{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T14:48:01Z","timestamp":1791470881651,"version":"4.3.4"},"reference-count":46,"publisher":"National Academy of Sciences","issue":"26","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2003,12,23]]},"abstract":"<jats:p>\n                    Previous studies of genome evolution usually have involved one or two genomes and have thus been limited in their ability to detect the direction and rate of evolutionary change. Here, we use complete genome data from 20 poxvirus genomes to build a robust phylogeny of the\n                    <jats:italic>Poxviridae<\/jats:italic>\n                    and to study patterns of genome evolution. We show that, although there has been little gene order evolution, there are substantial differences between poxviruses in terms of genome content. Furthermore, we show that the rate of gene acquisition is not constant over time and that it has increased in the orthopox lineage (which includes smallpox and vaccinia). We also tested for positive selection on 204 groups of genes and show that a disproportionately high proportion of genes in the orthopox clade are under positive selection. The association of an increased rate of gene gain and positive selection is indicative of adaptive genome evolution. Many of the genes involved in these processes are likely to be associated with host\u2013parasite coevolution.\n                  <\/jats:p>","DOI":"10.1073\/pnas.2136653100","type":"journal-article","created":{"date-parts":[[2003,12,23]],"date-time":"2003-12-23T12:58:11Z","timestamp":1072184291000},"page":"15655-15660","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":155,"title":["Extensive gene gain associated with adaptive evolution of poxviruses"],"prefix":"10.1073","volume":"100","author":[{"given":"Aoife","family":"McLysaght","sequence":"first","affiliation":[{"name":"Departments of Ecology and Evolutionary Biology and Biological Chemistry, Institute for Genomics and Bioinformatics, and School of Information and Computer Science, University of California, Irvine, CA 92697"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre F.","family":"Baldi","sequence":"additional","affiliation":[{"name":"Departments of Ecology and Evolutionary Biology and Biological Chemistry, Institute for Genomics and Bioinformatics, and School of Information and Computer Science, University of California, Irvine, CA 92697"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brandon S.","family":"Gaut","sequence":"additional","affiliation":[{"name":"Departments of Ecology and Evolutionary Biology and Biological Chemistry, Institute for Genomics and Bioinformatics, and School of Information and Computer Science, University of California, Irvine, CA 92697"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2003,12,5]]},"reference":[{"key":"e_1_3_2_1_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng1088"},{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1007\/PL00006428"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF02099948"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/42711"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.290.5499.2114"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng884"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.81.3.814"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1006\/geno.1995.9873"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.757503"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.182432999"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1086568"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00239-001-0021-1"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1567-1348(02)00040-0"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msg107"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1006\/viro.2000.0761"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.76.2.783-790.2002"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1006\/viro.2001.1343"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1099\/0022-1317-83-4-855"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.273.5276.813"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.74.8.3815-3831.2000"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1006\/viro.2000.0449"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0076-6879(96)66035-2"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2000.4042"},{"key":"e_1_3_2_25_2","first-page":"823","volume":"12","year":"1995","unstructured":"Takezaki, N., Rzhetsky, A. & Nei, M. 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