Short tandem repeat polymorphisms (STRPs) are highly variable markers that have proven to be very useful in resolving population structure. However, single-nucleotide polymorphism (SNP) assays are efficient and inexpensive, and the use of SNPs has become widespread. The resolving power of a set of SNPs will depend upon both the density of the markers and their frequencies. SNPs with minor allele frequencies (MAFs) of near 0.50 are assumed to be more ancient, while SNPs with low MAFs are assumed to be much more recent [4]. One hypothesis is that those SNPs with high MAFs predate the origins of modern human races and carry little useful information about population structure. It follows that SNPs with low MAFs, being much more recent polymorphisms, may be more informative in resolving population structure. Alternatively, the low heterozygosity of these SNPs may limit their usefulness (since the allele frequency differences between two populations would perforce be low); in this case, SNPs with high MAFs will be far more informative.
