Abstract
Among the major goals of research in evolutionary biology are the identification of genes targeted by natural selection and understanding how various regimes of evolution affect the fitness of an organism. In particular, adaptive evolution enables organisms to adapt to changing ecological factors such as diet, temperature, habitat, predatory pressures and prey abundance. An integrative approach is crucial for the identification of non-synonymous mutations that introduce radical changes in protein biochemistry and thus in turn influence the structure and function of proteins. Performing such analyses manually is often a time-consuming process, due to the large number of statistical files generated from multiple approaches, especially when assessing numerous taxa and/or large datasets. We present IMPACT_S, an easy-to-use Graphical User Interface (GUI) software, which rapidly and effectively integrates, filters and combines results from three widely used programs for assessing the influence of selection: Codeml (PAML package), Datamonkey and TreeSAAP. It enables the identification and tabulation of sites detected by these programs as evolving under the influence of positive, neutral and/or negative selection in protein-coding genes. IMPACT_S further facilitates the automatic mapping of these sites onto the three-dimensional structures of proteins. Other useful tools incorporated in IMPACT_S include Jmol, Archaeopteryx, Gnuplot, PhyML, a built-in Swiss-Model interface and a PDB downloader. The relevance and functionality of IMPACT_S is shown through a case study on the toxicoferan-reptilian Cysteine-rich Secretory Proteins (CRiSPs). IMPACT_S is a platform-independent software released under GPLv3 license, freely available online from http://impact-s.sourceforge.net.
Highlights
The nature and strength of evolutionary selection pressures can be estimated at the molecular level, as a non-synonymous to synonymous substitution rate ratio omega (v = dN/dS), where v greater than, equal to and less than 1 is indicative of positive, neutral and negative selection, respectively [1]
The manual integration of results from various approaches is time-consuming. To address these shortcomings and to facilitate the integration of results from various selection assessments, we propose IMPACT_S, a free platform-independent user-friendly Graphical User Interface (GUI) software that integrates results of nucleotide and amino acid-level assessments by employing three widely used softwares: Codeml from Phylogenetic Analysis by Maximum Likelihood (PAML) package [17], Datamonkey, a web-server of the HyPhy [20] package - www.datamonkey.org [18,19], and Selection on Amino Acid Properties using phylogenetic trees (TreeSAAP) [15]
Site-specific models, which are the current focus of this work, comprise the alternative models – model 2a (M2a) and model 8 (M8) and the null models – model 1a (M1a) and model 7 (M7)
Summary
The nature and strength of evolutionary selection pressures can be estimated at the molecular level, as a non-synonymous to synonymous substitution rate ratio omega (v = dN/dS), where v greater than, equal to and less than 1 is indicative of positive, neutral and negative selection, respectively [1] This approach often fails to detect subtle adaptations that only affect certain regions of the protein and/or take place over a very short period of evolutionary time [2]. Non-synonymous substitutions introduce variations in coding regions, a novel amino acid could have identical or similar biochemical and/or structural properties to that of the ancestral residue Such substitutions are unlikely to influence the structure or the function of the protein and are least likely to affect the fitness of an organism. The manual integration of results from various approaches is time-consuming
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