Y-chromosome haplotype mismatch in different haplogroups: Coincidence or evidence of SNP mutation?

The analysis of 240 individuals from the populations of the Madeira and Azores archipelagos for both Y-chromosome STRs and SNPs allows the determination of a correlation between the haplotype and haplogroup for each individual.The variability within each haplogroup was analysed and coalescence age calculated. These results led to the detection of some founder effects in both populations.It was found that some individuals share the same haplotype but belong to different Y-chromosome haplogroup suggesting that SNP mutations may occur frequently. We propose using SNP and STR information together, which provides a more reliable characterization of an individual in terms of Y-chromosome origin, minimizing the risk of misassigment due to mutation.