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141 results for “invasion genomics”
Mitochondrial genome sequencing and analysis of the invasive Microstegium vimineum: a resource for systematics, invasion history, and management
<p>Table S1: Accession data for Microstegium samples included in this study.</p> <p>File S1: Alignment of Mitochondrial CDS for Poales mitochondrial sequences.</p> <p>File S2: SNP data for Microstegium vimineum mitochondrial variants.</p> <p>Figure S1: Transposable element content in the Microstegium vimineum mitogenome.</p> <p>Figure S2: Summary of Kraken2 output.</p> <p> </p>
Genomic analyses of phenotypic differences between native and invasive populations of diffuse knapweed (Centaurea diffusa)
<p>Invasive species represent excellent opportunities to study the evolutionary potential of traits important to success in novel environments. Although some ecologically-important traits have been identified in invasive species, little is typically known about the genetic mechanisms that underlie invasion success in non-model species. Here, we use a genome-wide association (GWAS) approach to identify the genetic basis of trait variation in the non-model, invasive, diffuse knapweed (<i>Centaurea diffusa </i>Lam.<i> </i>[Asteraceae]). To assist with this analysis, we have assembled the first draft genome reference and fully annotated plastome assembly for this species, and the one of the first from this large, weedy, genus, which is of major ecological and economic importance. We collected phenotype data from 372 individuals from four native and four invasive populations of <i>C. diffusa </i>grown in a common environment. Using these individuals, we produced reduced-representation genotype-by-sequencing (GBS) libraries and identified 7058 SNPs. We identify two SNPs associated with leaf width in these populations, a trait which significantly varies between native and invasive populations. In this rosette forming species, increased leaf width is a major component of increased biomass, a common trait in invasive plants correlated with increased fitness. Finally, we use annotations from <i>Arabidopsis thaliana</i> to identify 98 candidate genes that are near the associated SNPs and highlight several good candidates for leaf width variation.</p>
Data from: The genome of a globally invasive passerine, the common myna, Acridotheres tristis
<p>In an era of global climate change, biodiversity conservation is receiving increased attention. Conservation efforts are greatly aided by genetic tools and approaches, which seek to understand patterns of genetic diversity and how they impact species health and their ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions regarding adaptive potential, with a particular focus on how changes in genetic diversity and effective population size interact with novel selection regimes. The common myna (<em>Acridotheres tristis</em>) is a globally invasive passerine and is an excellent model species for research both into the persistence of low-diversity populations and the mechanisms of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna. We describe the genomic landscape of this species, including genome wide allelic diversity, methylation, repeats, and recombination rate, as well as an examination of gene family evolution. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, and reveal artefactual impacts of genetic bottlenecks on demographic analysis.</p>
Dataset for: The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range
<p>Data and analyses for Thia et al. "The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range" submitted to <em>Journal of Evolutionary Biology</em>.</p> <p>This repository comprises data and scripts used to replicate the analyses in this paper.</p> <p>The goals of this study were to: (1) assemble a draft reference genome for <em>Halotydeus destructor</em>; (2) perform a comparative analysis of acetylcholinesterase genes among different agricultural arthropod pests; (3) characterise the population genetic patterns among Australian <em>H. destructor</em> populations; and (4) perform demographic modelling to understand the evolutionary relationships between eastern and western populations of <em>H. destructor</em> in Australia.</p>
Tracing the introduction of the invasive common myna using population genomics
<p>The common myna (<em>Acridotheres tristis</em>) is one of the most invasive bird species in the world, yet its colonisation history is only partly understood. We identified the introduction history and population structure, and quantified the genetic diversity of myna populations from the native range in India and the introduced populations in New Zealand, Australia, Fiji, Hawaii, and South Africa, based on thousands of single nucleotide polymorphism markers in 814 individuals. We were able to identify the source population of mynas in several invasive locations: mynas from Fiji and Melbourne, Australia, were likely founded by individuals from a subpopulation in Maharashtra, India, while mynas in Hawaii and South Africa were likely independently founded by individuals from other localities in India. Our findings suggest that New Zealand mynas were founded by individuals from Melbourne, which, in turn, were founded by individuals from Maharashtra. We identified two genetic clusters among New Zealand mynas, divided by New Zealand's North Island's axial mountain ranges, confirming previous observations that mountains and thick forests may form barriers to myna dispersal. Our study provides a foundation for other population and invasion genomic studies and provides useful information for the management of this invasive species.</p>
Genomic analyses of phenotypic differences between native and invasive populations of diffuse knapweed (Centaurea diffusa)
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Data from: Population genomic insights into recent nutria (<em>Myocastor coypus</em>) invasion dynamics
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Data from: The genome of a globally invasive passerine, the common myna, Acridotheres tristis
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Dataset for: The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range
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Tracing the introduction of the invasive common myna using population genomics
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Data from: Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia
Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of α and ß diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the unit of spreading and invasion. Both genomic compartments support the hypotheses of a unique accidental introduction in the Mediterranean and of multiple invasion events in Southern Australia. In addition to helping with tracing the origin of invasion, bacterial communities exhibit metabolic functions that can potentially enhance adaptability and competitiveness of the consortium they form with their host. We thus hypothesize that low genetic diversities of both host and symbiont communities may contribute to the recent regression in the Mediterranean, in contrast with the persistence of highly diverse assemblages in southern Australia. This study supports the importance of scaling up from the host to the holobiont for a comprehensive understanding of invasions.
Data from: Genomic survey provides insights on the evolutionary changes during invasive European expansion of the mosquitofish (Gambusia holbrooki)
Biological invasions rank among the main global threats for biodiversity. The Eastern mosquitofish (Gambusia holbrooki) is considered one of the 100 world worst invasive species due to its high adaptation capability to new environments. Using the restriction-site-associated DNA tags (RADtags), introduced European locations were compared against native US mosquitofish populations to analyse genomic changes that occurred during invasive process of European locations. After filtering, 7724 RADtags containing only one SNP were retained for population studies. Comparative genomics indicated that 186 of these RADtags matched sequences in the transcriptome of Xyphophorus maculatus, the most closely related genome available. Genomic analyses showed that invasive populations show high reductions in diversity. Further, analyses of population structuring based on these data are concordant with previous analyses based on microsatellites. It is concluded that during the invasion process genetic drift was the main evolutionary force affecting patterns of diversity and population structure. While recognizing that positive selection could be masked by the strong drift during founder events, adaptive processes were evidenced in a reduced number of RADtags (<2%), with only one of these in a putative coding region. Surprisingly, balancing selection was detected in several coding RADtags, suggesting that the preservation of polymorphism in specific genes could be more important than the average population diversity for the population maintenance at any location, particularly for the survival of introduced populations.
Whole genome sequencing (WGS) data from invasive pine sawfly Diprion similis
<p>Biological introductions are unintended "natural experiments" that provide unique insights into evolutionary processes. Invasive phytophagous insects are of particular interest to evolutionary biologists studying adaptation, as introductions often require rapid adaptation to novel host plants. However, adaptive potential of invasive populations may be limited by reduced genetic diversity—a problem known as the "genetic paradox of invasions". One potential solution to this paradox is if there are multiple invasive waves that bolster genetic variation in invasive populations. Evaluating this hypothesis requires characterizing genetic variation and population structure in the invaded range. To this end, we assemble a reference genome and describe patterns of genetic variation in the introduced white pine sawfly, <em>Diprion</em> <em>similis</em>. This species was introduced to North America in 1914, where it has rapidly colonized the thin-needled eastern white pine (<em>Pinus</em> <em>strobus</em>), making it an ideal invasion system for studying adaptation to novel environments. To evaluate evidence of multiple introductions, we generated whole-genome resequencing data for 64 <em>D</em>. <em>similis</em> females sampled across the North American range. Both model-based and model-free clustering analyses supported a single population for North American <em>D</em>. <em>similis</em>. Within this population, we found evidence of isolation-by-distance and a pattern of declining heterozygosity with distance from the hypothesized introduction site. Together, these results support a single-introduction event. We consider implications of these findings for the genetic paradox of invasion and discuss priorities for future research in <em>D</em>. <em>similis</em>, a promising model system for invasion biology.</p>
Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti
<p><strong>* These authors contributed equally: </strong>Alejandro N. Lozada-Chávez, Irma Lozada-Chávez.</p> <h3> </h3> <h1>Supplementary Dataset</h1> <p> </p> <p>This repository contains the <strong> Supplementary Data (from 1 to 12) </strong>cited in our paper "Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti" in <em>Nature Ecology and Evolution</em>: <a title="Aedes aegypti domestication." href="https://doi.org/10.1038/s41559-025-02643-5">https://doi.org/10.1038/s41559-025-02643-5</a></p> <p>These datasets are available in the section "Supplementary Information" of our paper, but with the absence of the SD-9 due its large big size (~3Gb after decompressed). Here you can find the complete set of datasets in a single ZIP file:</p> <p><strong>41559_2025_2643_MOESM5_ESM_Supplementary_Data.zip</strong></p> <p> </p> <p><strong>LIST OF DATASETS:</strong></p> <p>1) Supplementary Data 1. SNP statistics for populations through genomic regions (TXT). <br>2) Supplementary Data 2. Sequences of new detected nrEVEs (FASTA). <br>3) Supplementary Data 3. Phylogenetic trees for populations and individuals (NEWICK). <br>4) Supplementary Data 4. Information for 8,120 hard selective sweeps detected with RAiSD in out-of-Africa populations (TXT). <br>5) Supplementary Data 5. Information for 1,030 SNP outliers detected with PCAdapt within 2,266 genes (VCF format). <br>6) Supplementary Data 6. Matrix with DoS scores for 11,651 orthologous protein-coding genes in AaegL5 and each Ae. aegypti population (TXT). <br>7) Supplementary Data 7. Matrix with MKT scores for 11,651 orthologous protein-coding genes in AaegL5 and each Ae. aegypti population (TXT). <br>8) Supplementary Data 8. Matrix with DoS scores used to estimate relaxed selection (TXT). <br>9) Supplementary Data 9. Matrix with SNPs and genomic coordinates within adaptive protein-coding genes and ncRNAs that are shared or private for out-of-Africa populations against African populations (TXT). <br>10) Supplementary Data 10. Matrix with 483 nonsynonymous SNPs and their allele frequencies for our 40 populations Florida and Colombia (TXT).<br>11) Supplementary Data 11. Genomic coordinates of SNPs in AaegL5 obtained from the literature and VectorBase (TXT). <br>12) Supplementary Data 12. Source data of metrics used to plot Figure 4b (TXT).</p> <p> </p> <p><strong>UPDATES NOTE:</strong></p> <ul> <li><strong>Repository version 3.</strong> Final version of datasets for the accepted manuscript.</li> <li><strong>Repository version 2.</strong> Incomplete datasets: Files as prelimary versions and their content may vary. The SD-10 is not present (matrix with 483 SNPs) was added. The SD-7 is a broken file (cannot be opened).</li> <li><strong>Repository version 1. </strong> Incomplete datasets: Files as prelimary versions and their content may vary. Two final SD files are not present.</li> </ul> <p> </p> <p><strong>CITATION OF THIS REPOSITORY:</strong></p> <p>Lozada-Chávez, A. N., Lozada-Chávez, I., Alfano, N., Palatini, U., Sogliani, D., Elfekih, S., Degefa, T., Sharakhova, M. V., Badolo, A., Patchara, S., Casas-Martinez, M., Carlos, B. C., Carballar-Lejarazú, R., Lambrechts, L., Souza-Neto, J. A., & Bonizzoni, M. (2024). Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti [Data set]. Zenodo. https://doi.org/10.5281/zenodo.14948092</p> <p> </p> <p> </p>
Non-invasive genomics of respiratory pathogens infecting wild great apes using hybridization capture
<p>This dataset complements a manuscript reporting genomic analyses of respiratory pathogens cuasing lethal outbreaks in the wild chimpanzee community living in Tai National Park, Ivory Coast.</p>
Data from: Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs
<p>The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of Single Nucleotide Polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics' Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA isolated from fecal swabs. Total and host-specific DNA were quantified for 989 samples collected as part of a long-term individual-based study of feral horses on Sable Island, Nova Scotia, Canada, using dsDNA fluorescence and a host-specific qPCR assay, respectively. Forty-eight samples representing 44 individuals containing at least 10ng of host DNA (ATG's recommended minimum input) were genotyped using a custom multiplex panel targeting 279 SNPs. Genotyping accuracy and consistency were assessed by contrasting ATG genotypes with those obtained from the same individuals with SNP microarrays, and from multiple samples from the same horse, respectively. 62% of swabs yielded the minimum recommended amount of host DNA for ATG. Ignoring samples that failed to amplify, ATG recovered an average of 86.7% targeted sites per sample, while genotype concordance between ATG and SNP microarrays was 98.5%. The repeatability of genotypes from the same individual approached unity with an average of 99.9%. This study demonstrates the suitability of ATG for genome-wide, non-invasive targeted SNP genotyping, and will facilitate further ecological and conservation genetics research in equids and related species.</p>
Data associated to: Uncovering the genomic basis of an extraordinary plant invasion
<p><span>Invasive species are a key driver of the global biodiversity crisis but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in <em>Ambrosia artemisiifolia</em> (ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related <em>Ambrosia</em> species, escape from specific microbial enemies likely favoured the plant's remarkable success as an invasive species.</span></p>
Data for: (Epi)genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions
<p><span>Elucidating processes and mechanisms involved in rapid local adaptation to varied environments is a poorly understood but crucial component in management of invasive species. Recent studies have proposed that genetic and epigenetic variation could both contribute to ecological adaptation, yet it remains unclear on the interplay between these two components underpinning rapid adaptation in wild animal populations. To assess their respective contributions to local adaptation, we explored epigenomic and genomic responses to environmental heterogeneity in eight recently colonized ascidian (<em>Ciona intestinalis</em>) populations at a relatively fine geographical scale. Based on MethylRADseq data, we detected strong patterns of local environment-driven DNA methylation divergence among populations, significant epigenetic isolation by environment (IBE), and a large number of local environment-associated epigenetic loci. Meanwhile, multiple genetic analyses based on single nucleotide polymorphisms (SNPs) showed genomic footprints of </span><span>divergent selection</span><span>. </span><span>In addition, for five genetically similar populations, we detected significant methylation divergence and local environment-driven methylation patterns, indicating strong effects of local environments on epigenetic variation. From a functional perspective, a majority of functional genes, gene ontology (GO) terms, and biological pathways were largely specific to one of these two types of variation, suggesting partial independence between epigenetic and genetic adaptation. The methylation quantitative trait loci (mQTL) analysis showed that the genetic variation explained only 18.67% of methylation variation, further confirming the autonomous relationship between these two types of variation. Altogether, we highlight the complementary interplay of genetic and epigenetic variation involved in local adaptation, which may jointly promote populations' rapid adaptive capacity and successful invasions in different environments. The findings here provide valuable insights into interactions between invaders and local environments to allow invasive species to rapidly spread, thus contributing to better prediction of invasion success and development of management strategies.</span></p>
Data for isolation-by-environment and its consequences for range shifts with global change: Landscape genomics of the invasive common tansy
<p>Invasive species are a growing global economic and ecological problem. However, it is not well understood how environmental factors mediate invasive range expansion. In this study, we investigated the recent and rapid range expansion of common tansy across environmental gradients in Minnesota, U.S.A. We densely sampled individuals across the expanding range and performed reduced representation sequencing to generate a dataset of 3071 polymorphic loci for 176 individuals. The dataset includes additional samples from the native range in Finland that were not used in the downstream analysis but are contributed for completeness. The dataset includes the genotype calls for all individuals sampled and sequenced. The genotype file was generated by stacks2.59 running the denovo pipeline and then using the populations function where we kept loci that were in 70% of populations and had a minor allele frequency of at least 1%. We used non-spatial and spatially-explicit analyses to determine the relative influences of geographic distance and environmental variation on patterns of genomic variation. We found no evidence for isolation-by-distance (IBD) but strong evidence for isolation-by-environment (IBE), indicating that environmental factors may have modulated patterns of range expansion.</p>
Genome-wide association study Summary statistics of Invasive melanoma vs controls, In situ Melanoma vs controls and In situ vs invasive melanoma (case-case)
<p>Genome-wide association study Summary statistics of Invasive melanoma vs controls, In situ Melanoma vs controls and In situ vs invasive melanoma (case-case). The first GWAS meta-analysis combines GWAS summary statistics of invasive melanoma from UK Biobank (as of August 2022), FinnGen release 9, QSkin Sun and Health Study and The Queensland Study of Melanoma: environmental and genetic associations (Q-MEGA) study.</p> <p>The second GWAS meta-analysis combines GWAS summary statistics of in situ melanoma from UK Biobank (as of August 2022), FinnGen release 9, QSkin Sun and Health Study and The Queensland Study of Melanoma: environmental and genetic associations (Q-MEGA) study.</p> <p>The third GWAS meta-analysis combines GWAS summary statistics of in situ vs invasive (case-case; in situ code 0, invasive code 1) melanoma from UK Biobank (as of August 2022), QSkin Sun and Health Study and The Queensland Study of Melanoma: environmental and genetic associations (Q-MEGA) study.</p> <p>Columns</p> <p>CHR Chromosome</p> <p>SNP rsid</p> <p>POS Base position HG Build 37</p> <p>A1 effect allele</p> <p>A2 Non-effect allele</p> <p>A1FREQ Allele frequency of effect allele</p> <p>BETA effect estimate of effect allele</p> <p>SE standard error of effect estimate</p> <p>PVAL two-tailed p value</p> <p>DIRECTION the Direction of effect of the SNP in each cohort ( in the order UKBB, FINNGEN, QSKIN, QMEGA 610k, QMEGA OMNI)</p> <p>N sample size</p> <p>See </p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.