I know that markers such as M45, M89, etc. are Y SNPs but I'm not clear on how they are used in pop. genetics. How do they know that a base change is a mutation? It seems that there is an implication that there is a "template" order of bases that defines the "original" model? I have read alot of articles and several books that sort of gloss over the exact process of using markers to define haplogroups but none have explained it clearly. Does anyone know where there is some good information on this subject?