Genealogical and evolutionary inference with the human Y chromosome

Population genetics has emerged as a powerful tool for unraveling human his tory. In addition to the study of mitochondrial and autosomal DNA, attentio n has recently focused on Y-chromosome variation. Ambiguities and inaccurac ies in data analysis, however, pose an important obstacle to further develo pment of the field. Here we review the methods available for genealogical i nference using Y-chromosome data. Approaches can be divided into those that do and those that do not use an explicit population model in genealogical inference. We describe the strengths and weaknesses of these model-based an d model-free approaches, as well as difficulties associated with the mutati on process that affect both methods. In the case of genealogical inference using microsatellite Loci, we use coalescent simulations to show that relat ively simple generalizations of the mutation process can greatly increase t he accuracy of genealogical inference. Because model-free and model-based a pproaches have different biases and Limitations, we conclude that there is considerable benefit in the continued use of both types of approaches.