Research article
Topology of evolving, mutagenized viral populations: quasispecies expansion, compression, and operation of negative selection
-
* Corresponding author: Esteban Domingo edomingo@cbm.uam.es
1 Centro de Biología Molecular "Severo Ochoa", UAM-CSIC. Campus de Cantoblanco, 28049, Madrid, Spain
2 Laboratorio de Evolución Molecular, Centro de Astrobiología (CSIC/INTA), Instituto Nacional de Técnica Aeroespacial, Ctra de Torrejón a Ajalvir, km 4, 28850 Torrejón de Ardoz, Madrid, Spain
3 Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Spain
4 Institute of Virology, University of Cologne, Fuerst-Pueckler Str. 56, D-50935 Cologne, Germany
5 MRC Laboratory for Molecular Cell Biology & Cell Biology Unit, University College London, Gower Street, London, WC1E 6BT, UK
6 Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
BMC Evolutionary Biology 2008, 8:207 doi:10.1186/1471-2148-8-207
Published: 17 July 2008Additional files
Additional file 1:
Neighbour-joining, maximum likelihood and maximum parsimony analysis of populations RAp35 and RA0p35. Strains in the tree are shown by name. Consensus sequence of each population is indicated with an asterisk. Bar at the bottom of the trees denote distance A) and D) Neighbour joining trees with Kimura 2-parameter. Bootstrap resampling values (1000 replicas) higher than 50 are shown in red in the tree. B) and E) Maximum likelihood trees constructed with the Tamura-Nei substitution model and the Gamma distributed rates with eight parameters (TN-8Γ) as heterogeneity model. C) and F) Maximum parsimony trees, confidence values higher than 50 are shown in red in the tree.
Format: TIFF Size: 18.2MB Download file
Additional file 2:
Maximum likelihood phylogenetic analysis of mutagenized populations of FMDV. Strains in the tree are shown by name. Bar at the bottom of the trees denote distance. Consensus sequence indicated by *. The model used was GTR [61]. As a measure of the robustness of each node an approximate Likelihood Ratio Test was used.
Format: TIFF Size: 10.3MB Download file
Additional file 3:
Standard errors. Average Hamming distance of the components of each population (with respect to the central sequence selected by PAQ). Standard errors are plotted with boxes around the mean, as depicted in the legend.
Format: TIFF Size: 9.6MB Download file