Comparisons of the human genome to the genomes of Neandertals and apes can help identify features that set modern humans apart from other hominin species. In particular, the Neandertal genome sequence can now be used to catalog changes that have become "fixed" (are invariant within a population or species) in modern humans during the last few hundred thousand years and should be helpful for identifying genes affected by positive selection since humans diverged from Neandertals.
To help make informative comparisons, Green et al. sequenced the genomes of 5 present-day individuals from different parts of the world: southern Africa, West Africa, Papua New Guinea, China, and western Europe (see map). They then compared the genomes of these individuals with the genomes of the Neandertal and the chimpanzee, and looked both for specific regions shared by present-day humans but lacking in Neandertals and regions showing high frequencies of more recently evolved (derived) sequences. These regions signal the presence of mutations that occurred and swept to either high frequency or fixation after humans and Neandertal diverged, and that may have contributed to modern human-specific traits.
Using this comparative approach, Green et al. came up with a list of 20 candidate regions that may have been affected by positive selection in ancestral modern humans. Five of these regions contain no protein-coding genes and may thus include structural or regulatory elements. Among the remaining 15 regions, the team identified genes involved in metabolism and cognitive and cranial development, which suggests that aspects of these processes may have been functionally important for the evolution of modern humans.
For more on Neandertal-modern human comparisons see the News story by A. Gibbons.