host, resulting in coadaptation among several phylogenetically distant genomes.
Genomic sequence data, coupled with evolutionary analyses, have brought major new insights to our understanding of biological evolution. One of the biggest revelations is the extent to which biological adaptation and phenotypic innovation within a particular genetic lineage have depended on adopting already highly honed functional systems from other lineages, often only distantly related to the recipient. Traditional views of the evolutionary process, forged during the neo-Darwinian synthesis, focused on adaptation occurring as the result of natural selection acting on existing genes within a species. Most such adaptation occurs in small steps, although mutations in existing genes can sometimes cause major phenotypic changes. But the ability to reconstruct evolution at the molecular level, and especially the analysis of full genome sequences, has revealed that integration of genes originating from disparate sources has occurred on a very large scale.
Gene uptake confers novel adaptive capabilities, thereby enabling ecological expansion into new niches. But it also confers phenotypic complexity that is manifested at the genomic, the physiological, and the morphological levels. In many cases, and specifically in multicellular eukaryotes, the route to recruiting foreign genes and novel metabolic capabilities involves symbiotic association, that is, a persistent close interaction with another species. Comparative genomic studies now allow us to reconstruct the history of symbioses and episodes of genome amalgamation and to elucidate their contribution to the complexity evident in the dominant forms of life on earth.
Below, I briefly describe the routes by which organisms stably acquire capabilities evolved in other lineages, with emphasis on insights that have come from recent genome sequencing. I end with examples of the complex phenotypes generated by hereditary symbiosis in insects and with the consequences of this genome integration through symbiosis for animal evolution.
The evolutionary motivation for assimilating foreign genes stems from the obvious fact that species differ in gene sets and corresponding capabilities. Thus, intimate association between two lineages can readily arise through natural selection acting within each species to fix alleles that promote close association with the other species. Although differences in metabolic capacities among species have long been evident, genomics is