Convergence of Y chromosome STR haplotypes from different SNP haplogroups compromises accuracy of haplogroup prediction

TL;DR

This study investigates how converging Y chromosome STR haplotypes from different SNP-defined haplogroups can reduce the accuracy of haplogroup prediction in forensic and population genetics.

Contribution

It identifies specific haplotype similarities across haplogroups that compromise the reliability of STR-based haplogroup prediction methods.

Findings

Identified multiple haplotype similarities among different haplogroups.

Convergence of haplotypes reduces prediction accuracy.

Highlights limitations of using STRs alone for haplogroup inference.

Abstract

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.