The foot-and-mouth disease RNA virus as a model in experimental phylogenetics Authors Mario A. Fares Department of Genetics, and Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Spain Eladio Barrio Department of Genetics, and Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Spain Nelsson Becerra Department of Ecology and Evolutionary Biology, University of California, Irvine, USA Cristina Escarmís Center of Molecular Biology Severo Ochoa, CSIC, Autonomous University of Madrid, Spain Esteban Domingo Center of Molecular Biology Severo Ochoa, CSIC, Autonomous University of Madrid, Spain Andrés Moya Department of Genetics, and Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Spain Keywords: foot-and-mouth disease virus (FMDV), RNA virus evolution, distancebased methods, molecular phylogenies, convergent evolution Abstract Phylogenetic reconstruction methods are subject to two types of limitations: our knowledge about the true history of organisms and the gross simplification implied in the numerical simulation models of the relationships between them. In such a situation, experimental phylogenetics provides a way to assess the accuracy of the phylogenetic reconstruction methods. Nonetheless, this capacity is only feasible for organisms in which replication and mutation rates are high enough to provide valuable data. On the other hand, experimental phylogenetics also provides insights on the main evolutionary processes acting on viral variability under different population dynamics. Our study with the foot-and-mouth disease virus (FMDV) strongly suggests that the phylogenetic reconstruction methods can infer erroneous phylogenies due to nucleotide convergences between isolates belonging to different experimental lineages. We also point out that the diverse evolutionary mechanisms acting in different experimental dynamics generate alterations and change the frequencies of genetic variants, which can lead to the misinterpretation of the real evolutionary history. Downloads PDF Published 2010-03-17 Issue Vol. 1 No. 4 (1998) Section Review Articles License Submission of a manuscript to International Microbiology implies: that the work described has not been published before, including publication in the World Wide Web (except in the form of an Abstract or as part of a published lecture, review, or thesis); that it is not under consideration for publication elsewhere; that all the coauthors have agreed to its publication. The corresponding author signs for and accepts responsability for releasing this material and will act on behalf of any and all coauthors regarding the editorial review and publication process.If an article is accepted for publication in International Microbiology, the authors (or other copyright holder) must transfer to the journal the right–not exclusive–to reproduce and distribute the article including reprints, translations, photographic reproductions, microform, electronic form (offline, online) or any other reproductions of similar nature. Nevertheless, all article in International Microbiology will be available on the Internet to any reader at no cost. The journal allows users to freely download, copy, print, distribute, search, and link to the full text of any article, provided the authorship and source of the published article is cited. The copyright owner's consent does not include copying for new works, or resale. In these cases, the specific written permission of International Microbiology must first be obtained.Authors are requested to create a link to the published article on the journal's website. The link must be accompanied by the following text: "The original publication is available on LINK at <http://www.im.microbios.org>. Please use the appropiate URL for the article in LINK. Articles disseminated via LINK are indexed, abstracted, and referenced by many abstracting and information services, bibliographic networks, subscription agencies, library networks, and consortia.
