Ethnic fragmentation and degree of urbanization strongly affect the discrimination power of Y-STR haplotypes in central Sahel

•431 males from Cameroon and Chad analysed by using 27 Y-STRs and 82 Y-SNPs.•Extensive haplotype sharing for males from the same ethnic group and location.•Significant correlation between location census size and discrimination capacity.•Genetic differentiation among neighbouring villages exceeded that among countries.•Implications for the choice of the appropriate reference population database.