hundreds of genomes have been sequenced. As an illustration of the extent of foreign-gene uptake, a study reconstructing the sources of genes in the genomes of numerous species in the Gammaproteobacteria showed that the overwhelming majority of genes in most genomes were acquired from external sources after these lineages diverged from a common ancestor (Lerat et al., 2005). The impact of gene uptake can be massive even on short time scales. For example, in comparisons of gene sets of distinct Escherichia coli strains, for which orthologous DNA sequences are 99% identical, indicating recent shared ancestry, 25% or more of the genes in one genome are absent from other strains, having arrived recently from more distant (often unidentified) sources (Welch et al., 2002). In Bacteria, such incorporation of foreign genes is the major route to the origination of novel capacities (Ochman et al., 2000), as illustrated in E. coli, in which recently acquired genes are the basis for strain-specific pathogenicity (e.g., Welch et al., 2002).
Firm estimates are not yet possible for rates of gene acquisition by eukaryotic genomes. For Bacteria, the evidence for rampant gene acquisition is primarily based on comparing related genomes by using complete gene inventories, sequence features, and gene arrangements. To date, the numbers of sequenced genomes for clusters of related eukaryotic species are relatively small for estimating total gene uptake by using comparisons of gene inventories and gene arrangements. Currently, the extent of foreign gene uptake, and specifically genes arriving from Bacteria, does appear to be substantial in certain groups of unicellular eukaryotes, including Dictyostelium (Eichinger et al., 2005) and other lineages of amoebae (Andersson et al., 2006). But even in unicellular eukaryotes, duplication and divergence of existing genes appear to be more prominent than gene uptake as a process generating change in genome contents (e.g., Kellis et al., 2004; Aury et al., 2006). Similarly, plant nuclear and plastid genomes have not been found to contain substantial numbers of acquired genes, although acquisition of genes by plant mitochondrial genomes does occur relatively frequently and is currently the major category of gene incorporation by multicellular eukaryotes (Richardson and Palmer, 2007). Despite increasing findings of horizontal transfer even in eukaryotes, the capacity to incorporate new genes underlying enzymatic pathways and processes has severe limits (Kurland et al., 2003). Some groups of organisms rarely incorporate foreign genes, and, even in those that do, such as most free-living Bacteria, many genes underlying important informational and metabolic processes seem to resist horizontal transfer, as illustrated by the case of the tryptophan biosynthetic pathway (Xie et al., 2003).