Maximum Likelihood Estimation on Large Phylogenies and Analysis of Adaptive Evolution in Human Influenza Virus A |
| |
Authors: | Ziheng Yang |
| |
Institution: | (1) Galton Laboratory, Department of Biology, University College London, 4 Stephenson Way, London NW1 2HE, UK, GB |
| |
Abstract: | Algorithmic details to obtain maximum likelihood estimates of parameters on a large phylogeny are discussed. On a large tree,
an efficient approach is to optimize branch lengths one at a time while updating parameters in the substitution model simultaneously.
Codon substitution models that allow for variable nonsynonymous/synonymous rate ratios (ω=d
N/d
S) among sites are used to analyze a data set of human influenza virus type A hemagglutinin (HA) genes. The data set has 349
sequences. Methods for obtaining approximate estimates of branch lengths for codon models are explored, and the estimates
are used to test for positive selection and to identify sites under selection. Compared with results obtained from the exact
method estimating all parameters by maximum likelihood, the approximate methods produced reliable results. The analysis identified
a number of sites in the viral gene under diversifying Darwinian selection and demonstrated the importance of including many
sequences in the data in detecting positive selection at individual sites.
Received: 25 April 2000 / Accepted: 24 July 2000 |
| |
Keywords: | : Large phylogenies — Maximum likelihood — Molecular adaptation — Nonsynonymous substitution — Phylogenetics — Positive selection — Synonymous substitution |
本文献已被 PubMed SpringerLink 等数据库收录! |
|