providing a far more detailed view of how these differences have arisen. First, many genes and corresponding capabilities arose after lineage diversification had begun, so that some species descend from ancestors that never possessed the corresponding genes. Examples include fundamental metabolic innovations such as phototrophy (Mulkidjanian et al., 2006) and methanogenesis as well as specialties such as production of particular toxins or pathogenicity mechanisms, including the type III secretion system used by many bacteria for infecting host cells (Saier, 2004).
A second reason that species differ in gene sets and capabilities is that ancestral genes are often lost. Comparisons of genomic content among closely related species are now revealing that gene loss has been an important and ongoing process in evolution in all lineages. For example, tryptophan, required in proteins of all organisms, is produced by a single pathway requiring several enzymatic steps, and reconstructions of the evolution of this pathway point to a single origin before the divergence of the three domains of life (Xie et al., 2003). Many descendant lineages, including all animals and a variety of prokaryotes and parasitic protists, have lost the pathway and are dependent on acquiring tryptophan from ecologically associated species.
The loss of such useful capabilities may seem counterintuitive. But another major insight from comparative genomics is that genes are constantly being eliminated by mutation combined with insufficient purifying selection. The pathways lost most frequently are those with more enzymatic steps and higher energy requirements, suggesting that selection may favor pathway inactivation when the end products can be environmentally acquired. Outstanding examples of gene loss include many host-dependent microbial lineages; obligate pathogens, both bacterial and eukaryotic, lose genes for using substrates not encountered in their restricted environment and lose genes for synthesis of metabolic products that are dependably provided by the host cells (Shigenobu et al., 2000; Gardner et al., 2002; Tamas et al., 2002; Liu et al., 2006; Payne and Loomis, 2006). As a group, animals are unusual in lacking the ability to produce numerous universally required metabolic compounds such as vitamins and amino acids and also in lacking capabilities for producing bioactive secondary compounds that can act as toxins and defenses.
For many genes, the distribution among species reflects not only the lineage of origin and subsequent losses in some descendants but also transfer to new lineages. Thus, a species can acquire, more or less instantaneously, traits that originated in unrelated lineages or that were lost ancestrally. Gene transfer is clearly important in prokaryotes, for which