Minimal hierarchical analysis of global human Y-chromosome SNP diversity by PCR-RFLP

Phylogenetically informative binary polymorphisms on the Y-chromosome have become a standard source of markers for molecular anthropology studies. Although several analytical methods are currently available, most methodologies rely on specialized equipment or expensive reagents that research groups with a primarily anthropological focus often cannot afford. Here I present 15 Y-chromosome lineage assays based on a more widely accessible technique-Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). In conjunction with eight pre-existing tests, these validated protocols allow the assignment of unknown men to every major branch of the global Y-chromosome tree, including the 18 haplogroups/paragroups defined by the Y-Chromosome Consortitum. While not intended to supplant the high-throughput technologies adopted by advanced research units, these minimal protocols will allow smaller molecular anthropology groups to survey male variation in a broader range of human populations, thereby furthering our understanding of global human Y-chromosome diversity.