but 40 km SW in Esperstedt (samples from the Corded Ware culture of 2500-2050) gave 8 R1a and a R1b1a2, then 40 km SE from Esperstedt, in Eulau, two samples pertaining also to the Corded Ware from 2600 were R1a (total CW = 10 R1a + 1 R1b)
That alleged CWC R1b from Esperstedt was in fact R1a.
SNP calls suggest that he was in fact R1a-M198* (basal paragroup M198):
https://genetiker.wordpress.com/y-snp-calls-for-i1534/
And on Anthrogenica user Smal explained why he was not R1b - le'ts cite him:
http://www.anthrogenica.com/showthread.php?5605-R1b-in-Corded-Ware&p=125343&viewfull=1#post125343
Quote:
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I1534 is not R1b. CTS11468 and many other R1b specific SNPs are negative for this sample.
I1534 has the following negative R1b SNPs:
L1349/PF6268/YSC0000231-
CTS2702/PF6099/Z8132-
CTS2703-
L1345/PF6266/YSC0000224-
CTS9018/FGC188/PF6484-
CTS2466/PF6453-
CTS2704/PF6100-
CTS8052/FGC45/PF6473-
L749/PF6476/YSC0000290-
PF6496/YSC0000213-
L1350/PF6505/YSC0000225-
PF6507-
CTS11468/FGC49/PF6520-
CTS12972/FGC52/PF6532-
CTS11468 is a mutation from “G” to “T”. All R1b1a2 (R-M269) have “T” in this position. I1534 has 1”G” read.
I am looking at the actual reads from bam files.
It is easy to explain.
A difference between Reference Sequence and Sample Sequence can arise in 2 cases
1) Ancestral (RS) -> Derived (SS) [positive SNP in SS]
2) Ancestral (SS) -> Derived (RS) [negative SNP in SS]
If there are no differences between Reference Sequence and Sample Sequence that can mean
3) Ancestral -> Derived (RS) = Derived (SS) [positive SNP in SS]
4) Ancestral (RS) = Ancestral (SS) -> Derived [negative SNP in SS]
Probably you know that Reference Sequence is a mix from the actual R1b-P312 (mainly) and G sequences.
As a result, the most of R1b1a2 specific SNPs belong to the variant 3. But in case of CTS11468 we see the variant 2.
However, Mathieson et al have recorded it wrongly as the variant 1.
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End of quote