We are analyzing https://link.springer.com/article/10.1007/s00239-004-2597-8.

Title:
A Maximum Likelihood Method for Detecting Functional Divergence at Individual Codon Sites, with Application to Gene Family Evolution | Journal of Molecular Evolution
Description:
The tailoring of existing genetic systems to new uses is called genetic co-option. Mechanisms of genetic co-option have been difficult to study because of difficulties in identifying functionally important changes. One way to study genetic co-option in protein-coding genes is to identify those amino acid sites that have experienced changes in selective pressure following a genetic co-option event. In this paper we present a maximum likelihood method useful for measuring divergent selective pressures and identifying the amino acid sites affected by divergent selection. The method is based on a codon model of evolution and uses the nonsynonymous-to-synonymous rate ratio (ω) as a measure of selection on the protein, with ω = 1, <1, and >1 indicating neutral evolution, purifying selection, and positive selection, respectively. The model allows variation in ω among sites, with a fraction of sites evolving under divergent selective pressures. Divergent selection is indicated by different ω’s between clades, such as between paralogous clades of a gene family. We applied the codon model to duplication followed by functional divergence of (i) the ε and γ globin genes and (ii) the eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN) genes. In both cases likelihood ratio tests suggested the presence of sites evolving under divergent selective pressures. Results of the ε and γ globin analysis suggested that divergent selective pressures might be a consequence of a weakened relationship between fetal hemoglobin and 2,3-diphosphoglycerate. We suggest that empirical Bayesian identification of sites evolving under divergent selective pressures, combined with structural and functional information, can provide a valuable framework for identifying and studying mechanisms of genetic co-option. Limitations of the new method are discussed.
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Keywords {🔍}

google, scholar, cas, pubmed, article, gene, evolution, mol, evol, yang, genes, biol, likelihood, sites, selection, duplication, molecular, functional, bielawski, sci, goodman, detecting, divergent, proc, usa, maximum, divergence, genetic, genetics, natl, acad, codon, cooption, selective, model, evolutionary, science, schneider, privacy, cookies, journal, research, method, family, amino, acid, pressures, ratio, globin, evidence,

Topics {✒️}

month download article/chapter zhang hf rosenberg neiswanger dl gumucio czelusniak sl page gamma-globin gene sequences gamma-globin gene mediated redundant gamma-globin gene shh-bmp2 signalling module fetal globin expression goodman ca porter full article pdf goldman a-mk pedersen evolutionary rate shifts human eosinophil-derived neurotoxin sieu jl slightom detecting molecular adaptation detecting functional divergence hemoglobin beta-chain genes gene duplication proc detecting positive selection intronless coding sequences detecting adaptive evolution privacy choices/manage cookies predicting functional divergence long ch langley γ globin genes likelihood ratio tests knudsen mm miyamoto molecular evolution aims article bielawski host-specific selection amino acid sites protein-coding genes maximum-likelihood approach article journal positive darwinian selection maximum likelihood method genome coding regions eosinophil cationic protein synonymous rate ratio likelihood ratio test maximum likelihood methods gene family evolution eosinophil-derived neurotoxin anisimova jp bielawski article log heterogeneous selection pressure codon-based model codon based model dna evidence complemented

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