tive modern human features as long life spans and enlarged brains in the ancestries of both humans and elephants.
Charles Darwin (1859) proposed that natural selection favors inherited modifications that better adapt the organisms of a species to the environment of that species. Darwin also proposed the tree model for life’s evolution. In this model, natural selection adaptively modifies newly arisen species as they branch apart from their common ancestor (Darwin, 1859). Although there is now evidence that symbiotic merges produced the first eukaryotes and that prokaryotic species engage in reticulate evolution (Doolittle, 1999; Margulis and Sagan, 2002; Avise, 2008), Darwin’s model of tree-like branching appears to hold for the evolution of primates and other vertebrates. Having deduced that species share common ancestors, Darwin also reasoned that a truly natural system for classifying species would be genealogical, that is, species should be classified according to how recently they last shared a common ancestor. The hierarchical ranking in such a genealogical system could then be used to indicate how relatively close or distant in geological time extant species are from their last common ancestor (LCA).
In accord with this Darwinian framework, the phylogenomic approach to elucidating adaptive evolution in the ancestry of modern humans involves identifying the changes in genes and genomes on a phylogenetic tree that accurately places humans within the order Primates and, more widely, within the class Mammalia. Viewing the ancestries of many mammals, not just the ancestry of modern humans, could provide examples of convergent adaptive evolution, which may point to specific categories of genetic changes that are associated with important phenotypic changes. This phylogenomic approach could help identify the positively selected genetic changes that shaped such distinctive modern human features as prolonged prenatal and postnatal development, lengthened life spans, strong social bonds, enlarged brains, and high cognitive abilities. In this article, we first briefly sketch out the historical background of ideas and findings that have led to phylogenomic studies of human evolution. We then highlight the concepts that motivate our own efforts and discuss how phylogenomic evidence has enhanced our understanding of adaptive evolution in the ancestry of modern humans.
In The Descent of Man, and Selection in Relation to Sex, Charles Darwin (1874) suggested that Africa was the birthplace for humankind. The fol-