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42 results for “substitution models”
Main model fits and substitution rate predictions for: A quantitative genetic model of background selection in humans
<p>Across the human genome, there are large-scale fluctuations in genetic diversity caused by the indirect effects of selection. This can be thought of as a "linked selection signal" that reflects the impact of selection varying according to the placement of functional regions and recombination rates along the genome. Previous work has shown that negative selection against the steady influx of new deleterious mutations into conserved regions is the predominant mode of selection in humans. However, the theoretic model that underpins these results, classic Background Selection theory, is only applicable when new mutations are so deleterious that they cannot fix in the population. Here, we develop a statistical method based on a quantitative genetics view of the linked selection, which models the effects of weak draft created according to how polygenic additive fitness variance is distributed along the genome. We use a recent model that jointly predicts the equilibrium fitness variance and substitution rates due to both strong and weakly deleterious mutations, we estimate the distribution of fitness effects (DFE) and mutation rate across three human populations. While our model can accommodate weaker selection, we initially find evidence across three human populations of very strong selection against deleterious mutations consistent with previous work. However, the corollary predicted substitution rates for conserved regions are unreasonably low, and in disagreement with observed rates. We hypothesize this could be due to selected sites experiencing a further diminished population size due to selective interference. When we account for this in our method, we find evidence of weakly deleterious mutations in conserved regions which brings the predicted substitution rate into agreement with observations. However, these models lead to implausibly large mutation rate estimates. Overall, while our model of the genomic linked selection signal brings us a step towards uniting population and quantitative genetic selection models with the substitution process, our work suggests considerable uncertainty remains about the processes generating fitness variance in humans.</p>
Structure and stability constrained substitution models outperform traditional substitution models used for evolutionary inference
<p>The current knowledge about how protein structures influence sequence evolution is rarely incorporated into substitution models adopted for phylogenetic inference, which are commonly based on independent with the same substitution process and ignore the known variation of the evolutionary rates across sites with different structural properties. In previous works, we presented site-specific substitution models of protein evolution based on selection on the folding stability of the native state (Stab-CPE), which predict more realistically the evolutionary variability across protein sites. However, those Stab-CPE present qualitative differences from observed data, probably because they ignore changes in the native structure, despite empirical studies suggesting that conservation of the native structure is a strong selective force. Here we present novel structurally constrained substitution models (Str-CPE) based on Julián Echave's model of the structural change due to a mutation as the linear response of the protein to a perturbation and on the explicit model of the perturbation generated by a specific amino-acid mutation. Compared to our previous Stab-CPE models, the novel Str-CPE models are more stringent (they predict lower sequence entropy and substitution rate), provide higher likelihood to multiple sequence alignments (MSA) of the wild-type protein, and better predict the observed substitution rates. Next, we combine Str-CPE and Stab-CPE models to obtain structure and stability constrained substitution models (SSCPE) that fit the empirical MSAs even better. Importantly, these SSCPE models present a relevant improvement of the phylogenetic likelihood for all ten protein families that we analyzed with the program RAxML-NG. We implemented the SSCPE models in the program Prot evol, freely available at <a href="https://github.com/ugobas/Prot_evol">https://github.com/ugobas/Prot_evol</a>.</p>
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.
Site-specific structure and stability constrained substitution models improve phylogenetic inference
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Main model fits and substitution rate predictions for: A quantitative genetic model of background selection in humans
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Model executable, output, drivers and parameters for modeling organism acclimation to changing availability of and requirements for substitutable and interdependent resources
Files used to generate the data for figures in: Rastetter, EB, Kwiatkowski, BL. An approach to modeling resource optimization for substitutable and interdependent resources. Ecological Modelling (2020). https://doi.org/10.1016/j.ecolmodel.2020.109033. This paper presents a hierarchical approach to modeling organism acclimation to changing availability of and requirements for substitutable and interdependent resources. Substitutable resources are resources that fill the same metabolic or stoichiometric need of the organism. Interdependent resources are resources whose acquisition or expenditure are tightly linked (e.g., light, carbon dioxide, and water in photosynthesis and associated transpiration). We illustrate the approach by simulating the development of vegetation with four substitutable sources of nitrogen that differ only in the cost of their uptake and assimilation.
Data from: N-mixture models estimate abundance reliably: a field test on Marsh Tit using time-for-space substitution
<p>Imperfect detection in field studies on animal abundance, including birds, is common and can be corrected for in various ways. The binomial N-mixture (hereafter binmix) model developed for this task is widely used in ecological studies owing to its simplicity: it requires replicated count results as the input. However, it may overestimate abundance and be sensitive to even small violations of its assumptions. We used a 33-year dataset on the Marsh Tit, Poecile palustris, a sedentary forest passerine, from Białowieża Forest, Poland to validate inference from binmix models by comparing model-estimated abundances to the true number of breeding pairs within the plots, determined by exhaustive population study. The abundance estimates, derived from six springtime (April-May) counts of males on each plot in each year, were highly reliable: 116 out of 132 year-plot estimates (88%) included the true number of pairs within the 95% confidence intervals. Over- and underestimations were thus rare and similarly frequent (9 and 12 cases, respectively), with a tendency to overestimate at low densities and underestimate at high densities. Marsh Tits sing rarely but the frequency of countersinging increases with abundance, leading to non-independence in detections. When accounted for in a submodel for detection, the per-survey number of countersinging events positively affected detection probability but only weakly affected abundance estimates. Simulations further demonstrate that this property, overestimation at low densities and underestimation at high densities, may be a systematic bias of binmix model even if density-dependent detection is absent. While the behaviour of binmix models in specific situations requires more study, we conclude that these models are a valid tool to estimate abundance reliably when intensive population monitoring is not feasible.</p>
The Effect of Bone Graft Substitute in Healing Fractures with Bone Defects Through Examination of Alkaline Phosphatase and Radiology in the Murine Model (Rattus norvegicus) Wistar strain
<p>Raw data for manuscript with the title <strong>The Effect of Bone Graft Substitute in Healing Fractures with Bone Defects Through Examination of Alkaline Phosphatase and Radiology in the Murine Model (<em>Rattus norvegicus</em>) Wistar strain </strong></p>
Experimental data for Understanding frictional behavior in fascia tissues through tribological modeling and material substitution
<p>Dataset (experimental data) for publication titled: Understanding frictional behavior in fascia tissues through tribological modeling and material substitution. The article deals with the development of a tribological model of fascia. As in the paper, the dataset is divided into the three phenomena studied: Effect of geometry, Models, Hyaluronic acid - model E. </p>
Data from: N-mixture models estimate abundance reliably: a field test on Marsh Tit using time-for-space substitution
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Data from the article "The mitochondrial phylogeny of land plants shows support for Setaphyta under non-stationary substitution models"
<p>Data from the article:</p> <p>"The mitochondrial phylogeny of land plants shows support for Setaphyta under non-stationary substitution models"</p> <p>Filipe de Sousa, Peter Civáň, João Brazão, Peter G. Foster, Cymon J. Cox</p> <p> </p> <p>These data are divided in four folders:</p> <p>* 1_36_gene_nt_alignments_&_trees - contains 36 single gene nucleotide alignments and the corresponding trees inferred from a MCMC analysis on the program p4</p> <p>* 2_36_gene_aa_alignments_&_trees - contains 36 single gene amino acid alignments and the corresponding trees inferred from a MCMC analysis on the program p4</p> <p>* 3_concatenated_alignments_&_trees - contains the nucleotide, codon-degenerate and amino acid alignments of 36 concatenated genes and the corresponding trees inferred from MCMC analyses on the programs p4 and phylobayes with composition homogeneous, tree-heterogeneous and site-heterogeneous models; trees correspond to figures S1-S7 on the online supplemental file.</p> <p>* 4_concatenated_ML_trees - contains the ML trees from the analyses of the concatenated datasets (nucleotide, codon degenerate and amino acid).</p> <p> </p> <p> </p> <p> </p>
FIGURE5. Maximum likelihood tree based on the Kimura 2-parameter model of the COI sequences from the Siphamia species with P. kauderni as the outgroup. Tree shown here has the highest log likelihood following 10 000 replications. The percentage of trees in which the associated taxa clustered together is shown next to the branches, branch lengths are measured in the number of substitutions per site and all positions containing gaps and missing data have been eliminated. in Redescription and distributional range extension of the Speckled Siphonfish, Siphamia guttulata (Pisces: Apogonidae)
FIGURE5. Maximum likelihood tree based on the Kimura 2-parameter model of the COI sequences from the Siphamia species with P. kauderni as the outgroup. Tree shown here has the highest log likelihood following 10 000 replications. The percentage of trees in which the associated taxa clustered together is shown next to the branches, branch lengths are measured in the number of substitutions per site and all positions containing gaps and missing data have been eliminated.
Ions release from hydroxyapatite and substituted hydroxyapatites in different immersion liquids: In vitro experiments and theoretical modelling study
<p>The multi-substituted hydroxyapatites (ms-HAPs) are currently gaining more consideration due to their multifunctional properties and biomimetic structure, owning thus an enhanced biological potential in orthopedic and dental applications. In this study, nano hydroxyapatite (HAP) substituted with multiple cations (Sr2+, Mg2+ and Zn2+) for Ca2+ and anion (SiO44-) for PO43- and OH-, specifically HAPc-5%Sr and HAPc-10%Sr (where HAPc is HAP-1.5%Mg-0.2%Zn-0.2%Si), both lyophilized noncalcined and lyophilized calcined, were evaluated for their in vitro ions release. These nanomaterials were characterized by SEM, FE-SEM and EDX, as well as by AFM images and by surface-specific areas and porosity. Further, the release of cations and of phosphate anions were assessed from nano HAP and ms-HAPs, both in water and in simulated body fluid (SBF), in static and simulated dynamic conditions, using inductively coupled plasma optical emission spectrometry (ICP-OES). The release profiles were analyzed and the influence of experimental conditions was determined for each of the six nanomaterials and for various periods of time. The pH of the samples soaked in the immersion liquids was also measured. The ions release mechanism was theoretically investigated using the Korsmeyer-Peppas model. The results indicated a mechanism principally based on diffusion and dissolution, with possible contribution of ion exchange. The surface of ms-HAP nanoparticles is more susceptible to dissolution into immersion liquids due to the lattice strain provoked by simultaneous multi-substitution in HAP structure. According to the findings, it is rational to suggest that both materials HAPc-5%Sr and HAPc-10%Sr are bioactive and can be potential candidates in bone tissue regeneration.</p>
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.
Data for Standard Codon Substitution Models Overestimate Purifying Selection for Non-Stationary Data
<p>Codon-aligned, filtered alignments for Kaehler et al. (2016) (https://peerj.com/preprints/2218/). Please refer to preprint for preparation details.</p> <p>Data obtained from Ensembl (http://www.ensembl.org/) and antbase (http://antbase.org).</p> <p> </p> <p> </p>
Supplementary material for: nQMaker: estimating time non-reversible amino acid substitution models
<p><span>Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly-used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups. In this paper, we introduce a maximum likelihood approach nQMaker, an extension of the recently published QMaker method, that allows the estimation of time non-reversible amino acid substitution models and rooted phylogenetic trees from a set of protein sequence alignments. We show that the non-reversible models estimated with nQMaker are a much better fit to empirical alignments than pre-existing reversible models, across a wide range of datasets including mammals, birds, plants, fungi, and other taxa, and that the improvements in model fit scale with the size of the dataset. Notably, for the recently published plant and bird trees, these non-reversible models correctly recovered the commonly estimated root placements with very high statistical support without the need to use an outgroup. We provide nQMaker as an easy-to-use feature in the IQ-TREE software (<a href="http://www.iqtree.org">http://www.iqtree.org</a>), allowing users to estimate non-reversible models and rooted phylogenies from their own protein datasets.</span></p>
Data-specific substitution models improve protein-based phylogenetics - data
<p>Amino-acid sequence data sets, estimated data-specific amino-acid substitution models, and optimal ML trees.</p> <p>Data are divided in five folders, each one with a readme.txt file describing it.</p> <p>├── 1_simulated_data_sets<br> │ ├── 1500-site_alignments<br> │ ├── 400-site_alignments<br> │ └── 8000-site_alignments<br> ├── 2_simulated_data_specific_models<br> │ ├── Codeml_models<br> │ ├── FastMG_models<br> │ ├── IQTREE_models<br> │ ├── P4_BI_models<br> │ └── P4_ML_models<br> ├── 3_optimal_ML_trees_simulated_data<br> │ ├── commonly-used_empirical_models<br> │ │ ├── cpREV_model_analyses<br> │ │ └── WAG_model_analyses<br> │ ├── data_specfic_model_analyses<br> │ │ ├── Codeml-estimated_model_analyses<br> │ │ ├── FastMG-estimated_model_analyses<br> │ │ ├── IQTREE-estimated_model_analyses<br> │ │ ├── P4BI-estimated_model_analyses<br> │ │ └── P4ML-estimated_model_analyses<br> │ └── simulation_model_analyses<br> ├── 4_data_specific_models_empirical_data<br> │ └── Toussaint18_data_specific_models_27partitions<br> └── 5_optimal_ML_trees_empirical_data</p>
Modeling wetland functions: Is space-to-time substitution of perimeter-area relation appropriate?
<p>Wetlands' morphometric or shape properties such as their area and perimeter impact a multitude of ecosystem functions and services. However, current models used to quantify these functions often only use area as an independent variable, as the static area and perimeter of different wetlands have been found to be closely related. The study uses monthly satellite-based inundation maps to assess the temporal covariation of geographically isolated wetlands' perimeter and surface area. The results show that using static representations of wetlands to evaluate temporal dynamic perimeter-area relations can introduce significant discrepancies and that these discrepancies can be reduced if evaluations using static data are performed separately for each wetlandscape. The study concludes that current models that use implicit area-perimeter relations based on static wetland representations should be used with caution and that incorporating perimeter-area relations from temporally dynamic data can improve wetland function estimates.</p>
FIGURE4. Maximum-likelihood tree inferred from 694 bp of COI using a HKY+G substitution model implemented in MEGAX (Kumar et al. 2018). Bootstrap values are indicated on the nodes. in --Molecular--and--acoustic--evidence--support--the--species--status--of--Anthus rubescens rubescens and--Anthus [rubescens] japonicus--(Passeriformes:--Motacillidae)
FIGURE4. Maximum-likelihood tree inferred from 694 bp of COI using a HKY+G substitution model implemented in MEGAX (Kumar et al. 2018). Bootstrap values are indicated on the nodes.
FIGURE3. Maximum-likelihood tree inferred from 998 bp of CR using a HKY+G substitution model implemented in MEGAX (Kumar et al. 2018). Bootstrap values are indicated on the nodes. in --Molecular--and--acoustic--evidence--support--the--species--status--of--Anthus rubescens rubescens and--Anthus [rubescens] japonicus--(Passeriformes:--Motacillidae)
FIGURE3. Maximum-likelihood tree inferred from 998 bp of CR using a HKY+G substitution model implemented in MEGAX (Kumar et al. 2018). Bootstrap values are indicated on the nodes.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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