Notes on SNP P25


Reliability of P25 marker

A new study deals with some problems of the P25 marker which defines haplogroup R1b. Normally, a SNP is considered rare enough that its presence unambiguously establishes descent from a common ancestor, and its absence establishes non-descent. However, it is possible for a back-mutation to occur. In this case, there is a relationship of descent, but it appears that there is no such relationship. The authors of the new study discovered at least two cases of this happening, and they recommend that a different marker, M269 be used in the future.
Forensic Sci Int. 2005 Jul 15; [Epub ahead of print]

The case of the unreliable SNP:
Recurrent back-mutation of Y-chromosomal marker P25 through gene conversion.
Adams SM et al.

The Y-chromosomal binary marker P25 is a paralogous sequence variant, rather than a SNP: three copies of the P25 sequence lie within the giant palindromic repeats on Yq, and one copy has undergone a C to A transversion to define haplogroup R1b (designated C/C/A). Since gene conversion is known to be active in the palindromic repeats, we reasoned that P25 might be liable to back-mutation by gene conversion, yielding the ancestral state C/C/C. Through analysis of a set of binary markers in Y-chromosomes in two large samples from Great Britain and the Iberian Peninsula we show that such conversion events have occurred at least twice, and provide preliminary evidence that the reverse conversion event (yielding C/A/A) has also occurred. Because of its inherent instability, we suggest that P25 be used with caution in forensic studies, and perhaps replaced with the more reliable binary marker M269.