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Author Topic: mt-DNA Haplogroup H from Mesolithic sample from Guipuzcoa, Basque Country  (Read 1764 times)
JeanL
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« on: June 07, 2012, 04:42:17 PM »

Her thesis La Néolithisation du bassin méditerranéen : Apports de l'ADN ancien

Here is Table-1(Pages 48-49) with a description of all the sites analyzed by them, and the dates, as well as number of samples.



http://i1133.photobucket.com/albums/m582/jeanlohizun/Lacanetal2011-Table-1.jpg

So here it goes, Pages-93 and 94.

Quote from: Marie.Lacan.et.al.2011
Nous avons donc voulu confirmer l’authenticite de ces haplotypes en etudiant des positions diagnostiques, localisees sur la region codante cet ADN, par spectrometrie de masse. Sur les 5 echantillons, seuls deux ont livre des polymorphismes coherents avec les sequences HVI prealablement obtenues : les echantillons provenant des sites de Linatzeta (LTZ-T7) et Franchthi (Fr-63), ont ainsi permis de determiner l’haplogroupe mitochondrial des individus. L’absence de donnees supplementaires sur ces prelevements, comme l’ADN des fouilleurs et des differentes personnes en contact avec les collections, ou autres echantillons renfermant un ADN different, ne permet toutefois pas de savoir si l’ADN extrait correspond bien, pour chaque prelevement, a des molecules endogenes. Pour l’echantillon de Teviec, l’analyse de positions
supplementaires n’a pas permis de conforter l’authenticite de l’haplotype, ni de determiner l’haplogroupe. Enfin pour les echantillons de Rendina (R-T5) et de Los Canes (LC-T9) qui avaient pourtant livre une sequence HVI claire, l’analyse des positions diagnostiques a mis en evidence la presence d’un melange d’ADN, dont les polymorphismes caracterisent plusieurs haplogroupes, c'est-a-dire probablement un melange de molecules appartenant a des personnes differentes.

Table-9



http://i1133.photobucket.com/albums/m582/jeanlohizun/Lacanetal2011-Table-9.jpg

Table-10



http://i1133.photobucket.com/albums/m582/jeanlohizun/Lacanetal2011-Table-10.jpg

Table 9 shows that the Mesolithic (dated to 6230-6100 cal. B.C using C14) settlement of Linatzeta, Deba, Guipuzcoa is Haplogrup H, with HVR-I 16309G, and it tested positive for SNPs: H-C7028T having a C in there, and also H-C7028T also having a C in there too.

On the other hand the two samples from Santimamine(Dated to 4000 ybp using C14) tested H1, and U5.

So for all those that were skeptical of the results of Hervella.et.al.2012, now you have it there was indeed mt-DNA H in the FC region pre-Neolithic. It is likely that H and U5 were the two major players in the region.
« Last Edit: June 07, 2012, 04:53:11 PM by JeanL » Logged
GST
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« Reply #1 on: June 15, 2012, 03:33:19 PM »

I'll agree this is the first good evidence of H in the FC at an early date, around 6200 BC.

This work also shows the challenge of conclusively identifying ancient samples with some results appearing to be mixes of U and H.  I still want to see more than 2 SNPs for a conclusive identification.  U5b1a also has T7028C, and that shows the difficulty of relying on a test of a very small number of SNPs.

This also shows why it is so important to report the results of all SNPs tested (and not simply say you ran a test but not show the results.)

It might be challenging to sequence the full genome but that is what they have to attempt to do.
« Last Edit: June 15, 2012, 03:39:32 PM by GST » Logged
JeanL
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« Reply #2 on: June 15, 2012, 07:26:38 PM »


This work also shows the challenge of conclusively identifying ancient samples with some results appearing to be mixes of U and H.  I still want to see more than 2 SNPs for a conclusive identification.  U5b1a also has T7028C, and that shows the difficulty of relying on a test of a very small number of SNPs.


Well they it seems that the sample from Linatzeta, Deba, Guipuzcoa has HVR-I: 16309G, C in SNP H-C7028T and C  in SNP HV-C14766T, plus add to it that it had T in SNP U5-T3197T, and A in SNP U-A12308T.

So technically it is not just 2 SNP which distinguishes it from being U5b1a, but 4 SNPs, what are the odds that it would test negative for the SNPs that define U and U5, and positive for the SNPs that define HV and H, and still be U5b1a?
« Last Edit: June 15, 2012, 07:26:57 PM by JeanL » Logged
GST
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« Reply #3 on: June 16, 2012, 10:04:09 AM »

I agree - I think you can rule out U5 for this sample based on the lack of other U SNPs, and you have 2 SNPs for a positive ID of H, which I think is good evidence for H in Europe around 6200 BC.   I would like to see more SNPs tested for a better ID and to assign an H daughter group.

The test results in this studt that were a "melange" of U and H really highlight the challenge of using a small number of SNPs when you have both the problem of accurate testing and the difficulty of identifying a haplogroup testing a small part of the mtDNA genome.
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Isidro
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« Reply #4 on: August 01, 2012, 09:02:41 AM »

National Genographic publications:

Apologies if posted before:

BASQUE ROOTS REVEALED THROUGH DNA ANALYSIS

WASHINGTON (March 6, 2012)—The Genographic Project announced today the most comprehensive analysis to date of Basque genetic patterns, showing that Basque genetic uniqueness predates the arrival of agriculture in the Iberian Peninsula some 7,000 years ago. Through detailed DNA analysis of samples from the French and Spanish Basque regions, the Genographic team found that Basques share unique genetic patterns that distinguish them from the surrounding non-Basque populations.

NOTES: To view this publication (http://www.ncbi.nlm.nih.gov/pubmed/22365151) contact American Journal of Human Genetics. The Genographic Project will publish additional publications on the population history of Basques based on mtDNA and Y-chromosome variation in the coming months.
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Haplogroups
Y-DNA    R1b1a2a1a1b5    Shorthand    R-L176.2 mtDNA    HV  23andMe: HV0

M269+ P312+ Z196+ L176.2+ Z198+

Z262- U152- U106- SRY2627- P66- M65- M37- M222- M153- L21- L165-

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