Analyses of complete genomes of 10 French Late Mesolithic individuals form the sites

[alanarchae]

just checking it’s not April the 1st. Makes no sense on any level including SNP dating. It’s obviously wrong.

[jdean]

I can tell just by the number of valid markers teepean posted that hoe004 and hoe005 are females, there's no need to check the BAMs.

Somebody posted on Eurogenes that it must be contamination which made me smile.

Even if they weren't the wrong gender the calls quoted are C to T and G to A and should be treated with extreme caution anyway : )

[alanarchae]

I can tell just by the number of valid markers teepean posted thatbe  hoe004 and hoe005 are females, there's no need to check the BAMs.

Somebody posted on Eurogenes that it must be contamination which made me smile.

Even if they weren't the wrong gender the calls quoted are C to T and G to A and should be treated with extreme caution anyway : )

At least one hold out Franco-Cantabrian model guy will be screaming yesssssss and hitting the bottle now but will be in for a rude awakening once he sobers up. These snp reads look several multiples too young to fit the archaeological dates. Got to be wrong or contamination.

[jdean]

At least one hold out Franco-Cantabrian model guy will be screaming yesssssss and hitting the hitter now but will be in for a rude awakening once he sobers up. These snp reads look several multiples too young to fit the archaeological dates. Got to be wrong or contamination.

I don't think he ever sobers up : )

[alanarchae]

At least one hold out Franco-Cantabrian model guy will be screaming yesssssss and hitting the hitter now but will be in for a rude awakening once he sobers up. These snp reads look several multiples too young to fit the archaeological dates. Got to be wrong or contamination.

I don't think he ever sobers up : )

well if he actually lives in Spain (I doubt it) then at least alcohol is super cheap compared to northern Europe

[Qrts]

Their autosomal results look rather typical.
Can someone check tev002? Is it actually A1*(xA1a) or could it be A1b downstream?

[rmstevens2]

At least one hold out Franco-Cantabrian model guy will be screaming yesssssss and hitting the hitter now but will be in for a rude awakening once he sobers up. These snp reads look several multiples too young to fit the archaeological dates. Got to be wrong or contamination.

I don't think he ever sobers up : )

well if he actually lives in Spain (I doubt it) then at least alcohol is super cheap compared to northern Europe

I recall that someone with sufficient computer expertise said the person in question is actually an Hispanic-American who lives in Houston, Texas. I can't confirm that, but it wouldn't surprise me.

[Capsian20]

Their autosomal results look rather typical.
Can someone check tev002? Is it actually A1*(xA1a) or could it be A1b downstream?

Maybe low_coverage ?

[rmstevens2]

I can tell just by the number of valid markers teepean posted thatbe  hoe004 and hoe005 are females, there's no need to check the BAMs.

Somebody posted on Eurogenes that it must be contamination which made me smile.

Even if they weren't the wrong gender the calls quoted are C to T and G to A and should be treated with extreme caution anyway : )

At least one hold out Franco-Cantabrian model guy will be screaming yesssssss and hitting the bottle  now but will be in for a rude awakening once he sobers up. These snp reads look several multiples too young to fit the archaeological dates. Got to be wrong or contamination.

What does Common Sense say to that guy when he meets him on the street?

"Howdy, stranger!"

[AimSmall]

All fun aside... let's get back on topic.

[rmstevens2]

I can tell just by the number of valid markers teepean posted that hoe004 and hoe005 are females, there's no need to check the BAMs.

Serious question: what is it about the number of valid markers that makes you think those two samples are female?

Sorry I sound ignorant asking that question, but I'd really like to know.

For me the great weight of the evidence says they cannot be any kind of L52, and certainly not members of modern L52 subclades. Based on what you wrote, I wonder if they are in fact female, and I'd like to have this controversy resolved before the usual goofballs make a nuisance of themselves with these erroneous results.

Thanks!

[VladMC]

Apparently there are very few "valid markers":
hoe004 R-L52 14992
hoe005 R-L52 18903
tev002 A-1* 1717

…………

hoe002 I-Y3104 94608
hoe003 I-Y3104 128055
stp001 I-STS616 127816
tev001 I-L460 61589
tev003 I-Y3104 128063

[JMcB]

Apropos of the above, Göran Runström posted the following on the Big Y Facebook page a little earlier today:


Göran Runström
Admin Top Contributor

  ·  ·

Many are asking about French DNA and here is some aDNA data from what looks like a new upcoming paper from Uppsala University. All 5 ancient men in the study belong to Y-DNA haplogroup I2.


Analyses of complete genomes of 10 French Late Mesolithic individuals form the sites of Hoedic, Téviec and Champigny

Since the early Holocene, western and central Europe was inhabited by a genetically distinct group of Western Hunter-Gatherers (WHGs). These groups were eventually replaced and assimilated by the incoming Neolithic farmers. The western Atlantic façade was home to some of the last Mesolithic sites of mainland Europe, represented by the iconic open-air sites at Hoedic and Téviec in southern Brittany, France. These sites are known for the unusually well-preserved and rich burials. Genomic studies of Mesolithic European hunter-gatherers have been limited to single or a few individuals per site and our understanding of the social dynamics of the last Mesolithic hunter-gatherers of Europe and their interactions with incoming farmers is limited. We sequenced and analyzed the complete genomes of 10 individuals from the Late Mesolithic sites of Hoedic, Téviec, and Champigny, in France, four of which sequenced to between 23- and 8-times genome coverage. The analysis of genomic, chronological and dietary data revealed that the Late Mesolithic populations in Brittany maintained distinct social units within a network of exchanging mates. This resulted in low intra-group biological relatedness that prevented consanguineous mating, despite the small population size of the Late Mesolithic groups. We found no genetic ancestry from Neolithic farmers in the analyzed hunter-gatherers, even though some of them may have coexisted with the first farming groups in neighboring regions. Hence, contrary to previous conclusions based on stable isotope data from the same sites, the Late Mesolithic forager community was limited in mate-exchange to neighboring hunter-gatherer groups, to the exclusion of Neolithic farmers.

https://www.ebi.ac.uk/ena/browser/view/PRJEB71770

[rmstevens2]

Apropos of the above, Göran Runström posted the following on the Big Y Facebook page a little earlier today:


Göran Runström
Admin Top Contributor

  ·  ·

Many are asking about French DNA and here is some aDNA data from what looks like a new upcoming paper from Uppsala University. All 5 ancient men in the study belong to Y-DNA haplogroup I2.


Analyses of complete genomes of 10 French Late Mesolithic individuals form the sites of Hoedic, Téviec and Champigny

Since the early Holocene, western and central Europe was inhabited by a genetically distinct group of Western Hunter-Gatherers (WHGs). These groups were eventually replaced and assimilated by the incoming Neolithic farmers. The western Atlantic façade was home to some of the last Mesolithic sites of mainland Europe, represented by the iconic open-air sites at Hoedic and Téviec in southern Brittany, France. These sites are known for the unusually well-preserved and rich burials. Genomic studies of Mesolithic European hunter-gatherers have been limited to single or a few individuals per site and our understanding of the social dynamics of the last Mesolithic hunter-gatherers of Europe and their interactions with incoming farmers is limited. We sequenced and analyzed the complete genomes of 10 individuals from the Late Mesolithic sites of Hoedic, Téviec, and Champigny, in France, four of which sequenced to between 23- and 8-times genome coverage. The analysis of genomic, chronological and dietary data revealed that the Late Mesolithic populations in Brittany maintained distinct social units within a network of exchanging mates. This resulted in low intra-group biological relatedness that prevented consanguineous mating, despite the small population size of the Late Mesolithic groups. We found no genetic ancestry from Neolithic farmers in the analyzed hunter-gatherers, even though some of them may have coexisted with the first farming groups in neighboring regions. Hence, contrary to previous conclusions based on stable isotope data from the same sites, the Late Mesolithic forager community was limited in mate-exchange to neighboring hunter-gatherer groups, to the exclusion of Neolithic farmers.

https://www.ebi.ac.uk/ena/browser/view/PRJEB71770

That apparently backs up Pribislav's earlier assertion that the samples with bogus L52 calls are females.

[TanTin]

Serious question: what is it about the number of valid markers that makes you think those two samples are female?

I did a quick verification for the number of non-zero  markers for chr 24 (Y).
hoe004  1201
hoe005  1639

There are near 65 000 markers in total but almost all are 0 except for the numbers above. 
At my level I can't tell for sure if these are males or females. 
Please note that for HO dataset  there are only 500 markers included for CHR 24 .