Hi Ewenn,
This kind of analysis take some time, thanks a lot for this.
Why do you think it is probably unlikely that KOS015 belong to a "pre-R-FGC17460" ?? With only 2 positive SNPs out of 11 SNPs, I would tend to think it is highly probable.
It is true that there is also a low rate of positive SNPs among the higher levels, FGC17465 and above, and I believe that it is generally the case with ancient DNA.
Le lun., juil. 22, 2024 ¨¤ 5:46, Ewenn <gwenng008@...> a ¨¦crit: Erratum: *KOS015 could possibly belong to R-FTC75933, a branch for which it only has NO reads for the 11 equivalent SNPs of this block.
Hi Bertram, Shane,
?
Yes, indeed, FTDNA should, in principle, and to my knowledge, have checked these clades / SNPs downstream of R-FGC17460. Similarly, FTDNA also checks, in principle, for a possible match with Private Variants of downstream testers.
?
I tried to perform on my side an analysis of the KOS015¡¯s fastQ file, in comparison with the current version of the FTDNA¡¯s Y-DNA Haplotree (2024-07-20). I find the same result. In details:
Consistent path from A-PR2921 (root) to R-L151 (including with R-PF6538, intermediate clade between R-P310 and R-L151, which only appears at Yfull).
?
R-U106 and downstream clades?: consistent path to R-FGC17460?:
-
R-U106?:
-
R-FGC3861?:
-
R-S1855?:
-
R-FGC17465?:
-
FGC17465 1 positive read (BQ:0, mapQ:60, 51M, 5th position from the 3¡¯end of the aDNA¡¯s segment)
-
FGC68717 1 positive read (BQ:23, mapQ:12, 67M)
-
R-FGC17460?:
-
A4654 1 positive read (BQ:37, mapQ:60, 78M)
-
FGC17472 1 positive read (BQ:BQ:37, mapQ:29, 69M)
Downstream of R-FGC17460?: only negative (37/272 SNPs) or no reads. For equivalent SNPs to the current 6 known child haplogroups of R-FGC17460 (NOTA?: 2 currently unnamed branches, from England and Ireland, not taken into account):
-
R-FTA62881 (3 negative reads / 3 SNPs)
-
R-BY11544 (3 negative reads / 3 SNPs)
-
R-FTC75933 (terminal haplogroup, only no reads)
-
R-FT115916 (1 negative read / FT113203)
-
R-BY122236 (5 negative reads / 5 SNPs)
-
R-FGC17464 (6 negative reads / 4 SNPs)
?
As a result, it seems to me quite likely that KOS015 does not belong to the 5 child branches for which we have negative reads. It is however not totally impossible that KOS015 could belong to an extinct or unidentified branch splitting one of these blocks of equivalent SNPs. KOS015 could possibly belong to R-FTC75933, a branch for which it only has negative reads at the 11 equivalent SNPs. Finally, KOS015 could potentially belong to an unidentified or extinct branch downstream of R-FGC17460. With 2 positive SNPs out of 11 SNPs equivalent to R-FGC17460, and only no reads for the other 9 SNPs in this haplogroup, it is however not totally impossible (but probably unlikely) that KOS015 could be a "pre-R-FGC17460". In other words, that this aDNA belongs to an unidentified or extinct branch that would potentially split the R-FGC17460 block in two.
?
Ewenn
|
Hi Bertram,
Indeed, KOS015 possibly remains pre-R-FGC17460. As to the probability of this being the case, compared to the other possibilities, I am certainly not competent enough to decide the question. I was only expressing a personal opinion, not necessarily informed.
Regarding aDNA, the DNA recovered is very fragmented, partial, and partly altered. This is due both to the processes of DNA degradation over time, but also to sampling and analysis techniques. Consequently, the status of this aDNA for a large number of SNPs remains undetermined (no calls).
Regarding R-FGC17460, the TMRCA of this haplogroup is currently estimated around 200 BCE [650 BCE, 200 CE] 95% CI. The dating of KOS015 is around 800 CE [710 CE, 888 CE] (radiocarbon dating). Or somewhere around 1000 years after the most recent common ancestor of all R-FGC17460+ testers.
Without being in any way a specialist, I suppose that the probability of extinction (according to the Galton-Watson process) of the other potential branches coming from the R-FGC17460 block (therefore divergent between R-FGC17465 and the MRCA of R- FGC17460, between perhaps 1500 BCE and 200 BCE) was probably very high, and close to 1, around 800 CE.
There is however, in my humble opinion, nothing certain, and you are potentially right that KOS015 could be pre-R-FGC17460. With luck, and the addition of new testers to the Y tree, creating new branches, and the identification of new associated SNPs, perhaps FTDNA will be one day able to refine the placement of KOS015.
Ewenn
Hi Ewenn,
This kind of analysis take some time, thanks a lot for this.
Why do you think it is probably unlikely that KOS015 belong to a "pre-R-FGC17460" ?? With only 2 positive SNPs out of 11 SNPs, I would tend to think it is highly probable.
It is true that there is also a low rate of positive SNPs among the higher levels, FGC17465 and above, and I believe that it is generally the case with ancient DNA.
Bertram?
Le lun., juil. 22, 2024 ¨¤ 5:46, Ewenn Erratum: *KOS015 could possibly belong to R-FTC75933, a branch for which it only has NO reads for the 11 equivalent SNPs of this block.
Hi Bertram, Shane,
?
Yes, indeed, FTDNA should, in principle, and to my knowledge, have checked these clades / SNPs downstream of R-FGC17460. Similarly, FTDNA also checks, in principle, for a possible match with Private Variants of downstream testers.
?
I tried to perform on my side an analysis of the KOS015¡¯s fastQ file, in comparison with the current version of the FTDNA¡¯s Y-DNA Haplotree (2024-07-20). I find the same result. In details:
Consistent path from A-PR2921 (root) to R-L151 (including with R-PF6538, intermediate clade between R-P310 and R-L151, which only appears at Yfull).
?
R-U106 and downstream clades?: consistent path to R-FGC17460?:
-
R-U106?:
-
R-FGC3861?:
-
R-S1855?:
-
R-FGC17465?:
-
FGC17465 1 positive read (BQ:0, mapQ:60, 51M, 5th position from the 3¡¯end of the aDNA¡¯s segment)
-
FGC68717 1 positive read (BQ:23, mapQ:12, 67M)
-
R-FGC17460?:
-
A4654 1 positive read (BQ:37, mapQ:60, 78M)
-
FGC17472 1 positive read (BQ:BQ:37, mapQ:29, 69M)
Downstream of R-FGC17460?: only negative (37/272 SNPs) or no reads. For equivalent SNPs to the current 6 known child haplogroups of R-FGC17460 (NOTA?: 2 currently unnamed branches, from England and Ireland, not taken into account):
-
R-FTA62881 (3 negative reads / 3 SNPs)
-
R-BY11544 (3 negative reads / 3 SNPs)
-
R-FTC75933 (terminal haplogroup, only no reads)
-
R-FT115916 (1 negative read / FT113203)
-
R-BY122236 (5 negative reads / 5 SNPs)
-
R-FGC17464 (6 negative reads / 4 SNPs)
?
As a result, it seems to me quite likely that KOS015 does not belong to the 5 child branches for which we have negative reads. It is however not totally impossible that KOS015 could belong to an extinct or unidentified branch splitting one of these blocks of equivalent SNPs. KOS015 could possibly belong to R-FTC75933, a branch for which it only has negative reads at the 11 equivalent SNPs. Finally, KOS015 could potentially belong to an unidentified or extinct branch downstream of R-FGC17460. With 2 positive SNPs out of 11 SNPs equivalent to R-FGC17460, and only no reads for the other 9 SNPs in this haplogroup, it is however not totally impossible (but probably unlikely) that KOS015 could be a "pre-R-FGC17460". In other words, that this aDNA belongs to an unidentified or extinct branch that would potentially split the R-FGC17460 block in two.
?
Ewenn
|
Ewenn