  Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) are
two kinds of commonly used markers in Y chromosome studies of forensic and
population genetics. There has been increasing interest in the cost saving
strategy by using the STR haplotypes to predict SNP haplogroups. However, the
convergence of Y chromosome STR haplotypes from different haplogroups might
compromise the accuracy of haplogroup prediction. Here, we compared the
worldwide Y chromosome lineages at both haplogroup level and haplotype level to
search for the possible haplotype similarities among haplogroups. The similar
haplotypes between haplogroups B and I2, C1 and E1b1b1, C2 and E1b1a1, H1 and
J, L and O3a2c1, O1a and N, O3a1c and O3a2b, and M1 and O3a2 have been found,
and those similarities reduce the accuracy of prediction.
