Find research datasets worth reusing

opencc-by-4.0Aug 2021View details →

Data for "Unfolding the structural stability of nanoalloys via symmetry-constrained genetic algorithm and neural network potential"

PtNi_alloy_eam.db is the dataset (ase.db object) consisting of 55982 intially sampled Pt-Ni alloy structures with EAM energies and forces. PtNi_alloy_dft.db is the dataset (ase.db object) consisting of the final 6828 resampled Pt-Ni alloy structures with DFT energies and forces calculated by VASP. This is the training set for the NNP, and could be very useful for fitting other machine learning models. PtNi_nanoalloy_vertices_nnp.db is the dataset (ase.db object) consisting of all the vertices (stable structures) on the convex hulls obtained from NNP-based SCGA runs on 36 Pt-Ni nanoalloy systems. The energies are given by the NNP. Additional information such as mixing energy, motif and symmetry axis are also saved in the dataset and can be queried by the 'data' keyword. An xyz format trajectory of these stable structures is also uploaded. All the input files and scripts for hybrid MC-MD simulations, QBC resampling, DFT calculations, NNP training, NNP-based SCGA runs and convex hull analysis are provided in inputs_and_scripts.zip.

opencc-by-4.0Nov 2021View details →

The genetic basis of structural colour variation in mimetic Heliconius butterflies

Raw USAXS data from discal region of Heliconius butterflies (H. erato and H. melpomene). The data comes from wings of individuals of two intercross families, one from each species and was used to estimate scale structure variation and a QTL analysis.

opencc-by-4.0Aug 2021View details →

Simulated genetic data in a hierarchical metapopulation structure

The data are linked to a research article entitled: “Interactions between microenvironment, selection and genetic architecture drive multiscale adaptation in a simulation experiment” in Journal of Evolutionary Biology (see References). In this research on multiscale adaptation, we simulated a hierarchical metapopulation structure with four populations, two environments per population and three patches per environment, in a two-step procedure: <ul> <li>an initialization step without selection, with eight combinations of mutation type, selfing rate and QTL number parameters (2 modes each); out of 200,000 simulated generations in each case, we chose one with appropriate characteristics as a starting point for the next step;</li> <li>a selection step with all possible combinations of the following parameters: environmental pattern (4 modes), environmental range (5 modes), selection intensity (4 modes), fecundity (3 modes).</li> </ul> This resulted in 240 scenarios for each initialized metapopulation, i.e. 1,920 scenarios in total. Each scenario was replicated 10 times, i.e. 19,200 simulation runs. The archive includes all data needed to reproduce the simulations and analyses, or to re-use the simulated metapopulations for other analyses. It has the following structure (further detailed below): <ol> <li>NemoScripts directory contains the Nemo input files used to perform simulations for the initialization step and the selection step;</li> <li>RScripts directory contains the R scripts to read the Nemo output files, compute synthetic variables(*), and produce the figures as they appear in the publication and supplementary material (*: long computations, therefore we also directly provide those synthetic variables in the Data directory);</li> <li>Data directory contains the Nemo output files, the synthetic variables, and other data needed to reproduce the figures; this directory can be used as a working directory for the R scripts (recommended).</li> </ol> Running the following command in a terminal tar –xzvf Archive_PC_SOM_IS_FL.tar  will create a directory named Archive_PC_SOM_IS_FL, which detailed content is described in the README.pdf file. Warning: the extracted archive is large (460Go, >40,000 files) and extraction may take some time.

opencc-by-4.0Jul 2022View details →

Microsatellite genotypes for «Genetic diversity and spatial genetic structure support the specialist‑generalist variation hypothesis in two sympatric woodpecker species»

Species are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (Dendrocopos major), lower genetic diversity was found in the specialist middle spotted woodpecker (Dendrocoptes medius). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.

opencc-by-4.0Apr 2024View details →

Role of environmental factors in the genetic structure of a highly mobile seabird

Aim: Environmental features can act as selection pressures and barriers to gene flow between populations. The genetic structuring of highly mobile but philopatric seabirds creates a paradox, and the role of oceanographic and geographic variables is still poorly understood. In this study, we investigate the influence of environmental and geographic variables in the genetic and phenotypic diversity of a pantropical seabird breeding in islands and archipelagos separated by different geographic distances, up to thousand kilometers, and which differ in environmental characteristics. Location: Islands and archipelagos in the southwestern Atlantic Ocean. Taxon: Sula dactylatra, Lesson, 1831 (masked booby). Methods: The population structure of the species was accessed through mitochondrial and nuclear DNA. To test Isolation by Environment (IBE) vs. by Distance (IBD), sea surface temperature, primary productivity, and salinity, as well as isotopic niche based on carbon and nitrogen, and distances between colonies and from the continent, were used. We also tested the correlation between the genetic structure and the morphometry of individuals in each colony. Results: We identified the presence of low genetic structure between populations. Nevertheless, differences were identified between inshore and offshore colonies, with the influence of landscape characteristics of these two types of environment. The morphometric and isotopic niche variations are consistent with this segregation. Main conclusions: Environmental variables of coastal and oceanic environments seem to influence the genetic structure of masked boobies, even though it is low in the SW Atlantic Ocean, highlighting the role of environmental heterogeneity in shaping biodiversity.

opencc-by-4.0Mar 2023View details →

Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra- and interspecific genetic diversity in Mediterranean invertebrates

Sequence data and stepwise pipeline outputs associated with the article "Spineless and overlooked: DNA metabarcoding of autonomous reef monitoring structures reveals intra- and interspecific genetic diversity in Mediterranean invertebrates". Preprint available here: <a href="https://doi.org/10.22541/au.167085544.47638352/v1">10.22541/au.167085544.47638352/v1</a> Sequence data is deposited in fastq-format in folders by region (Palinuro.tar.gz, Livorno.tar.gz, and Rovinj.tar.gz) and a separate folder for controls (Controls.tar.gz). Each fastq-file contains sequences for a single PCR replicate named by sample and replicate number. Sample names are described in spineless_sample_names.csv. Positive control sequences are described in SM1_positive_controls.csv. Stepwise pipeline outputs are available in the folder Pipeline_outputs_stepwise.zip Scripts used to generate pipeline outputs as well as other aspects of the final article are available at <a href="https://github.com/thomasdotter/spineless-haplotypes">https://github.com/thomasdotter/spineless-haplotypes</a>.

opencc-by-4.0Sep 2023View details →

Genetic diversity, population structure, and linkage disequilibrium among tropical quality protein maize (QPM) lines assessed with high-density SNP markers

The study of genetic diversity (GD), population structure, and linkage disequilibrium (LD) provides a better understanding of the genetic relationships between individuals in a population which can be utilized in crop research and improvement. Genotyping-by-sequencing (GBS) was used to detect and genotype single nucleotide polymorphisms (SNPs) in a collection of 74 quality protein maize (QPM) lines and further to characterize their genetic diversity, population structure, and linkage disequilibrium. A total of 235,214 high-quality SNPs were used for different genetic analyses except for structure analysis where 11,950 SNPs were used. Analysis of molecular variance (AMOVA) based on these SNPs revealed high genetic heterozygosity among the five populations with 1% of the total genetic variation present among the subpopulations and 99% of the variation among individuals within the populations.  Population structure analysis using Bayesian-based clustering revealed that the 74 lines could be clustered into four groups. However, neighbor-joining trees indicate the lines are grouped into three major clusters.  Further analysis using principal component analyses (PCA) clustered the genotypes into five groups which are concordant with the groups based on pedigree information. Higher genetic diversity was detected in population 1 with a GD value of 0.484 and the lowest in population 5 (0.396) and overall, with a mean of 0.434. The LD pattern in the quality protein maize was investigated and we observed a relatively rapid LD decay of 3.53kb and 10.66kb at r2 =0.2 and r2= 0.1, respectively. Our findings provide important information for future Linkage mapping studies, genome-wide association analyses, and marker-assisted selective breeding of maize as well as genomic prediction-based selection in tropical germplasm.

opencc-by-4.0Apr 2019View details →

Fig. 3 in Genetic diversity and population structure of Brycon nattereri (Characiformes: Bryconidae): a Neotropical fish under threat of extinction

Fig. 3. Haplotype network based on partial sequencing of the D-loop region (mtDNA) of 92 individuals of Brycon nattereri from the Laranjinha River. Circle sizes are pro- portional to haplotype frequency.

opencc-zeroJul 2020View details →

Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs

The multi-subunit bacterial RNA polymerase (RNAP) and its associated regulators carry out transcription and integrate myriad regulatory signals. Numerous studies have interrogated the inner workings of RNAP, and mutations in genes encoding RNAP drive adaptation of Escherichia coli to many health- and industry-relevant environments, yet a paucity of systematic analyses has hampered our understanding of the fitness benefits and trade-offs from altering RNAP function. Here, we conduct a chemical-genetic analysis of a library of RNAP mutants. We discover phenotypes for non-essential insertions, show that clustering mutant phenotypes increases their predictive power for drawing functional inferences, and demonstrate that some RNA polymerase mutants both decrease average cell length and confer insensitivity to killing by cell-wall targeting antibiotics. Our findings demonstrate that RNAP chemical-genetic interactions provide a general platform for interrogating structure-function relationships in vivo and for identifying physiological trade-offs of mutations, including those relevant for disease and biotechnology. This strategy should have broad utility for illuminating the role of other important protein complexes.

opencc-zeroJul 2018View details →

Genetic structuring in a Neotropical palm analyzed through an Andean orogenesis‐scenario

Andean orogenesis has driven the development of very high plant diversity in the Neotropics through its impact on landscape evolution and climate. The analysis of the intraspecific patterns of genetic structure in plants would permit inferring the effects of Andean uplift on the evolution and diversification of Neotropical flora. In this study, using microsatellite markers and Bayesian clustering analyses, we report the presence of four genetic clusters for the palm Oenocarpus bataua var. bataua which are located within four biogeographic regions in northwestern South America: (a) Chocó rain forest, (b) Amotape-Huancabamba Zone, (c) northwestern Amazonian rain forest, and (d) southwestern Amazonian rain forest. We hypothesize that these clusters developed following three genetic diversification events mainly promoted by Andean orogenic events. Additionally, the distinct current climate dynamics among northwestern and southwestern Amazonia may maintain the genetic diversification detected in the western Amazon basin. Genetic exchange was identified between the clusters, including across the Andes region, discarding the possibility of any cluster to diversify as a distinct intraspecific variety. We identified a hot spot of genetic diversity in the northern Peruvian Amazon around the locality of Iquitos. We also detected a decrease in diversity with distance from this area in westward and southward direction within the Amazon basin and the eastern Andean foothills. Additionally, we confirmed the existence and divergence of O. bataua var. bataua from var. oligocarpus in northern South America, possibly expanding the distributional range of the latter variety beyond eastern Venezuela, to the central and eastern Andean cordilleras of Colombia. Based on our results, we suggest that Andean orogenesis is the main driver of genetic structuring and diversification in O. bataua within northwestern South America.

opencc-zeroJul 2019View details →

Data from: Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex

Taxonomy has traditionally relied on morphological and ecological traits to interpret and classify biological diversity. Over the last decade, technological advances and conceptual developments in the field of molecular ecology and systematics have eased the generation of genomic data and changed the paradigm of biodiversity analysis. Here we illustrate how traditional taxonomy has led to species designations that are supported neither by high throughput sequencing data nor by the quantitative integration of genomic information with other sources of evidence. Specifically, we focus on Omocestus antigai and O. navasi, two montane grasshoppers from the Pyrenean region that were originally described based on quantitative phenotypic differences and distinct habitat associations (alpine vs. Mediterranean-montane habitats). To validate current taxonomic designations, test species boundaries, and understand the factors that have contributed to genetic divergence, we obtained phenotypic (geometric morphometrics) and genome-wide SNP data (ddRADSeq) from populations covering the entire known distribution of the two taxa. Coalescent-based phylogenetic reconstructions, integrative Bayesian model-based species delimitation, and landscape genetic analyses revealed that populations assigned to the two taxa show a spatial distribution of genetic variation that do not match with current taxonomic designations and is incompatible with ecological/environmental speciation. Our results support little phenotypic variation among populations and a marked genetic structure that is mostly explained by geographic distances and limited population connectivity across the abrupt landscapes characterizing the study region. Overall, this study highlights the importance of integrative approaches to identify taxonomic units and elucidate the evolutionary history of species.

opencc-zeroDec 2016View details →

Data from: Different genetic structures revealed resident populations of a specialist parasitoid wasp in contrast to its migratory host

Genetic comparisons of parasitoids and their hosts are expected to reflect ecological and evolutionary processes that influence the interactions between species. The parasitoid wasp, Cotesia vestalis, and its host diamondback moth (DBM), Plutella xylostella, provide opportunities to test whether the specialist natural enemy migrates seasonally with its host or occurs as resident population. We genotyped 17 microsatellite loci and two mitochondrial genes for 158 female adults of C. vestalis collected from 12 geographical populations, as well as nine microsatellite loci for 127 DBM larvae from six separate sites. The samplings covered both the likely source (southern) and immigrant (northern) areas of DBM from China. Populations of C. vestalis fell into three groups, pointing to isolation in northwestern and southwestern China and strong genetic differentiation of these populations from others in central and eastern China. In contrast, DBM showed much weaker genetic differentiation and high rates of gene flow. TESS analysis identified the immigrant populations of DBM as showing admixture in northern China. Genetic disconnect between C. vestalis and its host suggests that the parasitoid did not migrate yearly with its host but likely consisted of resident populations in places where its host could not survive in winter.

opencc-by-4.0Dec 2020View details →

Convergent geographic patterns between grizzly bear population genetic structure and Indigenous language groups in coastal British Columbia

Microsatellite loci calls, sex, and mean centre detection per individual (GrizzlyMicroLociMeanXY.csv) and code associated with the paper: "Convergent geographic patterns between grizzly bear population genetic structure and Indigenous language groups in coastal British Columbia". All code is from published R packages or GitHub repositories not created by the author. Code used is best described in these alternate resources.

opencc-zeroDec 2023View details →

Data for: Genetic structuring and species boundaries in the Atlantic stony coral Favia (Scleractinia, Faviidae)

Scleractinian corals are the main modern builders of coral reefs, dynamic ecosystems that are hot spots of marine biodiversity. Southern Atlantic reef corals are understudied compared to their Caribbean and Indo-Pacific counterparts and many hypotheses about their population dynamics demand further testing. We employed thousands of single nucleotide polymorphisms (SNPs) recovered via ezRAD to characterize genetic population structuring and species boundaries in the amphi-Atlantic hard coral genus Favia. Coalescent-based species delimitation (BFD* - Bayes factor delimitation) recovered F. fragum and F. gravida as separate species. Although our results agree with depth-related genetic structuring in F. fragum, they did not support incipient speciation of the "tall" and "short" morphotypes. The preferred scenario revealed a split between two main lineages of F. gravida, one from Ascension Island and the other from Brazil. The Brazilian lineage is further divided into a species that occurs throughout the Northeastern coast and another that ranges from the Abrolhos Archipelago to the state of Espírito Santo. BFD* scenarios were supported by analysis of datasets with varying levels of missing data. Our results challenge current notions about Atlantic reef corals because they uncovered surprising genetic diversity in Favia and rejected the long-standing hypothesis that Abrolhos Archipelago may have served as a Pleistocenic refuge during the last glaciations.

opencc-by-4.0Apr 2024View details →

Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts

Genetic variations are instrumental for unraveling phage evolution and deciphering their functional implications. Here we explore the underlying fine-scale genetic variations in the gut phageome, especially structural variations (SVs). By employing virome-enriched long-read metagenomics sequencing across 91 individuals, we identified a total of 14,438 non-redundant phage SVs, and revealed their prevalence within the human gut phageome. These SVs are mainly enriched in genes involved in recombination, DNA methylation, and antibiotic resistance. Strikingly, a substantial fraction of phage SV sequences share close homology with bacterial fragments, with most SVs enriched for horizontal gene transfer (HGT) mechanism. Further investigations showed that these SV sequences were genetic exchanged between specific phage-bacteria pairs, particularly between phages and their respective bacterial hosts. Temperate phages exhibits a higher frequency of genetic exchange with bacterial chromosomes then virulent phages. Collectively, our findings provide novel insights into the genetic landscape of the human gut phageome.

opencc-zeroDec 2021View details →

Data from: Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe

Context. Plant populations in agricultural landscapes are mostly fragmented and their functional connectivity often depends on seed and pollen dispersal by animals. However, little is known about how the interactions of seed and pollen dispersers with the agricultural matrix translate into gene flow among plant populations. Objectives. We aimed to identify effects of the landscape structure on the genetic diversity within, and the genetic differentiation among, spatially isolated populations of three temperate forest herbs. We asked, whether different arable crops have different effects, and whether the orientation of linear landscape elements relative to the gene dispersal direction matters. Methods. We analysed the species' population genetic structures in seven agricultural landscapes across temperate Europe using microsatellite markers. These were modelled as a function of landscape composition and configuration, which we quantified in buffer zones around, and in rectangular landscape strips between, plant populations. Results. Landscape effects were diverse and often contrasting between species, reflecting their association with different pollen- or seed dispersal vectors. Differentiating crop types rather than lumping them together yielded higher proportions of explained variation. Some linear landscape elements had both a channelling and hampering effect on gene flow, depending on their orientation. Conclusions. Landscape structure is a more important determinant of the species' population genetic structure than habitat loss and fragmentation per se. Landscape planning with the aim to enhance the functional connectivity among spatially isolated plant populations should consider that even species of the same ecological guild might show distinct responses to the landscape structure.