproportionately high frequencies in some other ancient mtdna studies.

    U5 has a high frequency, 17%. France and Spain each have 7% U5. This pattern has been observed before in ancient mtdna studies. Not to speak of the hunter-gatherer study that was all U4/U5, plus the recent study of Danish mtdna which tested 3 samples from 3000 or 4000 years ago, and they were all U5, a 1 in 1000 possibility if Denmark had the same frequency of U5 as it does today.

    And H is very low, just 20%. This too is a feature of several previous ancient mtdna studies. H is 45% to 50% in both France and Spain.

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  14. I could not find where does it say that M201 was not tested satisfactorily. That would be strange indeed considering that we are before 20 individuals each of which was tested separately. However P15 clearly indicates G2a and is coincident with the inference from STR haplotype sequences.

    "There's no N1a (mtdna)".

    It's not the only case: some Danubian populations also had no N1a but their numbers were smaller. Also after more samples were tested from the Elbe group the apportion of N1a has been greatly reduced and I think that today we can shake off the notion that N1a was so important re. Neolithic (though it was indeed more important than it is today). Maps here.

    At this moment, N1a appears in the Neolithic of:
    - Tisza (1/1)
    - Loire (1/3)
    - Rhine (2/8)
    - Elbe (4/33)

    And nowhere else (not in Austria, not in Moravia, not in Italy, not in Andalusia, not in Portugal and not in Britain).

    "H is 45% to 50% in both France and Spain".

    For what I can tell H might be in the Neolithic as much as (assuming all or most R* is H):

    - Andalusia: 1/1
    - Austria: 1/1
    - Portugal: 18/23
    - Tyrol: 1/2
    - Rhine: 2/8
    - Moravia: 1/4
    - Elbe: maybe 8/33

    Some of these are H for sure but others we can't be sure.

    What I find most important is that in Southern Europe, notably the Iberian Peninsula, H was even more dominant than today. H was also documented in Portugal in the Epipaleolithic and could have been present at similarly high frequencies.

    Of course, there could be other factors such as functionality. For example this 2008 paper argues that U5a and J are associated with accelerated AIDS progression, H3 and "IWX" with delay of AIDS onset and K ("Uk") with protection against AIDS. So maybe some odd changes in frequencies, like the reduction of mtDNA I in Denmark, have epidemic reasons and not demographic ones.

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  15. Maju said:
    “Based on the same data (and being absolutely strict in my filtering of it) I have detected for sure H in Europe in two pre-Neolithic cases: Sunghir in Russia (parsimoniously two H17'27 indivdiuals) and then in Epipaleolithic Portugal (Chandler 2005), with two unmistakable H1b individuals.”

    Maju this is what she said on a page regarding Genetic debate:

    “Even more significantly, H1 and H3 have a low diversity in Cantabrian Spain and in particular among the Basques. Instead the highest diversity and allelic richness of H1 and H3 in Europe is found in north-eastern and north-central regions, while the Near East has the greatest overall diversity of H1, and North Africa that for H3. The once-popular idea of the Basques as the source population for most of modern-day Europe is not supported by this closer examination.

    Instead it suggests that H1 and possibly H3 arrived in Europe with the first farmers. Against this is one sample of H1b reported in Mesolithic DNA in Portugal. However this comes from a study carried out some years ago, when ancient DNA studies were less reliable.”

    In her references in this write up she provides Garcia et al(2011), Ennafaa et al(2009), and Chandler et al(2005). The interesting part is that she completely dismisses the proof that H1b was already present on a Mesolithic Portuguese population (Chandler et al.2005), because “Back then ancient DNA were less reliable" ....

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  16. I have read multiple times the study done by Ennafaa et al(2009), the one that she puts up as a reference that H3 is most diverse in North African, and that H1 is most diverse in the Middle East. However nowhere does it say in that study that H1 is more diverse in the ME, or that H3 is more diverse in NA. A look at Table-1 reveals that the diversity values are highest for Tunisia Berbers(hHG ± se = 85 ± 3), however this table is for the overall diversity of Haplogroup H, not for that of Haplogroups H1 or H3. In fact the regions with greater overall diversity than the Iberian Peninsula(hHG ± se = 74 ± 2) are Morrocan Berbers (hHG ± se = 79 ± 3) and the Arabian Peninsula(hHG ± se = 76 ± 3), North Africa as a whole has the same diversity as the Iberian Peninsula(hHG ± se = 74 ± 2), and the Middle East has less diversity(hHG ± se = 72 ± 3), on the other hand many other places in North Africa have far lower diversity than the Iberian Peninsula such as Morocco, Mauritania, Saharans:

    http://www.biomedcentral.com/1471-2156/10/8/table/T1

    So I wonder, why Jean M made such claim, and provided that study as reference, when the study itself doesn’t support her claim. In fact the authors of the study conclude the following:

    Ennafaa et al(2009):
    “Although there is no archaeological evidence to justify such a demic flow from Iberia to North Africa, based on the phylogeographic range, comparative gene diversity and ages of several mitochondrial haplogroups such as V, H1, H3, and U5b1b [25,37,26], the presence of these haplogroups in North Africa is thought to be the result of a southward expansion of Palaeolithic hunter-gatherers from the Franco-Cantabrian refuge after the Last Glacial Maximum.”
    ……

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  17. In fact other studies that have come out after the Ennafaa et al(2009) study seem to agree in the expansion of Haplogroups H1 and H3 from Iberia to North Africa.

    Cherni et al(2009) concluded the following:

    “Although no signs of local expansion were detected, which would allow a clear dating of their introduction, the younger and less diverse Tunisian H1 and H3 lineages indicate Iberia as the radiating centre.”

    Also Ottoni et al(2010):

    “Coalescence time estimates suggest an arrival of the European H1 mtDNAs at about 8,000–9,000 years ago, while phylogenetic analyses reveal three novel H1 branches, termed H1v, H1w and H1x, which appear to be specific for North African populations, but whose frequencies can be extremely different even in relatively close Tuareg villages. Overall, these findings support the scenario of an arrival of haplogroup H1 in North Africa from Iberia at the beginning of the Holocene, as a consequence of the improvement in climate conditions after the Younger Dryas cold snap, followed by in situ formation of local H1 sub-haplogroups.”

    So why does Jean M so happily ignores these studies, and makes the baseless claim that H1/H3 is most diverse in the Middle East/North Africa based on a study that doesn’t support such statement?

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  18. Ask her for a link, for a reference. You need to know what is she founding such ideas on if you want to clarify the matter.

    Anyhow, H3 has a very SW distribution so no idea of what she may be talking about. H3 almost does not exist in Nothern Europe.

    "The once-popular idea of the Basques as the source population for most of modern-day Europe is not supported by this closer examination".

    In my opinion it is true that Basques alone cannot considered ancestral. Occitans and Gascons are the true ancestors. Basques are just placeholders.

    But this is difficult to discern because France is not well researched. There's been a fetish on Iberia, Basques and such and also there are restrictive laws in France re. genetic research, it seems. But France is crucial for anyone who wants to study European anthropology, history, prehistory and genetics. There's no other single region in Europe so central across the ages.

    "However this [H1b] comes from a study carried out some years ago, when ancient DNA studies were less reliable".

    Go and repeat it. That's how science is done. Also it's two individuals, not one.

    If we have to trust Chandler and Zilhao in this one, almost all Epipaleolithic Portuguese were H. But I (not her) did bother filtering the straw from the grain and found that only two of the cases were safe H and these were H1b without any reasonable doubt.

    "The interesting part is that she completely dismisses the proof that H1b was already present on a Mesolithic Portuguese population (Chandler et al.2005), because “Back then ancient DNA were less reliable" ....

    It is ideological, totally biased. We stopped exchanging when I told her that there was a (two) quite clear H case in Sunghir. She just rejects it because Zilhao, a friend of hers or her late husband, thinks that there was replacement. It's a preconception.

    She does a good job as archivist but her opinions regarding genetics and prehistory are not really solid.

    "however this table is for the overall diversity of Haplogroup H"...

    Indeed. That's what I meant.

    "So I wonder, why Jean M made such claim"...

    Ask her because I can't recall what paper may that one be.

    "So why does Jean M so happily ignores these studies"...

    Because she has a prejudice which has become to dominate her thought: for some reason she cannot accept (and she is not the only one) that Paleolithic people may have survived the Neolithic expansion.

    But anyhow: ask her.

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  19. "There's been a fetish on Iberia, Basques and such and also there are restrictive laws in France re. genetic research, it seems. But France is crucial for anyone who wants to study European anthropology, history, prehistory and genetics. There's no other single region in Europe so central across the ages. "

    Are you sure? I'm saying this because nearly 99% of "prehistoric" entertainment centered in Europe (neanderthals, upper paleolithic art and so on) has some French background. I'm reading J.M.Auel's last book: the history is placed in France. Nearly all neanderthal films, documentaries, comics and books have some ties in France as well. I think France is a widely accepted fetish regarding prehistory. Now people claim there must be continuity in France and/or origins of all Europeans recall there, because there's a lot of prehistoric art.

    Genetic studies don't seem to support this as far as I know. I find hard to believe it's because there are some nationalistic restrictions to take samples from France. While it can be the case, there's no evidence that the amount of prehistoric art strictly correlates with the French genetics: they seem to be a bridge between different European populations, such as southern and northern Europeans, which is nothing unexpected at all. But I don't understand why should be France more crucial, than, for example Italy or Germany.

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  20. Precisely: about 80% of European Paleolithic archaeology is in Southern France (plus the Cantabrian strip between San Sebastian and Oviedo, and to some extent Girona province).

    Basques are "a fossil" in that context but they are not nor can be representative of the whole region. Not at all. For example, Gascons alone when sampled have provided interesting insights (being suggestinve of origin of some lineages common in Catalonia, Aragon and the Basque Country). And Gascony is just a fraction of all that region as well.

    Basques cannot hold all the FC diversity (partly because of the fact of being a sub-region, partly because of local drift) and that is apparent for example in R1b-L11 and S116 scatter: some key clades are found further East in Languedoc. If we are to track the origins of R1b-M222 to the sub-Pyrenean region (hypothetical at the moment), it won't be the Basque country... but it may be the Loire or Languedoc.

    "Genetic studies don't seem to support this as far as I know".

    Which ones? There are not so many really.

    "I find hard to believe it's because there are some nationalistic restrictions to take samples from France".

    Actually we do have a serious problem of lack of info re. France. We have plenty of data from all West, Central and even East Europe. All but France.

    "there's no evidence that the amount of prehistoric art strictly correlates with the French genetics"...

    I'm not talking "art" but Paleolithic sites with or without art (see Boucquet-Appel 2005). Also even in the Middle Ages a plurality of Europeans were "French"... it's a region with a lot of history and demography.

    "they seem to be a bridge between different European populations"

    That's the interesting part. And if I recall properly, when Dienekes began digging deep enough, the French (and only them) began splitting in regional groups (where sampled), while for example Northern Europeans remained one single cluster. There's much more diversity in France, specially the South than normally acknowledged.

    "But I don't understand why should be France more crucial, than, for example Italy or Germany".

    I do not wish to take or give but if you know a bit the European Upper Paleolithic (I insist that you read Boucquet-Appel, linked above) you realize that it's like comparing Barcelona with Andorra (exaggerating a bit? maybe but not that much)

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  21. What does jeanm think of the Haak 2005 ancient mtdna study of Neolithic farmers? Does she also think it's "too old" to be considered valid? Can someone check, just for laughs?

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  22. "Precisely: about 80% of European Paleolithic archaeology is in Southern France (plus the Cantabrian strip between San Sebastian and Oviedo, and to some extent Girona province). "

    Interesting information, but east Africa is also a very rich archaeologycal site, yet genetic studies seem to suggest the oldest clades are from south-western Africa (or central/north Africa Africa, lately).

    "Basques are "a fossil" in that context but they are not nor can be representative of the whole region. "

    Why do you think they're a fossil? From what I've read recently, they look pretty much like their neighbours. No one denies they have their own peculiarities, but whether these are due to a "fossil" context or not is something still unknown.

    "And Gascony is just a fraction of all that region as well."

    With "that" region, you mean Occitania? Because French from Paris seem to be way different.

    "Which ones? There are not so many really."

    The French are often included in European genetic studies. They just look transitional between northern europeans (germans, english, dutch) and iberians.

    http://spittoon.23andme.com/wp-content/uploads/2008/09/novembreblogpostfig.jpg

    http://blogs.discovermagazine.com/gnxp/files/genmapeuropeA.jpg

    http://i129.photobucket.com/albums/p217/dpwes/Lao2008.jpg

    "Actually we do have a serious problem of lack of info re. France. We have plenty of data from all West, Central and even East Europe. All but France. "

    What about Treilles, or another work with neolithic samples found in France, with high N2a, I think? Of course some regions seem more interesting than others. Maybe we have relatively few info about the French, but what about the southern Italians, or corsicans, or Swiss or even north africans?

    "I'm not talking "art" but Paleolithic sites with or without art (see Boucquet-Appel 2005). Also even in the Middle Ages a plurality of Europeans were "French"... it's a region with a lot of history and demography. "

    I know this paper, but again, we have the same problem: East Africa also seemed to have been populated since the origins of mankind. Yet genetics tell a different history, at least for the moment. If the French are so special I think we should have some knowledge already of it. Genetic studies with haplogroups and so on are being published since late 90's.

    "There's much more diversity in France, specially the South than normally acknowledged. "

    Yes, that's for sure. Just look at their faces: Gascons look much like Basques and Iberians. Parisians look much like Germans.

    "you realize that it's like comparing Barcelona with Andorra"

    I'm not denying France has a very interesting archaeological sites, but I'm talking about genetics: do they correlate well with archaeology, or perhaps not at all?

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  23. "... but east Africa is also a very rich archaeologycal site, yet genetic studies seem to suggest the oldest clades are from south-western Africa".

    MtDNA still points to East Africa (and for me it is potentially more reliable than the others). But anyhow Africa is not Europe: BA begins explaining why he and colleagues believe that Europe has been researched in a quite balanced and throughly way and that means that his conclusions are likely to be close to reality (or at least proportional to reality).

    "Why do you think they're a fossil?"

    It's just a shorthand to mean that Basques have (quite obviously) less "recent" inputs than nearby areas, lacking R1a and all the Neolithic Y-DNA lineages (G, J, E). Also mtDNA-wise Basque samples keep that intense "pure" flavor. And in autosomal genetics, even Dienekes has to admit that Basques show to lack the "Indian" component (or something like that - "West Asian"?).

    In other words: Basques seem to represent the "untainted" form of ancient Europeans - but they are also different from most other Europeans, even in those aboriginal elements to some extent (so they cannot be taken as sole representative, even if the others are usually more mixed).

    "With "that" region, you mean Occitania? Because French from Paris seem to be way different".

    Specially Occitania but also Gascony and the areas between the Garonne and the Loire. And maybe even groups from further North (as the matter has not been researched, I cannot say for sure).

    "The French are often included in European genetic studies".

    OK but that was not what I was considering most: mtDNA, Y-DNA, regional samples and not just "French" (is the same a French from Paris as French from Lyon and a French from Bordeaux, etc.? I don't think so).

    The sample may be always the same anyhow. I haven't bothered researching that.

    "What about Treilles, or another work with neolithic samples found in France, with high N2a, I think?"

    Some stuff is coming but that's not modern French.

    "but what about the southern Italians, or corsicans, or Swiss or even north africans?"

    We have a lot more info on Italy and its regional structure than on France (incl. Corsica). Even the info on North Africa may be more detailed than France. I have no idea why Switzerland would be of any particular importance (it's a tiny country and colonized only since Holocene).

    None of these cases seem to be comparable to France in any way: neither in their relevance to understand the origins of West Europeans nor in the systematic lack of regionalized studies.

    "Just look at their faces: Gascons look much like Basques and Iberians".

    Not really. If you look at Anthrofrance, you'll realize it's not always the case: Gascons and Occitans and the peoples between Dordogne and the Loire... are very diverse (in looks too).

    "... but I'm talking about genetics: do they correlate well with archaeology, or perhaps not at all?"

    That's what I'd like to know. And we do not know almost at all.

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  24. About France : there is a clear problem with legislation. Genetic tests are forbidden if not allowed by a judge (for scientific purposes for instance). Add that most French scientists are not that interested in their country's own history (you cannot change "tropisms" : France is supposed to be a homogeneous and uninteresting entity while the whole world is an exotic place to excavate).

    It's true that some French samples are included in some studies now and then but the modern French sample used by Dienekes and likes is clearly insufficient : no geographic/genealogic data (just "Lyons") for instance.

    Maju is right that when Dienekes tried to dig a bit further and used splitting algorithms, the French were split into numerous clusters while most Northern Europeans (or Iberians) clustered together. Still, most French people from that Lyons sample clustered together (about half of them). As for me (I'm Gascon), depending on runs, I either defined a cluster of my own (along with a Frenchman from Lyons, probably that one on 23andme showing Basque affinities) or was put into the Iberian cluster by default (the algorithm clearly hinted to the fact that it was an approximation).

    Maju is also right that Dienekes has proved in his worldwide affinity analyzes that the Basques lacked his "West Asian" component (I also lack that component : I'm DOD133 for those interested). It's about 10% amongst the French. Note that such component is not interesting IMO : comparing Europeans with Middle-Easterners is not that relevant as much "Neolithic" variation could very be comprised within what was attributed to European variation by the algorithm for being unique to Europe. Comparing some Western Europeans with Greeks or Balkanic people could more interesting.

    Phenotypically wise, the Basques are quite unique : I always recognize a Basque face. It's clear that Basque physical features disappear somewhere in Cantabria, La Rioja and around Soria. The Pyrenees are somehow more transitional with a smooth transition towards "East-Pyrenean" types (read : Catalan). In the North, it's more blurry : I'm not sure peripheral Gascon people have retained Basque features, maybe they looked different in the first place, I must check. My feelings is that SW France is a vast continuum with Basque features disappearing as one gets further from the Basque Country. Quite clearly, Poitevin people are very distinct, Provençal people are as well, intermediate areas not so much. There are very interesting pockets where people have their own peculiar looks : I'm thinking of Pasiegos in Cantabria, Foix in the Pyrenees. People in Périgord are very strange-looking for instance. In some samples (I'm thinking of obscure areas such as Velay or Berry), you see faces that cannot be seen elsewhere.

    Still, I'm not claiming the Basques are "unique" per se : they're unique for being Basque but each area of Europe - depending on its history - has developped its own peculiarities. Well there are areas of Europe more or less interesting : France is surely remarkable for being that internally diverse. I'm not persuaded Slavic lands are that fascinating.

    Eventually what cannot be denied is that France is not being properly studied which is a shame for what seems to be the source for many modern populations (the Brits might originate from NW France).

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  25. Argiedude said:
    "What does jeanm think of the Haak 2005 ancient mtdna study of Neolithic farmers? Does she also think it's "too old" to be considered valid? Can someone check, just for laughs?"

    Yeah, that would be good to ask her? Does anyone know how one can communicate with her? I do think her saying that H1 and H3 is most diverse in ME and NA respectively, and giving Ennafaa et al(2009) as the reference for that, even though Ennafaa et al(2009) says nothing about H1 or H3 being most diverse in ME/NA says something about her. Most people wouldn't even check and take her word for it, but a quick check of the study reveals that she pretty much BS that part, and hoped to get away with it. So while she is ok with Haak et al(2005) given that it goes along with her line of thinking, Chandler et al(2005) is a big No-no, because it contradicts her with solid proof that H and as Maju pointed out H1b was already present in Iberia in pre-Neolithic people.

    On a different subject, I would be interested to see what the diversity value is for the R-M269 of Basques from Alava. Alava seems to be a region that has been undersampled. So far only Alonso et al (2005) took a mixed sample of Alava and Navarra, but the sample was too small (n=22). I have a feeling that Alava Basques should have a much older TMRCA for R-M269 that other Basques, perhaps I'm wrong. That is why I'm interested in the SJAPL burial chamber; I hope they do a Y-DNA Haplogroup test on that ancient sample.

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  26. I don't think TMRCA estimates are of any use but in any case Araba has the most recent colonization time of all the Basque Country: since Epipaleolithic. This trait is shared with most of Navarre, though the NW corner has UP habitation.

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  27. Maju said:

    "I don't think TMRCA estimates are of any use but in any case Araba has the most recent colonization time of all the Basque Country: since Epipaleolithic. This trait is shared with most of Navarre, though the NW corner has UP habitation."

    Well I think that given that Alava has received much more external influences than Eastern Vizcaya, NW Navarra, or Guipuzcoa, then their Genetic pool and their R-M269 should be more diverse, and hence have an older TMRCA. I know the area along the Ebro valley did experience demic influxes during the Neolithic. I was recently reading this paper:

    http://www.aranzadi-zientziak.org/fileadmin/docs/Munibe/1988105112.pdf

    The paper talks about signs of violence in the bodies found in SJAPL, which is why I'm interested in their Y-DNA Haplogroup, because most likely those people from SJAPL were either early farmers or hunter-gatherers that came face to face with the incoming tribes.

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  29. I just went to Eupedia, and the latest thread made by Maciamo is almost laughable.

    http://www.eupedia.com/forum/showthread.php?26522-Looking-at-European-genes-Paleolithic-vs-Neolithic

    According to his Theory, where R1b in Western Europe is the result of Bronze Age expansions, which is why it wasn't found in this French Burial, the populations with the most Paleolithic Genes in Europe are:
    "
    - Iceland : 94.5% Paleolithic vs 0% Middle Eastern (+ 5.5% Mongoloid)
    - Norway : 84% Paleolithic vs 7% Middle Eastern (+ 9% Mongoloid)
    - Denmark : 83.5% Paleolithic vs 15.5% Middle Eastern (+ 3.5% Mongoloid)
    - Croatia : 81% Paleolithic vs 19% Middle Eastern
    - Ireland 74.5% Paleolithic vs 25% Middle Eastern (+ 0.5% Mongoloid)
    - Scotland 74% Paleolithic vs 23.5% Middle Eastern (+ 2.5% Mongoloid)
    - England : 73.5% Paleolithic vs 26% Middle Eastern (+ 1.5% Mongoloid)
    - Sweden : 69.5% Paleolithic vs 10% Middle Eastern (+ 19.5% Mongoloid)
    (- Brittany : 69% Paleolithic vs 31% Middle Eastern)"

    Then followed by Basques:

    (- Basque country : 64% Paleolithic vs 36% Middle Eastern)

    Spaniards apparently are big on the Middle Eastern part:

    - Spain : 24.5% Paleolithic vs 75.5% Middle Eastern


    So I wonder how come if Basques have such percentage of Neolithic genes, why is it that in Behar et al(2010) they seemed to lack that Green component that showed up in all other Europeans, including Orcadians who are supposed to have much less Middle Eastern admixture according to Maciamo. I for once wish these whole issue with Haplogroup R-M269 was settled for once, and this people would for once give an objective opinion, instead of basing their opinions on personal fetishes. How clever that every time one considers I to be the solely European Paleolithic Haplogroup Scandinavia and most of the UK end up being the most Paleolithic Europeans according to all this forumites, yet in reality, logic indicates that there is no way Basques are less Paleolithic than Croatians. These people completely ignore historical facts about the Neolithic transition, or society in the Basque Country, and presume to go ahead and claim whatever comes to their mind about Basques. The most absurd one that I have seen so far, was Klyosov claiming Basques to have been Turkic speakers from Altai who came to Europe from Africa about 3000-4000 ybp.

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  30. "their Genetic pool and their R-M269 should be more diverse, and hence have an older TMRCA".

    Maybe but that would only be another argument against TMRCA having any use.

    But, anyhow most of the extra diversity should not be in form of R-M269 but as other lineages, specially if the theory of Franco-Cantabrian origin of this clade is correct.

    And another caveat: I recently mentioned a paper in which the Araban sample showed extremely low diversity. It was on mtDNA and not Y-DNA but anyhow the extremely low diversity (80% H1) could suggest strong founder effects in the event of Epipaleolithic (or other?) colonization (would need to be confirmed), i.e. just the opposite you are proposing.

    Without doubt the Ebro valley was a corridor for migrations, conquests and massacres (La Hoya, for instance) but, excepting Arabako Errioxa, most of Araba (Arabako Lautada or Llanada alavesa) is relatively protected as a (quite cold) plain surrounded by mountains. So I would actually expect more intense migrant flows further south in La Rioja and Erribera (Southern Navarre). This area is actually documented to have been influenced by "Gracile Mediterranean" types (as opposed to "Pyrenean" or "Basque" type) since the Neolithic and these were still dominant in La Hoya (Biasteri, near modern Logroño) when it was destroyed c. 300 BCE.

    But this site is in is Araba only accidentally: it could well have been La Rioja or Navarre. This is also the case of San Juan Ante Porta Latinam (what a name!), so in both cases rather than genuine Arabans or Basques what we have there is a peculiar crossroads zone. I would imagine both massacres to be similar in nature: product of warfare for the control of a most strategic route along the Ebro and very rich fields in the surrounding areas. However there are almost 3000 years of difference between them.

    Whatever the case this is La Rioja/Erribera rather than Araba proper.

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  31. Maju Said:

    "And another caveat: I recently mentioned a paper in which the Araban sample showed extremely low diversity. It was on mtDNA and not Y-DNA but anyhow the extremely low diversity (80% H1) could suggest strong founder effects in the event of Epipaleolithic (or other?) colonization (would need to be confirmed), i.e. just the opposite you are proposing.
    "

    I just took a look at their Table-S1, and it seems they only analyzed 2 samples from Alava, both of which belong to Haplogroup H. It seems in Table-S3 they combined the data with other studies as the sample size seems to increase for Vizcaya, Guipuzcoa and Alava. Now Alava with (n=51) which the authors claim comes from:

    "47 (Corte-Real et al., 1996), 2 (Alvarez et al., 2007) and 2 (this study)"

    From what I see, they seem to have 25.5 Haplogroup H with CRS, and 54.9% Haplogroup H without CRS, but since the samples come from another study, they do not go into details as into the diversity of the samples. So I don't know if all of those 54.9% that did not have the CRS in the HVI motif, had the same motif. Anyways, when I was referring to Alava, I was referring to the area along the Ebro Valley, where most Neolithic settlements in the Basque Country are found.

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  33. I just looked at the diversity value for Alava, and you are correct it is very low indeed (35+-8). Now here is something interesting that I just realized by looking at the diversity values of Table-S3; Jean M said the following on her site:

    "Even more significantly, H1 and H3 have a low diversity in Cantabrian Spain and in particular among the Basques. Instead the highest diversity and allelic richness of H1 and H3 in Europe is found in north-eastern and north-central regions, while the Near East has the greatest overall diversity of H1, and North Africa that for H3. "

    Yet I just looked at the overall diversity of the other two Basque samples, and Guipuzcoa seems to have a somewhat intermediate value (67+-3), but Vizcaya has a high diversity value (80+-3). Now this diversity values, is for the overall Haplogroups, not just H1 and H3. However a look at Table-S5 reveals that the Basques weren't used in the analysis of diversity for H1 and H3. The Iberian Peninsula (n=333) was made up of Madrid(n=36), León(n=36), Portugal(n=194), and south Iberia(n=67). So I wonder why Jean M made such a claim, when it is very clear that not a single Basque was used in the analysis of diversity for H1 and H3. However Vizcayans do not seem any less diverse overall than most other Europeans.

    PS: I'm sorry about deleted posts, is just that I usually write my responses in word, and then paste them here. Sometimes, I seem to leave an important chunk out of it, so I have to repaste it again.

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  34. Ok, to be fair, I just looked at Table-S11, and it seems Basque were indeed analyzed under the big NorthWestern Iberia umbrella, but I see no reason to think that they are any less diverse than anyone else from North Western Iberia. Vizcaya Basques seem to contribute 22 Samples of Haplogroup H1*, 2 samples of Haplogroup H1b, and 4 samples of Haplogroup H3.

    Now the Haplotypes for H3 found in Vizcaya Basques from Table-S1:

    1:H3 HVI:CRS HVII: 263 311i
    1:H3 HVI:519 HVII:152 263 303i 311i
    1:H3 HVI:519 HVII:263 303i 311i
    1:H3 HVI: 176 192 HVII:263 311i

    Now the Haplotypes for H1b found in Vizcaya Basques from Table-S1:

    1:H1b HVI:189 356 519 HVII:263 303i 311i
    1:H1b HVI:189 356 519 HVII:263 303ii 311i

    Now the Haplotypes for H1* found in Vizcaya Basques from Table-S1

    3: H1* HVI:CRS HVII:73 152 263 303i 311i
    2: H1* HVI:399 HVII:73 152 263 303i 311i
    1: H1* HVI:519 HVII:64 263 303i 311i
    1: H1* HVI:519 HVII:93 263 303i 311i
    1: H1* HVI:519 HVII:150 152 215 263 303i 311i
    1: H1* HVI:519 HVII: 150 263 311i
    1: H1* HVI:519 HVII: 204 263 311i
    4: H1* HVI:519 HVII: 263 303i 311i
    1: H1* HVI:519 HVII: 204 311i
    1: H1* HVI: 093 519 HVII: 93 263 303i 311i
    1: H1* HVI: 107 519 HVII: 152 263 303ii 311i
    1: H1* HVI: 129 519 HVII: 19 114 263 303i 311i
    1: H1* HVI: 129 519 HVII: 152 263 303i 311i
    1: H1* HVI: 221 519 HVII: 152 263 311i
    1: H1* HVI: 278 519 HVII: 146 263 303i 311i
    1: H1* HVI: 187 192 519 HVII: 263 303i 311i

    In Table-S11 and Table-S12 Basques are included under the big umbrella of NWIP. For the sample including H1 (H1*+H1a+H1b) the Gene diversity (by 100) for NWIP is 75. The Gene Diversity value for Vizcaya Basques for H1(H1*+H1a+H1b) is 75 (i.e. 18/24*100), so with respect to H1 in General the Vizcaya Basques do not seem any less diverse than the average for the whole NWIP. Now for H1*(without H1a and H1b) the Gene Diversity (by 100) for NWIP is 71.3. The Gene Diversity value for Vizcaya Basques for H1* (Without H1a and H1b) is actually higher than the average 72.72(i.e. 16/22*100). The Gene diversity value for H1b for NWIP is 71.1, the same value for Vizcaya Basques is 100 (i.e. 2/2*100), so in that sense Vizcaya Basque are bringing the average up not down. Finally the Gene Diversity value (by 100) for H3 for NWIP is 55.8, yet the same value for Vizcaya Basque is 100(i.e. 4/4*100), so again Vizcaya Basque are bringing the average up not down. What this shows is that Vizcaya Basques have the highest diversity for Haplogroups H1b, and H3, meaning that every single haplogroup found belonged to a different haplotype, the diversity value for H1* wasn’t the highest (84) amongst Europeans, however it wasn’t the lowest amongst FC populations. This contradicts Jean M claim that the diversity values for H1 and H3 were lowest amongst FC populations, and especially amongst Basques. Perhaps, I’d do the same analysis afterwards with Guipuzcoa Basques.

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  35. "Anyways, when I was referring to Alava, I was referring to the area along the Ebro Valley, where most Neolithic settlements in the Basque Country are found".

    I don't think Araba has more Neolithic settlements than other areas in the Basque Country. This Wiki-article is essentially my work of several years ago (based on more academic stuff) and you can see that neither in the extremely brief Basque Neolithic and the longer Chalcolithic Araba seems to have more settlements.

    They were a bit more advanced and prosperous probably but that's about it.

    Your observations about Basque samples' diversity are very keen. I would not draw too many conclusions in one direction or the other because there's always an element of randomness in any sample we should be able to assume as natural.

    But I think this bit is particularly valuable:

    "... Vizcaya Basques have the highest diversity for Haplogroups H1b, and H3, meaning that every single haplogroup found belonged to a different haplotype"

    Every single individual within these haplogroups you mean, right?

    "... the diversity value for H1* wasn’t the highest (84) amongst Europeans, however it wasn’t the lowest amongst FC populations. This contradicts Jean M claim that the diversity values for H1 and H3 were lowest amongst FC populations, and especially amongst Basques".

    I have the impression that Jean, like so many other people with a preconception they choose to serve (instead of to observe, which would be much fairer), likes to put the cart before the oxen. We should meditate on the data not use the data as some sort of weapon, because that betrays the spirit of scientific research.

    Anyhow, do you know which is the population that has the greatest known H1* diversity? Is it within the Franco-Cantabrian region or Central Europe? I ask because I really do not know if H1 originated in the FC region: it could also be, together with other H subclades, an aftershock of the original colonization of Europe (which began in Central Europe (Hungary, Moravia...) with North Italy playing a major role as well). But I have many doubts about this.

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  36. Maju Said:
    "I don't think Araba has more Neolithic settlements than other areas in the Basque Country. This Wiki-article is essentially my work of several years ago (based on more academic stuff) and you can see that neither in the extremely brief Basque Neolithic and the longer Chalcolithic Araba seems to have more settlements.
    "

    Well Maju in the same article you redirect me too says the following:

    "Overall the vast majority of important Neolithic sites are placed in the southern part of the country (Ebro valley): Fuente Hoz, Peña Larga, Berniollo and La Renke in Araba; Zatoia, Abauntz, Peña, Padre Areso and Urbasa 11 in Navarre; Herriko Barra in Gipuzkoa.
    [...]
    The human type is sometimes defined as Western Pyrenean, yet in the Ebro valley it appears mixed with Gracil Mediterranean types. There are virtually no brachicephallic remains found in the Basque Country yet, in spite of being more common in other areas of Europe since this period
    "
    It seems to be based on the work done by:

    Xabier Peñalver, Euskal Herria en la Prehistoria, 1996. ISBN 84-89077-58-4

    So if it was you who wrote that based on Peñalver's work, then it is very clear there that the most important Neolithic happened in Alava, and Southern Navarra. Also didn't the Urnfield culture reach Alava?

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  37. Maju said:

    "Every single individual within these haplogroups you mean, right?
    "

    Yes that is exactly what I meant; every single individual present in the Vizcaya Basque sample has a different haplotype, at least for H1b and H3.

    Maju said:

    “Anyhow, do you know which is the population that has the greatest known H1* diversity? Is it within the Franco-Cantabrian region or Central Europe? I ask because I really do not know if H1 originated in the FC region: it could also be, together with other H subclades, an aftershock of the original colonization of Europe (which began in Central Europe (Hungary, Moravia...) with North Italy playing a major role as well). But I have many doubts about this.”

    I’ll have to check, but it takes time, I’m actually going to Table-S1 and counting how many Haplotypes each population has, and based on that, is that one can calculate the Gene Diversity. In Table-S11 the population with the highest Gene Diversity for H1 Complete (H1*+H1a+H1b) is Med with a Gene Diversity of 90, now their sample size is rather small 84 which in turn represents 8% of the total sample, but not only that, Med is made up of the following countries Corsica (n=100), Italy (n=946), Sicily (n=314), Macedonia (n=13), Greece (n=195), South-East Europe (n=233), Croatians from Italy (n=41), Croatia (n=96), Albania (n=42), and Mediterranean Center (n= 302). Now given that H1(H1* + H1a+H1b) only 84 sample, this means that the sample size was really small for every single population. Now as far as I know there isn’t any event that would link all those place as into make the whole region a possible source of Haplogroup H1, so analyzing the whole Mediterranean combo is rather misleading. It would me more interesting to see instead of the general Mediterranean region, the diversity break down for each single place. Anyhow the highest diversity value for H1* also happens at the same region Med with a Gene Diversity of 84.1. As for H3 the highest Gene Diversity value happens in the region deemed WIS, or West Islands of Europe, but here is the catch, the sample size is only 5, which in turn represents 5% of the total sample. The Gene diversity value for the region is 90, however I don’t see any reason to deem this region as the one with the highest diversity, when Vizcaya Basque alone with a sample size of 4, which isn’t really any smaller than 5, but instead a Gene Diversity of 100.

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  38. Here is the main problem with Table-S1 and FC region, the samples that are known to belong to the FC region have very small sample size, except for some Basques (Vizcaya and Guipuzcoa). For example Alava(n=2), Cantabria(n=6), France (n=6), Basque Country Miscellaneous (n=24), Asturias has a greater sample size(n=76), but I don’t know if Asturias could be considered part of the FC region.

    Anyhow looking at Table-S2 I can see that Asturias for example has 5 different haplotypes for the 5 different samples belonging to Haplogroup H3, so that is another population in the fringe that also has a Gene Diversity of 100 (i.e 5/5*100). Here are the haplotypes:

    1:H3 HVI: 180 519 HVII: 200 263 303i 311i
    1:H3 HVI: 189 519 HVII: 263 303i 311i
    1:H3 HVI: 111 129 256 519 HVII: 153 263 303i 311i
    1:H3 HVI: 129 145 HVII: n.a.
    1:H3 HVI: 519 HVII: 257 263 303i

    Thus, so far we have two populations from Northern Iberia that seem to have greater diversity for H3 than the UK, and both of them have a very similar sample size (i.e 4 and 5 vs. 5). On the other hand Asturias has 12 different haplotypes for 17 H1* samples found it them, so the gene diversity value for them seems to be 70.58 (i.e 12/17*100). This value seems to be lower than the average of 75, since the Vizcaya Basques have a value of 75 and a sample size of 22. The only conclusion that I can make thus far, is that while the FC region doesn’t seem to hold the greatest diversity as a whole, certain sub regions inside the FC do seem to have great diversity.

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  39. One of the regions that seems to have a rather low diversity and is probably causing the general diversity to decrease because it does have somewhat big sample size is Guipuzcoa. The number of sample that have Haplogroup H1* in Guipuzcoa are 27, yet only 17 different haplotypes are present according to Table-S2, so that gives it a Gene Diversity value of 62.96 (i.e. 17/27*100). However for H1b, Guipuzcoa and Vizcaya both a 2 samples belonging to H1b, and the two samples being of different haplotypes, meaning a 100 Gene Diversity. Nonetheless any conclusions about H1b can be misleading because of the small sample sizes so far. However the authors seem not to care about this given that their highest Gene diversity for H1b happens in WIS (UK Islands) as shown in Table-S11, yet if one looks at the sample size it is 2. Now here is something interesting, when one looks at Table-S4 one can see that H1b represents 5.4% of the Vizcaya Basques (n=37) which means 2, it also represents 3.2% of the Guipuzcoa Basques(n=63) which means 2. However on Table-S11 it seems that the total sample size for H1b for NWIP is 10, this comes from 3 from Miscellaneous Basques, 1 from Galicia/Asturias, 1 from Cantabria, and 1 from Potes Cantabria. The Gene Diversity value given for NWIP for H1b in Table-S11 is 71.1, so this means that the 3 Miscellaneous Basques that had H1b, probably had some Haplotype sharing, or at least partial haplotype sharing. However those 3 Basques having H1b are coming from Pereira et al(2005), given that the 24 Basques analyzed in that study did not have H1b. In case you are wondering this is all from Garcia et al(2011). Anyways as you can see the Authors of the study did a little manipulation themselves, because if only Guipuzcoa and Vizcaya Basques analyzed in their study were included for the Gene Diversity Value, it would have been the same as that of the WIS at 100, yet the sample size would have been twice that of WIS. Guipuzcoa Basques also seem to have a lower Gene diversity for H3 at 66.67 (i.e 8/12*100) as seen in Table-S2

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  40. "So if it was you who wrote that based on Peñalver's work"...

    Years ago (as Sugaar). It surely suffered some modifications since then.

    "then it is very clear there that the most important Neolithic happened in Alava, and Southern Navarra".

    I understand that Arabako Lautada (most of Araba), while being part of the Ebro basin is not part of the Ebro valley, which begins near Logroño (or as high as Miranda at the most) and is a rather narrow strip until it opens up around Tutera (Tudela).

    Southern Navarre would more within the Ebro Valley than Araba actually. Ebro Valley and Ebro Basin are not the same, naturally.

    Anyhow, as the maps show, the archaeological sites of Basque Neolithic/Chalcolithic are quite evenly distributed. Admittedly the south hosted larger towns at times and had more sophisticated burial customs (gallery dolmens instead of the simple ones of the coast/mountain). I do think La Hoya (Biasteri) was particularly important since the late Chalcolithic and maybe was the hegemonic polis of the area but I am not aware of any extreme contrast between the Mediterranean and Atlantic basins.

    "Also didn't the Urnfield culture reach Alava?"

    Yes but in a very modified variant, strongly influenced by the Aquitanian cultural substrate. It is in any case a brief episode of the early Iron Age (we are talking the latest Urnfields here, not the much longer lived ones of Catalonia).

    In any case, it is true that Araba has been more open to outer influences from the Ebro Valley and the Plateau but, as everything else, it is relative (the coast would have been more exposed to sea routes for example).

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  41. As for your other comment, Jeanlohizun, it is very interesting. I recall now having gone through all that data back in the day and feeling the same frustration about the regional groupings and the difficulty of analysis.

    Still I also feel that this outlines also the difficulty of measuring diversity by haplotype in small or with irregularly sized samples.

    Following your methods, I get maximum (100% unless otherwise specified) diversities (for n>1):

    H*: Asturias (n=9), Biscay (n=3), Catalonia (n=3) and Normandy (n=5).

    H1*: Galicia (n=4), Normandy (n=3)

    H1b: Biscay (n=2), Gipuzkoa (n=2) [adding up too, with n=4, GUI and VIZ haplotypes are different and most of H1b detected in this paper, the other one is from Asturias]

    H2a: Asturias (n=3)

    H3: Asturias (n=5), Biscay (n=4), Normandy (n=3), Valencia (n=3)

    H4: Biscay (n=3, div=67%)

    H5a: La Rioja (n=2), Valencia (n=2) [H5 as a whole also Asturias, n=2]

    H7: Valencia (n=3)

    So it looks like H1b, H2a, H4 and H5 could be from the Franco-Cantabrian region. H5a and H7 could be from the Iberian province. I withhold my judgment on H, H1 and H3 because of Normandy and lack of data on Central Europe/Italy but they could be from the Franco-Cantabrian region as well (surely the case with H3, as it's concentrated in SW Europe).

    For the casual reader, just remember we are discussing here the supplemental material in García 2011, which I mentioned in this entry.

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  42. I have recently know that my father (Bruno Tognoni: 1920-2008) was mtDNA H* by a test of my cousin Monica De Conti at 23andme. By Relative Finder there are many H* whic match me or my relatives, also by my wife side who comes from Sicily. Then I think that H* is massive overall in Italy.

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  43. It's possible. My best hunch is that H expanded with the first colonization of Europe, because there is no other mtDNA haplogroup (phylogenetic node) with so many basal sublineages as H, excepting M (huge star-like structures).

    M's huge basal diversity almost for sure represents the great expansion that happened to the Eurasian humankind upon arrival to South Asia. Similarly H must represent a huge sudden expansion, which IMO is most likely to have happened in the colonization of Europe (Aurignacian/-oid very possibly).

    In that early process, North Italy played a major role surely in the spread of both proto-Aurignacian and then Aurignacian proper in Westward direction. The abundance of H* (unlike M*) suggests that the basal diversity of H is even greater than so far explored (33 known basal sublineages), representing a brutal explosion with only one comparison in all the phylogenetic tree (M).

    In Álvarez Iglesias, Mosquera Miguel et al. 2009, we see however that H* is very common in Italy but also Central and SE Europe and Europe in general (but not Iberia). So it's not just an Italian thing.

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  44. Just for the record, after looking at how H subclades are distributed (I lack info on many small clades however) it looks to me that H (as a whole) surely boomed from the Mid Danube (and that was probably also the case of H1 and some other sublineages H5a, H7, H11 (and for whatever is worth H*, though this one is more like Slovenia and Slovenia was not inhabited back then).

    H3, H4 and H6a look too specific from SW Europe to have originated anywhere else. In turn H2a, H8 and H13 look from Eastern Europe instead.

    This would all fit with a expansion in the context of the Aurignacian/-oid colonization, from a root in the West Asian highlands where other HV and R0 are still found now.

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  45. I didn’t want to say that H* is “Italian”, only that probably it is in Italy from very ancient times. This said to those who say that Italy didn’t exist, that was peopled from elsewhere in recent times. I have only my data and I cannot pay for everyone. I invite many friends to pay for their tests. Anyway every result arrives to me, it is always a surprise. Also the K1c1* of my wife (and my sons) has the mutations in 310T and 16180T (and 23andme tests only 3000 SNPs out of 16569) not found elsewhere over the world. My cousin Fabrizio Federighi is R0a, but with the mutations in 16230G and 16497G not found elsewhere all over the world.
    Amongst the Relative Finder of my wife (100% Sicilian) there are 26 H haplogroup out of 53= 49%. Even though I don’t know their origin (they could be of mixed origin amongst the millions of descendants of Sicilians all over the world), I found many of these haplogroups also in my cousin Monica (50% Tuscan and %0% Venetian):

    1 HV
    4 H*
    2 H1
    1 H1e
    2 H1e1a
    1 H2a2
    3 H3
    1 H4a
    1 H4a1a
    1 H5’36
    1 H6a1a
    4 H7
    1 H10
    1 H11
    1 H17

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  46. "But I don't understand why should be France more crucial, than, for example Italy or Germany."

    I think people just mean in the context of LGM refugia. Germany has the earliest finds of art and music (Vogelherd, Geißenklösterle), but these are all the same people roughly, with some clines, naturally, until the ice age separated them. It is still not known; the southern Rhine valley would have been warm enough to survive, but other than that most assume that the number of people who could have made it and then expand would have been small. Then you have the Czech lowlands, some weird climatological island, and that's it for Central Europe. Everyone agrees Italy was important and preserved basal lineages, the same as (probably the NW) Balkans. What is weird is that Italy and the NW Balkans don't look all that similar, today, even if you subtract R1a and neolithic lineages. You would have thought the Po valley and its extension, the-then dry part of the Adriatic, would have formed a continuum with the coastal NW Balkans (surely one of the mildest areas of the time). And that latter area has access to rich, nearby planes which could have been hunted seasonally. The Balkans have similar basal lineage groups, but for the most part their members seem different from those in Italy.

    'Also even in the Middle Ages a plurality of Europeans were "French"...'

    That's stretching it, a bit. First of all, the combined areas of central and eastern Europe are huge, so even with a sparser population density, things add up quickly. Secondly (thus perhaps your use of quotes), the central, narrow strip of the Frank kingdom was mixed Gallic/Germanic, under Dutch/Germanic rule. As it had been mixed since before Roman times (Caesar just liked to only call the Germanic tribes east of the Rhine Germanii, for political reasons). You can even today look at a map and draw a (slightly curved) line from Dunkerque to Basel, and see that the toponymy is Germanic to the right of that line.

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  47. Instead of saying "Germany" or "France", modern names of modern implications and strict borders, I tend to use the real Paleolithic provinces, i.e. Franco-Cantabrian (most of France but also parts of Spain), Rhine-Danub (Germany but also Belgium, border areas of France and, crucially, the Mid-Danube, with its many key sites in Moravia and Hungary), Iberia (minus the Cantabrian strip), Italy (with extension to the Adriatic?), Eastern Europe (Ukraine and much of European Russia)...

    Germany also has a duality, with the Lower part of the country having at least in the late UP a distinct culture (Hamburgian-Ahrensburgian) to that of the Middle and Upper country (Magdalenian, a culture of Franco-Cantabrian origin).

    In general, specially since the LGM, the Franco-Cantabrian region hosts most of the population, surely because of special climatic and ecological reasons (milder climate with diversity of environments).

    In this case we have to insist in the modern concept of France because it is a legal entity and no other reason. A legal entity that, because of ideological reasons (fear of its own ethnic and genetic diversity, potentially destructive of the polity), hinders the research on the origin of Europeans in general.

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  48. "What is weird is that Italy and the NW Balkans don't look all that similar, today, even if you subtract R1a and neolithic lineages. You would have thought the Po valley and its extension, the-then dry part of the Adriatic, would have formed a continuum with the coastal NW Balkans (surely one of the mildest areas of the time)".

    There are two things here: one is whether there was really an Italo-Adriatic province or not. There is no rock art in Italy (and not for lack of caves) and instead there is in the Adriatic area, which has been proposed as cultural corridor towards Anatolia, where again we see rock art of a late period.

    (Yes, believe it or not, there may have been some lesser flows from Europe to West Asia in the UP and not just unidirectional ones from East to West).

    But I'm not sufficiently knowledgeable on the UP of either region and particularly not that of the Balcans, so I can't say for sure. In any case I do have the feeling that both areas may have suffered large repetitive replacements that hide their substrate. You can still see a connection in form of, for instance: I2a, R1b (transitional clades), etc. But I agree that is not much, specially not much pre-Neolithic.

    One of the things about the Balcans is the they hosted low population densities most of the time, because the area was dry steppe (like North France) instead of the much more productive loess steppe of the Rhine-Danube (down to the Iron Gates) and Eastern Europe (Dniepr-Don essentially). And then you have the Balcans getting the bulk of the Neolithic demic impact. But still they retain enough diversity to show up as a most likely candidate for the origin or R1b1b2a (old nomenclature) if we are to follow my (quite straightforward) interpretation of Morelli 2009.

    So what the Balcans (and Italy and parts of Central Europe like Moravia) lack in frequency (as new waves have rolled over), they seem to keep in rare clades near the root, specially in relation with R1b (-1b and -1a).

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  49. As for the population, according to N.G. Pound 1981, in the 15th century (right after the Hundred Years' War), France had 17-18 million people, while the second most important area, the HRE (described as "Germany, incl. Netherlands, Austria and Bohemia") had some 10-12 million, next was Italy with some 8 million, Iberia with 6 million, the Balcans 5 million, historical Hungary 4 million... No data is offered for either Britain nor Eastern Europe.

    It's not a brutal difference but it's clear that at that time France was the largest country in Europe by population by a lot. And that was even more true earlier in the Middle Ages proper most probably as Northern European agricultural and commercial development kicked off then and most of the largest cities were in the South.

    Note: cited as "giant" cities (>50,000 people est.) in the Middle Ages are: Constantinople, Cordoba, Seville, Granada, Venice, Genoa, Florence, Milan, Paris, Ghent and Bruggen.

    Anyhow, this debate would divert us. What really matters is the population densities in the Upper Paleolithic, and these do concentrate intensely in the Franco-Cantabrian region, specially since the LGM (cf. Bocquet-Appel 2005).

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  50. Excellent analysis Maju, both in the original post and in your comments. This is really one of the finest bits of analysis that I've seen at your blog or anywhere on this subject.

    The notion that a late megalithic community was lactose intolerant, makes the case for the entire megalithic cultural complex being lactose intolerant, at least for most of its history, and is suggestive that the same was true of the cardial pottery food producers, although I'd be very interested to know what other evidence can be marshalled for or against this inference from food animal remains, ancient DNA, etc. in addition to the Southern French lactose intolerant rate which generally seems to fit the olive oil-butter line in Europe.

    This example is, as you note, pre-Bell Beaker, but it would also be interesting to look at those evideence of lactose tolerance in Bell Beaker populations, ideally from ancient DNA, but also from other inferrences. It looks like lactose tolerance, in places that experienced the Neolithic revolution via megalithic or cardial pottery sources, probably started to acquire it will Bell Beaker which is often inferred to be Indo-European probably Celtic or proto-Celtic-Italic.

    This would point a search for the cultural ancestors of the Basque and the source of their lactose tolerance not in Epipaleolithic Iberians or Franco-Cantabrian refugees (although they certainly could have been part of the mix), but in dairy farmers from some non-Indo-European society somewhere to the East.

    Given the apparently lack of a continuous Vasconic cultural area from the Danubian dairy farmers to Iberia, it would seem to make more sense that they arrived by sea as part of a maritime culture that is post-cardial pottery and post-early megalithic. (You've done an excellent job now and in the past of making the point that the Basque ancestors were not part of the megalithic cultural complex.)

    Looking around for a dairy using, maritime culture in that time frame that is not Indo-European or Semitic linguistically, I'm hard pressed to find any candidate that fits the bill better than the Minoans, who are also notable for sharing with the ancient Basque, a very special cultural (and perhaps religious) place for the bull relative to some of the other candidate cultures (e.g. Danubian dairy farmers or Kassites or Hurrians). This could also explain the low levels of R1a in the Basque relative to R1a in some of the other possible dairy farmer source populations.

    Any thoughts on that line of reasoning?

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  51. Thanks for your compliments, Andrew. They are surely undeserved but always feel good.

    "The notion that a late megalithic community was lactose intolerant, makes the case for the entire megalithic cultural complex being lactose intolerant, at least for most of its history"...

    Not for me.

    (1) We cannot conclude that all Megalithic peoples were genetically related, at least not too intensely: Megalithism is a "super-culture" like Christianism, Islam or Buddhism, not (generally at least) a pattern of systematic colonization. In general, Megalithism appears on pre-existent cultures and that is clear the case of Treilles.

    (2) Basques are the most lactose-tolerant peoples on Earth (another stupid Basque genetic record) but crucially Iberians and British follow close behind - unlike "South French". So I think that this finding reflects at most a trait of some South French, trait that remains in some local populations up to this day. Hence genetics have not changed substantially in all the area and the patterns of Neolithic can still be seen today (and vice versa).

    "... it would also be interesting to look at those evideence of lactose tolerance in Bell Beaker populations"...

    There's no such thing as "Bell Beaker" populations: there were Bell Beaker individuals within other populations, just like today there are Jews or Parsis within other populations. While Megalithism may have been associated locally to some limited colonizations, Bell Beaker was not with nearly all certainty

    (And by the way, Bell Beaker might have originated in Iberia after all - a matter I need to research further).

    "Given the apparently lack of a continuous Vasconic cultural area from the Danubian dairy farmers to Iberia, it would seem to make more sense that they arrived by sea as part of a maritime culture that is post-cardial pottery and post-early megalithic"...

    IF Bell Beaker is also of Iberian origin (and Megalithism is already widely accepted to be), you may want to consider linguistic flow from Portugal (as alternative to Paleolithic continuity for Vascoid languages). However I do not think that much genetic flow can be attributed to this cultural expansion from SW Iberia (not enough E-M81 along the Atlantic).

    "Looking around for a dairy using, maritime culture in that time frame that is not Indo-European or Semitic linguistically, I'm hard pressed to find any candidate that fits the bill better than the Minoans"....

    Impossible. Minoans lasted just a few centuries before being conquered and hellenized, and Greeks (including Cretans AFAIK) are mostly lactose intolerant.

    Lactose tolerance is either a Paleolithic genetic accident (most likely) or a Paleolithic product of forgotten horse domestication in the Magdalenian period (not impossible). I do not think it is a product of Neolithic because Neolithic remains consistently test as lactose intolerant and because too many peoples unrelated since at least the UP have the same mutation at dominant levels.

    I must therefore consider that it is a genetic accident and not (mostly not) positive selection, just like high concentrations of Rh- or Y-DNA R1b appear to be genetic accidents as well and not the product of any evolutionary logic.

    It's not impossible that, beginning from high prevalence, it has increased its frequency to almost 100% by selection - but why here and not there? I'm more inclined to think in mere chance.

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  52. "I do not think it is a product of Neolithic because Neolithic remains consistently test as lactose intolerant and because too many peoples unrelated since at least the UP have the same mutation at dominant levels."

    Why not simply late Neolithic, with early Neolithic, particularly in the olive oil belt being lactose intolerant at first, and late Neolithic including a wave of people descended from later dairy farmers?

    Even if it was a paleolithic genetic accident, it wouldn't have been a mutation with selective advantage until the advent of dairy farming and would have remained rare, except due to genetic drift.

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  53. "Why not simply late Neolithic"...

    The Treilles' burials are "late Neolithic" or early Chalcolithic in fact. We are getting dangerously close to the line when written history begins. It's barely double of the age of Alexander the Great or Plato, same age as the earliest pharaohs... we are getting contemporary.

    True that some changes still happened in that time but there is only room for so many changes, most notably the Celtic migrations.

    "the olive oil belt being lactose intolerant"...

    It would imply a massive replacement in Iberia, where most are lactose tolerant. I strongly feel that this "adaption" is only so much an adaption and mostly pure chance. Essentially we see that lactose tolerance follows the same pattern in Europe, roughly, as high concentration of Rh- or R1b, so it's more of a random genetic fonder effect - just that genes often have a function, in this case an unusual ability to digest milk in adulthood.

    "Even if it was a paleolithic genetic accident, it wouldn't have been a mutation with selective advantage until the advent of dairy farming and would have remained rare, except due to genetic drift".

    That's what I think it happened: it became fixated by accident and not selection - though I cannot discard this last reinforced the fixation a posteriori, but only somewhat.

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  54. Hey Maju what do you think of this?
    http://euskararenjatorria.eu/2-Sergio_Cardoso_Marian_Mtez_Pancorbo.pdf
    Whao, I have to say there are really good papers coming our way, anyways read over that, especially the following part:
    "4. La población vasca y su relación genética con otras poblaciones"
    Here is an excerpt from it:
    "El análisis del cromosoma Y en las poblaciones autóctonas del refugio también ha permitido determinar la existencia linajes paternos representados de forma muy significativa (Alonso et al. 2005; López-Parra et al. 2009), cuyo origen podría estar al final del último periodo glacial. Así, en nuestros estudios hemos observado que el haplogrupo R1b1b2 alcanza una frecuencia del 91% en la población vasca (Valverde et al. 2011), es decir, existe una baja diversidad tanto de linajes maternos como paternos. Asimismo, nuestros cálculos proporcionan una estima del origen del haplogrupo R1b1b2-M269 a finales del Paleolítico, hace aproximadamente 12.000 años, lo que apoya la expansion post-glacial de este linaje de forma coetánea con los haplogrupos H1 y H3 del AND mitocondrial desde el refugio Franco-Cantábrico. Esto podría igualmente explicar la alta frecuencia de este haplogrupo existente en la población irlandesa, puesto que la población irlandesa conservaría el acervo génico pre-neolítico consecuencia de la expansión del R1b1b2-M269 por el oeste de Europa (Wilson et al. 2001; Alonso et al. 2005; Oppenheimer, 2006). Nuestro grupo está realizando un análisis en mayor profundidad del haplogrupo R1b1b2-M269 con el objetivo de ayudar a mejorar las aproximaciones en cuanto al lugar de origen, periodo de llegada al refugio Franco-Cantábrico y horizontes de expansión de este linaje paterno en Europa.
    […]
    En síntesis, las poblaciones autóctonas del País Vasco y norte de Navarra presentan un marcado aislamiento genético reflejado en una baja diversidad de los linajes maternos de
    ADNmt (Alfonso-Sánchez et al. 2008; Cardoso et al. 2011), así como una baja diversidad
    de los linajes paternos del cromosoma Y (Valverde et al. 2011). Por otro lado, un elevado
    porcentaje de los linajes maternos encontrados en las poblaciones vascas son de origen
    paleolítico y algunos de ellos presentan además máximos de frecuencia en el contexto
    europeo; este el caso de los haplogrupos U5b, J1c, H1 y H3.
    "
    Here are the studies that have been sent to be published:
    Cardoso et al. (2011b). Mitochondrial DNA phylogeny of the Franco-Cantabrian Refuge: beyond the postglacial resettlement of Western Europe
    Valverde et al. (2011) Y Chromosome lineages in the Basque Diaspora in the Western USA
    ADN antiguo: una mirada al pasado. Resultados preliminares del yacimiento Calcolítico Las Yurdinas II. Munibe, 2010.

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  55. My first impression is that their sampling strategy is highly unoriginal (Basque Country and the highly peculiar Valle del Pas, c'mon, we have seen that a zillion times before!)

    However there are novel interesting results, facts that I did not know about, notably that U5b and J1c appear to be centered in the Basque Country (notwithstanding possible 'South French' missing data - the perennial blank of European pop. genetics). Also they find low tier lineages that appear specific to the Basque area: H1j1 and V10.

    I also appreciate that they do not allow themselves to be carried away by Anglosaxon recentist fashions but that is, as we all know by now, arguable (though I agree, of course).

    I will discuss the paper later, thanks for the link, Jeanlohizun.

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  56. This is the old theory we know, but what makes me think is what the authors say: “En síntesis, las poblaciones autóctonas del País Vasco y norte de Navarra presentan un marcado aislamiento genético reflejado en una baja diversidad de los linajes maternos de
    ADNmt (Alfonso-Sánchez et al. 2008; Cardoso et al. 2011), así como una baja diversidad
    de los linajes paternos del cromosoma Y (Valverde et al. 2011) ». A low diversity is a sign of recent origin and not ancient. I think having demonstrated, also by the 1000 Genome project new SNPs, that for instance R-U152 is more ancient in Tuscany than in Iberia, and I am R1b1b2a , Italy has the highest variance and percentage of R-L51+ etc. We shall see.

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  57. Low Y-DNA diversity may mean 90% R1b and 10% I, that's lower than 50% R1b, 10% R1a, 20% I, 10% J2, 5% G and 5% E, for example.

    Similarly, the USA or Brazil are much more unqualifiedly diverse than Europe as a whole, becauste to a varied array of European lineages, they add African, Native American and other diverse lineages. Without doubt New York is more diverse than Bordeaux but Bordeaux is much older than New York for European-specific lineages.

    I'm not sure what the authors had in mind when they wrote that, because no particular tabulated data is provided as support for that assessment, but this may be it.

    The question is not diversity as such but what specific kind of diversity we are talking about. I do not think that Basques have low basal diversity for R1b1a2a1a1b (P312/S116), and I do not think that South French or Iberians are either in that same category. And this is what matters: diversity within the phylogeny, "orange" diversity and not random diversity in which the proverbial "apples and oranges" and a dozen other kinds of fruits are put together without any criterion.

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  58. "R-U152 is more ancient in Tuscany than in Iberia"

    It's possible. I'm quite sure that it should be most diverse somewhere in France actually but I do not have the data (do you?). Iberia (or most of it) should be rather irrelevant, France (Gascony, Occitania, Guyenne) is what really matters here (and incidentally Basques too but not as centrally as sometimes claimed).

    I'd ask geneticists to stop debating Basques and Iberians and start debating Dordogne, the Garonne, the Loire, the Rhône... that is the true Franco-Cantabrian refuge, there is where most Europeans lived in the Ice Age.

    "Italy has the highest variance and percentage of R-L51+"...

    R-L51(xR-L11)? Or just generic R-L51? How does it compare with the Mid-Danube area (the former Austro-Hungarian Empire, roughly)?

    Whatever the case this is consistent with the Proto-Aurignacian, Aurignacian and then Gravettian waves flowing Westward from the Balcans and Central Europe, at least partly, through North Italy. IMO Italy's diversity refers along with that of the Mid-Danube (quite comparable at least), to the pre-LGM flows, while SW European R1b1a2a1a1b (P312/S116) diversity corresponds to LGM and post-LGM flows.

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  59. About R-U152 I can say the case I examined recently: an American of French surname (Pommier) asked me about his STRs. It seemed R1b1b2a of an Armenian clade, even thought only with 37 markers and without DYS461, but with DYS393=11, which presupposed a 12.
    Examined by FTDNA, and now also by 23andMe (see “Adriano’s spreadsheet”), he resulted R-L2+.
    This for saying what I have said also in the past, when forums banned me, and this I have written many times also to Whit Athey, that only a SNP exam can be resolutive. The Athey’s calculator can calculate the medium but not the border line, which is the most interesting.
    This for saying that we know a few of the variance, and, being Pommier a French, France of course has yet a lot to say. But for this also Tuscany. I have written many posts on this, on “Dienekes’Anthropology blog”, when I find it open to me, or on 23andMe, on Worldfamilies, etc.

    P.S. R-L51 in Italy is R-L51*, the ancestor of all the subclades.

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  60. "R-L51 in Italy is R-L51*, the ancestor of all the subclades".

    It is not "the ancestor" but one or several parallel lineages. The ancestors are all dead (and their Y-DNA peculiar sequences too). However I get your point.

    AFAIK, R1b-L51* is found in relatively large numbers in North Italy and the Mid-Danube. And in lesser frequencies in the Upper Danube, Provence and several regions of Iberia.

    You claim that R1b-L51* is most diverse in Italy than anywhere else, even more diverse than Hungary/Moravia/Slovakia, right? How sure you are of this? Can you document this claim? I think it is potentially important to clarify where R1b1a2a1a (L51/M412/S167) coalesced. I am undecided between Hungary or North Italy but I tend to favor Hungary because it has oldest dates for Aurignacian (but North Italy has them for proto-Aurignacian (in competition with Catalonia and Cantabria, this is an unsolved C14 dating matter), so the documentation you can provide in this matter may slide my opinion in one side or the other. I would need to see that data first anyhow.

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  61. Probably you should ask Argiedude, but he is a strange boy. Sometimes he writes, sometimes not. He did a map of R-L51 and frequently carries data which seems to go in this direction. Lastly on “Dienekes’ Anthropology blog”. To calculate the variance we should have certain STRs passed by a SNP test. We are working above all with “presumed” R-L51+, by DYS426=13, but, as the case of Pommier has demonstrated, nothing is sure. If we consider only the R-L51 tested on the ht35 project of Vizachero (you know he was my worst enemy, but what ever happened to him?), the Italian ones are very few, but we know that they are much more.

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  62. he is a strange boy

    lol, I like to investigate things, but not so much writing about what I find.

    By the way, so FTDNA has decided to accept L150 (was it?) as valid? You were wondering about Vincent. He abandoned all his (quite a few) y-dna Projects that he was managing for FTDNA as a protest because they didn't agree with him regarding L150, but much more regarding an SNP at the base of R1b, that splits the "African" R1b1* lineages from the rest, it was a huge division, and FTDNA didn't agree with him, something like that.

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  63. I thank you for all what you are doing and saying. I thank you also for what you have said about Vincent. As you see, you are more informed than me. In Italian we say: “Chi la dura la vince”. “Vince” didn’t win.
    About L150, we have discussed much about in the past, I am not seeing something clear by the “ht35 project”. Do you know something more careful about its meaning?
    And what about the SNP which separate the African R1b1* from the rest? It will be a Cruciani SNP, like V88+. Perhaps you know that I hypothesized that the African R1b1* (V88+) had come from Italy (or Spain) and of course descend from some R1b1/V88- not found in Africa, but in Italy yes, just from Cruciani in Sardinia etc. The same Cruciani, by a letter, said he would have taken in consideration my hypothesis. You know that Vincent was a supporter of a Middle Eastern origin of hg. R perhaps to justify some Jewish haplotypes and that just FTDNA has given up him is very meaningful. Those presumed Jewish haplotypes are disproved in other way, the last that H6a1 we have discussed about on “Dienekes’ Anthropology blog”.

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  64. I'm very concentrated in mtdna, at the moment, but anyhow, remember to always check here for the latest, up to date info on R1b:

    ISOGG R1b page

    And here for the best tree on mtdna:

    phylotree main page

    Notice in the ISOGG page that L150 has been provisionally added.

    You should rejoin dna-forums, with a new account, not necessarily to post, but to keep up to date on developments regarding SNP discoveries.

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  65. I thank you, but of course I know and consult every day Isogg and Phylotree: How could I write about these arguments without knowing this? And I of course saw that L150 was put in the tree. It happened many time ago. What I was saying was that it isn’t clear by the data FTDNA has given out lastly which is its function. From 23andMe (and in the “Adriano’s spreadsheet”) the unique L150 is Romitti (and this was for me one of the points in favour of an Italian origin), but then also Sutherland (R1b1b2*) was found 150- and this SNP seemed having lost its meaning.
    The fact that V88+ has determined a new branch in the tree is clear also from Isogg, but this I wrote to Sam Vass many years ago, that he hadn’t anything to do with us R1b1b2, and that we derived from some R-V88- I supposed having lived in Italy. Isogg continues to believe and to say that this haplogroup was born in Asia, that it is between 4000 and 8000 years old etc. If this would be true, why Vizachero abandoned his place of fighting?
    About Dna-forums I could do what you say many years ago. I didn’t and I wont do. I disdain those persons and who put my destiny into the hands of such a person. I fight my battles elsewhere. It isn’t said that amongst the know-alls of that site will be who will win the final war.

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