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Recently, the first evidence of phylogenetic incongruence between interspecific members of the MBFV was reported in ZIKV and its close relative, Spondweni virus. Uniquely, these hybrid proteomes were derived from four incongruent trees involving an Aedes-associated DENV node (1 tree) and three different Culex-associated flavivirus nodes (3 trees). This analysis has now been extended across a wider spectrum of viruses within the MBFV lineage targeting the breakpoints between phylogenetic incongruent loci originally identified in ZIKV. Interspecies phylogenetic incongruence at these breakpoints was identified in 10 of 50 viruses within the MBFV lineage, representing emergent Aedes and Culex-associated viruses including JEV, West Nile virus, yellow fever virus, and insect-specific viruses. Thus, interspecies phylogenetic incongruence is widespread amongst the flaviviruses and is robustly associated with the specific breakpoints that coincide with the interspecific phylogenetic incongruence previously identified, inferring they are \u2018hotspots\u2019. The incongruence amongst the emergent MBFV group was restricted to viruses within their respective associated epidemiological boundaries. This MBFV group was RY-coded at the third codon position (\u2018wobble codon\u2019) to remove transition saturation. The resulting \u2018wobble codon\u2019 trees presented a single topology for the entire genome that lacked any robust evidence of phylogenetic incongruence between loci. Phylogenetic interspecific incongruence was therefore observed for exactly the same loci between amino acid and the RY-coded \u2018wobble codon\u2019 alignments and this incongruence represented either a major part, or the entire genomes. Maximum likelihood codon analysis revealed positive selection for the incongruent lineages. Positive selection could result in the same locus producing two opposing trees. These analyses for the clinically important MBFV suggest that robust interspecific phylogenetic incongruence resulted from amino acid selection. Convergent or parallel evolutions are evolutionary processes that would explain the observation, whilst interspecific recombination is unlikely.<\/jats:p>","DOI":"10.1093\/ve\/veac027","type":"journal-article","created":{"date-parts":[[2022,4,17]],"date-time":"2022-04-17T19:06:31Z","timestamp":1650222391000},"source":"Crossref","is-referenced-by-count":3,"title":["Widespread interspecific phylogenetic tree incongruence between mosquito-borne and insect-specific flaviviruses at hotspots originally identified in Zika virus"],"prefix":"10.1093","volume":"8","author":[{"given":"Michael W","family":"Gaunt","sequence":"first","affiliation":[{"name":"Department of Infection Biology London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John H-O","family":"Pettersson","sequence":"additional","affiliation":[{"name":"Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, 751 23 Uppsala, Sweden"},{"name":"Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Goro","family":"Kuno","sequence":"additional","affiliation":[{"name":"1648 Collindale Dr., Fort Collins, CO 80525, USA Formerly, Centers for Disease Control, Fort Collins, CO 80521, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bill","family":"Gaunt","sequence":"additional","affiliation":[{"name":"Aeon-Sys, MBCS 29 Kensington Road, Barnsley S75 2TU, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7895-2720","authenticated-orcid":false,"given":"Xavier","family":"de Lamballerie","sequence":"additional","affiliation":[{"name":"UMR \u201cUnit\u00e9 des Virus Emergents\u201d, Aix-Marseille Universit\u00e9-IRD 190-Inserm 1207-IHU M\u00e9diterran\u00e9e Infection, Marseille, France"},{"name":"APHM Public Hospitals of Marseille, Institut Hospitalo-Universitaire M\u00e9diterran\u00e9e Infection, 13005 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ernest A","family":"Gould","sequence":"additional","affiliation":[{"name":"UMR \u201cUnit\u00e9 des Virus Emergents\u201d, Aix-Marseille Universit\u00e9-IRD 190-Inserm 1207-IHU M\u00e9diterran\u00e9e Infection, Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,4,18]]},"reference":[{"key":"2022051715165534800_R1","doi-asserted-by":"crossref","first-page":"3334","DOI":"10.1099\/vir.0.83122-0","article-title":"Multiple Recombinant Dengue Type 1 Viruses in an Isolate from a Dengue Patient","volume":"88","author":"Aaskov","year":"2007","journal-title":"Journal of General Virology"},{"key":"2022051715165534800_R2","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1093\/molbev\/msg028","article-title":"Bayes or Bootstrap? 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