Inferring human history: clues from Y-chromosome haplotypes.

molecules are organic elements of information storage imbued with imperfect copying processes. Thus, they are fundamental repositories of an organism's evolutionary history. The field of human molecular evolution is predicated on the concept that patterns of DNA sequence variation in living populations encode aspects of human heritage shaped by a constellation of evolutionary influences. The framework of genetic variability in the genome reflects both evolutionary adaptive processes that are locus-specific and population-level forces that affect all the components of the genome equally. Genetic research often focuses on distinguishing inconsistencies in patterns of variation between genomic regions to help bridge the gap between particular genes and traits, including matters of function and malfunction. Alternatively , genomic DNA is also an archive of those aspects of human evolutionary processes reflective of population level forces like drift, subdivision, size fluctuation, and migration. By studying the degree of genetic molecular variation, one can, in principle, reconstruct past events such as expansions and settlements from which origins of specific populations can be predicted (Cavalli-Sforza et al. 1994). However, since the bulk of common variation in the genome occurs between individuals, the difference between populations is low, making it more challenging to investigate ambiguities concerning affinities and origins of populations. It is the component of between population variance that best provides insights into the evolution of the spectrum of extant populations (Cav-alli-Sforza and Feldman 2003). In addition, determining the migratory patterns of our ancestors and their timing, as well as the amount of population admixture due to such migrations, has been experimentally less tractable. Consequently , such issues are often simply ignored when reconstructing population phylogenies where little or no migration is implicitly assumed. Progress in understanding the spectrum of human DNA sequence variation and its causes, especially when integrated with other knowledge from historians, archaeologists , anthropologists, and linguists, can help recapit-ulate human population histories (Owens and King 1999; Cann 2001). In particular, informative haplotypes, immune from the scrambling effects of recurrent mutation and recombination, provide a promising way forward. In the early genetic studies, both protein and matrilineal inherited mitochondrial DNA (mtDNA) loci have provided much of the initial evidence. However, considerable recent progress in elucidating Y-chromosome sequence variation from the nonrecombining region (NRY) has made it possible to more fully investigate the parallel paternal heritage that underlies the central theme of this paper. Although extrapolating variation associated with a single gene to population …