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Probably Genotyping Error affects TMRCA calculation

Posted by vineviz on 08 Feb 2008 at 00:53 GMT

We also assessed the TMRCA for the rare Sardinia-specific R-M18 haplogroup, and obtained a value of 8.1 (7.8–10.5) KYA.

I did notice, however, what appears to be a genotyping error in haplogroup R-M18. One of the Cagliari haplotypes appears to have been classified as R-M18 when it should have been classified as R-M269.

This haplotype does not match any of the other seven haplotypes at five of the eight reported STRs, yet matches the majority allele for R-M269 at seven of the eight STRs. In a UPGMA phylogeny constructed using the haplotypes from this paper, it also clustered with R-M269 in all of the trees.

Including this R-M269 haplotype in the R-M18 TMRCA calculation dramatically increases the STR variance, thus producing an errantly large TMRCA calculation.