title: Detecting recombination in TT virus: a phylogenetic approach.
abstract: TT virus (TTV) has a remarkable genetic heterogeneity. To study TTV evolution, phylogenetic analyses were performed on 739 DNA sequences mapping in the N22 region of ORF1. Analysis of neighbor-joining consensus trees shows significant differences between DNA and protein phylogeny. Median joining networks phylogenetic clustering indicates that DNA sequence analysis is biased by homoplasy (i.e., genetic variability not originated by descent), indicative of either hypermutation or recombination. Statistical analysis shows that the significant excess of homoplasy is due to frequent recombination among closely related strains. Recombination events imply that the transmission of TTV is not clonal and provide the necessary basis to explain (i) the high degree of genetic divergence between TTV isolates, (ii) the lack of population structure on a world scale, and (iii) the number of highly divergent strains that seems typical of this virus. We show that recombination phenomena can be detected by phylogenetic analyses in very short sequences when a sufficiently large data set is available.
authors.affiliation: Laboratoire d'Anthropologie Biologique (CNRS FRE 2292), Musée de I'Homme MNHN, 17 Place du Trocadéro, 75016 Paris, France. manni@mnhn.fr
authors.forename: Franz
authors.initials: F
authors.lastname: Manni
authors.forename: Antonella
authors.initials: A
authors.lastname: Rotola
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Caselli
authors.forename: Giorgio
authors.initials: G
authors.lastname: Bertorelle
authors.forename: Dario
authors.initials: D
authors.lastname: Di Luca
mesh_terms: D004279:DNA, Viral / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation; D010802:Phylogeny; D011995:Recombination, Genetic; D022783:Torque teno virus / Q000235:genetics*; D014764:Viral Proteins / Q000235:genetics
chemical_list: D004279:DNA, Viral; C446939:ORF1 protein, TT virus; D014764:Viral Proteins