What do our genes tell us about our past?

The use of DNA sequences to elucidate the history of relationships of organisms is widespread, and focus on our species has been intense. This paper examines some simple aspects of using genetic information to analyze relationships within and amongst humans. Clonal markers (mtDNA and Y chromosomal DNA) have always shown a high degree of structure and robustness when analyzed for hierarchical structure. Results from genome wide phylogenetic structure in many organismal systems suggests instead that recombining genetic elements like the X chromosome and the autosomes will give conflicting information from genome region to genome region. In addition, the evolutionary signal from the different chromosomal regions will show a high degree of incongruence with each other, as do adjacent regions of chromosomes. This incongruence and lack of hierarchical structure is discussed in the context of what we know about human populations and the theoretical underpinnings of tree building based analysis of human populations.