and most animal phyla (McFall-Ngai, 2002; Brundrett, 2003; Schardl et al., 2004). Many of these symbioses are vertically transmitted, resulting in continuous association of individual genetic lineages across generations and facilitating the evolution of mutually beneficial features. Others are reestablished each host generation from a dispersing symbiont population.
Animals stand out as a group having lost many ancestral capabilities, making them unusually dependent on other organisms. In the Metazoa generally, gene loss has resulted in the inability to synthesize essential metabolic compounds, yielding a long list of required dietary components, including numerous cofactors (vitamins) as well as the 10 essential amino acids (Payne and Loomis, 2006). The losses of these pathways reflect the evolution of a digestive cavity by animals, which acquire diverse nutrients by eating tissues and cells of other organisms. If nutrients are readily available in the diet, selection to maintain pathways for production of these compounds will be relaxed, resulting in the inactivation of the underlying genes. Comparisons of recently sequenced animal genomes reveal that particular animal lineages have continued to eliminate particular sets of genes. For example, the Drosophila genome lacks many genes that are present in both honeybee and mammals, reflecting gene loss in the dipteran lineage (Honeybee Genome Sequencing Consortium, 2006).
Animals also appear to be limited in the ability to incorporate foreign genes directly into their nuclear genomes. To date, the complete genomes of several mammals, nematodes, and insects have not revealed large numbers of foreign genes. [In fact, the initial report that the human genome contains numerous genes acquired from Bacteria (Lander et al., 2001) was later shown to be unwarranted, reflecting artifacts of analysis and limited data from eukaryotic genomes (e.g., Stanhope et al., 2001).]. So, although uptake of nonfunctional DNA does occur (e.g., Sunnucks and Hales, 1996; Kondo et al., 2002) and sometimes may result in adaptive incorporation of functional genes from exogenous sources (e.g., Mallet et al., 2003; Daimon et al., 2003), current evidence indicates that this process is limited in animals. Duplication of existing genes and regulatory changes are far more important. Among potential barriers to gene acquisition in animals are the need for regulating expression in the context of the more complex development and also the separation of germ line. In contrast to organelles (mitochondria and plastids) that arose in single-celled hosts and are present in most or all cells in modern multicellular hosts, symbionts acquired by animals are typically restricted to specialized organs and often live primarily in somatic tissues, where they may be intracellular or