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While lineage I is more commonly found among human listeriosis cases, lineage II appears to be overrepresented among isolates from foods and environmental sources. This study used the genome sequences for one<jats:italic>L. innocua<\/jats:italic>strain and four<jats:italic>L. monocytogenes<\/jats:italic>strains representing lineages I and II, to characterize the contributions of positive selection and recombination to the evolution of the<jats:italic>L. innocua<\/jats:italic>\/<jats:italic>L. monocytogenes<\/jats:italic>core genome.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Among the 2267 genes in the<jats:italic>L. monocytogenes\/L. innocua<\/jats:italic>core genome, 1097 genes showed evidence for recombination and 36 genes showed evidence for positive selection. Positive selection was strongly associated with recombination. Specifically, 29 of the 36 genes under positive selection also showed evidence for recombination. Recombination was more common among isolates in lineage II than lineage I; this trend was confirmed by sequencing five genes in a larger isolate set. Positive selection was more abundant in the ancestral branch of lineage II (20 genes) as compared to the ancestral branch of lineage I (9 genes). Additional genes under positive selection were identified in the branch separating the two species; for this branch, genes in the role category \"Cell wall and membrane biogenesis\" were significantly more likely to have evidence for positive selection. Positive selection of three genes was confirmed in a larger isolate set, which also revealed occurrence of multiple premature stop codons in one positively selected gene involved in flagellar motility (<jats:italic>flaR<\/jats:italic>).<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>While recombination and positive selection both contribute to evolution of<jats:italic>L. monocytogenes<\/jats:italic>, the relative contributions of these evolutionary forces seem to differ by<jats:italic>L. monocytogenes<\/jats:italic>lineages and appear to be more important in the evolution of lineage II, which seems to be found in a broader range of environments, as compared to the apparently more host adapted lineage I. Diversification of cell wall and membrane biogenesis and motility-related genes may play a particularly important role in the evolution of<jats:italic>L. monocytogenes<\/jats:italic>.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2148-8-233","type":"journal-article","created":{"date-parts":[[2008,8,13]],"date-time":"2008-08-13T06:13:36Z","timestamp":1218608016000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":63,"title":["Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes"],"prefix":"10.1186","volume":"8","author":[{"given":"Renato H","family":"Orsi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Wiedmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2008,8,12]]},"reference":[{"key":"802_CR1","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.1093\/oxfordjournals.molbev.a003991","volume":"19","author":"R Urwin","year":"2002","unstructured":"Urwin R, Holmes EC, Fox AJ, Derrick JP, Maiden MC: Phylogenetic evidence for frequent positive selection and recombination in the meningococcal surface antigen PorB. 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