occurred between ancestral and descendent genomes. Of particular interest will be those adaptive genetic changes in protein-coding sequences, promoters, and other regulatory sequences.
Phylogenomic research provides an opportunity to identify those parallel or convergent patterns of adaptive genetic evolution that correlate with parallel or convergent patterns of adaptive phenotypic evolution. As an example, brain size increased in parallel in the stem catarrhines and stem platyrrhines (Kay et al., 1997). Encephalization then increased further in ape ancestry, in some Old World monkeys and some New World monkeys (e.g., Cebus) (Marino, 1998). In addition to humans, a number of primate species also exhibit a great deal of phenotypic and behavioral plasticity, including chimpanzees, baboons, macaques, and capuchins. Parallel or convergent patterns of adaptive genetic evolution among these species might help elucidate mechanisms contributing to enhanced brain plasticity in modern humans during childhood when the capacity for learning is greatest. Nevertheless, the search for genetic correlates of distinctive human phenotypic features should explore the possibility that some molecular aspects of modern human brain plasticity might be uniquely human. The hypothesis could be tested that adaptive evolution in our recent ancestry increased the diversity of macromolecular specificities involved in neuronal connectivity and neural plasticity. In testing this hypothesis, genes such as those concerned with cell–cell interaction, adhesion, and receptor–ligand binding and their cis-regulatory motifs should be examined. However, we would not be surprised if phylogenomic studies reveal that the genetic underpinnings for the basic mechanisms of brain plasticity are essentially the same as in other catarrhine primates and that the modern human mind differs from the other species primarily because of the modern human brain’s larger number of neurons and dendritic connections and much longer periods of postnatal development in a social nurturing environment.
With the advent of large-scale sequencing technologies and new bioinformatic tools for processing genomic sequence data, we are poised to embark on a new voyage of exploration and inquiry just as Darwin did in 1831. The last decade in particular has seen exponential growth in genome sequence collection and characterization. As we work toward a more complete understanding of genome structure, biology, and evolution, we become better able to develop and test hypotheses concerning a number of fundamental questions in evolutionary biology and human evolution. At the forefront of our interests are those molecular mechanisms and adaptations that have resulted in the modern human mind.