A Phylogenetic Method for Detecting Positive Epistasis in Gene Sequences and Its Application to RNA Virus Evolution

@article{citeulike:783261, abstract = {RNA virus genomes are compact, often containing multiple overlapping reading frames and functional secondary structure. Consequently, it is thought that evolutionary interactions between nucleotide sites are commonplace in the genomes of these infectious agents. However, the role of epistasis in natural populations of RNA viruses remains unclear. To investigate the pervasiveness of epistasis in RNA viruses, we used a parsimony-based computational method to identify pairs of co-occurring mutations along phylogenies of 177 RNA virus genes. This analysis revealed widespread evidence for positive epistatic interactions at both synonymous and nonsynonymous nucleotide sites and in both clonal and recombining viruses, with the majority of these interactions spanning very short sequence regions. These findings have important implications for understanding the key aspects of RNA virus evolution, including the dynamics of adaptation. Additionally, many comparative analyses that utilize the phylogenetic relationships among gene sequences assume that mutations represent independent, uncorrelated events. Our results show that this assumption may often be invalid. 10.1093/molbev/msl037}, author = {Shapiro, Beth and Rambaut, Andrew and Pybus, Oliver G. and Holmes, Edward C. }, citeulike-article-id = {783261}, doi = {http://dx.doi.org/10.1093/molbev/msl037}, journal = {Mol Biol Evol}, keywords = {evolution, phylogeny, positiveepistasis}, month = {September}, number = {9}, pages = {1724--1730}, posted-at = {2007-04-16 14:16:08}, priority = {1}, title = {A Phylogenetic Method for Detecting Positive Epistasis in Gene Sequences and Its Application to RNA Virus Evolution}, url = {http://dx.doi.org/10.1093/molbev/msl037}, volume = {23}, year = {2006} }

TY - JOUR ID - citeulike:783261 L3 - citeulike-article-id:783261 TI - A Phylogenetic Method for Detecting Positive Epistasis in Gene Sequences and Its Application to RNA Virus Evolution JF - Mol Biol Evol VL - 23 IS - 9 SP - 1724 EP - 1730 N2 - RNA virus genomes are compact, often containing multiple overlapping reading frames and functional secondary structure. Consequently, it is thought that evolutionary interactions between nucleotide sites are commonplace in the genomes of these infectious agents. However, the role of epistasis in natural populations of RNA viruses remains unclear. To investigate the pervasiveness of epistasis in RNA viruses, we used a parsimony-based computational method to identify pairs of co-occurring mutations along phylogenies of 177 RNA virus genes. This analysis revealed widespread evidence for positive epistatic interactions at both synonymous and nonsynonymous nucleotide sites and in both clonal and recombining viruses, with the majority of these interactions spanning very short sequence regions. These findings have important implications for understanding the key aspects of RNA virus evolution, including the dynamics of adaptation. Additionally, many comparative analyses that utilize the phylogenetic relationships among gene sequences assume that mutations represent independent, uncorrelated events. Our results show that this assumption may often be invalid. 10.1093/molbev/msl037 KW - evolution KW - phylogeny KW - positiveepistasis AU - Shapiro, Beth AU - Rambaut, Andrew AU - Pybus, Oliver AU - Holmes, Edward PY - 2006/09/01/ UR - http://dx.doi.org/10.1093/molbev/msl037 ER -