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

[Manofthehour]

Code:

Hoe004:
Result (5.3% 1 -0 +18): R-FT87109
R1b -> R-L754 -> R-L389 -> R-P297 -> R-M269 -> R-L23 -> R-L51 -> R-L52 -> R-PF6538 -> R-L151 -> R-P312 -> R-U152 -> R-L2 -> R-Z258 -> R-L20 -> R-Z1909 -> R-Y6789 -> R-Y15103 -> R-BY137174 -> R-FT87109 (ISOGG: )
Extra: P279/PF5065:A FT74184/PR4337(H):G FT319138(H):G FTC60807(H):G FT129821(H):T FT195078:T FT307459(H):T FT148647:T FT184689:G Y4847/A3242:A FT45000:C Z37822:C FGC58892:T Z9083(H):T CTS5707:G CTS10207:G Z29483:T CTS12954:G

Code:

Hoe005:
Result (3.0% 4 -1 +29): R-FGC37088
R1b -> R-L754 -> R-L389 -> R-P297 -> R-M269 -> R-L23 -> R-L51 -> R-L52 -> R-PF6538 -> R-L151 -> R-A8053 -> R-A8051 -> R-FGC57291 -> R-FGC37108 -> R-FGC37090 -> R-FGC37084 -> R-FGC37088 (ISOGG: )
Extra: Y172006:T FT203261:T FT97603(H):T FT100401(H):T FGC7862:T Z18652/FGC23610(H):T Y367008(H):G A22122:T FTA34303:T FTD87509/Y433063:G L687:A FT45000:C Z37822:C TY133092:A Y29212:G FTB33009:T MF93894:C TY135350/Y300104:G BY14580:A FTA18624:T Y144103:T Y151158/FGC91133:T F19771:T CTS5707:G CTS8072:T ZS2704(H):G CTS10207:G Y76781:C CTS12954:G

Would these Y-dna calls be due to contamination from male workers? If so, at least we get two more modern Y-dna samples from an undertested country (assuming they are French) lol.

[TanTin]

So here is the number of non-zero records for CHR 24 for all 10 individuals:

hoe001 173
hoe002 57515
hoe003 64687
hoe004 1201
hoe005 1639
hoe006 51
stp001 64839
tev001 45879
tev002 1313
tev003 64875

Please note, that we should substract 3 from this number (because of first 6 identifiers) and then we should divide the number on 2, because there is only 1 marker for Y chromosome, 1 allele, but it is written twice in plink files with the same value for both alleles.
So the worst are hoe006 hoe001 . However not all the snips are counted for the Y chromosome detection. So I guess the software used by Pribislav doesn't find any valid marker to be counted, at the same time the worst samples were able to qualify..

[TanTin]

I can assure you there is no contamination for all 10 samples. Autosomal they projected near the best WHG that we have.
And all 10 of them were projected very closely near each other. Not far from Bichon..
If there was any contamination, the contaminated individual would be projected very far from the other WHG , because these days we don't have modern humans with pure WHG DNA... However all these 10 from France are clear WHG..
And if any contamination , it would affect not only Y, but Autosomal  as well.

[TanTin]

The worst contaminated individual that I've seen so far is PCA010. (from NagelePosthScience2020)
It is in V54 database . It seems to be a mixture of some kind of chimp or else with human.  There are no related individuals and no other individuals aroung this one. 
Every time when I see this one to appear in my PCA I am confused what could be this one ? Then I find it is the same one .. I am not sure why they included this one in the last dataset.  It doesn't appear to be a valid one.
If you check further, you may notice this individual PCA010  was not even included in the publication:

Individuals visibly shifted from the American cluster, suggesting non- 9/39 American admixture or contamination, were removed from further analyses (CAO004, PDI003, PCA010).

So they removed this sample from the analysis in their publication, but the data is still there in V54 and it is not very helpful to have it.  In my opinion the contamination for this one is from chimp.

[Pribislav]

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!

So I guess the software used by Pribislav doesn't find any valid marker to be counted, at the same time the worst samples were able to qualify..

I didn't use any software here, I just compared the number of valid markers to the BAM size of each sample. Those females with L52 reads have disproportionately low number of valid markers compared to their BAM size, that's all.

[Pribislav]

hoe002, hoe003 and tev003 all belong to the same lineage, the very earliest form of I2-L161. They have 37, 41 and 41 SNP(s) covered at L161 level, respectively, and all three of them have just this one derived: AMM055/FGC8129/S2662+  (G>A), with 6, 17 and 11 derived reads, respectively.

[TanTin]

tev002 hoe004 hoe005 don't seems to be valid.
hoe002 stp001 tev003 hoe003 tev001 are all within I .

[Mitchell-Atkins]

Dang, I was all excited to break out the popcorn to watch the fireworks lol

If L52 did turn up this early, he would surely have Steppe ancestry. If they could make it to Mongolia they could make it to France.

[jdean]

Dang, I was all excited to break out the popcorn to watch the fireworks lol

If L52 did turn up this early, he would surely have Steppe ancestry.  If they could make it to Mongolia they could make it to France.

They would have had to have stowed away on the Tardis so the distance wouldn't have been an issue : )

Spect it'll turn up near a black obelisk on the moon next : ))))

[rmstevens2]

I asked at FTDNA's Big Y Facebook group about the two alleged "R-L52" French Mesolithic samples, hoe004 and hoe005. Vincent Vizachero responded that those are two of the study's five female samples. 

So, there you go. If you just knew those "Y-DNA" results had to be bogus, you were right.

[ArmandoR1b]

I asked at FTDNA's Big Y Facebook group about the two alleged "R-L52" French Mesolithic samples, hoe004 and hoe005. Vincent Vizachero responded that those are two of the study's five female samples. 

So, there you go. If you just knew those "Y-DNA" results had to be bogus, you were right.

Before coming back to this thread I looked at the X chromosome in the BAM files and it showed to be female for both of those. I definitely had my doubts about R-L52 which is dated to the Neolithic showing up in Mesolithic samples. Anybody that didn't doubt the validity need to hone their deductive reasoning skills.

[ArmandoR1b]

Sooo?!
L52 in Mesolithic France? Autosomal these guys fit rest of samples.

Earliest L52 so far was found in France and none was found in Yamnaya (?). That is quite interesting.

Ok, both seem to be L151 as per teepan’s post, which is normally dated 3,500 BCE at yfull. What is happening here?

The Mesolithic site Téviec was dated   between 6740 and 5680 years BP, so up to 3600BC, which is not that old, It was not only Chalcolithic, but even beginning of the Bronze on the Balkans, so the dates are not that far off. Maybe R1b-L52 was native to Europe after all.
https://en.wikipedia.org/wiki/T%C3%A9viec

Even though the samples are female and the R-L52 results are invalid the fact that R-P310 appeared in Afanasievo about 3000 BC means that it likely came from the Steppe region. So it is European but not western European. It does not appear in western Europe until Auvernier A297/MX304 which is dated to 2866-2601 BC.

[ArmandoR1b]

Y-DNA with Yleaf (two read minimum)

Code:

Sample_name    Hg    Hg_marker    Total_reads    Valid_markers
hoe004    R-L52    CTS7650    402728620    14992
hoe005    R-L52    CTS7650    652343679    18903

L52 in French hunter-gatherers? This would be a first if correct.

No way that is correct.

That's Yleaf's interpretation and needs manual checking. Snipsa gives these results.

Code:

Hoe004:
Result (5.3% 1 -0 +18): R-FT87109
R1b -> R-L754 -> R-L389 -> R-P297 -> R-M269 -> R-L23 -> R-L51 -> R-L52 -> R-PF6538 -> R-L151 -> R-P312 -> R-U152 -> R-L2 -> R-Z258 -> R-L20 -> R-Z1909 -> R-Y6789 -> R-Y15103 -> R-BY137174 -> R-FT87109 (ISOGG: )
Extra: P279/PF5065:A FT74184/PR4337(H):G FT319138(H):G FTC60807(H):G FT129821(H):T FT195078:T FT307459(H):T FT148647:T FT184689:G Y4847/A3242:A FT45000:C Z37822:C FGC58892:T Z9083(H):T CTS5707:G CTS10207:G Z29483:T CTS12954:G

Code:

Hoe005:
Result (3.0% 4 -1 +29): R-FGC37088
R1b -> R-L754 -> R-L389 -> R-P297 -> R-M269 -> R-L23 -> R-L51 -> R-L52 -> R-PF6538 -> R-L151 -> R-A8053 -> R-A8051 -> R-FGC57291 -> R-FGC37108 -> R-FGC37090 -> R-FGC37084 -> R-FGC37088 (ISOGG: )
Extra: Y172006:T FT203261:T FT97603(H):T FT100401(H):T FGC7862:T Z18652/FGC23610(H):T Y367008(H):G A22122:T FTA34303:T FTD87509/Y433063:G L687:A FT45000:C Z37822:C TY133092:A Y29212:G FTB33009:T MF93894:C TY135350/Y300104:G BY14580:A FTA18624:T Y144103:T Y151158/FGC91133:T F19771:T CTS5707:G CTS8072:T ZS2704(H):G CTS10207:G Y76781:C CTS12954:G

Why did you not check the X chromosome? Why did you not compare the file size with the number of hits on the Y chromosome? The latter could have easily been done after running Yfleaf and Snipsa and the difference was an obvious clue. The former is definitive that the R-L52 samples are female.

[ArmandoR1b]

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.

The person trying to determine who he is has unreliable data. There are things that I know about him that I won't post that proves he is who he says he is and that he lives in Spain and that he is Basque. We shouldn't be trying to dox people, which is why I won't post details, but I felt that he shouldn't be accused of being someone he isn't. He is who he has said he is. He has posted plenty of self identifying information. He is definitely not an Hispanic-American in Houston. Apart from what I have already pointed out, Hispanic-Americans and Mexicans do not care about details that he writes about and most of the time wouldn't even know about those details.

[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.

The person trying to determine who he is has unreliable data. There are things that I know about him that I won't post that proves he is who he says he is and that he lives in Spain and that he is Basque. We shouldn't be trying to dox people, which is why I won't post details, but I felt that he shouldn't be accused of being someone he isn't. He is who he has said he is. He has posted plenty of self identifying information. He is definitely not an Hispanic-American in Houston. Apart from what I have already pointed out, Hispanic-Americans and Mexicans do not care about details that he writes about and most of the time wouldn't even know about those details.

All that doesn't really matter. In fact, if he were from Houston, he might be less of a rabid ethno-nationalist. What matters is that over many years now he has proven himself to be not only a person immune to evidence and reason, but an inveterate liar, as well.