PDA

View Full Version : Cardoso et al: The Expanded mtDNA Phylogeny of the Franco-Cantabrian Region



GailT
07-04-2013, 10:41 PM
The Expanded mtDNA Phylogeny of the Franco-Cantabrian Region Upholds the Pre-Neolithic Genetic Substrate of Basques (link) (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0067835#pone.0 067835.s002)

We have been waiting for this paper for two years - the finding of U5b1f among the Basques was first discussed in a web doc by Cardoso and blogged at this link (http://forwhattheywereweare.blogspot.com/2011/06/basque-specific-mtdna-lineages.html). Perhaps it took a long time to get it published because the paper makes some claims that are entirely unsupported and almost certainly incorrect. I'll post more after I look at their data.

GailT
07-04-2013, 10:59 PM
The ten U5b1f samples are a closely related subclade with an age estimate of about 3000 ybp.

edit: Age estimates for U5b1f depend on you define it to include 16319 or not. If this is stable mutation site and defines a subclade of U5b1f, the age estimate of about 3000 years would apply to the 16319 subclade.

GailT
07-07-2013, 04:18 PM
Jean, have you looked at the El Agar civilization (http://en.wikipedia.org/wiki/El_Argar) and any thoughts on their origins. According to wikipedia, they were early adopters of bronze which allowed them to dominate local copper age peoples. The age of this group matches well with the beginning of rapid expansion of the Basque mtDNA groups, around 3500 ybp.
http://en.wikipedia.org/wiki/El_Argar

thanks,
Gail

Jean M
07-07-2013, 04:42 PM
El Agar is in the wrong place to link to Basque, and much more likely to be linked to the Iberes. The sudden creation c. 2200 BC of the fearsomely fortified town of La Bastida in south-east Iberia in a style reminiscent of the second phase of Troy and the urban world of the Levant suggests arrivals from the Near East. So say the discoverers of same. Universitat Autonoma de Barcelona, press release 27 September 2012.

Jean M
07-07-2013, 06:16 PM
Saw your post on Rootsweb (http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2013-07/1373048725) Gail. Hope you don't mind if I repost here:


The results from the Behar et al 2012 Basque paper are similar with about 18% of the Basque in mtDNA U5, and 2/3 of them in a single rare subclade U5b1f. The Behar paper did not, however, have full sequences for the U5 samples, so the new Cardoso data allows us to estimate the age of U5b1f in the Basque. There is very little diversity in the 10 Basque U5b1f samples with an average of 1.2 mutations (most of these are in HVR) and an age estimate for this group of about 3,000 years. So this really does not support the authors claim that the Basque were part of the Paleolithic population of Europe.

Although U5b1f is rare, it is widely distributed from Germany to Portugal, and the oldest branches are in Germany (the authors discount the German origin of one of the two U5b1f samples from GenBank that they include in the analysis of their 10 new U5b1f samples). A likely scenario is that U5b1f married into the Basque community before 3,000 years ago and that U5b1f became dominant through population drift in a small, isolated population.

If the Basque were part of the Paleolithic Europeans, we should have seen much more diversity and older age estimates in the U5 samples. However, the U5 samples (excluding U5b1f) in the Basque are very similar in age and distribution to other countries in southern and central Europe.


Proves me wrong before I'm in print! But that's life.

GailT
07-07-2013, 07:11 PM
Thanks for reposting, and not proved yet, as we still have a very small sample of U5b1f, and the key German sample is not yet in GenBank. In any case, I think the U5b1f results are consistent with your section on the Basque where you speculate on a possible Neolithic or Copper age arrival of the Basques. It seems to me that this new Cardoso et al paper is consistent with a late copper or bronze age arrival, with the mtDNA diversity expanding around 3500 ybp, although they interpret the results differently, using the illogical concept of a "splitting age".

mtDNA has poor temporal resolution ability, so their estimate of 3500 ybp could easily be off by 1000 years or more, so could still be consistent with an earlier Copper Age arrival of the Basques. In any case, it does seem the DNA evidence clearly shows that the idea of the Basque as a Paleolithic or even a Mesolithic relict is probably wrong.

Jean M
07-07-2013, 07:37 PM
As you know I plumped for mixed genetic origins for the Basques, with perhaps:

1. A locally ancient element, based on the mtDNA U5.
2. A Neolithic Cardial Ware element, based on some of the Y-DNA haplogroups.
3. A Copper to Bronze Age element, based again on Y-DNA, and bringing the ancestor to the Basque language.

It's no. 1 that is now looking shaky.

GailT
07-07-2013, 09:01 PM
I'm not quite sure if I understand your thoughts in no.1 - I think that U5b1f does reflect a locally ancient subclade (it has only been found in the region from Portugal to Germany) and it descends from U5b1 which seems to have an Iberian LGM refugium origin, based on the high diversity of U5b1 in that region. So I'd interpret this, possibly, as newly arrived Basque men mating with local U5b1f women, consistent with no. 1 above.

If you exclude U5b1f, the remaining U5 in the Basque is remarkably similar to other southern European populations - I can you send more details on this via email.

Gail

Jean M
07-07-2013, 09:17 PM
It's OK Gail. I understand you now. Thanks.

jeanL
07-07-2013, 10:01 PM
Basques certainly do have more mt-DNA than U5b1f, and while JeanM you think that mt-DNA H isn't pre-Neolithic in Europe, and you and I have already been through it, I would like however to bring forth something that perhaps we missed before, and it was that the mt-DNA H typed in a Mesolithic sample from Guipuzcoa, which you said that it could have been subject to contamination infact comes from a recently(year 2000) unearthed remain, so contamination isn't likely an issue. I actually do not disagree with GailT position that some mt-DNA H in Europe is pre-neolithic, some is post. I do however think that the age of mt-DNA H (20 kya-23 kya as per Fu.et.al.2013), puts its origin in Europe, as in, it arose in Europe, since we have plenty of mt-DNA HV from ancient remains in Europe, in fact most upper Paleolithic remains in Europe are indeed either R0 or HV, but probably some clades went to the middle east and then back again into Europe. My point is that the idea that U5 is the only link the to Mesolithic isn't very viable, and in order to do so one has to ignore some papers.

Let's focus on U5 then, then 10 FullMT came from 1 Vizcayan, 2 Guipuzcoans, 6 Northern Navarrans, 1 Lower Navarran(French Basque), so not only is the sample size small at 10, but it is mostly dominated by 6 Northern Navarrans. Now even in the 76 haplotypes of the fullMT DNA sequences more U5 lineages show up, so the idea that all of the Basque U5 is mostly U5b1f is not substantiated, for example from Table-S1:

Vizcaya
U5a1a1:1
U5b1c1a: 2
U5b1f: 2

Guipuzcoa

U5b1f: 2

Northern Navarra
U5b1f: 6
U5b1c1a: 1

French Basque Lower Navarra

U5b1f: 1

If I recall correctly there was a sample from Aizpea, Navarra from the Mesolithic dated to 6600 ybp that was U5b1c.

Now as per Table-S3 where the frequencies of all haplogroups are listed we see that:

Guipuzcoa(n=228)

U5b1f: 27 or 11.8%

These data comes from a combination of Behar.et.al.2012, Cardoso.et.al.2012, Garcia.et.al.2011, Alfonso.Sanchez.et.al.2008

From Table-S1 in Cardoso.et.al.2012 we see that Guipuzcoans(n=34) have 1-U5a1, and 6-U5b.
From Table-S3 in Martinez-Cruz.et.al.2012 we see that Guipuzcoans (n=57) 1-U5a, and 10-U5b
From Table-S1 in Garcia.et.al.2011 we see that Guipuzcoans(n=113) have 2-U5a1a, and 21-U5b
From the Alfonso-Sanchez.et.al.2008 there are 24 Guipuzcoan but they don't give their frequency, instead it is combined with the Vizcayans, and in any case their combined frequency is 1-U5b2, 1-U5b1c, 1-U5a.

South-West Guipuzcoa (n=63)

U5b1f: 6 or 9.5%

Vizcaya (n=251)

U5b1f: 9 or 3.6%

West Vizcaya (n=21)

U5b1f: 0

Alava (n=193)

U5b1f: 1 or 0.05%

Northern Navarra (n=210)

U5b1f: 32 or 15.2%

Central-West Navarra (n=64)

U5b1f: 5 or 7.8%

North-East Navarre (n=55)
U5b1f: 13 or 23.6%

North-West Navarre (n=53)
U5b1f: 9 or 17.0%

The other places where it is high is in:

Lower Navarre (French Basque Country) (n=73)
U5b1f: 6 or 8.2%

Labourdin (French Basque Country) (n=58)
U5b1f: 14 or 24.1%

Soule (French Basque Country) (n=62)
U5b1f: 11 or 17.7%

Bearn (n=56)
U5b1f: 7 or 12.5%

Bigorre (n=48)
U5b1f: 4 or 8.3%

Chalosse (n=60)
U5b1f: 9 or 15.0%

Now since it is more than obvious that this Haplogroup has a founders effect in the area around Northern Navarra, it would be good to calculate the rho without the 6 Navarrans samples, and also calculate it on the 6 Navarran samples.

In any case from Garcia.et.al.2011 Table-S1 we see evidence of multiple lineages of U5b amongst some Basques(namely Guipozcoans, and Vizcayans):

Guipuzcoa (n=113)

U5/U5b

HVR-I--------------------HVR-II------------------------------------------------------n
192 270-----------73 150 151 152 263 311i--------------------------------------------1
192 270 519-------73 150 151 228 263 303i 311i---------------------------------------1
192 270 519 ------73 150 151 228 263 311i--------------------------------------------2
192 270 319-------73 150 263 311i---------------------------------------------------10
192 270 319 362---73 150 263 303i 311i-----------------------------------------------3
192 270 319 362 --73 150 263 311i---------------------------------------------------1
192 270 319 362---73 150 263 303i---------------------------------------------------1
189 192 270-------73 150 263 311i---------------------------------------------------1
037 189 192 270 311 336---55A 73 150 263 303i 311i----------------------------------1

Vizcayans (n=91)

U5/U5b

HVR-I--------------------HVR-II------------------------------------------------------n
192 270---------------73 152 263 311i ------------------------------------------------1
192 270 519--------73 150 151 228 263 303i 311i--------------------------------------1
192 270 319-----------73 150 263 311i------------------------------------------------4

Rathna
07-08-2013, 01:32 AM
Welcome here, Jean. I had the bullock and you the horn.

Gioiello

GailT
07-08-2013, 03:52 AM
jeanL - have you tried to do age estimates based on the HVR results? The sample size of FMS results is quite small. I've sorted the results from the Behar et al 2012 Basque sample, and can share that spreadsheet with you. It looks like your results include additional samples from other papers?

thanks,
Gail

GailT
07-08-2013, 04:12 AM
This is how I'm currently defining U5b1f and its subclades:

U5b1f - C3507a: one sample, kit N27754 from Germany

U5b1f1 - A533G: two samples, HQ675036 from Spain and kit 195997, also waiting for a Portugal FMS test

U5b1f1a: - G16319A: three samples from Germany, Spain and France. (DQ156208, JX286537 and kit N45715. We also have the 10 new sample from Cardoso that all fall into U5b1f1a.

This is still uncertain, I'd like to see a larger number of FMS samples to determine if 533 and 16319 are subject to reversions.

Rathna
07-08-2013, 06:04 AM
I don't know if this may help, but in the 1KGP, whereas in Iberians (they were only 14) no Hg. U5 was detected, Tuscans were 105 and hg. U5 were 8 (7,62%):
U5a1a1b [NA20812]
U5a1g [NA20805]
U5a1b1a [NA20774], [NA20515]
U5a2b [NA20760]
U5a2b2 [NA20765]without 13269G, not known if 12308A! was detected
U5b1a [NA20540]without 15097C
U5b2a3 [NA20517]
Some of these hgs are older than LGM, others than Younger Dryas. Others split subclades known so far.

Rathna
07-08-2013, 07:45 AM
And it is clear how the Eastern European U5a2b2 derive from the Italian Refugium, what Malyarchuk did know well:

U5a2b2 8281-8289d 10685 11984 12308! 12654 13269 13285 16234

61. GU296587(Poland) Malyarchuk U5a2b2 04-MAY-2010
A73G A263G 309.1C 315.1C A750G A1438G A2706G T3197C A4769G C7028T C8281-9d A8860G G9477A G9548A G10685A A11467G G11719A T11984C G12372A A12654G A13269G A13285G T13617C C14766T A14793G A15326G C16192T C16234T C16256T C16270T T16491C G16526A
62. GU296646(Slovakia) Malyarchuk U5a2b2 04-MAY-2010
A73G A263G 309.1C 315.1C A750G A1438G A2706G T3197C A4769G C7028T C8281-9d C8778T A8860G G9477A G9548A G10685A A11467G G11719A T11984C G12372A A12654G A13269G A13285G T13617C C14766T A14793G A15326G C16192T C16234T C16256T C16270T G16526A

The Tuscan sample NA20765:
A73G T152C A263G A750G A1438G A2706G T3197C A4769G C7028T C8281-9d A8860G G9477A G9548A G10685A A11467G G11719A T11984C T12128C G12372A A12654G A13285G T13617C C14766T A14793G A15326G C16192T C16256T C16270T G16526A

Jean M
07-08-2013, 09:37 AM
JeanM you think that mt-DNA H isn't pre-Neolithic in Europe, and you and I have already been through it .... I actually do not disagree with GailT position that some mt-DNA H in Europe is pre-neolithic, some is post.

Welcome to this forum Jean L.

I didn't get the impression that Gail was arguing that any mtDNA H was pre-Neolithic in Europe. There is general agreement that H was born in the Near East. Its expansion in the Neolithic is visible in the "star-burst" of subclades about that time (as best we can calculate.) See Soares 2009 and Behar 2012 for dating. But that discussion is for another thread really.

GailT
07-08-2013, 01:25 PM
I think it is unlikely that H was a major haplogroup present in Mesolithic Europe (probably not part of the first wave of people to repopulate northern Europe after the LGM), but it seems possible that H might have arrived in southern Europe in the Mesolithic based on some reports of ancient H samples in Italy or Spain. As far as I know, they have not been published so it will be interesting to see if they can be, or have been, confirmed.

I try to be very cautious in any conclusions, as we all know that new discoveries can change our understanding. I'm also cautious in interpreting the results of mtDNA tests, as the current distribution and the sparse testing of ancient remains provides an incomplete record of human history.

Today I was called an "ignorant, stupid, racist" and was the victim of a massive spam attack because I said that being in U5 is not proof of Saami ancestry, and that people in many U5 subclades are unlikely to have Saami ancestry. So I've been reminded again how important it is to be extremely careful in wording of comments that touch on a person's sense of identity.

jeanL
07-08-2013, 01:55 PM
Today I was called an "ignorant, stupid, racist" and was the victim of a massive spam attack because I said that being in U5 is not proof of Saami ancestry, and that people in many U5 subclades are unlikely to have Saami ancestry. So I've been reminded again how important it is to be extremely careful in wording of comments that touch on a person's sense of identity.

Whoao I'm sorry to hear that Gail!!! Anyhow I wanted to ask you. Did you have a chance to read the paper I sent you about Y-STR mutations??

jeanL
07-08-2013, 02:17 PM
jeanL - have you tried to do age estimates based on the HVR results?
thanks,
Gail

I was trying to do something like that yesterday, but truth be told I am not too comfortable doing age estimates based on HVR.

GailT
07-09-2013, 04:31 AM
I was trying to do something like that yesterday, but truth be told I am not too comfortable doing age estimates based on HVR.

Yeah, I also have doubts about the value of the HVR based age estimate. Sorry, I have not looked at the STR paper, it seems I don't have enough time to keep up with the mtDNA results.