Find research datasets worth reusing

opencc-by-4.0Nov 2021View details →

VCF data for genetic polyploid phasing

Used data for evaluation in pending Recomb 2022 submission "Genetic Polyploid Phasing using Marker Signals from Low-Depth Progeny Samples". Data was used in and partly created by the scripts from here: https://github.com/AlBi-HHU/genetic-phasing-scripts

opencc-by-4.0Jul 2021View details →

Local chromatin context dictates the genetic determinants of the heterochromatin spreading reaction. Analysis Code, Numerical and Primary data.

Uploaded under this Zenodo DOI is the following: 1. the Analysis Code used for Flow Cytometry analysis in the paper, GO complex analysis (Figure 3) and Hit visualization (Figure 1, 2 S1, S4 Figs). 2. The primary Flow Cytometry data from both the initial screen (ScreenFlowFCS) and validation experiments (ValidationFlowFCS) are included as .zip files. 3. a .zip folder is uploaded that contains all the analysis code for the ChIP-Seq experiments.  4. Excel worksheets that contain the numerical source data for all qPCR bar plots.

opencc-zeroMay 2022View details →

Data from: Inversion Invasions: when the genetic basis of local adaptation is concentrated within inversions in the face of gene flow

Across many species where inversions have been implicated in local adaptation, genomes often evolve to contain multiple, large inversions that arise early in divergence. Why this occurs has yet to be resolved. To address this gap, we built forward-time simulations in which inversions have flexible characteristics and can invade a metapopulation undergoing spatially divergent selection for a highly polygenic trait. In our simulations, inversions typically arose early in divergence, captured standing genetic variation upon mutation, and then accumulated many small-effect loci over time. Under special conditions, inversions could also arise late in adaptation and capture locally adapted alleles. Polygenic inversions behaved similarly to a single supergene of large effect and were detectable by genome scans. Our results show that characteristics of adaptive inversions found in empirical studies (e.g., multiple large, old inversions that are FST outliers, sometimes overlapping with other inversions) are consistent with a highly polygenic architecture, and inversions do not need to contain any large-effect genes to play an important role in local adaptation. By combining a population and quantitative genetic framework, our results give a deeper understanding of the specific conditions needed for inversions to be involved in adaptation when the genetic architecture is polygenic.

opencc-by-4.0Jun 2022View details →

Characterization data for the manuscript: "Using genetic algorithms to systematically improve the synthesis conditions of Al-PMOF"

This entry contains characterization data for the manuscript "Using genetic algorithms to systematically improve the synthesis conditions of Al-PMOF", which we exported from the electronic lab notebook (ELN). To visualize the data in this dataset: <a href="https://www.cheminfo.org/flavor/zenodo/index.html?id=6620502">open entry</a>

opencc-by-4.0Jul 2022View details →

data for "Plant genetic effects on microbial hubs impact host fitness in repeated field trials"

These are data tables required for the analysis of the paper "Plant genetic effects on microbial hubs impact host fitness in repeated field trials".  All scripts are available at https://forgemia.inra.fr/bbrachi/microbiota_paper.git The folder architecture in the zip files is the same as in the repository: https://forgemia.inra.fr/bbrachi/microbiota_paper.git The dataset includes:  - OTU count tables for 16S and ITS - taxonomic assignation - plant seed-set estimates - plant growth data from the B38 experiment.  - Metabolomics datasets

opencc-zeroJul 2022View details →

Data from: Genetic, maternal, and environmental influences on sociality in a pedigreed primate population

Various aspects of sociality in mammals (e.g., dyadic connectedness) are linked with measures of biological fitness (e.g., longevity). How within- and between-individual variation in relevant social traits arises in uncontrolled wild populations is challenging to determine but is crucial for understanding constraints on the evolution of sociality. We use an advanced statistical method, known as the 'animal model', which incorporates pedigree information, to look at social, genetic, and environmental influences on sociality in a long-lived wild primate. We leverage a longitudinal database spanning 20 years of observation on individually recognized white-faced capuchin monkeys (Cebus capucinus imitator), with a multi-generational pedigree. We analyze two measures of spatial association, using repeat sampling of 376 individuals (mean: 53.5 months per subject, range: 6-185 months per subject). Conditioned on the effects of age, sex, group size, seasonality , and El Niño–Southern Oscillation phases, we show low to moderate long-term repeatability (across years) of the proportion of time spent social (posterior mode [95% Highest Posterior Density interval]: 0.207 [0.169, 0.265]) and of average number of partners (0.144 [0.113, 0.181]) (latent scale). Most of this long-term repeatability could be explained by modest heritability (h2social: 0.152 [0.094, 0.207]; h2partners: 0.113 [0.076, 0.149]) with small long-term maternal effects (m2social: 0.000 [0.000, 0.045]; m2partners: 0.000 [0.000, 0.041]). Our models capture the majority of variance in our behavioral traits, with much of the variance explained by temporally changing factors, such as group of residence, highlighting potential limits to the evolvability of our trait due to social and environmental constraints.

opencc-by-4.0May 2022View details →

Data to accompany the publication "Combined biophysical and genetic modelling approaches reveal complementary information about population connectivity of New Zealand green-lipped mussels"

Data to accompany the publication "Combined biophysical and genetic modelling approaches reveal complementary information about population connectivity of New Zealand green-lipped mussels".  migrationmatrix14.txt contains the particle tracking matrix, with the total number of particles that migrated from row i to column j (out of a total of 2217864 particles released per population). mussel_microsat_Genepop.txt contains the microsatellite data for each population in Genepop format.

opencc-zeroSep 2022View details →

Epidendrum radicans - genetic data of 4 regional populations

Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (N = 690) of the terrestrial orchid, Epidendrum radicans, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (N = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (He = 0.092 – 0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 versus 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from in situ reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally larger on the older sites (≤ 8m versus ≤ 3m).

opencc-zeroSep 2022View details →

Epidendrum radicans – x, y coordinates and genetic data of individuals within 5 focal populations

Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (N = 690) of the terrestrial orchid, Epidendrum radicans, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (N = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (He = 0.092–0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 versus 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from in situ reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally larger on the older sites (≤ 8m versus ≤ 3m).

opencc-zeroMay 2024View details →

Data from: Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity

A paradoxical finding from genome-wide association studies (GWAS) in plants is that variation in metabolite profiles typically maps to a small number of loci, despite the complexity of underlying biosynthetic pathways. This discrepancy may partially arise from limitations presented by geographically diverse mapping panels. Properties of metabolic pathways that impede GWAS by diluting the additive effect of a causal variant, such as allelic and genic heterogeneity and epistasis, would be expected to increase in severity with the geographic range of the mapping panel. We hypothesized that a population from a single locality would reveal an expanded set of associated loci. We tested this in a French Arabidopsis thaliana population (< 1 km transect) by profiling and conducting GWAS for glucosinolates, a suite of defensive metabolites that have been studied in depth through functional and genetic mapping approaches. For two distinct classes of glucosinolates, we discovered more associations at biosynthetic loci than previous GWAS with continental-scale mapping panels. Candidate genes underlying novel associations were supported by concordance between their observed effects in the TOU-A population and previous functional genetic and biochemical characterization. Local populations complement geographically diverse mapping panels to reveal a more complete genetic architecture for metabolic traits.

opencc-by-4.0May 2024View details →

Data and codes from "Daniel et al. What can optimized cost distances based on genetic distances offer? A simulation study on the use and misuse of ResistanceGA"

Data and codes used for “Daniel et al. What can optimized cost distances based on genetic distances offer? A simulation study on the use and misuse of ResistanceGA”

opencc-zeroMay 2024View details →

Data and code from: Evaluating genomic offset predictions in a forest tree with high population genetic structure

Predicting how tree populations will respond to climate change is an urgent societal concern. An increasingly popular way to make such predictions is the genomic offset (GO) approach, which aims to use genomic and climate data to identify populations that may experience climate maladaptation in the near future. More precisely, GO tries to represent the change in allele frequencies required to maintain the current gene-climate relationships under climate change. However, the GO approach has major limitations and, despite promising validation of its predictions using height data from common gardens, it still lacks broad empirical testing. In the present study, we evaluated the consistency and empirical validity of GO predictions in maritime pine (Pinus pinaster Ait.), a tree species from southwestern Europe and North Africa with a marked population genetic structure. First, gene-climate relationships were estimated using 9,817 SNPs genotyped in 454 trees from 34 populations; and candidate SNPs potentially involved in climate adaptation were identified. Second, GO was predicted using four methods, namely Gradient Forest (GF), Redundancy Analysis (RDA), latent factor mixed model (LFMM) and Generalised Dissimilarity Modeling (GDM), two sets of SNPs (candidate and control SNPs) and five climate general circulation models (GCMs) to account for uncertainty in future climate predictions. Last, the empirical validity of GO predictions was evaluated within a Bayesian framework by estimating the associations between GO predictions and two independent data sources: mortality data from National Forest Inventories (NFI), and mortality and height data from five common gardens in contrasting environments. We found high variability in GO predictions across methods, SNP sets and GCMs. Regarding validation, GO predictions with GDM and GF (and to a lesser extent RDA) based on the candidate SNPs showed the strongest and most consistent associations with mortality rates in common gardens and NFI plots. We found almost no association between GO predictions and tree height in common gardens, most likely due to the overwhelming effect of population genetic structure on tree height in this species. Our study demonstrates the imperative to validate GO predictions with a range of independent data sources before they can be used as informative and reliable metrics in conservation or management strategies.

opencc-by-4.0Dec 2023View details →

Elution profiles and protein interaction data accompanying "Ancient eukaryotic protein interactions illuminate modern genetic disorders"

<div>   <table> <tbody> <tr> <td> <h2>DESCRIPTION</h2> </td> <td> <h2>FILENAME</h2> </td> <td> <h2>LOCATION</h2> </td> </tr> <tr> <td> LECA 10K OG set </td> <td> leca_ogs_annotated.xlsx </td> <td> Paper, Table S1 Zenodo </td> </tr> <tr> <td> Summary of biological resources </td> <td> resource_summary.xlsx </td> <td> Paper, Table S2 Zenodo </td> </tr> <tr> <td> LECA interactome (complexes) </td> <td> leca_ppis_fdr10_clustered_annotated.xlsx </td> <td> Paper, Table S3 Zenodo </td> </tr> <tr> <td> CFMS - ref proteomes </td> <td> cfms_ref_proteomes.xlsx </td> <td> Paper, Table S4 Zenodo </td> </tr> <tr> <td> ML - top algorithms </td> <td> tpot_top_algorithms.xlsx </td> <td> Paper, Table S5 Zenodo </td> </tr> <tr> <td> LECA interactome (pairwise) </td> <td> leca_ppis_fdr10_pairwise.csv </td> <td> Zenodo </td> </tr> <tr> <td> UniProt Subcellular Localization IDs </td> <td> uniprot_localization_codes.xlsx </td> <td> Zenodo </td> </tr> <tr> <td> Dollo parsimony - ref proteomes </td> <td> dollo_parsimony_ref_proteomes.xlsx </td> <td> Zenodo </td> </tr> <tr> <td> Dollo parsimony - input trait matrix </td> <td> dollo_parsimony_count_matrix.tsv </td> <td> Zenodo </td> </tr> <tr> <td> CFMS - raw elution profiles </td> <td> amorphea_raw_elution_vectors.csv excavata_raw_elution_vectors.csv tsar_raw_elution_vectors.csv archaeplastida_raw_elution_vectors.csv </td> <td> Zenodo </td> </tr> <tr> <td> CFMS - normalized elution profiles </td> <td> amorphea_norm_elution_vectors.csv excavata_norm_elution_vectors.csv tsar_norm_elution_vectors.csv archaeplastida_norm_elution_vectors.csv </td> <td> Zenodo </td> </tr> <tr> <td> CFMS/APMS - complete feature matrix </td> <td> feature_matrix.csv </td> <td> Zenodo </td> </tr> <tr> <td> ML - top features </td> <td> linearsvc_top_100_features.xlsx </td> <td> Zenodo </td> </tr> <tr> <td> OMIM disease propagation, statistics </td> <td> omim_disease_propagation_stats.xlsx </td> <td> Zenodo </td> </tr> <tr> <td> OMIM disease propagation, top 20 hits per disease </td> <td> omim_disease_propagation_top20hits_per_disease.xlsx </td> <td> Zenodo </td> </tr> <tr> <td> Curated OMIM gene-disease relationships for LECA OGs </td> <td> omim_disease_network.tsv </td> <td> Zenodo </td> </tr> <tr> <td>Curated OMIM gene-disease relationships for human UniProt IDs</td> <td>omim_disease_groups.csv</td> <td>Zenodo</td> </tr> </tbody> </table> </div>

opencc-zeroMay 2024View details →

Data from: Female-biased population sex ratios caused by genetic rather than ecological mechanisms in dwarf willow (Salix herbacea L.)

Biased sex ratios among reproductive individuals are common in plants, but the underlying mechanisms, as well as the evolutionary consequences, are not well understood. The classical theory of Düsing and Fisher predicts an equal primary sex ratio at seed production, based on the selective advantage of the rare sex. Biased sex ratios among reproductive plants can arise from sexual dimorphism in survival and flowering. Sex ratio biases can also be present from the seed stage; in these cases, assumptions of Düsing's and Fisher's theory, for example, random mating or demographic equilibrium, are thought to be violated. We investigated mechanisms leading to female-biased sex ratios in the arctic-alpine dwarf willow Salix herbacea L. We studied sex ratios in three natural populations over three years as well as in 29 crosses (full-sib families) under controlled conditions over four growth periods. We tested whether sex ratio was associated with habitat parameters (elevation and snowmelt time), or with germination, survival or flowering, and whether females and males differed in size or flowering that may cause observation bias. We detected a strong and consistent female bias, both in natural populations (sex ratio [proportion of females]: 0.71-0.82) and in our controlled experiment (overall sex ratio: 0.70-0-72). Female bias became more pronounced with increasing elevation. Our data did not support sexual dimorphism in size or flowering. Family sex ratios varied largely (from 0.25 to 1), including many female-biased families, unbiased families and two male-biased families. Families with lower germination, seedling establishment, survival or flowering did not have stronger female bias, indicating that intrinsically higher survival or flowering in females does not explain overall female bias. Synthesis: Our results suggest that sex ratio bias in S. herbacea is already present in seeds and does not arise through intrinsic differences between sexes. Candidate mechanisms that can lead to both overall female bias and variation in sex ratio among families are meiotic drive or cyto-nuclear interactions. The pioneer habit of Salix may lead to non-equilibrium population dynamics that allow for the long-term persistence of variable genetic sex ratio distortion systems that arise from genetic conflict.

FIGURE 4 in One step closer but still far from solving the puzzle - The phylogeny of marine associated mites (Acari, Oribatida, Ameronothroidea) inferred from morphological and molecular genetic data

FIGURE 4 Bayesian inference topology based on 66 morphological traits of 102 oribatid mite species. Posterior probability values are shown near nodes. Photographs of selected species are given to provide an insight into the basic morphology of each larger group. *Photograph shows Tegeocranellus knysnaensis, this species was not used for the analyses but is given here to visualize the typical habitus of Tegeocranellus species.

FIGURE 3 in One step closer but still far from solving the puzzle - The phylogeny of marine associated mites (Acari, Oribatida, Ameronothroidea) inferred from morphological and molecular genetic data

FIGURE 3 One of 14 most parsimonious trees based on 66 characters or character states of 98 ameronothroid and four terrestrial oribatid mite species. Bootstrap values are shown near nodes. Colours refer to different families and are the same as in preceding figures.

FIGURE 1 in One step closer but still far from solving the puzzle - The phylogeny of marine associated mites (Acari, Oribatida, Ameronothroidea) inferred from morphological and molecular genetic data

FIGURE 1 Bayesian inference tree of marine associated Ameronothroidea and terrestrial outgroups based on 18S sequences. Posterior probabilities>0.9 are shown near nodes; abbreviations: PRT – Portugal, DE – Germany, DR – Dominican Republic, JP – Japan, TW – Taiwan, MY – Malaysia; families are given in different colours. Photographs of selected species are given to provide an insight into the basic habitus of each larger group.

FIGURE 2 in One step closer but still far from solving the puzzle - The phylogeny of marine associated mites (Acari, Oribatida, Ameronothroidea) inferred from morphological and molecular genetic data

FIGURE 2 Bayesian topology based on the combined data set of coi, D3 and 18S sequences. Posterior probabilities>0.9 are shown near nodes; abbreviations: PRT – Portugal, DE – Germany, DR – Dominican Republic, TW – Taiwan.

opencc-by-4.0Nov 2021View details →

Fig. 2 in Morphological and genetic data suggest a complex pattern of inter-island colonisation and differentiation for mining bees (Hymenoptera: Anthophila: Andrena) on the Macaronesian Islands

Fig. 2 Median Joining network of Andrena species (Micrandrena) of the Canary Islands and the Madeira Archipelago. Circle size is relative to number of haplotype copies present in dataset. A branch represents a single nucleotide change (mutation); bars on branches represent inferred missing haplotypes (single nucleotide changes). LG La Gomera, LP La Palma. The colours correspond to those used to represent the location of species on islands in Fig. 1