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A codon model for associating phenotypic traits with altered selective patterns of sequence evolution
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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.
III Average nucleotide distances (%) based on the Kimura 2-parameter (K2P) model between Aselliscus spp., and associated outgroups based on complete mitochondrial Cytb (1,140 bp, below the diagonal) and COI (657 bp, above the diagonal) gene sequences in Description of a new species of the genus Aselliscus (Chiroptera, Hipposideridae) from Vietnam
III Average nucleotide distances (%) based on the Kimura 2-parameter (K2P) model between Aselliscus spp., and associated outgroups based on complete mitochondrial Cytb (1,140 bp, below the diagonal) and COI (657 bp, above the diagonal) gene sequences
The genome sequence of Samia ricini, a new model species of lepidopteran insect
<p><span><span><span><span><span><span><span><span><span><span><span><i>Samia ricini</i>, a gigantic saturniid moth, has the potential to be a novel lepidopteran model species. Since <i>S. ricini </i>is much more tough and resistant to diseases than the current model species <i>Bombyx mori</i>, the former can be easily reared compared to the latter. In addition, genetic resources available for <i>S. ricini</i> rival or even exceed those for <i>B. mori</i>: at least 26 eco-races of <i>S. ricini</i> are reported and <i>S. ricini</i> can hybridize with wild <i>Samia</i> species, which are distributed throughout Asian countries, and produce fertile progenies. Physiological traits such as food preference, integument colour, larval spot pattern, etc. are different between<i> S. ricini</i>and wild <i>Samia</i> species so that those traits can be the target for forward genetic analysis.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span> In order to facilitate genetic research in <i>S. ricini</i>, we determined the whole genome sequence of <i>S. ricini</i>. The assembled genome of <i>S. ricini</i> was 458 Mb with 155 scaffolds, and the N50 length of the assembly was approximately 21 Mb. 16,702 protein coding genes were predicted in the assembly. Although the gene repertoire of <i>S. ricini</i> was not so different from that of <i>B. mori</i>, some genes, such as chorion genes and fibroin genes, seemed to have specifically evolved in <i>S. ricin</i></span></span></span></span></span></span></span></span></span></span></span><em>i</em>.</p>
TA B L E 2 Estimates of pairwise sequence divergence (cyt-b gene) in pale-bellied Micronycteris, where M. minuta is divided in three clades. Below the diagonal: pairwise distance using the Kimura 2-parameter model (percentage). On the diagonal: within-clade distance using the Kimura 2-parameter model (percentage). Above the diagonal: pairwise p-distance values. Number of specimens sequenced in parenthesis. *Chimeric sequence obtained from two paratypes (Siles et al., 2013). in Revision of the pale-bellied Micronycteris Gray, 1866 (Chiroptera, Phyllostomidae) with descriptions of two new species
TA B L E 2 Estimates of pairwise sequence divergence (cyt-b gene) in pale-bellied Micronycteris, where M. minuta is divided in three clades. Below the diagonal: pairwise distance using the Kimura 2-parameter model (percentage). On the diagonal: within-clade distance using the Kimura 2-parameter model (percentage). Above the diagonal: pairwise p-distance values. Number of specimens sequenced in parenthesis. *Chimeric sequence obtained from two paratypes (Siles et al., 2013).
Data from: Utility of pooled sequencing for association mapping in non-model organisms
High density genome-wide sequencing increases the likelihood of discovering genes of major effect and genomic structural variation in organisms. While there is an increasing availability of reference genomes across broad taxa, the greatest limitation to whole-genome sequencing of multiple individuals continues to be the costs associated with sequencing. To alleviate excessive costs, pooling multiple individuals with similar phenotypes and sequencing the homogenized DNA (Pool-Seq) can achieve high genome coverage, but at the loss of individual genotypes. Although Pool-Seq has been an effective method for association mapping in model organisms, it has not been frequently utilized in natural populations. To extend bioinformatic tools for rapid implementation of Pool-Seq data in non-model organisms, we developed a pipeline called PoolParty and illustrate its effectiveness in genetic association mapping. Alignment expectations based on five pooled Chinook salmon (Oncorhynchus tshawytscha) libraries showed that approximately 48% genome coverage per library could be achieved with reasonable sequencing effort. We additionally examined male and female O. tshawytscha libraries to illustrate how Pool-Seq techniques can successfully map known genes associated with functional differences among sexes such as growth hormone 2. Finally, we compared pools of individuals of different spawning ages for each sex to discover novel genes involved with age at maturity in O. tshawytscha such as opsin4 and transmembrane protein19. While not appropriate for every system, Pool-Seq data processed by the PoolParty pipeline is a practical method for identifying genes of major effect in non-model organisms when high genome coverage is necessary and cost is a limiting factor.
Data from: "Genome-wide microsatellite marker development from next-generation sequencing of two non-model bat species impacted by wind turbine mortality: Lasiurus borealis and L. cinereus (Vespertilionidae)" in Genomic Resources Notes accepted 1 October 2013 to 30 November 2013
Tree-roosting bats in the genus Lasiurus are widespread, migratory species that have not been well characterized for population genetic diversity and structure due to a lack of genetic resources. Generating genetic resources in Lasiurus is made pressing by the need for conservation genetic assessments of demographic trends in this genus, which comprise a large percentage of bat mortalities at wind turbine sites across North America. We report on marker development from whole-genome Illumina sequencing of the red bat (Lasirus borealis) and the hoary bat (L. cinereus). We generated paired-end libraries for a single individual of each species, sequenced on the Illumina HiSeq platform. We mapped a total of 46.6 million reads to the Myotis lucifigus reference genome, and used bioinformatics searches to identify tends of thousands of simple sequence repeats (SSRs) distributed across the bat genome. We selected 48 candidate microsatellite loci to develop cross-species primer sequences for Lasiurus, assembled these into multiplex combinations, and tested for amplification and polymorphism levels in a sample of 23 individuals from each of L. borealis and L. cinereus. In total, we identified 42 highly polymorphic loci that could be robustly amplified and scored, the majority of which (39) were also combinable into highly multiplexed assays of 4-8 loci each. The combination of new genomic sequence assemblies, a large set of highly polymorphic microsatellite loci, and the ability to efficiently multiplex represents a significant contribution to the genetic resources available for population and comparative genetic studies of bats.
Data from: Genotyping-by-sequencing for estimating relatedness in non-model organisms: avoiding the trap of precise bias
There has been remarkably little attention to using the high resolution provided by genotyping-by-sequencing (i.e. RADseq and similar methods) datasets for assessing relatedness in wildlife populations. A major hurdle is the genotyping error, especially allelic dropout, often found in this type of dataset that could lead to downward-biased, yet precise, estimates of relatedness. Here we assess the applicability of genotyping-by-sequencing datasets for relatedness inferences given their relatively high genotyping error rates. Individuals of known relatedness were simulated under genotyping error, allelic dropout, and missing data scenarios based on an empirical ddRAD dataset, and their true relatedness was compared to that estimated by seven relatedness estimators. We found that an estimator chosen through such analyses can circumvent the influence of genotyping error, with the estimator of Ritland (1996) shown to be unaffected by allelic dropout and to be the most accurate when there is genotyping error. We also found that the choice of estimator should not rely solely on the strength of correlation between estimated and true relatedness as a strong correlation does not necessarily mean estimates are close to true relatedness. We also demonstrated how even a large SNP dataset with genotyping error (allelic dropout or otherwise) or missing data still performs better than a perfectly genotyped microsatellite dataset of tens of markers. The simulation-based approach used here can be easily implemented by others on their own genotyping-by-sequencing datasets to confirm the most appropriate and powerful estimator for their dataset.
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 from: Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African buffalo representative of the four subspecies. We identified 2534 SNPs with high confidence within the panel by aligning the short sequences to the cattle genome (Bos taurus). The average sequencing depth of the complete aligned set of reads was estimated at 5x, and at 13x when only considering the final set of putative SNPs that passed the filtering criterion. Our set of SNPs was validated by PCR amplification and Sanger sequencing of 15 SNPs. Of these 15 SNPs, 14 amplified successfully and 13 were shown to be polymorphic (success rate: 87%). The fidelity of the identified set of SNPs and potential future applications are finally discussed.
Integration of protein and coding sequences enables mutual augmentation of the language model
<p><strong>The file structure is as follows:</strong></p> <p>Project Root<br>├── TE_MRL<br>│ ├── MRL_dataset.zip<br>│ └── TE_dataset.zip<br>│<br>├── finetuned_model<br>│ ├── FoldP<br>│ ├── LocP<br>│ ├── SSP<br>│ └── SolP<br>│<br>├── tax_tsne<br>│ └── emb_3models.zip<br>│<br>└── training_data<br> ├── FoldP.csv<br> ├── LocP.csv<br> ├── SolP.csv<br> ├── SSP.pkl<br> └── pretrain_source_GCF.txt</p>
scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution - Supplementary data and code
<p>Data and code to reproduce the analyses from the study: "scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution". </p>
BSO-GBD:Behavior Sequence-Oriented GitHub Bot Detection model
<p>Our dataset is primarily divided into three parts. Firstly, there are human accounts (Human) and bot accounts (Bot). Both of these types appear similar to regular developer accounts, lacking any distinctive markings. The second category comprises self-bot accounts, typically formed by GitHub apps. These accounts generally bear an explicit "bot" label, and we exclude them in our classification.</p> <p>The dataset is structured as follows: a total of 4786 ordinary accounts, with 4325 being Human accounts and 461 being Bot accounts. Each account internally consists of a CSV table with the following fields: user_name; repo_name; event_type_L1; event_type_L2; event_type_L3; timestamp. These data constitute our raw dataset.</p>
Antibody-Antigen Models for McCoy 2024 Paper: "A Comparison of Antibody-Antigen Complex Sequence-to-Structure Prediction Methods and their Systematic Biases"
<p>Up to the top 20 models generated for each method tested in the 2024 Paper: "A Comparison of Antibody-Antigen Complex Sequence-to-Structure Prediction Methods and their Systematic Biases"</p>
Supplementary data: Predicting grid frequency short-term dynamics with Gaussian processes and sequence modeling
<p>This repository contains data and result files for the paper "Predicting grid frequency short-term dynamics with Gaussian processes and sequence modelling". The code to generate the models and reproduce the results of the comparative study in the above paper is available on this <a href="https://github.com/bolin-liu/sequence-model-and-gaussian-process-for-frequency-prediction">github repository</a></p> <p><strong>Supplementary data</strong>:</p> <p>- The <strong>trained_models</strong> folder contains the results of the trained models.</p> <p>- The folder <strong>data</strong> contains data needed for for the comparative study for the year 2019 in the paper above. This data set (except knn_point_predictions.npy) is generated with the code in this <a href="https://github.com/johkruse/PIML-for-grid-frequency-modelling">github repository</a>. knn_point_predictions.npy is generated with the code in this <a href="https://github.com/bolin-liu/sequence-model-and-gaussian-process-for-frequency-prediction">github repository </a>.</p>
FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined. in Morphological and phylogenetic relations of members of the genus Coelastrella (Scenedesmaceae, Chlorophyta) from the Ural and Khentii Mountains (Russia, Mongolia)
FIGURE. Variable positions in the ITS2 secondary structure of some Coelastrella sensu lato species. The ITS2 model of Coelastrella striolata strain CAUP H 3602 (JX513881) was used to map sequence differences. Variable positions of analyzed strains (GenBank numbers can be found in Table 3, 4 are given next to the main structure and are marked in bold. Hemi- Compensatory Base Changes in conservative regions are circled and Compensatory Base Change is contoured. Sequences of strains with GenBank numbers JX513879 (C. aeroterrestrica), JX513882 (C. terrestris), JX513884 (C. rubescens), MH176120 (C. rubescens var. oocystiformis), JX513880 (C. multistriata), JX513887 (C. oocystiformis) were used as representatives of Coelastrella species. The strains analyzed in this study are underlined.
Orca: Sequence-based modeling of genome 3D architecture from kilobase to chromosome-scale (Part1)
<p>This dataset (Part 1) provide the core resource files required for using the code of Orca, including models and the hg38 reference genome (resources_core.tar.gz), and the micro-C mcool files required for extracting the experimental observations (resources_mcools.tar.gz). Orca is a sequence-based deep learning modeling framework for multiscale genome 3D architecture.</p>
Modeling Sequences of Earthquakes and Aseismic Slip (SEAS) in Elasto-Plastic Fault Zones With a Hybrid Finite Element Spectral Boundary Integral Scheme
<p>This repository contains the results of 2D simulations of the earthquake cycles accounting for off-fault plasticity.</p> <p>Folder Case1 contains the slip rate and time history for all simulations with cohesion c = 47 MPa</p> <p>Folder Case2 contains the slip rate and time history for all simulations with cohesion c = 25 MPa</p> <p>the mat files contain equivalent plastic strain of each element stored at the start and end of each event with element connectivity and node coordinates.</p>
Modeling the Organic Carbon Oxidation and Redox Sequence under the Partial- Equilibrium Approach: a Discussion by means of a Semi-Analytical Solution
<p>Filename: Analytical_solution.xls<br> File format: Excel<br> Description: It contains the calculation of the analytical model, programmed by means of excel. The sheet "advection" contains the calculation of the advection model and the sheet "diffusion" that of the diffusion model. The sheet "Phreeqc results" contains the results of the Phreeqc batch model (see Batch.pqi). Input data are highlighted in yellow.</p> <p>Filename: Batch.pqi<br> File format: Phreeqc<br> Description: It contains the input file for the calculation of the batch model by Phreeqc. It requires the Phreeqc database file Phreeqc.dat</p> <p>Filename: PEA_om_adv.pqi<br> File format: Phreeqc<br> Description: It contains the input file for the numerical calculation of the advection model by Phreeqc using the PEA (Partial Equilibrium Assumption). It requires the Phreeqc database file Phreeqc.dat</p> <p>Filename: PEA_om_dif.pqi<br> File format: Phreeqc<br> Description: It contains the input file for the numerical calculation of the diffusion model by Phreeqc using the PEA (Partial Equilibrium Assumption). It requires the Phreeqc database file Phreeqc.dat</p> <p>Filename: KIN_om_adv.pqi<br> File format: Phreeqc<br> Description: It contains the input file for the numerical calculation of the advection model by Phreeqc using the fully kinetic approach. It requires the Phreeqc database file PhreeqcKIN.dat</p> <p>Filename: KIN_om_dif.pqi<br> File format: Phreeqc<br> Description: It contains the input file for the numerical calculation of the diffusion model by Phreeqc using the fully kinetic approach. It requires the Phreeqc database file PhreeqcKIN.dat</p> <p>Filename: phreeqc.dat<br> File format: Phreeqc database<br> Description: It contains thermodynamic data for the batch model (see Batch.pqi) and the PEA models (see PEA_om_adv.pqi and PEA_om_dif.pqi). It is the default thermodynamic database of Phreeqc, dat), from which we removed ammonium to avoid the unrealistic reduction of NO3- and N2 to NH4+</p> <p>Filename: phreeqcKIN.dat<br> File format: Phreeqc database<br> Description: It contains thermodynamic data for the fully kinetic models (see KIN_om_adv.pqi and KIN_om_dif.pqi). It is the default thermodynamic database of Phreeqc, dat), from which we removed the relevant equilibrium redox reaction, so that they can be treated kinetically.</p> <p> </p> <p> </p>
Scalable mixed model approaches for set-based association studies on large-scale categorical data analysis and its application to 450k exome sequencing data in UK Biobank
<p>The ongoing release of large-scale sequencing data in the UK Biobank allows for identifying associations between rare variants and complex traits. SAIGE-GENE+ is a valid approach to conducting set-based association tests for quantitative and binary traits. However, for ordinal categorical phenotypes, applying SAIGE-GENE+ with treating the trait as quantitative or binarizing the trait can cause inflated type I error rates or power loss. In this study, we propose a novel method for rare-variant association tests, POLMM-GENE, in which a proportional odds logistic mixed model was used to characterize ordinal categorical phenotypes while adjusting for sample relatedness. POLMM-GENE fully utilizes the categorical nature of phenotypes and thus can well control type I error rates while remaining powerful. In the analyses of UK Biobank 450k whole exome-sequencing data for 5 ordinal categorical traits, POLMM-GENE identified 54 gene-phenotype associations.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
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