The phylogenetic information profile of HIV-1 and the degradation effect of recombination.
HIV-1, while known to recombine frequently and evolve rapidly, is one of the most sequenced organisms. The availability of many and long sequences (almost full-length) renders HIV-1 as a good model for studying theoretical predictions linked to evolution and phylogenetic inferences. Here we study the effects of rapid and through-recombination evolution on phylogenetic information in order to confirm theoretical predictions of the characteristics of phylogenetic information on a real dataset. Firstly we study the fluctuation of the phylogenetic information along the HIV-1 genome showing that genomic regions such as the first part and the last part of the pol gene contain less phylogenetic information, while the vpr, vpu and the first exon of the tat gene contain more phylogenetic information compared to the rest of the genome. Moreover, we provide evidence that phylogenetic information is correlated to the sequence similarity of the dataset used and is degraded by the effect of recombination.
Magiorkinis
G
G
Medical School, National and Kapodistrian University of Athens, Greece. gmagi@med.uoa.gr
Paraskevis
D
D
Schmidt
H A
HA
Hatzakis
A
A
D000163:Acquired Immunodeficiency Syndrome / Q000453:epidemiology / Q000821:virology; D014644:Genetic Variation; D005843:Geography; D015497:HIV-1 / Q000235:genetics*; D006801:Humans; D015233:Models, Statistical; D010802:Phylogeny; D011995:Recombination, Genetic; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid