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

[AimSmall]

Guys... let's move on from speculating about a person not even on this forum to the best of my knowledge.

[ArmandoR1b]

I mostly look at the Y chromosome data in BAM files although I have at times looked at the mtDNA but they are almost always male specimens. Before today, I don't remember if I have ever looked to see if BAM files of female specimens showed Y chromosome data. I don't have information on which Y chromosome positions can be affected by the X chromosome but would like to have it. Does anyone here have any idea if there is another explanation besides contamination being the cause of the Y chromosome data in the BAM files of the females? Are there some other BAM files of female specimens with low contamination that I can download and review?

The BAM files for hoe004 and hoe005 are 15.4 GB and 24.6 GB respectively. The largest BAM files I had ever downloaded prior to today were about 14 GB. I wonder if the excellent coverage allowed for details to be captured that normally wouldn't.

[rmstevens2]

I mostly look at the Y chromosome data in BAM files although I have at times looked at the mtDNA but they are almost always male specimens. Before today, I don't remember if I have ever looked to see if BAM files of female specimens showed Y chromosome data. I don't have information on which Y chromosome positions can be affected by the X chromosome but would like to have it. Does anyone here have any idea if there is another explanation besides contamination being the cause of the Y chromosome data in the BAM files of the females? Are there some other BAM files of female specimens with low contamination that I can download and review?

The BAM files for hoe004 and hoe005 are 15.4 GB and 24.6 GB respectively. The largest BAM files I had ever downloaded prior to today were about 14 GB. I wonder if the excellent coverage allowed for details to be captured that normally wouldn't.

I'm curious about all that, too: i.e., how females can acquire spurious results that look like Y-DNA, results that are good enough to fool otherwise intelligent and well-informed people (better informed than I am, for example).

[TanTin]

I mostly look at the Y chromosome data in BAM files although I have at times looked at the mtDNA but they are almost always male specimens. Before today, I don't remember if I have ever looked to see if BAM files of female specimens showed Y chromosome data. I don't have information on which Y chromosome positions can be affected by the X chromosome but would like to have it. Does anyone here have any idea if there is another explanation besides contamination being the cause of the Y chromosome data in the BAM files of the females? Are there some other BAM files of female specimens with low contamination that I can download and review?

The BAM files for hoe004 and hoe005 are 15.4 GB and 24.6 GB respectively. The largest BAM files I had ever downloaded prior to today were about 14 GB. I wonder if the excellent coverage allowed for details to be captured that normally wouldn't.

I'm curious about all that, too: i.e., how females can acquire spurious results that look like Y-DNA, results that are good enough to fool otherwise intelligent and well-informed people (better informed than I am, for example).

There are few publication explaining that. There is a limited recombination between X and Y chromosomes.  There are some regeions on Y chromosome where this may happen.

Y chromosome does not experience crossing over, it undergoes a different type of recombination called gene conversion. While crossing over involves the shuffle and exchange of genes between two different chromosomes, gene conversion is not reciprocal

“You don’t have two chromosomes that exchange material, you have one chromosome that donates its sequence to the other part of the chromosome” and the sequences become identical.

This is one of the articles:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2706966/

The process is also explained here:
https://en.wikipedia.org/wiki/Gene_conversion

I was checking for the possibility to transfer Y markers by using X chromosome as intermediare.
For example E-chaplogroup males may have some markers that belongs to J haplogroup, or opposite. And the only valid explanation could be that such were transferred through the X chromosome . 
May be here  we see such examples of X chromosomes, carriers of small number of Y-markers.

[ArmandoR1b]

For example E-chaplogroup males may have some markers that belongs to J haplogroup, or opposite. And the only valid explanation could be that such were transferred through the X chromosome .

Are you confounding recurrent SNPs with what is going on with hoe004 and hoe005? Recurrent SNPs are when the same mutation exists in two different haplogroups. Recurrent SNPs have nothing to do with the X chromosome.

[Capsian20]

mtDNA Haplogroups this samples all its belong a U5

[rmstevens2]

mtDNA Haplogroups this samples all its belong a U5

That's not surprising. U5 is an old European hunter-gatherer mtDNA haplogroup.

[Capsian20]

mtDNA Haplogroups this samples all its belong a U5

That's not surprising. U5 is an old European hunter-gatherer mtDNA haplogroup.

Yes of course, i was hoping that there are samples of V or at least HV

[TanTin]

For example E-chaplogroup males may have some markers that belongs to J haplogroup, or opposite. And the only valid explanation could be that such were transferred through the X chromosome .

Are you confounding recurrent SNPs with what is going on with hoe004 and hoe005. Recurrent SNPs are when the same mutation exists in two different haplogroups. Recurrent SNPs have nothing to do with the X chromosome.

Recurrent SNPs  don't appear from nowhere.   There should be is some explanation how they first appear.

And when we see such  recurrent SNPs in some distant chaplogroups,  at the same time such  are missing in the root of the tree, so what could be the explanation ? 
BTW, it is not for a single  recurrent SNP,  there are examples for many  recurrent SNPs which appear for very specific population where some contact existed between male carriers of such SNPs..

[ArmandoR1b]

For example E-chaplogroup males may have some markers that belongs to J haplogroup, or opposite. And the only valid explanation could be that such were transferred through the X chromosome .

Are you confounding recurrent SNPs with what is going on with hoe004 and hoe005. Recurrent SNPs are when the same mutation exists in two different haplogroups. Recurrent SNPs have nothing to do with the X chromosome.

Recurrent SNPs  don't appear from nowhere.   There should be is some explanation how they first appear.

And when we see such  recurrent SNPs in some distant chaplogroups,  at the same time such  are missing in the root of the tree, so what could be the explanation ? 
BTW, it is not for a single  recurrent SNP,  there are examples for many  recurrent SNPs which appear for very specific population where some contact existed between male carriers of such SNPs..

Where do you think regular SNP mutation appear from? They just happen. Recurrent SNPs are simply in positions that are more apt to have a mutation. They also happen in the mtDNA. This is a confounding of recurrent SNPs and what is happening with hoe004 and hoe005.

[Kale]

BTW, it is not for a single  recurrent SNP,  there are examples for many  recurrent SNPs which appear for very specific population where some contact existed between male carriers of such SNPs..

Can you give specific examples, I'm interested in looking into this.
Quick tally of yfull showed 0 shared snps between those that define haplogroup G and those that define J, J1, L, or T.

[ArmandoR1b]

I mostly look at the Y chromosome data in BAM files although I have at times looked at the mtDNA but they are almost always male specimens. Before today, I don't remember if I have ever looked to see if BAM files of female specimens showed Y chromosome data. I don't have information on which Y chromosome positions can be affected by the X chromosome but would like to have it. Does anyone here have any idea if there is another explanation besides contamination being the cause of the Y chromosome data in the BAM files of the females? Are there some other BAM files of female specimens with low contamination that I can download and review?

The BAM files for hoe004 and hoe005 are 15.4 GB and 24.6 GB respectively. The largest BAM files I had ever downloaded prior to today were about 14 GB. I wonder if the excellent coverage allowed for details to be captured that normally wouldn't.

I'm curious about all that, too: i.e., how females can acquire spurious results that look like Y-DNA, results that are good enough to fool otherwise intelligent and well-informed people (better informed than I am, for example).

I looked at two 9 GB BAM files of Roman females from Antonio et al. 2019 and they both have Y-DNA results but don't have most of the results of hoe004 and hoe005. I still think, but could be wrong, that the higher coverage of hoe004 and hoe005 caused the appearance of the other Y-DNA results. By the way, all of the positions that I looked at of the Y-DNA R results of hoe004 and hoe005 are either highly recurrent and unreliable or are mutations that can be caused by deamination.

I did find a thread by someone, here, that was confused by Y-DNA results showing up in females even though the VCF files exclude the pseudo-autosomal regions on chrY.

There is another thread here where they mention they have seen the issue.

Luckily in the cases of hoe004 and hoe005 the positions on the X chromosome that have alleles that differ between the first and second proves they are females. Hopefully in the future everyone that looks at BAM files thinks to check that before announcing false results.

[ArmandoR1b]

My last post that I deleted was due to my own confusion about the order of events. I apologize if anyone saw it.

[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.

tev001 could be in the same clade as those three above, but unfortunately he doesn't have AMM055/FGC8129/S2662 covered. He could also be pre-Y3104 since he has 4 ancestral SNPs at this level, but there are false calls at a lot of levels, so these four could aslo be false negatives.

stp001 is splitting level I2-M284, with 17 derived and 17 ancestral SNPs.

[TanTin]

BTW, it is not for a single  recurrent SNP,  there are examples for many  recurrent SNPs which appear for very specific population where some contact existed between male carriers of such SNPs..

Can you give specific examples, I'm interested in looking into this.
Quick tally of yfull showed 0 shared snps between those that define haplogroup G and those that define J, J1, L, or T.

It took me some time to re-run my report and to reproduce the previous  results.
As this is a new topic,  I am going to open a new discussion in new topic and will provide more examples there.