The human Y chromosome haplogroup tree: Nomenclature and phylogeography of its major divisions

In this review we discuss the recent construction of a highly resolved tree of the nonrecombining portion of the Y chromosome (NRY), and the development of a cladistic nomenclatural system to name the resulting haplogroups. This phylogenetic gene tree comprises 18 major haplogroups that are defined by 48 binary polymorphisms. We also present results from a phylogeographic analysis of NRY haplogroups in a global sample of 2007 males, as well as from a regional study focusing on Siberia (n = 902). We use the following statistical techniques to explicate our presentation: analysis of molecular variance, multidimensional scaling, comparative measures of genetic diversity, and phylogeography-based frequency distributions. Our global results, based on the 18 major haplogroups, are similar to those from previous analyses employing additional markers and support the hypothesis of an African origin of human NRY diversity. Although Africa exhibits greater divergence among haplogroups, Asia contains the largest number of major haplogroups (N = 15). The multidimensional scaling analysis plot indicates that the Americas, Africa, and East Asia are outliers, whereas the rest of the world forms a large central cluster. According to our new global-level analysis of molecular variance, 43% of the total variance of NRY haplogroups is attributable to differences among populations (i.e., Phi(ST) = 0.43). The Siberian regional analysis of 62 binary markers exhibits nonrandom associations between geographically restricted NRY haplogroups and language families. We conclude with a list of typing recommendations for laboratories that wish to use the Y chromosome as a tool to investigate questions of anthropological interest.