{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:49:43Z","timestamp":1792788583400,"version":"4.5.0"},"reference-count":85,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2016,12,15]],"date-time":"2016-12-15T00:00:00Z","timestamp":1481760000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004963","name":"Seventh Framework Programme","doi-asserted-by":"publisher","award":["278433"],"award-info":[{"award-number":["278433"]}],"id":[{"id":"10.13039\/501100004963","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["BSV3-0019"],"award-info":[{"award-number":["BSV3-0019"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR10-INBS-09-08"],"award-info":[{"award-number":["ANR10-INBS-09-08"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","award":["653316"],"award-info":[{"award-number":["653316"]}],"id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007601","name":"Horizon 2020","doi-asserted-by":"publisher","award":["653316"],"award-info":[{"award-number":["653316"]}],"id":[{"id":"10.13039\/501100007601","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Universtiy of Melbourne McKenzie fellowship"}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"DOI":"10.1371\/journal.ppat.1006041","type":"journal-article","created":{"date-parts":[[2016,12,16]],"date-time":"2016-12-16T03:10:08Z","timestamp":1481857808000},"page":"e1006041","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":225,"title":["Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts"],"prefix":"10.1371","volume":"12","author":[{"given":"C\u00e9cile","family":"Troupin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurent","family":"Dacheux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marion","family":"Tanguy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claude","family":"Sabeta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Herv\u00e9","family":"Blanc","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christiane","family":"Bouchier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Vignuzzi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2863-0907","authenticated-orcid":true,"given":"Sebasti\u00e1n","family":"Duchene","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward C.","family":"Holmes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Herv\u00e9","family":"Bourhy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2016,12,15]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1146\/annurev.micro.62.081307.162912","article-title":"Evolutionary history and phylogeography of human viruses","volume":"62","author":"EC Holmes","year":"2008","journal-title":"Annual review of microbiology"},{"issue":"6","key":"ref2","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1016\/j.copbio.2003.10.010","article-title":"Emerging viral infections in a rapidly changing world","volume":"14","author":"T Kuiken","year":"2003","journal-title":"Current opinion in biotechnology"},{"key":"ref3","first-page":"85","article-title":"Overviews of pathogen emergence: which pathogens emerge, when and why?","volume":"315","author":"S Cleaveland","year":"2007","journal-title":"Current topics in microbiology and immunology"},{"issue":"1411","key":"ref4","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1098\/rstb.2001.0889","article-title":"Diseases of humans and their domestic mammals: pathogen characteristics, host range and the risk of emergence","volume":"356","author":"S Cleaveland","year":"2001","journal-title":"Philosophical transactions of the Royal Society of London Series B, Biological sciences"},{"key":"ref5","first-page":"1","article-title":"Introduction: conceptualizing and partitioning the emergence process of zoonotic viruses from wildlife to humans","volume":"315","author":"JE Childs","year":"2007","journal-title":"Current topics in microbiology and immunology"},{"key":"ref6","unstructured":"(ICTV) ICoToV. Virus Taxonomy: 2015 Release 2016. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.ictvonline.org\/virustaxonomy.asp\" xlink:type=\"simple\">http:\/\/www.ictvonline.org\/virustaxonomy.asp<\/ext-link>."},{"key":"ref7","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1146\/annurev.mi.41.100187.002205","article-title":"Rapid evolution of RNA viruses","volume":"41","author":"DA Steinhauer","year":"1987","journal-title":"Annual review of microbiology"},{"issue":"17","key":"ref8","doi-asserted-by":"crossref","first-page":"8096","DOI":"10.1128\/JVI.75.17.8096-8104.2001","article-title":"Host switching in Lyssavirus history from the Chiroptera to the Carnivora orders","volume":"75","author":"H Badrane","year":"2001","journal-title":"Journal of virology"},{"issue":"1614","key":"ref9","doi-asserted-by":"crossref","first-page":"20120196","DOI":"10.1098\/rstb.2012.0196","article-title":"Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints","volume":"368","author":"NR Faria","year":"2013","journal-title":"Philosophical transactions of the Royal Society of London Series B, Biological sciences"},{"issue":"2","key":"ref10","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1006\/viro.2001.1271","article-title":"Genetic constraints and the adaptive evolution of rabies virus in nature","volume":"292","author":"EC Holmes","year":"2002","journal-title":"Virology"},{"issue":"6","key":"ref11","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1016\/j.coviro.2011.10.014","article-title":"A perspective on lyssavirus emergence and perpetuation","volume":"1","author":"CE Rupprecht","year":"2011","journal-title":"Curr Opin Virol"},{"issue":"4","key":"ref12","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1080\/10408410701647602","article-title":"Lyssaviruses","volume":"33","author":"LH Nel","year":"2007","journal-title":"Critical reviews in microbiology"},{"issue":"Pt 11","key":"ref13","doi-asserted-by":"crossref","first-page":"2673","DOI":"10.1099\/vir.0.2008\/003913-0","article-title":"The origin and phylogeography of dog rabies virus","volume":"89","author":"H Bourhy","year":"2008","journal-title":"The Journal of general virology"},{"issue":"6","key":"ref14","doi-asserted-by":"crossref","first-page":"e1002786","DOI":"10.1371\/journal.ppat.1002786","article-title":"Molecular inferences suggest multiple host shifts of rabies viruses from bats to mesocarnivores in Arizona during 2001\u20132009","volume":"8","author":"IV Kuzmin","year":"2012","journal-title":"PLoS pathogens"},{"issue":"19","key":"ref15","doi-asserted-by":"crossref","first-page":"7993","DOI":"10.1073\/pnas.0700741104","article-title":"A high-resolution genetic signature of demographic and spatial expansion in epizootic rabies virus","volume":"104","author":"R Biek","year":"2007","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"1\u20132","key":"ref16","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.virusres.2013.02.008","article-title":"Genetic characterization and phylogenetic analysis of skunk-associated rabies viruses in North America with special emphasis on the central plains","volume":"174","author":"R Davis","year":"2013","journal-title":"Virus research"},{"issue":"12","key":"ref17","doi-asserted-by":"crossref","first-page":"e82348","DOI":"10.1371\/journal.pone.0082348","article-title":"The phylogeography and spatiotemporal spread of south-central skunk rabies virus","volume":"8","author":"NA Kuzmina","year":"2013","journal-title":"PloS one"},{"issue":"Pt 10","key":"ref18","doi-asserted-by":"crossref","first-page":"2545","DOI":"10.1099\/0022-1317-80-10-2545","article-title":"Ecology and evolution of rabies virus in Europe","volume":"80","author":"H Bourhy","year":"1999","journal-title":"The Journal of general virology"},{"issue":"2","key":"ref19","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.virusres.2004.12.003","article-title":"Mongoose rabies in southern Africa: a re-evaluation based on molecular epidemiology","volume":"109","author":"LH Nel","year":"2005","journal-title":"Virus research"},{"issue":"3","key":"ref20","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1007\/s11262-013-0923-1","article-title":"Complete genome sequences of three rabies viruses isolated from rabid raccoon dogs and a cow in Korea","volume":"47","author":"JK Oem","year":"2013","journal-title":"Virus genes"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.vetmic.2015.10.030","article-title":"Emergence of a sylvatic enzootic formosan ferret badger-associated rabies in Taiwan and the geographical separation of two phylogenetic groups of rabies viruses","volume":"182","author":"KJ Tsai","year":"2016","journal-title":"Veterinary microbiology"},{"issue":"8","key":"ref22","doi-asserted-by":"crossref","first-page":"2059","DOI":"10.1007\/s00705-014-2044-0","article-title":"Molecular characterization of three ferret badger (Melogale moschata) rabies virus isolates from Jiangxi province, China","volume":"159","author":"J Zhao","year":"2014","journal-title":"Archives of virology"},{"issue":"4","key":"ref23","doi-asserted-by":"crossref","first-page":"e0003709","DOI":"10.1371\/journal.pntd.0003709","article-title":"Estimating the global burden of endemic canine rabies","volume":"9","author":"K Hampson","year":"2015","journal-title":"PLoS neglected tropical diseases"},{"issue":"2","key":"ref24","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1006\/viro.2002.1492","article-title":"Lyssavirus P gene characterisation provides insights into the phylogeny of the genus and identifies structural similarities and diversity within the encoded phosphoprotein","volume":"298","author":"SA Nadin-Davis","year":"2002","journal-title":"Virology"},{"issue":"11","key":"ref25","doi-asserted-by":"crossref","first-page":"e2560","DOI":"10.1371\/journal.pntd.0002560","article-title":"Recent emergence and spread of an Arctic-related phylogenetic lineage of rabies virus in Nepal","volume":"7","author":"GR Pant","year":"2013","journal-title":"PLoS neglected tropical diseases"},{"issue":"48","key":"ref26","doi-asserted-by":"crossref","first-page":"19715","DOI":"10.1073\/pnas.1203456109","article-title":"Variable evolutionary routes to host establishment across repeated rabies virus host shifts among bats","volume":"109","author":"DG Streicker","year":"2012","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"Pt 4","key":"ref27","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1099\/vir.0.007765-0","article-title":"Evolutionary history and dynamics of dog rabies virus in western and central Africa","volume":"90","author":"C Talbi","year":"2009","journal-title":"The Journal of general virology"},{"issue":"3","key":"ref28","doi-asserted-by":"crossref","DOI":"10.1128\/genomeA.00192-13","article-title":"Complete Genome Sequence of a Rabies Virus Isolate from a Ferret Badger (Melogale moschata) in Jiangxi, China","volume":"1","author":"J Zhao","year":"2013","journal-title":"Genome Announc"},{"issue":"10","key":"ref29","doi-asserted-by":"crossref","first-page":"e3251","DOI":"10.1371\/journal.pntd.0003251","article-title":"The phylogeography of rabies in Grenada, West Indies, and implications for control","volume":"8","author":"U Zieger","year":"2014","journal-title":"PLoS neglected tropical diseases"},{"issue":"1","key":"ref30","doi-asserted-by":"crossref","first-page":"vev011","DOI":"10.1093\/ve\/vev011","article-title":"Elucidating the phylogynamics of endemic rabies virus in eastern Africa using whole-genome sequencing","volume":"1","author":"K Brunker","year":"2015","journal-title":"Virus Evolution"},{"issue":"4","key":"ref31","doi-asserted-by":"crossref","first-page":"e2057","DOI":"10.1371\/journal.pone.0002057","article-title":"Genomic diversity and evolution of the lyssaviruses","volume":"3","author":"O Delmas","year":"2008","journal-title":"PloS one"},{"issue":"3","key":"ref32","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1007\/s11262-014-1108-2","article-title":"Characterization of the biological properties and complete genome sequence analysis of a cattle-derived rabies virus isolate from the Guangxi province of southern China","volume":"49","author":"HB Tang","year":"2014","journal-title":"Virus genes"},{"issue":"3","key":"ref33","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1007\/s12250-012-3251-z","article-title":"The full-length genome analysis of a street rabies virus strain isolated in Yunnan province of China","volume":"27","author":"J Zhang","year":"2012","journal-title":"Virologica Sinica"},{"issue":"10","key":"ref34","doi-asserted-by":"crossref","first-page":"e1001166","DOI":"10.1371\/journal.ppat.1001166","article-title":"Phylodynamics and human-mediated dispersal of a zoonotic virus","volume":"6","author":"C Talbi","year":"2010","journal-title":"PLoS pathogens"},{"issue":"4","key":"ref35","doi-asserted-by":"crossref","first-page":"e1005525","DOI":"10.1371\/journal.ppat.1005525","article-title":"Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting","volume":"12","author":"H Bourhy","year":"2016","journal-title":"PLoS pathogens"},{"issue":"5","key":"ref36","doi-asserted-by":"crossref","first-page":"e1002720","DOI":"10.1371\/journal.ppat.1002720","article-title":"Rates of viral evolution are linked to host geography in bat rabies","volume":"8","author":"DG Streicker","year":"2012","journal-title":"PLoS pathogens"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1186\/s12862-015-0410-5","article-title":"Avian influenza virus exhibits distinct evolutionary dynamics in wild birds and poultry","volume":"15","author":"M Fourment","year":"2015","journal-title":"BMC evolutionary biology"},{"issue":"9951","key":"ref38","doi-asserted-by":"crossref","first-page":"1389","DOI":"10.1016\/S0140-6736(13)62707-5","article-title":"Current status of rabies and prospects for elimination","volume":"384","author":"AR Fooks","year":"2014","journal-title":"Lancet"},{"issue":"1","key":"ref39","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.virusres.2005.03.007","article-title":"Molecular epizootiology of rabies associated with terrestrial carnivores in Mexico","volume":"111","author":"A Velasco-Villa","year":"2005","journal-title":"Virus research"},{"issue":"4","key":"ref40","doi-asserted-by":"crossref","first-page":"923","DOI":"10.7589\/2015-04-090","article-title":"Rabies Virus Infection in Ferret Badgers (Melogale moschata subaurantiaca) in Taiwan: A Retrospective Study","volume":"51","author":"JC Chang","year":"2015","journal-title":"Journal of wildlife diseases"},{"issue":"5","key":"ref41","doi-asserted-by":"crossref","first-page":"790","DOI":"10.3201\/eid2005.131389","article-title":"Molecular characterization of cryptically circulating rabies virus from ferret badgers, Taiwan","volume":"20","author":"HY Chiou","year":"2014","journal-title":"Emerging infectious diseases"},{"issue":"7","key":"ref42","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1007\/s00705-007-0962-9","article-title":"The evolutionary dynamics of canid and mongoose rabies virus in Southern Africa","volume":"152","author":"PL Davis","year":"2007","journal-title":"Archives of virology"},{"issue":"1\u20132","key":"ref43","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.virusres.2010.02.018","article-title":"Evolutionary history of African mongoose rabies","volume":"150","author":"N Van Zyl","year":"2010","journal-title":"Virus research"},{"issue":"1\u20132","key":"ref44","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/j.virusres.2010.02.019","article-title":"Temporal and spatial dynamics of rabies viruses in China and Southeast Asia","volume":"150","author":"W Gong","year":"2010","journal-title":"Virus research"},{"issue":"1","key":"ref45","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1093\/molbev\/msj021","article-title":"Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences","volume":"23","author":"B Shapiro","year":"2006","journal-title":"Molecular biology and evolution"},{"issue":"5","key":"ref46","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1080\/10635150390238879","article-title":"Hierarchical phylogenetic models for analyzing multipartite sequence data","volume":"52","author":"MA Suchard","year":"2003","journal-title":"Systematic biology"},{"issue":"5","key":"ref47","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1093\/molbev\/msi105","article-title":"Not so different after all: a comparison of methods for detecting amino acid sites under selection","volume":"22","author":"SL Kosakovsky Pond","year":"2005","journal-title":"Molecular biology and evolution"},{"issue":"5","key":"ref48","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1093\/molbev\/mst030","article-title":"FUBAR: a fast, unconstrained bayesian approximation for inferring selection","volume":"30","author":"B Murrell","year":"2013","journal-title":"Molecular biology and evolution"},{"issue":"7","key":"ref49","doi-asserted-by":"crossref","first-page":"e1002764","DOI":"10.1371\/journal.pgen.1002764","article-title":"Detecting individual sites subject to episodic diversifying selection","volume":"8","author":"B Murrell","year":"2012","journal-title":"PLoS genetics"},{"issue":"1","key":"ref50","doi-asserted-by":"crossref","first-page":"e2039","DOI":"10.1371\/journal.pntd.0002039","article-title":"National borders effectively halt the spread of rabies: the current rabies epidemic in China is dislocated from cases in neighboring countries","volume":"7","author":"Z Guo","year":"2013","journal-title":"PLoS neglected tropical diseases"},{"issue":"2","key":"ref51","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/j.virol.2010.12.011","article-title":"Evolutionary dynamics of rabies viruses highlights the importance of China rabies transmission in Asia","volume":"410","author":"S Meng","year":"2011","journal-title":"Virology"},{"issue":"1","key":"ref52","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1016\/j.virusres.2009.02.014","article-title":"Molecular characterization of the complete genome of a street rabies virus isolated in China","volume":"143","author":"P Ming","year":"2009","journal-title":"Virus research"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/j.meegid.2013.02.009","article-title":"Genetic diversity and molecular evolution of the rabies virus matrix protein gene in China","volume":"16","author":"H Wu","year":"2013","journal-title":"Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases"},{"issue":"12","key":"ref54","doi-asserted-by":"crossref","first-page":"3355","DOI":"10.1093\/molbev\/msr170","article-title":"Purifying selection can obscure the ancient age of viral lineages","volume":"28","author":"JO Wertheim","year":"2011","journal-title":"Molecular biology and evolution"},{"issue":"2","key":"ref55","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1128\/JVI.01520-09","article-title":"Structure of the nucleoprotein binding domain of Mokola virus phosphoprotein","volume":"84","author":"R Assenberg","year":"2010","journal-title":"Journal of virology"},{"issue":"4","key":"ref56","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1016\/j.jmb.2004.08.071","article-title":"Structure and function of the C-terminal domain of the polymerase cofactor of rabies virus","volume":"343","author":"M Mavrakis","year":"2004","journal-title":"J Mol Biol"},{"key":"ref57","first-page":"1","article-title":"The Natural History of Rabies","volume":"2","author":"JH Steele","year":"1991"},{"key":"ref58","first-page":"289","article-title":"Histoire de la Rage","author":"J Theodorides","year":"1986"},{"key":"ref59","unstructured":"History APW. Key Concept 4.1 Globalizing Networks of Communication and Exchange. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/apworldipedia.com\/index.php?title=Key_Concept_4.1_Globalizing_Networks_of_Communication_and_Exchange\" xlink:type=\"simple\">http:\/\/apworldipedia.com\/index.php?title=Key_Concept_4.1_Globalizing_Networks_of_Communication_and_Exchange<\/ext-link>."},{"issue":"5992","key":"ref60","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1126\/science.1188836","article-title":"Host phylogeny constrains cross-species emergence and establishment of rabies virus in bats","volume":"329","author":"DG Streicker","year":"2010","journal-title":"Science"},{"issue":"1","key":"ref61","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1006\/viro.2000.0381","article-title":"Acute and persistent viral life strategies and their relationship to emerging diseases","volume":"272","author":"LP Villarreal","year":"2000","journal-title":"Virology"},{"issue":"3","key":"ref62","doi-asserted-by":"crossref","first-page":"746","DOI":"10.7589\/0090-3558-39.3.746","article-title":"Population monitoring in support of a rabies vaccination program for skunks in Arizona","volume":"39","author":"RM Engeman","year":"2003","journal-title":"Journal of wildlife diseases"},{"issue":"8","key":"ref63","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.3201\/eid1208.051526","article-title":"Bat-associated rabies virus in Skunks","volume":"12","author":"MJ Leslie","year":"2006","journal-title":"Emerging infectious diseases"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1016\/j.coviro.2014.07.004","article-title":"The role of viral evolution in rabies host shifts and emergence","volume":"8","author":"N Mollentze","year":"2014","journal-title":"Curr Opin Virol"},{"issue":"11","key":"ref65","doi-asserted-by":"crossref","first-page":"e2555","DOI":"10.1371\/journal.pntd.0002555","article-title":"Ultra-deep sequencing of intra-host rabies virus populations during cross-species transmission","volume":"7","author":"MK Borucki","year":"2013","journal-title":"PLoS neglected tropical diseases"},{"issue":"3","key":"ref66","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1128\/MMBR.00004-08","article-title":"Cross-species virus transmission and the emergence of new epidemic diseases","volume":"72","author":"CR Parrish","year":"2008","journal-title":"Microbiol Mol Biol Rev"},{"issue":"5","key":"ref67","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1016\/j.tree.2005.02.009","article-title":"Emerging pathogens: the epidemiology and evolution of species jumps","volume":"20","author":"ME Woolhouse","year":"2005","journal-title":"Trends Ecol Evol"},{"issue":"3","key":"ref68","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1534\/genetics.105.040741","article-title":"Epistasis and the adaptability of an RNA virus","volume":"170","author":"R Sanjuan","year":"2005","journal-title":"Genetics"},{"issue":"11","key":"ref69","doi-asserted-by":"crossref","first-page":"1744","DOI":"10.1093\/infdis\/jit829","article-title":"Interaction of rabies virus P-protein with STAT proteins is critical to lethal rabies disease","volume":"209","author":"L Wiltzer","year":"2014","journal-title":"J Infect Dis"},{"issue":"18","key":"ref70","doi-asserted-by":"crossref","first-page":"9557","DOI":"10.1128\/JVI.00771-10","article-title":"Application of broad-spectrum resequencing microarray for genotyping rhabdoviruses","volume":"84","author":"L Dacheux","year":"2010","journal-title":"Journal of virology"},{"issue":"5\u20136","key":"ref71","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1016\/j.ygeno.2013.07.011","article-title":"AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads","volume":"102","author":"A Criscuolo","year":"2013","journal-title":"Genomics"},{"issue":"8","key":"ref72","doi-asserted-by":"crossref","first-page":"R86","DOI":"10.1186\/gb-2010-11-8-r86","article-title":"Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences","volume":"11","author":"J Goecks","year":"2010","journal-title":"Genome biology"},{"key":"ref73","first-page":"19 0 1","article-title":"Galaxy: a web-based genome analysis tool for experimentalists","volume":"Chapter 19","author":"D Blankenberg","year":"2010","journal-title":"Current protocols in molecular biology"},{"issue":"10","key":"ref74","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1101\/gr.4086505","article-title":"Galaxy: a platform for interactive large-scale genome analysis","volume":"15","author":"B Giardine","year":"2005","journal-title":"Genome research"},{"issue":"21","key":"ref75","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","article-title":"Clustal W and Clustal X version 2.0","volume":"23","author":"MA Larkin","year":"2007","journal-title":"Bioinformatics"},{"issue":"8","key":"ref76","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1038\/nmeth.2109","article-title":"jModelTest 2: more models, new heuristics and parallel computing","volume":"9","author":"D Darriba","year":"2012","journal-title":"Nat Methods"},{"issue":"5","key":"ref77","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","article-title":"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood","volume":"52","author":"S Guindon","year":"2003","journal-title":"Systematic biology"},{"issue":"3","key":"ref78","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0","volume":"59","author":"S Guindon","year":"2010","journal-title":"Systematic biology"},{"issue":"4","key":"ref79","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1080\/10635150600755453","article-title":"Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative","volume":"55","author":"M Anisimova","year":"2006","journal-title":"Systematic biology"},{"key":"ref80","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"A Rambaut","year":"2016","journal-title":"Virus Evolution"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1186\/1471-2148-7-214","article-title":"BEAST: Bayesian evolutionary analysis by sampling trees","volume":"7","author":"AJ Drummond","year":"2007","journal-title":"BMC evolutionary biology"},{"issue":"7","key":"ref82","doi-asserted-by":"crossref","first-page":"1459","DOI":"10.1093\/molbev\/msn090","article-title":"Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics","volume":"25","author":"VN Minin","year":"2008","journal-title":"Molecular biology and evolution"},{"issue":"3","key":"ref83","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1093\/molbev\/mss265","article-title":"Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci","volume":"30","author":"MS Gill","year":"2013","journal-title":"Molecular biology and evolution"},{"issue":"19","key":"ref84","doi-asserted-by":"crossref","first-page":"2455","DOI":"10.1093\/bioinformatics\/btq429","article-title":"Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology","volume":"26","author":"W Delport","year":"2010","journal-title":"Bioinformatics"},{"issue":"10","key":"ref85","doi-asserted-by":"crossref","first-page":"2531","DOI":"10.1093\/bioinformatics\/bti320","article-title":"Datamonkey: rapid detection of selective pressure on individual sites of codon alignments","volume":"21","author":"SL Pond","year":"2005","journal-title":"Bioinformatics"}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.ppat.1006041","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,24]],"date-time":"2018-10-24T04:08:03Z","timestamp":1540354083000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1006041"}},"subtitle":[],"editor":[{"given":"Colin","family":"Parrish","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,12,15]]},"references-count":85,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2016,12,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1006041","relation":{},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,12,15]]}}}