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The<jats:italic>Wolbachia<\/jats:italic>strains that infect nematodes are phylogenetically distinct, strictly vertically transmitted, and required by their hosts for growth and reproduction. Insects in contrast form more fluid associations with<jats:italic>Wolbachia<\/jats:italic>. In these taxa, host populations are most often polymorphic for infection, horizontal transmission occurs between distantly related hosts, and direct fitness effects on hosts are mild. Despite extensive interest in the<jats:italic>Wolbachia<\/jats:italic>system for many years, relatively little is known about the molecular mechanisms that mediate its varied interactions with different hosts. We have compared the genomes of the<jats:italic>Wolbachia<\/jats:italic>that infect<jats:italic>Drosophila melanogaster<\/jats:italic>,<jats:italic>w<\/jats:italic>Mel and the nematode<jats:italic>Brugia malayi<\/jats:italic>,<jats:italic>w<\/jats:italic>Bm to that of an outgroup<jats:italic>Anaplasma marginale<\/jats:italic>to identify genes that have experienced diversifying selection in the<jats:italic>Wolbachia<\/jats:italic>lineages. The goal of the study was to identify likely molecular mechanisms of the symbiosis and to understand the nature of the diverse association across different hosts.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The prevalence of selection was far greater in<jats:italic>w<\/jats:italic>Mel than<jats:italic>w<\/jats:italic>Bm. Genes contributing to DNA metabolism, cofactor biosynthesis, and secretion were positively selected in both lineages. In<jats:italic>w<\/jats:italic>Mel there was a greater emphasis on DNA repair, cell division, protein stability, and cell envelope synthesis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Secretion pathways and outer surface protein encoding genes are highly affected by selection in keeping with host:parasite theory. If evidence of selection on various cofactor molecules reflects possible provisioning, then both insect as well as nematode<jats:italic>Wolbachia<\/jats:italic>may be providing substances to hosts. Selection on cell envelope synthesis, DNA replication and repair machinery, heat shock, and two component switching suggest strategies insect<jats:italic>Wolbachia<\/jats:italic>may employ to cope with diverse host and intra-host environments.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2148-7-68","type":"journal-article","created":{"date-parts":[[2007,5,1]],"date-time":"2007-05-01T06:13:42Z","timestamp":1178000022000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":34,"title":["Diversifying selection and host adaptation in two endosymbiont genomes"],"prefix":"10.1186","volume":"7","author":[{"given":"Jeremy C","family":"Brownlie","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcin","family":"Adamski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barton","family":"Slatko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth A","family":"McGraw","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2007,4,30]]},"reference":[{"key":"362_CR1","first-page":"xi, 214","volume-title":"Influential passengers : inherited microorganisms and arthropod reproduction","author":"SL O'Neill","year":"1997","unstructured":"O'Neill SL, Hoffmann AA, Werren JH: Influential passengers : inherited microorganisms and arthropod reproduction. 1997, Oxford ; New York, Oxford University Press, xi, 214-"},{"key":"362_CR2","doi-asserted-by":"publisher","first-page":"1989","DOI":"10.1126\/science.1094611","volume":"303","author":"T Tsuchida","year":"2004","unstructured":"Tsuchida T, Koga R, Fukatsu T: Host plant specialization governed by facultative symbiont. 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