scholarly journals Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection

2005 ◽  
Vol 22 (4) ◽  
pp. 1107-1118 ◽  
Author(s):  
Z. Yang
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Empirical Bayes ◽  
Acid Sites ◽  
Bayes Inference

scholarly journals A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection

2012 ◽  
Vol 28 (24) ◽  
pp. 3248-3256 ◽  
Author(s):  
Philippe Lemey ◽  
Vladimir N. Minin ◽  
Filip Bielejec ◽  
Sergei L. Kosakovsky Pond ◽  
Marc A. Suchard
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Empirical Bayes ◽  
Acid Sites ◽  
Stochastic Mapping

scholarly journals Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites

Genetics ◽  
2000 ◽  
Vol 155 (1) ◽  
pp. 431-449 ◽  
Author(s):  
Ziheng Yang ◽  
Rasmus Nielsen ◽  
Nick Goldman ◽  
Anne-Mette Krabbe Pedersen
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Selective Pressure ◽  
Acid Sites ◽  
Data Sets ◽  
Protein Coding ◽  
Important Indicator ◽  
Diversifying Selection ◽  
Codon Substitution ◽  
Neutral Mutations

AbstractComparison of relative fixation rates of synonymous (silent) and nonsynonymous (amino acid-altering) mutations provides a means for understanding the mechanisms of molecular sequence evolution. The nonsynonymous/synonymous rate ratio (ω = dN/dS) is an important indicator of selective pressure at the protein level, with ω = 1 meaning neutral mutations, ω < 1 purifying selection, and ω > 1 diversifying positive selection. Amino acid sites in a protein are expected to be under different selective pressures and have different underlying ω ratios. We develop models that account for heterogeneous ω ratios among amino acid sites and apply them to phylogenetic analyses of protein-coding DNA sequences. These models are useful for testing for adaptive molecular evolution and identifying amino acid sites under diversifying selection. Ten data sets of genes from nuclear, mitochondrial, and viral genomes are analyzed to estimate the distributions of ω among sites. In all data sets analyzed, the selective pressure indicated by the ω ratio is found to be highly heterogeneous among sites. Previously unsuspected Darwinian selection is detected in several genes in which the average ω ratio across sites is <1, but in which some sites are clearly under diversifying selection with ω > 1. Genes undergoing positive selection include the β-globin gene from vertebrates, mitochondrial protein-coding genes from hominoids, the hemagglutinin (HA) gene from human influenza virus A, and HIV-1 env, vif, and pol genes. Tests for the presence of positively selected sites and their subsequent identification appear quite robust to the specific distributional form assumed for ω and can be achieved using any of several models we implement. However, we encountered difficulties in estimating the precise distribution of ω among sites from real data sets.

scholarly journals Anopheles Immune Genes and Amino Acid Sites Evolving Under the Effect of Positive Selection

PLoS ONE ◽  
2010 ◽  
Vol 5 (1) ◽  
pp. e8885 ◽  
Author(s):  
Aristeidis Parmakelis ◽  
Marina Moustaka ◽  
Nikolaos Poulakakis ◽  
Christos Louis ◽  
Michel A. Slotman ◽  
...  
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Acid Sites ◽  
Immune Genes

Accuracy and Power of Bayes Prediction of Amino Acid Sites Under Positive Selection

2002 ◽  
Vol 19 (6) ◽  
pp. 950-958 ◽  
Author(s):  
Maria Anisimova ◽  
Joseph P. Bielawski ◽  
Ziheng Yang
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Acid Sites ◽  
Bayes Prediction

scholarly journals Introduction of Viral Hemorrhagic Septicemia Virus into Freshwater Cultured Rainbow Trout Is Followed by Bursts of Adaptive Evolution

2018 ◽  
Vol 92 (12) ◽  
Author(s):  
Anna A. Schönherz ◽  
Roald Forsberg ◽  
Bernt Guldbrandtsen ◽  
Albert J. Buitenhuis ◽  
Katja Einer-Jensen
Keyword(s):  
Rainbow Trout ◽  
Amino Acid ◽  
Positive Selection ◽  
Marine Species ◽  
Acid Sites ◽  
Viral Hemorrhagic Septicemia Virus ◽  
Neutralizing Epitope ◽  
Phylogenetic Groups ◽  
Viral Hemorrhagic Septicemia ◽  
Viral Emergence

ABSTRACTViral hemorrhagic septicemia virus(VHSV), a rhabdovirus infecting teleost fish, has repeatedly crossed the boundary from marine fish species to freshwater cultured rainbow trout. These naturally replicated cross-species transmission events permit the study of general and repeatable evolutionary events occurring in connection with viral emergence in a novel host species. The purpose of the present study was to investigate the adaptive molecular evolution of the VHSV glycoprotein, one of the key virus proteins involved in viral emergence, following emergence from marine species into freshwater cultured rainbow trout. A comprehensive phylogenetic reconstruction of the complete coding region of the VHSV glycoprotein was conducted, and adaptive molecular evolution was investigated using a maximum likelihood approach to compare different codon substitution models allowing for heterogeneous substitution rate ratios among amino acid sites. Evidence of positive selection was detected at six amino acid sites of the VHSV glycoprotein, within the signal peptide, the confirmation-dependent major neutralizing epitope, and the intracellular tail. Evidence of positive selection was found exclusively in rainbow trout-adapted virus isolates, and amino acid combinations found at the six sites under positive selection pressure differentiated rainbow trout- from non-rainbow trout-adapted isolates. Furthermore, four adaptive sites revealed signs of recurring identical changes across phylogenetic groups of rainbow trout-adapted isolates, suggesting that repeated VHSV emergence in freshwater cultured rainbow trout was established through convergent routes of evolution that are associated with immune escape.IMPORTANCEThis study is the first to demonstrate that VHSV emergence from marine species into freshwater cultured rainbow trout has been accompanied by bursts of adaptive evolution in the VHSV glycoprotein. Furthermore, repeated detection of the same adaptive amino acid sites across phylogenetic groups of rainbow trout-adapted isolates indicates that adaptation to rainbow trout was established through parallel evolution. In addition, signals of convergent evolution toward the maintenance of genetic variation were detected in the conformation-dependent neutralizing epitope or in close proximity to disulfide bonds involved in the structural conformation of the neutralizing epitope, indicating adaptation to immune response-related genetic variation across freshwater cultured rainbow trout.

scholarly journals Evidence for Heterogeneous Selective Pressures in the Evolution of the env Gene in Different Human Immunodeficiency Virus Type 1 Subtypes

2005 ◽  
Vol 79 (3) ◽  
pp. 1836-1841 ◽  
Author(s):  
Simon A. A. Travers ◽  
Mary J. O'Connell ◽  
Grace P. McCormack ◽  
James O. McInerney
Keyword(s):  
Human Immunodeficiency Virus ◽  
Amino Acid ◽  
Positive Selection ◽  
Human Immunodeficiency Virus Type ◽  
Purifying Selection ◽  
Acid Sites ◽  
Selective Pressures ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACT Recent studies have demonstrated the emergence of human immunodeficiency virus type 1 (HIV-1) subtypes with various levels of fitness. Using heterogeneous maximum-likelihood models of adaptive evolution implemented in the PAML software package, with env sequences representing each HIV-1 group M subtype, we examined the various intersubtype selective pressures operating across the env gene. We found heterogeneity of evolutionary mechanisms between the different subtypes with a category of amino acid sites observed that had undergone positive selection for subtypes C, F1, and G, while these sites had undergone purifying selection in all other subtypes. Also, amino acid sites within subtypes A and K that had undergone purifying selection were observed, while these sites had undergone positive selection in all other subtypes. The presence of such sites indicates heterogeneity of selective pressures within HIV-1 group M subtype evolution that may account for the various levels of fitness of the subtypes.

scholarly journals Molecular convergent and parallel evolution among four high-elevation anuran species from the Tibetan region

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Bin Lu ◽  
Hong Jin ◽  
Jinzhong Fu
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Convergent Evolution ◽  
Parallel Evolution ◽  
Amino Acid Level ◽  
High Elevation ◽  
Acid Sites ◽  
Anuran Species ◽  
Close Relatives ◽  
Relative Prevalence

Abstract Background To date, evidence for the relative prevalence or rarity of molecular convergent and parallel evolution is conflicting, and understanding of how these processes contribute to adaptation is limited. We compared four high-elevation anuran species (Bufo tibetanus, Nanorana parkeri, Rana kukunoris and Scutiger boulengeri) from the Tibetan region, and examined convergent and parallel amino acid substitutions between them and how they may have contributed to high-elevation adaptation. Results Genomic data of the four high-elevation species and eight of their low-elevation close relatives were gathered. A total of 1098 orthologs shared by all species were identified. We first conducted pairwise comparisons using Zhang and Kumar’s test. Then, the Rconv index was calculated and convergence/divergence correlation plotting was conducted. Furthermore, genes under positive selection and with elevated evolutionary rate were examined. We detected a large number of amino acid sites with convergent or parallel substitutions. Several pairs of high-elevation species, in particular, R. kukunoris vs N. parkeri and B. tibetanus vs S. boulengeri, had excessive amounts of convergent substitutions compared to neutral expectation. Nevertheless, these sites were mostly concentrated in a small number of genes (3–32), and no genome-wide convergence was detected. Furthermore, the majority of these convergent genes were neither under detectable positive selection nor had elevated evolutionary rates, although functional prediction analysis suggested some of the convergent genes could potentially contribute to high-elevation adaptation. Conclusions There is a substantial amount of convergent evolution at the amino-acid level among high-elevation amphibians, although these sites are concentrated in a few genes, not widespread across the genomes. This may attribute to the fact that all the target species are from the same environment. The relative prevalence of convergent substitutions among high-elevation amphibians provides an excellent opportunity for further study of molecular convergent evolution.

scholarly journals Delineation of the Crucial Evolutionary Amino Acid Sites in Trehalose-6-Phosphate Synthase From Higher Plants

2020 ◽  
Vol 16 ◽  
pp. 117693432091014
Author(s):  
Rong Wang ◽  
Congfen He ◽  
Kun Dong ◽  
Xin Zhao ◽  
Yaxuan Li ◽  
...  
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Higher Plants ◽  
Functional Divergence ◽  
Acid Sites ◽  
Evolutionary Analysis ◽  
Codon Substitution ◽  
Bioinformatics Tools ◽  
Amino Acid Properties ◽  
Phosphate Synthase

Trehalose-6-phosphate synthase (TPS) is a key enzyme in the biosynthesis of trehalose, with its direct product, trehalose-6-phosphate, playing important roles in regulating whole-plant carbohydrate allocation and utilization. Genes encoding TPS constitute a multigene family in which functional divergence appears to have occurred repeatedly. To identify the crucial evolutionary amino acid sites of TPS in higher plants, a series of bioinformatics tools were applied to investigate the phylogenetic relationships, functional divergence, positive selection, and co-evolution of TPS proteins. First, we identified 150 TPS genes from 13 higher plant species. Phylogenetic analysis placed these TPS proteins into 2 clades: clades A and B, of which clade B could be further divided into 4 subclades (B1-B4). This classification was supported by the intron-exon structures, with more introns present in clade A. Next, detection of the critical functionally divergent amino acid sites resulted in the isolation of a total of 286 sites reflecting nonredundant radical shifts in amino acid properties with a high posterior probability cutoff among subclades. In addition, positively selected sites were identified using a codon substitution model, from which 46 amino acid sites were isolated as exhibiting positive selection at a significant level. Moreover, 18 amino acid sites were highlighted both for functional divergence and positive selection; these may thus potentially represent crucial evolutionary sites in the TPS family. Further co-evolutionary analysis revealed 3 pairs of sites: 11S and 12H, 33S and 34N, and 109G and 110E as demonstrating co-evolution. Finally, the 18 crucial evolutionary amino acid sites were mapped in the 3-dimensional structure. A total of 77 sites harboring functionally and structurally important residues of TPS proteins were found by using the CLIPS-4D online tool; notably, no overlap was observed with the identified crucial evolutionary sites, providing positive evidence supporting their designation. A total of 18 sites were isolated as key amino acids by using multiple bioinformatics tools based on their concomitant functional divergence and positive selection. Almost all these key sites are located in 2 domains of this protein family where they exhibit no overlap with the structurally and functionally conserved sites. These results will provide an improved understanding of the complexity of the TPS gene family and of its function and evolution in higher plants. Moreover, this knowledge may facilitate the exploitation of these sites for protein engineering applications.

Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene

Genetics ◽  
1998 ◽  
Vol 148 (3) ◽  
pp. 929-936 ◽  
Author(s):  
Rasmus Nielsen ◽  
Ziheng Yang
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Acid Sites ◽  
Selection Model ◽  
Envelope Gene ◽  
Selection Intensity ◽  
Neutral Model ◽  
V3 Region ◽  
Hiv 1 ◽  
Positively Selected Sites

Abstract Several codon-based models for the evolution of protein-coding DNA sequences are developed that account for varying selection intensity among amino acid sites. The “neutral model” assumes two categories of sites at which amino acid replacements are either neutral or deleterious. The “positive-selection model” assumes an additional category of positively selected sites at which nonsynonymous substitutions occur at a higher rate than synonymous ones. This model is also used to identify target sites for positive selection. The models are applied to a data set of the V3 region of the HIV-1 envelope gene, sequenced at different years after the infection of one patient. The results provide strong support for variable selection intensity among amino acid sites The neutral model is rejected in favor of the positive-selection model, indicating the operation of positive selection in the region. Positively selected sites are found in both the V3 region and the flanking regions.

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