A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and its Application to Influenza A Virus.

@article{citeulike:2854651, abstract = {We develop a model-based phylogenetic maximum likelihood test for evidence of preferential substitution towards a given residue at individual positions of a protein alignment - Directional Evolution of Protein Sequences (DEPS). DEPS can identify both the target residue and sites evolving towards it, help detect selective sweeps and frequency dependent selection - scenarios that confound most existing tests for selection, and achieves good power and accuracy on simulated data. We applied DEPS to alignments representing different genomic regions of Influenza A virus (IAV), sampled from avian hosts (H5N1 serotype) and human hosts (H3N2 serotype) and identified multiple directionally evolving sites in 5/8 genomic segments of H5N1 and H3N2 IAV. We propose a simple descriptive classification of directionally evolving sites into 5 groups based on the temporal distribution of residue frequencies, and document known functional correlates, such as immune escape or host adaptation.}, address = {Department of Pathology, University of California San Diego, La Jolla, California, 92093.}, author = {Kosakovsky Pond, Sergei L L. and Poon, Art F Y F. and Leigh Brown, Andrew J J. and Frost, Simon D W D. }, citeulike-article-id = {2854651}, doi = {10.1093/molbev/msn123}, issn = {1537-1719}, journal = {Molecular biology and evolution}, keywords = {evolution, protein, sequence}, month = {May}, posted-at = {2008-06-27 03:55:48}, priority = {2}, title = {A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and its Application to Influenza A Virus.}, url = {http://dx.doi.org/10.1093/molbev/msn123}, year = {2008} }

TY - JOUR ID - citeulike:2854651 L3 - citeulike-article-id:2854651 TI - A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and its Application to Influenza A Virus. JF - Molecular biology and evolution AD - Department of Pathology, University of California San Diego, La Jolla, California, 92093. SN - 1537-1719 N2 - We develop a model-based phylogenetic maximum likelihood test for evidence of preferential substitution towards a given residue at individual positions of a protein alignment - Directional Evolution of Protein Sequences (DEPS). DEPS can identify both the target residue and sites evolving towards it, help detect selective sweeps and frequency dependent selection - scenarios that confound most existing tests for selection, and achieves good power and accuracy on simulated data. We applied DEPS to alignments representing different genomic regions of Influenza A virus (IAV), sampled from avian hosts (H5N1 serotype) and human hosts (H3N2 serotype) and identified multiple directionally evolving sites in 5/8 genomic segments of H5N1 and H3N2 IAV. We propose a simple descriptive classification of directionally evolving sites into 5 groups based on the temporal distribution of residue frequencies, and document known functional correlates, such as immune escape or host adaptation. KW - evolution KW - protein KW - sequence AU - Kosakovsky Pond, Sergei L AU - Poon, Art F Y AU - Leigh Brown, Andrew J AU - Frost, Simon D W PY - 2008/05/29/ UR - http://dx.doi.org/10.1093/molbev/msn123 ER -