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12 results for “Nucleotide substitution”
Figure. The phylogenetic tree showing the relationship among Brevibacillus parabrevis strains SA2.2 and TJ2.3, Bacillus licheniformis MG4.2, and their phylogenetically closest type strains. The GenBank accession numbers of the type strains and studied strains are shown following species names. Distance matrix was calculated by Kimura's 2-parameter model. The scale bar indicates 0.02 substitutions per nucleotide position. Alicyclobacillus pohliae AJ564766 served as an out-group. in Distribution of extracellular enzyme-producing bacteria in the digestive tracts of 4 brackish water fish species
Figure. The phylogenetic tree showing the relationship among Brevibacillus parabrevis strains SA2.2 and TJ2.3, Bacillus licheniformis MG4.2, and their phylogenetically closest type strains. The GenBank accession numbers of the type strains and studied strains are shown following species names. Distance matrix was calculated by Kimura's 2-parameter model. The scale bar indicates 0.02 substitutions per nucleotide position. Alicyclobacillus pohliae AJ564766 served as an out-group.
Data from: Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages
Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree. However, an increasing body of data suggests that evolution under these conditions is an exception, rather than the norm. To address this issue, several non-SRH models of molecular evolution have been proposed, but they either ignore heterogeneity in the substitution process across sites (HAS) or assume it can be modelled accurately using the Γ distribution. As an alternative to these models of evolution, we introduce a family of mixture models that approximate HAS without the assumption of an underlying predefined statistical distribution. This family of mixture models is combined with non-SRH models of evolution that account for heterogeneity in the substitution process across lineages (HAL). We also present two algorithms for searching model space and identifying an optimal model of evolution that is less likely to over- or under-parameterize the data. The performance of the two new algorithms was evaluated using alignments of nucleotides with 10,000 sites simulated under complex non-SRH conditions on a 25-tipped tree. The algorithms were found to be very successful, identifying the correct HAL model with a 75% success rate (the average success rate for assigning rate matrices to the tree's 48 edges was 99.25%) and, for the correct HAL model, identifying the correct HAS model with a 98% success rate. Finally, parameter estimates obtained under the correct HAL-HAS model were found to be accurate and precise. The merits of our new algorithms were illustrated with an analysis of 42,337 second codon sites extracted from a concatenation of 106 alignments of orthologous genes encoded by the nuclear genomes of Saccharomyces cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, S. castellii, S. kluyveri, S. bayanus, and Candida albicans. Our results show that second codon sites in the ancestral genome of these species contained 49.1% invariable sites, 39.6% variable sites belonging to one rate category (V1), and 11.3% variable sites belonging to a second rate category (V2). The ancestral nucleotide content was found to differ markedly across these 3 sets of sites, and the evolutionary processes operating at the variable sites were found to be non-SRH and best modelled by a combination of 8 edge-specific rate matrices (4 for V1 and 4 for V2). The number of substitutions per site at the variable sites also differed markedly, with sites belonging to V1 evolving slower than those belonging to V2 along the lineages separating the 7 species of Saccharomyces. Finally, sites belonging to V1 appeared to have ceased evolving along the lineages separating S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, implying that they might have become so selectively constrained that they could be considered invariable sites in these species.
Nucleotide substitutions during speciation may explain substitution rate variation
<p><span>Although molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which is just a statistical distribution of mutation rates without much underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life. </span></p>
FIGURE. Maximum clade credibility tree of a post-burnin Bayesian analysis (100 million generations), based on nuclear (agt1, ETS, g3pdh, phyC, rpb2) and plastid (atpB–rbcL, matK, rps16, ycf1 pos. 1113-2103, ycf1 pos. 4492-5440) data. Above the branches, Bayesian posterior probabilities (PP) and maximum-likelihood bootstrap support (BS) are shown (PP/BS). The scale bar below the tree shows the branch length for 0.004 substitutions per nucleotide position. Capital letters at the branches are referred to in the tree description. in Re-evaluation of the Amazonian Hylaeaicum (Bromeliaceae: Bromelioideae) based on neglected morphological traits and molecular evidence
FIGURE. Maximum clade credibility tree of a post-burnin Bayesian analysis (100 million generations), based on nuclear (agt1, ETS, g3pdh, phyC, rpb2) and plastid (atpB–rbcL, matK, rps16, ycf1 pos. 1113-2103, ycf1 pos. 4492-5440) data. Above the branches, Bayesian posterior probabilities (PP) and maximum-likelihood bootstrap support (BS) are shown (PP/BS). The scale bar below the tree shows the branch length for 0.004 substitutions per nucleotide position. Capital letters at the branches are referred to in the tree description.
FIGURE. RAxML tree based on a combined dataset of partial LSU and ITS sequence analyses. Bootstrap support values for ML equal to or greater than 60 %, Bayesian posterior probabilities (BYPP) equal to or greater than 0.95 are shown as ML/ BYPP above the nodes. New isolates are in red bold. The tree is rooted to Conioscypha lignicola and Conioschypha minutispora (FMR11245) and Conioscyphascus varius. The scale bar represents the expected number of nucleotide substitutions per site. in Yunnan-Guizhou Plateau: a mycological hotspot
FIGURE. RAxML tree based on a combined dataset of partial LSU and ITS sequence analyses. Bootstrap support values for ML equal to or greater than 60 %, Bayesian posterior probabilities (BYPP) equal to or greater than 0.95 are shown as ML/ BYPP above the nodes. New isolates are in red bold. The tree is rooted to Conioscypha lignicola and Conioschypha minutispora (FMR11245) and Conioscyphascus varius. The scale bar represents the expected number of nucleotide substitutions per site.
Data from: Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages
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Data from: A genome-wide scan study identifies a single nucleotide substitution in ASIP associated with white versus non-white coat-colour variation in sheep (Ovis aries)
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Nucleotide substitutions during speciation may explain substitution rate variation
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Data from: Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses
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Data from: ModelOMatic: fast and automated comparison between RY, nucleotide, amino acid, and codon substitution models
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High nucleotide substitution rates associated with retrotransposon proliferation drive dynamic secretome evolution in smut pathogens
GEO Series GSE206526. Ustilago hordei. 6 samples. Type: Expression profiling by high throughput sequencing.
Systems genetics of single nucleotide substitutions at the Drosophila Obp56h locus
GEO Series GSE178635. Drosophila melanogaster. 30 samples. Type: Expression profiling by high throughput sequencing.
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