Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
517
datasets available to search
ShareScore release 0.9.0
Dataset results
517 results for “Genomic adaptation”
Alignments from "Caecilian genomes reveal molecular basis of adaptation and convergent evolution of limblessness in vertebrates"
<p>Compressed file containing the alignments at both nucleotide and amino acid level for the manuscript "Caecilian genomes reveal molecular basis of adaptation and convergent evolution of limblessness in vertebrates" </p>
Adaptive changes in the genomes of wild rabbits after 16 years of viral epidemics
<p>Since its introduction to control overabundant alien rabbits (Oryctolagus cuniculus), the highly virulent Rabbit Haemorrhagic Disease Virus (RHDV) has caused regular annual disease outbreaks in Australian rabbit populations. Although initially reducing rabbit abundance by 60%, continent-wide, experimental evidence has since indicated increased genetic resistance in wild rabbits that have experienced RHDV-driven selection. To identify genetic adaptations, which explain the increased resistance to this biocontrol virus, we investigated genome-wide SNP (single nucleotide polymorphism) allele frequency changes in a South Australian rabbit population that was sampled in 1996 (pre-RHD genomes) and after 16 years of RHDV outbreaks. We identified several SNPs with changed allele frequencies within or in proximity of genes that have roles potentially important for increased RHD resistance. Many of the identified genes are known to be involved in virus infections or immunity, or had previously been identified as being differentially expressed in healthy vs. acutely RHDV-infected rabbits. Furthermore, we show in a simulation study that the allele/genotype frequency changes cannot be explained by drift alone, and that several candidate genes had also been identified as being associated with surviving RHD in a different Australian rabbit population. Our unique dataset allowed us to identify candidate genes for RHDV resistance that have evolved under natural conditions, and over a time span that would not have been feasible to study in an experimental setting. Moreover, it provides a rare example of host genetic adaptations to virus-driven selection in response to a suddenly emerging infectious disease.</p>
The genome of the Xingu Scale-backed Antbird (Willisornis vidua nigrigula) reveals lineage-specific adaptations
<p>Antbirds (Thamnophilidae) are a large neotropical family of passerine bird renowned for the ant-following foraging strategies of several members of this clade. The high diversity of antbirds provides ample opportunity for speciation studies, however these studies can be hindered by the lack of an annotated antbird reference genome. In this study, we produced a high-quality annotated reference genome for the Xingu Scale-backed Antbird (<em>Willisornis vidua nigrigula</em>) using 10X Genomics Chromium linked-reads technology. The assembly is 1.09 Gb, with a scaffold N50 of 12.1 Mb and 17,475 annotated protein coding genes. We compare the proteome of <em>W. v. nigrigula</em> to several other passerines, and produce annotations for two additional antbird genomes in order to identify genes under lineage-specific positive selection and gene families with evidence for significant expansions in antbirds. Several of these genes have functions potentially related to the lineage-specific traits of antbirds, including adaptations for thermoregulation in a humid tropical environment.</p>
Data from: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.
Data from: The spotted parrotfish genome provides evolutionary insight into the ecological adaptation of a keystone dietary specialist
<p>With over 600 valid species, the wrasses (family Labridae) are among the largest and most successful of the marine teleosts. They feature prominently on coral reefs where they are known not only for their impressive diversity in colouration and form, but also in their functional specialization and ability to occupy a wide variety of trophic guilds. Among the wrasses, the parrotfishes (tribe Scarini) display some one of the most dramatic examples of trophic specialization. Using abrasion-resistant biomineralized teeth, parrotfishes are able to mechanically extract protein-rich micro-photoautotrophs growing in and amongst reef carbonate material, a dietary niche that is inaccessible to most other teleost fishes. This ability to exploit an otherwise untapped trophic resource is thought to have played a role in the diversification and evolutionary success of the parrotfishes. In order to better understand the key evolutionary innovations leading to the success of these dietary specialists, we sequenced and analysed the genome of a representative species, the spotted parrotfish (<em>Cetoscarus ocellatus</em>). We find significant expansion, selection, and duplication within several detoxification gene families and a novel poly-glutamine expansion in the enamel protein ameloblastin, and we consider their evolutionary implications. Our genome provides a useful resource for comparative genomic studies investigating the evolutionary history of this highly specialized teleostean radiation.</p>
Data from: Genomic landscapes of divergence among island bird populations: evidence of parallel adaptation but at different loci?
<p>When populations colonise new environments they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes, and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (> 22X coverage) in Berthelot's pipit (<em>Anthus berthelotii</em>), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. Firstly, we quantify how genomic divergence accumulates across the speciation continuum, i.e., among Berthelot's pipit populations, between subspecies across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (<em>Anthus campestris</em>). Across these colonisation timeframes (2.1 million – <em>ca.</em> 8,000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non-neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism, and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism, and immune defence.</p>
Population genomics of a forest fungus reveals high gene flow and climate adaptation signatures
Genome sequencing of spatially distributed individuals sheds light on how evolution structures genetic variation. Populations of <i>Phellopilus nigrolimitatus</i>, a red-listed wood-inhabiting fungus associated with old-growth coniferous forests, have decreased in size over the last century due to a loss of suitable habitats. We assessed the population genetic structure and investigated local adaptation in<i> P. nigrolimitatus</i>, by establishing a reference genome and genotyping 327 individuals sampled from 24 locations in Northern Europe by RAD sequencing. We revealed a shallow population genetic structure, indicating large historical population sizes and high levels of gene flow. Despite this weak sub-structuring, two genetic groups were recognized; a western group distributed mostly in Norway and an eastern group covering most of Finland, Poland and Russia. This sub-structuring may reflect co-immigration with the main host, Norway spruce (<i>Picea abies</i>), into Northern Europe after the last ice age. We found evidence of low levels of genetic diversity in southwestern Finland, which has a long history of intensive forestry and urbanization. Numerous loci were significantly associated with one or more environmental factors, indicating adaptation to specific environments. These loci clustered into two groups with different associations with temperature and precipitation. Overall, our findings indicate that the current population genetic structure of P. nigrolimitatus results from a combination of gene flow, genetic drift and selection. The acquisition of similar knowledge especially over broad geographic scales, linking signatures of adaptive genetic variation to evolutionary processes and environmental variation, for other fungal species will undoubtedly be useful for assessment of the combined effects of habitat fragmentation and climate change on fungi strongly bound to old-growth forests. --
Supplementary Data - Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions
<p><strong>File: 50K_GenotypesEU_raw_UHOH_SoySNP50K.csv.tgz </strong></p> <p>Genotyping data of SoySNP50k SNP array of 170 European soybean varieties.</p> <p>The array includes 51.955 SNP markers.</p> <p>Genotypes of each variety are in columns and each row is a SNP marker. Naming of markers follows the annotation of the soybean genome.</p> <p><strong>File: EUvarieties_infos.csv </strong></p> <p>Description of European varieties</p> <p>Contains variety name, country of origin, EU region and maturity group assignment.</p> <p> </p> <p><strong>File: Supplementary_Data_Haupt_Schmid.xlsx</strong></p> <p>Additional data derived from data analysis. Description of data contained within file (Worksheet "Summary")</p> <p> </p>
Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds
<p>The current study was conducted from 2009 to 2019 in three hot and dry agroecological zones in Egypt: Western Desert coastal zone, New Valley desert oasis, and hot-dry Upper Egypt. Within these zones, three local sheep breeds were studied: Barki (83 ewes), Wahati (55 ewes) and Saidi (68 ewes). During the study period, the animals exercised under natural heat stress (simulating summer grazing on poor pasture). Meteorological and physiological parameters were measured and recorded. The heat tolerance index of the animals was calculated to identify animals with high and low heat tolerance based on the animals' response to the five main physiological parameters (scale from 0 to 5). DNA samples were extracted for genomic analysis. The genetic diversity measurements showed a significant influence of breed and location on the populations. The influence of breed is more significant than that of location. The inbreeding analysis shows that the desert breeds (Wahati and Barki) have lower values than the urban breed (Saidi). The high rate of sub-clustering indicates the process of sub-population through inbreeding pressure. Wahati and Barki are very distinct breeds with strong identification, while Saidi breed has crosses with other breeds. The most significant SNPs associated with heat tolerance were found in MYO5A, PRKG1, GSTCD, and RTN1 genes (P < 0.0001). MYO5A had an effect of 0.74 on the trait heat tolerance in the studied population. It produces a protein that is widely distributed in the melanin-producing neural crest of the skin. Genetic association between genetic and phenotypic variations showed that OAR1 18300122.1, located in ST3GAL3, had the greatest positive effect on heat tolerance. GWAS analysis identified SNPs associated with heat tolerance in the PLCB1, STEAP3, KSR2, UNC13C , PEBP4, and GPAT2 genes.</p>
Genomic changes underlying repeated niche shifts in an adaptive radiation
<p>In adaptive radiations, single lineages rapidly diversify by adapting to many new niches. Little is known yet about the genomic mechanisms involved, i.e. the source of genetic variation or genomic architecture facilitating or constraining adaptive radiation. Here, we investigate genomic changes associated with repeated invasion of many different freshwater niches by threespine stickleback in the Haida Gwaii archipelago, Canada, by re-sequencing single genomes from one marine and 28 freshwater populations. We find 89 likely targets of parallel selection in the genome that are enriched for old standing genetic variation. In contrast to theoretical expectations, their genomic architecture is highly dispersed with little clustering. Candidate genes and genotype-environment correlations match the three major environmental axes predation regime, light environment and ecosystem size. In a niche space with these three dimensions, we find that the more divergent a new niche from the ancestral marine habitat, the more loci show signatures of parallel selection. Our findings suggest that the genomic architecture of parallel adaptation in adaptive radiation depends on the steepness of ecological gradients and the dimensionality of the niche space.</p>
Genomic and chemical evidence for local adaptation in resistance to different herbivores in Datura stramonium
<p>Since most species are collections of genetically variable populations distributed to habitats differing in their abiotic/biotic environmental factors and community composition, the pattern and strength of natural selection imposed by species on each others' traits are also expected to be highly spatially variable. Here, we used genomic and quantitative genetic approaches to understand how spatially variable selection operates on the genetic basis of plant defenses to herbivores. To this end, an F2 progeny was generated by crossing Datura stramonium (Solanaceae) parents from two populations differing in their level of chemical defense. This F2 progeny was reciprocally transplanted into the parental plants' habitats and by measuring the Identity by Descent (IBD) relationship of each F2 plant to each parent, we were able to elucidate how spatially variable selection imposed by herbivores operated on the genetic background (IBD) of resistance to herbivory, promoting local adaptation. The results highlight that plants possessing the highest total alkaloid concentrations (sum of all alkaloid classes) were not the most well-defended or fit. Instead, specific alkaloids and their linked loci/alleles were favored by selection imposed by different herbivores. This has led to population differentiation in plant defenses and thus, to local adaptation driven by plant-herbivore interactions.</p>
Pollinator loss causes rapid adaptive evolution of selfing and dramatically reduces genome-wide genetic variability
<p>While selfing populations harbor little genetic variation limiting evolutionary potential, the causes are unclear. We experimentally evolved large, replicate populations of <em>Mimulus guttatus </em>for nine generations in greenhouses with or without pollinating bees and studied DNA polymorphism in descendants. Populations without bees adapted to produce more selfed seed yet exhibited striking reductions in DNA polymorphism despite large population sizes. Importantly, the genome-wide pattern of variation cannot be explained by a simple reduction in effective population size, but instead reflects the complicated interaction between selection, linkage, and inbreeding. Simulations demonstrate that the spread of favored alleles at few loci depresses neutral variation genome-wide in large populations containing fully selfing lineages. It also generates greater heterogeneity among chromosomes than expected with neutral evolution in small populations. Genome-wide deviations from neutrality were documented in populations with bees, suggesting widespread influences of background selection. After applying outlier tests to detect loci under selection, two genome regions were found in populations with bees, yet no adaptive loci were otherwise mapped. Large amounts of stochastic change in selfing populations compromise evolutionary potential and undermine outlier tests for selection. This occurs because genetic draft in highly selfing populations makes even the largest changes in allele frequency unremarkable.</p>
Supplementary Data of "Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?"
<p><strong>Datasets used in the analyses (see Table S5 for a detailed description).</strong></p> <p>► Dataset #1: phased SNPs with offspring.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle.vcf<br> ► Dataset #2: all SNPs with missing data.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_parents_oNA5.vcf<br> ► Dataset #3a: phased SNPs.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents.vcf<br> ► Dataset #3b: CDS version of “phased SNPs”.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents_SNP_CHRall.orf.cds<br> ► Dataset #3c: FASTA version of “phased SNPs”.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents_SNP_chr5.sub_${START}-${END}.fasta<br> ► Dataset #4: ancestry informative phased SNPs.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_phased_phasedBeagle_parents.frq.fixed.vcf<br> ► Dataset #5: all SNPs.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_parents_oNA.vcf<br> ► Dataset #6: all polarized SNPs.<br> joint_bwa_mem_mdup_IR_recal_variants_refine_HQ_denovo_Oad18ad31ad2.clean.biallelic.noindels_filter_parents_raw_refine_HQ_edwardsi_oNA3_polar.vcf<br> ► Dataset #7: unfiltered mapping files.<br> ciona_bwa-mapping_${IND}_bwa_mem_mdup_IR_chromosome5:700000-1500000_sorted_nodup.bam</p>
Supplementary Information of "Introgression between highly divergent sea squirt genomes: an adaptive breakthrough?"
<p><strong>Supplementary Figures</strong></p> <p><strong>Figure S1</strong> Population genetic statistics calculated in non-overlapping 10 Kb windows along the 14 chromosomes in the sea squirt genome.<br> <strong>Figure S2</strong> <em>C. robusta</em> introgression into <em>C. intestinalis</em> shown across the 14 chromosomes.<br> <strong>Figure S3</strong> Population genetic statistics of the <em>C. robusta</em> introgressed coding sequences.<br> <strong>Figure S4 </strong>ABBA-BABA introgression patterns using<em> C. edwardsi </em>as an outgroup.<br> <strong>Figure S5</strong> Inference of the divergence history between <em>C. robusta</em> and <em>C. intestinalis</em> with moments.<br> <strong>Figure S6 </strong>Selection tests.<br> <strong>Figure S7 </strong><em>C. robusta</em> ancestry along chromosome 5 in <em>C. intestinalis</em> individuals.<br> <strong>Figure S8</strong> Neighbor-joining trees of 50 Kb windows framing the “missing data region” (grey band) at the center of the chromosome 5 hotspot.<br> <strong>Figure S9</strong> Copy number variation at candidate SNPs in the introgression hotspot on chromosome 5 (700 Kb - 1.5 Mb).<br> <strong>Figure S10</strong> Structural analysis of the “missing data region” on chromosome 5 (from 1,009,000 to 1,055,000 bp).</p> <p> </p> <p><strong>Supplementary Tables</strong></p> <p><strong>Table S1</strong> Sample information.<br> <strong>Table S2 </strong>Correlation between chromosomes of the individual <em>C. robusta </em>ancestry fraction.<br> <strong>Table S3</strong> Demographic results with moments – excluding chromosome 5.<br> <strong>Table S4</strong> Demographic results with moments – including chromosome 5.<br> <strong>Table S5 </strong>Description of the Supplementary Data.</p> <p> </p> <p><strong>Supplementary Scripts</strong></p> <p><em>Bioinformatic pipeline used for genotyping and haplotyping.</em></p> <p><strong>Script #1</strong>: prepare the reference genome for BWA and GATK.<br> reference_bwa_GATK_CF.sh<br> <strong>Script #2</strong>: mapping the reads to the reference with BWA.<br> mapping_bwa-mem_CF.sh<br> <strong>Script #3</strong>: indel realignment with GATK.<br> indel_realignment_CF.sh<br> <strong>Script #4</strong>: individual variant calling in gVCF format with GATK.<br> snpindel_callingGVCF_raw_CF.sh<br> <strong>Script #5</strong>: joint genotyping with GATK.<br> joint_genotyping_raw_CF.sh<br> <strong>Script #6</strong>: genotype refinement with GATK.<br> genotype_refinement_raw_CF.sh<br> <strong>Script #7</strong>: SNPs and indels recalibration with GATK.<br> snpindel_recalibration_CF.sh<br> <strong>Script #8</strong>: genotype refinement after recalibration with GATK.<br> genotype_refinement_recal_CF.sh<br> <strong>Script #9</strong>: genotype correction.<br> phase_by_transmission_correctCalling_CF@2020.sh<br> <strong>Script #10</strong>: phasing with GATK and BEAGLE.<br> phase_by_transmission_clean_CF@2020.sh</p> <p><em>Pipeline used for the demographic inferences with moments.</em></p> <p><strong>Script #11</strong>: define the demographic models.<br> moments_models_2pop_bb_parallel_folded_2periods.py<br> <strong>Script #12</strong>: run the demographic inferences.<br> moments_inference_dualanneal_bb_parallel_folded_2periods_bounds.py</p>
Data from: Local adaptation in shell shape traits of a brooding chiton with strong population genomic differentiation
<p class="MsoNormal"><span>Comparing divergence in quantitative tr</span><span>aits and neutral m</span><span>olecular markers, such as <em>Q</em><sub>ST</sub><em>–F</em><sub>ST</sub> comparisons, provides a means to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. </span><em>Onithochiton neglectus</em> (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 (<em><span>F<sub>ST</sub></span></em><span>)</span> with an index of phenotypic differentiation (<em>P<sub>ST</sub></em>). We used 7,562 putatively neutral single nucleotide polymorphisms (SNPs) across 15 populations and three clades of <em>O. neglectus</em> throughout New Zealand to infer <em><span>F<sub>ST</sub></span></em>. <em>P<sub>ST</sub></em> was calculated from 18 shell shape traits and gave highly variable estimates across populations, clades and shape groups. By systematically comparing <em>P<sub>ST</sub></em> with <em>F<sub>ST</sub></em><sub>,</sub> we identified evidence of local adaptation in a number of the <em>O. neglectus </em>shell shape traits. This <span>supports the hypothesis that shell shape could be an adaptive trait, potentially correlated with the ability to live and raft in kelp holdfasts.</span></p>
Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia (The genome assembly and annotion fiile)
<p>The genome assembly and annotion fiile used in the manuscript: <strong>Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia</strong></p>
Data and source code for: Recent adaptation in a threatened salmonid revealed by museum genomics
<p>Steelhead/rainbow trout (Oncorhynchus mykiss) is an imperiled salmonid with two main life history strategies: migrate to the ocean or remain in freshwater. Domesticated hatchery forms of this species have been stocked into almost all California waterbodies, possibly resulting in introgression into natural populations and altered population structure. </p> <p>We compared whole-genome sequence data from contemporary populations against a set of museum population samples of steelhead from the same locations that were collected prior to most hatchery stocking. </p> <p>We observed minimal introgression and few steelhead-hatchery trout hybrids despite a century of extensive stocking. Our historical data show signals of introgression with a sister species and indications of an early hatchery facility. Finally, we found that migration-associated haplotypes have become less frequent over time, a likely adaptation to decreased opportunities for migration. Since contemporary migration-associated haplotype frequencies have been used to guide species management, we consider this to be a rare example of shifting baseline syndrome that has been validated with historical data. </p> <p>We suggest cautious optimism that a century of hatchery stocking has had minimal impact on California steelhead population genetic structure, but we note that continued shifts in life history may lead to further declines in the ocean-going form of the species. </p>
Adapter sequences used for trimming of genomic sequences in the assembly of the Northern Spotted Owl (<i>Strix occidentalis caurina</i>) genome assembly version 1.0
<p>These files provide the sequences of the adapters used in the construction of the genomic libraries Hanna et al. (2017a) sequenced and used to assemble the Northern Spotted Owl (<em>Strix occidentalis caurina</em>) genome assembly version 1.0 (Hanna et al. 2017b). These files also contain relevant supplemental adapter sequences from the adapter files included with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).</p> <p><strong>SRR4011595_adapters.fa</strong> : This FASTA format file contains the full length sequences of the adapters Hanna et al. (2017a) used to construct the genomic library they sequenced to produced the data uploaded as NCBI Sequence Read Archive (SRA) run accession SRR4011595. I have also included the partial adapter sequences provided in the "TruSeq3-PE-2.fa" and "NexteraPE-PE.fa" files distributed with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).</p> <p><strong>SRR4011596_adapters.fa</strong> : This FASTA format file contains the full length sequences of the adapters Hanna et al. (2017a) used to construct the genomic library they sequenced to produced the data uploaded as NCBI Sequence Read Archive (SRA) run accession SRR4011596. I have also included the partial adapter sequences provided in the "TruSeq3-PE-2.fa" and "NexteraPE-PE.fa" files distributed with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).</p> <p><strong>SRR4011597_adapters.fa</strong> : This FASTA format file contains the full length sequences of the adapters Hanna et al. (2017a) used to construct the genomic library they sequenced to produced the data uploaded as NCBI Sequence Read Archive (SRA) run accession SRR4011597. I have also included the partial adapter sequences provided in the "TruSeq3-PE-2.fa" and "NexteraPE-PE.fa" files distributed with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).</p> <p><strong>SRR4011614_adapters.fa</strong> : This FASTA format file contains the full length sequences of the adapters Hanna et al. (2017a) used to construct the genomic library they sequenced to produced the data uploaded as NCBI Sequence Read Archive (SRA) run accession SRR4011614. I have also included the partial adapter sequences provided in the "TruSeq3-PE-2.fa" and "NexteraPE-PE.fa" files distributed with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).</p> <p><strong>SRR4011615_adapters.fa</strong> : This FASTA format file contains the full length sequences of the adapters Hanna et al. (2017a) used to construct the genomic library they sequenced to produced the data uploaded as NCBI Sequence Read Archive (SRA) run accession SRR4011615. I have also included the partial adapter sequences provided in the "TruSeq3-PE-2.fa" file distributed with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).</p> <p><strong>SRR4011616_adapters.fa</strong> : This FASTA format file contains the full length sequences of the adapters Hanna et al. (2017a) used to construct the genomic library they sequenced to produced the data uploaded as NCBI Sequence Read Archive (SRA) run accession SRR4011616. I have also included the partial adapter sequences provided in the "TruSeq3-PE-2.fa" file distributed with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).<br> <br> <strong>SRR4011617_adapters.fa</strong> : This FASTA format file contains the full length sequences of the adapters Hanna et al. (2017a) used to construct the genomic library they sequenced to produced the data uploaded as NCBI Sequence Read Archive (SRA) run accession SRR4011617. I have also included the partial adapter sequences provided in the "TruSeq3-PE-2.fa" file distributed with Trimmomatic version 0.36 (Bolger, Lohse & Usadel, 2014).</p>
Supplementary Data for The salmon louse genome: copepod features and parasitic adaptations.
<p>This dataset contains supporting data for the manuscript: Skern-Mauritzen <em>et al. </em>The salmon louse genome: copepod features and parasitic adaptations.</p> <p>Copepods encompass a range of ecological roles from parasites to phytoplankton grazers linking primary producers to higher trophic levels. Despite these important roles, copepod genome assemblies are scarce. <em>Lepeophtheirus salmonis</em> is an economically and ecologically important ectoparasitic copepod found on salmonid fish. We present the 695.4 Mbp <em>L. salmonis</em> genome assembly containing ≈60% repetitive regions and 13081 annotated protein-coding genes. The genome comprises 14 autosomes and a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of the expected arthropod genes. Transcriptomics supported annotation and indicated a marked shift in gene expression after host attachment, including down-regulation of genes related to circadian rhythm coinciding with abandoning diurnal migration. The genome shows evolutionary signatures including loss of genes needed for peroxisome biogenesis, presence of numerous FNII domains, and an incomplete heme homeostasis pathway suggesting heme proteins to be obtained from the host. Despite large capacity to develop resistance against chemical treatments <em>L. salmonis</em> exhibits low numbers of many genes involved in detoxification.</p> <ul> <li>Supplementary data is explained in detail and referenced in the manuscript and the file Supplementary Material 30062021 REVISED.pdf</li> <li>BUSCO-V5-results-species-comparison.tar.gz contains the raw output and results of all BUSCO V 5.0.0 runs on the genomes in Table 1 of the manuscript and Supplementary_Table_GenomeStats.xlsx </li> <li>GCA_000181255.2_ASM18125v2_genomic.fna.RepMasker.o ..., GCA_001005205.1_lsal_atl_canada_female_v1_genomic. ..., GCA_001005235.1_lsal_atl_canada_male_v1_genomic.fn ... and TableS4-1-LSalAtl2s.fasta.RepMasker.out.gz contain original output from RepeatMasker</li> <li>Lsalmonis-RepeatModeler-families.fa.gz and Lsalmonis-RepeatModeler-families.stk.gz contain all repeat families as original output from RepeatModeler</li> </ul> <p> </p> <p> </p>
The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern
<p>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.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
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.