title: Applying phylogenetic analysis to viral livestock diseases: moving beyond molecular typing.
abstract: Changes in livestock production systems in recent years have altered the presentation of many diseases resulting in the need for more sophisticated control measures. At the same time, new molecular assays have been developed to support the diagnosis of animal viral disease. Nucleotide sequences generated by these diagnostic techniques can be used in phylogenetic analysis to infer phenotypes by sequence homology and to perform molecular epidemiology studies. In this review, some key elements of phylogenetic analysis are highlighted, such as the selection of the appropriate neutral phylogenetic marker, the proper phylogenetic method and different techniques to test the reliability of the resulting tree. Examples are given of current and future applications of phylogenetic reconstructions in viral livestock diseases.
authors.affiliation: Centre de Recerca en Sanitat Animal, UAB-IRTA, Campus de Bellaterra-Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain. Alex.Olvera@cresa.uab.cat
authors.forename: Alex
authors.initials: A
authors.lastname: Olvera
authors.forename: Núria
authors.initials: N
authors.lastname: Busquets
authors.forename: Marti
authors.initials: M
authors.lastname: Cortey
authors.forename: Nilsa
authors.initials: N
authors.lastname: de Deus
authors.forename: Llilianne
authors.initials: L
authors.lastname: Ganges
authors.forename: José Ignacio
authors.initials: JI
authors.lastname: Núñez
authors.forename: Bibiana
authors.initials: B
authors.lastname: Peralta
authors.forename: Jennifer
authors.initials: J
authors.lastname: Toskano
authors.forename: Roser
authors.initials: R
authors.lastname: Dolz