Find research datasets worth reusing

opencc-zeroOct 2022View details →

Data from: Local adaptation in shell shape traits of a brooding chiton with strong population genomic differentiation

Comparing divergence in quantitative traits and neutral molecular markers, such as QST–FST comparisons, provides a means to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. Onithochiton neglectus (Rochebrune, 1881) is a morphologically variable chiton endemic to New Zealand, with populations distributed over a broad latitudinal environmental gradient. In this species, the morphological variants cluster into two geographically separated shell shape groups, and the phenotypic variation in shell shape has been hypothesised to be adaptive. Here, we assessed this hypothesis by comparing neutral genomic differentiation between populations (FST) with an index of phenotypic differentiation (PST). We used 7,562 putatively neutral single nucleotide polymorphisms (SNPs) across 15 populations and three clades of O. neglectus throughout New Zealand to infer FST. PST was calculated from 18 shell shape traits and gave highly variable estimates across populations, clades and shape groups. By systematically comparing PST with FST, we identified evidence of local adaptation in a number of the O. neglectus shell shape traits. This supports the hypothesis that shell shape could be an adaptive trait, potentially correlated with the ability to live and raft in kelp holdfasts.

opencc-by-4.0Dec 2017View details →

Correcting for population stratification reduces false positive and false negative results in joint analyses of host and pathogen genomes [G2G-Simulator: Simulated dataset]

Data associated with the paper 'Correcting for population stratification reduces false positive and false negative results in joint analyses of host and pathogen genomes'. It contains the raw simulated data from the 'G2G-Simulator' program.  Those data need to be loaded in a R environment . You can reproduce plots present in the paper by parsing the R object using the script 'parse_paper_data.R' present in the G2G-Simulator GitHub repository (https://github.com/onaret/G2G-Simulator/paper/parse_paper_dataset.R).

opencc-by-4.0Nov 2023View details →

FIGURE 2 in Complete mitochondrial genome of four Scleromystax barbatus (Siluriformes: Callichthyidae) populations

FIGURE 2 | Phylogenetic analysis of 13 Corydoradinae and Hoplosternum littorale (Callichthyinae member) species as the outgroup based on the nucleotide sequences of 13 PCGs from the mitochondrial genome. Bootstrap values are shown next to nodes and the scale bar shows 0.03 changes. Population codes in Tab. 1.

opencc-by-4.0Nov 2023View details →

FIGURE 1 in Complete mitochondrial genome of four Scleromystax barbatus (Siluriformes: Callichthyidae) populations

FIGURE 1 | A. Geographic location of the Scleromystax barbatus populations in coastal Atlantic Rainforest rivers. B. Male of S. barbatus. Photo by Caio Feltrin. C. Complete mitochondrial genome of S. barbatus from the AR population. Population codes in Tab. 1.

opencc-by-4.0May 2024View details →

Data for publication: A pipeline for in-depth analysis of DNA virus populations by profiling the low abundant virus variants and partial genomic components

Raw and processed sequence data from Oxford Nanopore and BGI short read sequencing platforms used in the publication: "A pipeline for in-depth analysis of DNA virus populations by profiling the low abundant virus variants and partial genomic components".

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-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.

Fig. 3 in Partial molecular characterization of the mitochondrial genome of Baylisascaris columnaris and prevalence of infection in a wild population of Striped skunks

Fig. 3. Single nucleotide polymorphisms in the ND2 gene of B. columnaris, compared to B. procyonis. Nucleotide position numbers are shown at the top of the figure. Speciesspecific SNPs are shown in bold.

Fig. 1 in Partial molecular characterization of the mitochondrial genome of Baylisascaris columnaris and prevalence of infection in a wild population of Striped skunks

Fig. 1. Single nucleotide polymorphisms in the Cox1 gene of B. columnaris, compared to B. procyonis. Nucleotide position numbers are shown at the top of the figure. Italicized numbers represent the position number from a previously published partial sequence of the B. columnaris Cox1 gene (Franssen et al., 2013). Species-specific SNPs are shown in bold.

Fig. 2 in Partial molecular characterization of the mitochondrial genome of Baylisascaris columnaris and prevalence of infection in a wild population of Striped skunks

Fig. 2. Single nucleotide polymorphisms in the Cox2 gene of B. columnaris, compared to B. procyonis. Nucleotide position numbers are shown at the top of the figure. Italicized numbers represent the position number from a previously published partial sequence of the B. columnaris Cox2 gene (Franssen et al., 2013).

Fig. 4 in Partial molecular characterization of the mitochondrial genome of Baylisascaris columnaris and prevalence of infection in a wild population of Striped skunks

Fig. 4. Single nucleotide polymorphisms in several tRNA genes of B. columnaris, compared to B. procyonis, B. transfuga and B. schroederi. Nucleotide position numbers are shown at the top of the figure. SNPs which distinguish B. columnaris from other Baylisascaris species are shown in bold.

opencc-by-4.0Sep 2024View details →

Datasets: Population genomics and mitochondrial DNA reveal cryptic diversity in North American Spring Cavefishes (Amblyopsidae, Forbesichthys)

Forbesichthys_allsites.vcf: Dataset in VCF format used to perform Effective Population Size estimation. Forbesichthys_SNPs_NoLD.vcf: Dataset in VCF format used to perform PCA, fastStrucuture, and phylogenetic analyses. Files with extension .sfs contain site spectrum frequencies generated with the program easySFS.py.

opencc-by-4.0Feb 2024View details →

Genome streamlining: effect of mutation rate and population size on genome size reduction: simulated data

Lineages data of populations simulated with Aevol (<a href="https://gitlab.inria.fr/aevol/aevol">https://gitlab.inria.fr/aevol/aevol</a>), and the Wild-Types sequences used for that. Conditions: change of mutation rate, population size, or both. Mutational bias: none, insertion bias or deletion bias

openother-openJun 2021View details →

Code and data associated with Christiansen et al. 2021 "Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing"

All code and data input and output files (except reference genome and raw sequencing data) needed to reproduce the results of Christiansen et al. 2021 as released on <a href="https://github.com/notothen/radpilot">https://github.com/notothen/radpilot</a> alongside journal publication. See published paper: Christiansen, H., Heindler, F.M., Hellemans, B. et al. Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. BMC Genomics 22, 625 (2021). <a href="https://doi.org/10.1186/s12864-021-07917-3">https://doi.org/10.1186/s12864-021-07917-3</a>

opencc-zeroJul 2021View details →

The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern

Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels (Urocitellus brunneus – NIDGS, and U. endemicus - SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with restriction site-associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both the inter- and intraspecific level, and identified putatively adaptive SNPs using population structure outlier detection and genotype-environment association (GEA) analyses. At the interspecific level, we detected a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation putatively linked to torpor patterns. At the intraspecific level, we found evidence of both neutral and adaptive differentiation. For NIDGS, elevation appears to be the main driver of adaptive differentiation, while neutral variation patterns match and expand information on the low connectivity between some populations identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected natural geographic barriers, while adaptive variation reflected differences in land cover and temperature, as well as elevation. These results clearly highlight the roles of neutral and adaptive processes for understanding the complexity of the processes leading to species and population differentiation, which can have important conservation implications in susceptible and threatened species.

opencc-by-4.0Oct 2020View details →

REPIN population analysis in 4 Dokdonia genomes

This dataset is the output of RAREFAN (http://rarefan.evolbio.mpg.de/) a webserver to identify REPIN populations across an entire bacterial species. The data was created using the following command "java -jar -Xmx10g rarefan.jar dokdonia/in/ dokdonia/out/ 4h-3-7-5.fas 55 21 in/yafM_Ecoli.faa dokdonia.nwk 1e-10 true 1" All input files are located in the folder dokdonia/in/, all output data is located in dokdonia/out/. The input files include the 4 fasta formatted Dokdonia genome files (*.fas) and a RAYT protein sequence called yafM_Ecoli.faa. The output files include the following: A phylogenetic tree "dokdonia.nwk" of all genomes generated with andi (<a href="http://github.com/evolbioinf/andi/">http://github.com/evolbioinf/andi/</a>) and clustDist (http://guanine.evolbio.mpg.de/problemsBook/node1.html). A file containing the frequencies of all 21bp long sequences found in the 4h-3-7-5 genome: 4h-3-7-5.wfr A file containing all 21bp long sequences that occur more frequently than 55 times in the 4h-3-7-5 genome: 4h-3-7-5.overrep A file containing information on the RAYTs and their cooccurrence with different REPIN populations: prox.stats A file containing the nucleotide sequences of all yafM_Ecoli.faa relatives identified with BLAST+ in the Dokdonia species: yafM_relatives.fna maxREPIN_0.txt Contains the most frequent REPIN identified for each sequence type in each Dokdonia strain.  presAbs_0.txt Contains for each strain information on the number of RAYTs, the number of REPINs, the master sequence, the number of master sequences, the entire REP/REPIN population size, the number of REPIN clusters that contain more than 10 sequences, all REPINs in the population as well as all REPINs that differ to the master sequences in at most three nucleotides. rayt_[strain name].tab contains location information for each identified RAYT relative for each strain. The files can be viewed with artemis. results.txt contains for each strain the frequency of the six identified 21bp long seeds. There is one folder called groupSeedSequences, which includes the data for identifying the most common 21 bp long sequences in D. sp. 4h-3-7-5. All 21bp long sequences in the genome that occur more frequently than 55 times are sorted into 6 sequence groups. These sequence groups are stored in the files Group_4h-3-7-5_*.out and .out.fas. There is also a 4h-3-7-5_words.tab file, which contains the locations of all overrepresented 21bp long sequences in the 4h-3-7-5 genome. This file can be viewed in artemis (https://www.sanger.ac.uk/tool/artemis/) together with the 4h-3-7-5 genome file. The most common sequence in each group is used as a seed sequence to determine REPIN populations across all 4 genomes.   For each genome there is one output folder (ending in _0), for each sequence group one. Each folder contains the following files: *.dd: Degree distribution of the REPIN network, where each REPIN is a node. A REPIN is connected to another REPIN if they differ in exactly one position. The degree distribution is a histogram of the number of connections of all the nodes.  *.hist For the largest sequence cluster determined by mcl that consists of REPINs (two REPs in inverted orientation) this file contains the number of REPINs in each sequence class. Sequence class 0 is the master sequence. By definition the most common REPIN in the sequence population. Sequence class 1 contains all REPINs differing in exactly one position to the master sequence. Sequence class 2 contains REPINs differing in 2 positions etc. *.mcl Contains the clustering output by mcl. Each line contains the member of a cluster. Lines are sorted by cluster size. *.mw Contains the most common 21bp long sequence and its frequency in the genome, which is the basis for identifying first all related REP sequences and from those the REPINs formed by these REP sequences. *.nodes The identity and frequency of all REPINs and REP sequences for either all sequences or only for the largest sequence cluster. *.ss Contains REPINs and REP sequences as well as their positions in fasta format. Position information starts with the location in genome fasta file (first sequence is 0...) followed by the start and end position of the entire REPIN/REP sequence.   *.ss.REP REP sequence information in fasta format. *.tab Location in tab format. Can be used to display locations of REPs and REPINs in the genome via artemis. *_[0-9].ss Contains REPIN/REP sequence information for each subcluster separately. *_[0-9].tab Contains the location of REP/REPINs for each subcluster separately for viewing in artemis. *allSeed.nw Contains network connections between nodes of all sequences. Can be used to view network in for example R or cytoscape together with the nodes file. *largestCluster.nodes Information on nodes only from the largest REPIN cluster. *largestCluster.ss *.ss file for the largest REPIN cluster. *largestCluster.tab *.tab file for the largest REPIN cluster. *_rayt_repin_prox.txt shows which REPIN/REP cluster is in proximity to any of the RAYT genes identified in the genome (within 200bp). And a subfolder that contains the complete sequences (including the variable region) for all identified REPs and REPINs. The dataset was generated using the following external tools: andi for tree building: B Haubold, F Klötzl, and P Pfaffelhuber. andi: fast and accurate estimation of evolutionary distances between closely related genomes. Bioinformatics, 2015 vol. 31 (8) pp. 1169-1175. MCL for REPIN population clustering: A J Enright, S Van Dongen, and C A Ouzounis. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research, 2002 vol. 30 (7) pp. 1575-1584. BLAST+ for identifying RAYT relatives in the different genomes: C Camacho, G Coulouris, V Avagyan, N Ma, J Papadopoulos, K Bealer, and T L Madden. BLAST+: architecture and applications. BMC Bioinformatics, 2009 vol. 10 (1) pp. 421-9.

opencc-by-4.0Dec 2022View details →

Data from: Cost-saving population genomic investigation of Daphnia longispina complex resting eggs using whole genome amplification and pre-sequencing screening

This dataset contains all paired MiSeq sequences that were generated for the study "Cost-saving population genomic investigation of Daphnia longispina complex resting eggs using whole genome amplification and pre-sequencing screening" by Nickel and Cordellier. The sample names used in the study and the associated file names are explained in the table "Study_sample_names.xlsx"

opencc-zeroJan 2023View details →

Data for: Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia

Genomic diversity is a fundamental component of Earth's total biodiversity and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (Mesembriomys gouldii), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species' range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches.

opencc-zeroJan 2023View details →

Whole genome demographic models indicate divergent effective population size histories shape contemporary genetic diversity gradients in a montane bumble bee

Understanding historical range shifts and population size variation provides important context for interpreting contemporary genetic diversity. Methods to predict changes in species distributions and model changes in effective population size (Ne) using whole genomes make it feasible to examine how temporal dynamics influence diversity across populations. We investigate Ne variation and climate-associated range shifts to examine the origins of a previously observed latitudinal heterozygosity gradient in the bumble bee Bombus vancouverensis Cresson (Hymenoptera: Apidae: Bombus Latreille) in western North America. We analyze whole genomes from a latitude-elevation cline using sequentially Markovian coalescent models of Ne through time to test whether relatively low diversity in southern high-elevation populations is a result of long-term differences in Ne. We use Maxent models of the species range over the last 130,000 years to evaluate range shifts and stability. Ne fluctuates with climate across populations, but more genetically diverse northern populations have maintained greater Ne over the late Pleistocene and experienced larger expansions with climatically favorable time periods. Northern populations also experienced larger bottlenecks during the last glacial period which matched the loss of range area near these sites, however, bottlenecks were not sufficient to erode diversity maintained during periods of large Ne. A genome sampled from an island population indicated a severe postglacial bottleneck, indicating that large recent post-glacial declines are detectable if they have occurred. Genetic diversity was not related to niche stability or glacial-period bottleneck size. Instead, spatial expansions and increased connectivity during favorable climates likely maintain diversity in the north while restriction to high elevations maintains relatively low diversity despite greater stability in southern regions. Results suggest genetic diversity gradients reflect long-term differences in Ne dynamics and also emphasize the unique effects of isolation on insular habitats for bumble bees. Patterns are discussed in the context of conservation under climate change.