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183 results for “Genome conservation”
Lepidoptera genomics based on 88 chromosomal reference sequences informs population genetic parameters for conservation
<p>This repository contains (1) germline mutations called by the DeepVariant (v1.1.0) pipeline in VCF format; (2) rejected substitution scores calculated by the Genomic Evolutionary Rate Profiling (GERP++) software on each species and chromosome; and (3) the phylogenetic tree used as guide tree in the Cactus alignment.</p>
Anopheles gambiae (AgamP4) genome conservation score
<p>The conservation score storage is a result of a bioinformatics pipeline that integrates a systematic analysis of the data on genetic variation in more than 1,000 wild-caught Anopheles gambiae individuals and conserved syntenic regions of 19 Anopheles species and 3 phylogenetically more distant species of dipterans.</p> <p>The results of this analysis are gathered in the HDF5 data storage system that allows for flexible extraction and bioinformatic manipulation at each genomic position in AgamP4 reference genome.</p> <p> </p> <p> </p>
Supplementary data for: Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome
<p><strong><em>Myzus persicae </em>clone O v2 frozen release</strong></p> <p>Genome assembly: Myzus_persicae_O_v2.0.scaffolds.fa.gz</p> <p>BRAKER2 gene models: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3</p> <p>List of gene models containing internal stop codons (removed from the protein and cds fasta files): Myzus_persicae_O_v2.0.scaffolds.braker2.bad_genes.lst</p> <p>BRAKER2 protein sequences: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.cds.fa</p> <p>BRAKER2 coding sequences (longest transcript per gene only): Myzus_persicae_O_v2.0.scaffolds.braker2.gff3.filtered.cds.LTPG.fa</p> <p><em>De novo </em>repeat library (ReapeatModeler merged with repbase insecta): Myzus_persicae_O_v2.0_repeat_lib.repeatmodeler_merged_repbase_insecta.fa</p> <p>RepeatMasker transposable element annotation using the <em>M. persicae de novo</em> repeat library: Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff.out</p> <p>RepeatMasker transposable element annotation using the <em>M. persicae</em> <em>de novo r</em>epeat library (gff format): Myzus_persicae_O_v2.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff</p> <p><strong><em>Acyrthosiphon pisum</em> clone JIC1 v1 frozen release</strong></p> <p>Genome assembly: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.fa.gz</p> <p>BRAKER2 gene models: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff</p> <p>List of gene models containing internal stop codons (removed from the protein and cds fasta files): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.bad_genes.lst</p> <p>BRAKER2 protein sequences: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.cds.fa</p> <p>BRAKER2 coding sequences (longest transcript per gene only): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.braker2.gff.filtered.cds.LTPG.fa</p> <p><em>De novo </em>repeat library (ReapeatModeler merged with repbase insecta): Acyrthosiphon_pisum_JIC1_repeat_lib.repeatmodeler_merged_repbase_insecta.fa</p> <p>RepeatMasker transposable element annotation using the <em>A. pisum</em> <em>de novo</em> repeat library: Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.out</p> <p>RepeatMasker transposable element annotation using the <em>A. pisum de novo</em> repeat library (gff format): Acyrthosiphon_pisum_JIC1_v1.0.scaffolds.repeatmodeler_merged_repbase_insecta.repeatmasker.gff</p> <p><strong><em>Rhodnius prolixus</em> DNA zoo chromosome-scale genome assembly annotation</strong></p> <p><em>R. prolixus </em>chromosome-scale genome assembly was obtained here: <a href="https://www.dnazoo.org/assemblies/Rhodnius_prolixus">https://www.dnazoo.org/assemblies/Rhodnius_prolixus</a>.</p> <p>Genome assembly: Rhodnius_prolixus-3.0.3_HiC.fasta</p> <p>BRAKER2 gene models: Rhodnius_prolixus-3.0.3_HiC.braker2.gff</p> <p>BRAKER2 protein sequences: Rhodnius_prolixus-3.0.3_HiC.braker2.gff.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): Rhodnius_prolixus-3.0.3_HiC.braker2.gff.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: Rhodnius_prolixus-3.0.3_HiC.braker2.gff.cds.fa</p> <p><strong><em>Triatoma rubrofasciata</em> chromosome-scale genome assembly annotation</strong></p> <p><em>T. rubrofasciata </em>chromosome-scale genome assembly was obtained here: <a href="http://dx.doi.org/10.5524/100614">http://dx.doi.org/10.5524/100614</a></p> <p>Genome assembly: zhuichun_assembly.fasta</p> <p>BRAKER2 gene models: zhuichun_assembly.braker2.gff</p> <p>BRAKER2 protein sequences: zhuichun_assembly.braker2.gff.aa.fa</p> <p>BRAKER2 protein sequences (longest transcript per gene only): zhuichun_assembly.braker2.gff.aa.LTPG.fa</p> <p>BRAKER2 coding sequences: zhuichun_assembly.braker2.gff.cds.fa</p> <p><strong>Hemiptera orthogroups and species tree</strong></p> <p>OrthoFinder was used to cluster proteomes of 14 Hemiptera into orthogroups for phylogenomic analysis. All proteomes were reduced to the longest transcript per gene. See here for full details:</p> <p>Species included, taxon IDs and data source:</p> <p>Mcer = Myzus cerasi v1.1 (<a href="https://bipaa.genouest.org/sp/myzus_cerasi/">https://bipaa.genouest.org/sp/myzus_cerasi/</a>)</p> <p>MperO = Myzus persicae clone O v2 (This study)</p> <p>Dnox = Diuraphis noxia Thorpe et. al. gene predictions (<a href="https://bipaa.genouest.org/sp/diuraphis_noxia/">https://bipaa.genouest.org/sp/diuraphis_noxia/</a>)</p> <p>Apis = Acyrthosiphon pisum JIC1 v1 (This study)</p> <p>Pnig = Pentalonia nigronervosa (This study)</p> <p>Rmai = Rhopalosiphum maidis v0.1 (<a href="http://gigadb.org/dataset/100572">http://gigadb.org/dataset/100572</a>)</p> <p>Rpad = Rhopalosiphum padi v1.0 (<a href="https://bipaa.genouest.org/sp/rhopalosiphum_padi/">https://bipaa.genouest.org/sp/rhopalosiphum_padi/</a>)</p> <p>Agly = Aphis glycines biotype 4 v2.1 (<a href="https://zenodo.org/record/3453468#.XnpL5JOgLRY">https://zenodo.org/record/3453468#.XnpL5JOgLRY</a>)</p> <p>BtabMEAM1 = Bemissia tabacci MEAM1 v1.2 (<a href="http://www.whiteflygenomics.org/cgi-bin/bta/index.cgi">http://www.whiteflygenomics.org/cgi-bin/bta/index.cgi</a>)</p> <p>Trub = Triatoma rubrofasciata (This study)</p> <p>Rpro = Rhodnius prolixus (This study)</p> <p>Ofas = Oncopeltus fasciatus OGS v1.0 (<a href="https://i5k.nal.usda.gov/Oncopeltus_fasciatus">https://i5k.nal.usda.gov/Oncopeltus_fasciatus</a>)</p> <p>Sfuc = Sogatella furcifera v1 (<a href="http://dx.doi.org/10.5524/100255">http://dx.doi.org/10.5524/100255</a>)</p> <p>Nlug = Nilaparvata lugens (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0521-0#Sec42">https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0521-0#Sec42</a>)</p> <p>Files:</p> <p>Proteomes included in the analysis: proteomes.tar.gz</p> <p>Orthogroups: Orthogroups.txt</p> <p>Gene counts per orthogroup, per species: Orthogroups.GeneCount.csv</p> <p>Single copy conserved orthogroups used for species tree: SingleCopyOrthogroups.txt</p> <p>Species tree alignment: SpeciesTreeAlignment.fa</p> <p>r8s configuration file (includes time calibrations and OrthoFinder ML species tree with branch lengths): species_tree_rooted.r8s.nex</p> <p>r8s time calibrated species tree: r8s_tree.nwk</p>
Genomics‐informed delineation of conservation units in a desert amphibian
<p>Delineating conservation units (CUs, e.g., evolutionarily significant units, ESUs, and management units, MUs) is critical to the recovery of declining species because CUs inform both listing status and management actions. Genomic data have strengths and limitations in informing CU delineation and related management questions in natural systems. We illustrate the value of using genomic data in combination with landscape, dispersal, and occupancy data, to inform CU delineation in Nevada populations of the Great Basin Distinct Population Segment of the Columbia spotted frog (<em>Rana luteiventris</em>). <em>R</em>. <em>luteiventris</em> occupies naturally fragmented aquatic habitats in this xeric region, but beaver removal, climate change, and other factors have put many of these populations at high risk of extirpation without management intervention. We addressed three objectives: (1) assessing support for ESUs within Nevada; (2) evaluating and revising, if warranted, the current delineation of MUs; and (3) evaluating genetic diversity, effective population size, adaptive differentiation, and functional connectivity to inform ongoing management actions. We found little support for ESUs within Nevada but did identify potential revisions to MUs based on unique landscape drivers of connectivity that distinguish these desert populations from those in the northern portion of the species range. Effective sizes were uniformly small, with low genetic diversity and weak signatures of adaptive differentiation. Our findings suggest that management actions, including translocations and genetic rescue, might be warranted. Our study illustrates how a carefully planned genetic study, designed to address priority management goals that include CU delineation, can provide multiple insights to inform conservation action.</p>
Fig. 3 in Chloroplast genome of the conserved Aster altaicus var. uchiyamae B2015-0044 as genetic barcode
Fig. 3. The variable sites in the chloroplast genomes of Aster altaicus var. uchiyamae. Variable sequences are marked in red. GG: Yeoju, Gyeonggi Province, CB: Cheongju, Chungcheongbuk Province.
Fig. 2 in Chloroplast genome of the conserved Aster altaicus var. uchiyamae B2015-0044 as genetic barcode
Fig. 2. The sequence alignment of variable sites in the chloroplast genomes of Aster altaicus var. uchiyamae. Variable sequences are marked in red. GG: Yeoju, Gyeonggi Province, CB: Cheongju, Chungcheongbuk Province.
Conservation of animal genome structure is the exception not the rule
<p>Species from diverse animal lineages, including molluscs, annelids, echinoderms, hemichordates, and cephalochordates, have retained groups of orthologous genes on the same chromosomes for over half a billion years since the last common ancestor of bilaterians. Though there are notable exceptions, it has been proposed that the conservation of chromosome-scale gene linkages is the norm among animals. Here, by examining interchromosomal rearrangements in 64 chromosome-level genomes across 15 bilaterian phyla and at least 52 classes, we show that, though striking, cases of genome structure conservation are exceptionally rare. The ubiquity of massive genome rearrangements suggests that, in general, chromosome-scale gene linkages are of minimal importance to animal genome function.</p> <p>This project includes gene models for 14 genome assemblies annotated in this study, with files available for coding sequences (*.fasta), protein sequences (*.faa), and gene annotations in GTF format (*.gtf), as detailed below. Additionally, a spreadsheet containing all accession numbers and genome metadata for 64 bilaterian genomes and 3 cnidarian genomes is provided as a Supplemental Dataset.</p> <p>- Amphiscolops sp. MND2022 (acoel worm; phylum Xenacoelomorpha)<br>- Antedon bifida (crinoid; phylum Echinodermata)<br>- Carcinoscorpius rotundicauda (horseshoe crab; phylum Arthropoda)<br>- Convolutriloba macropyga (acoel worm; phylum Xenacoelomorpha)<br>- Emplectonema gracile (ribbon worm; phylum Nemertea)<br>- Gordius sp. MW1 (horsehair worm; phylum Nematomorpha)<br>- Hypsibius dujardini (water bear; phylum Tardigrada)<br>- Ophiura sarsii (brittle star; phylum Echinodermata)<br>- Schizocardium californicum (acorn worm, phylum Hemichordata)<br>- Schmidtea mediterranea (planarian; phylum Platyhelminthes)<br>- Strigamia acuminata (centipede; phylum Arthropoda)<br>- Styela plicata (tunicate; phylum Chordata)<br>- Trichinella spiralis (nematode; phylum Nematoda)<br>- Trididemnum miniatum (tunicate; phylum Chordata)</p> <p>Custom R scripts are available at our GitHub repository (https://github.com/symgenoevolab/animal_genome_structure) under the MIT License.</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>
Data for: Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia
<p>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 (<em>Mesembriomys</em> <em>gouldii</em>), 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.</p>
Supporting Data for: Ocean-wide conservation genomics of blue whales suggest new Northern Hemisphere subspecies
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Data from: Conservation prioritisation of genomic diversity to inform management of a declining mammal species
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Data for: Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia
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The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern
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Genomics‐informed delineation of conservation units in a desert amphibian
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Data from: Genomics-informed conservation units reveal spatial variation in climate vulnerability in a migratory bird
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Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny
<p class="BodyAA">The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead this research. Fortunately, integration of additional, independent streams of information, such as a marker-dense genetic map and conserved orthologous gene order from related taxa, can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a "chromonome". We demonstrate Chromonomer's performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality.</p>
Data from: The conservation genomics of the endangered distylous gypsophile Oreocarya crassipes (Boraginaceae)
The Chihuahuan Desert includes many endemic angiosperm species, some having very restricted geographic ranges. One of these species is Oreocarya crassipes (I. M. Johnst.) Hasenstab & M. G. Simpson, an endangered distylous gypsophile from the Trans-Pecos region in southern Brewster County, Texas, USA. The species is known from 10 populations, and this small number of populations, human development in the area, a distylous breeding system, and edaphic requirements threaten the long-term viability of the species. Using both hundreds of single nucleotide polymorphisms identified via tunable genotyping-by-sequencing (tGBS) and 10 microsatellite loci, patterns of genetic diversity, demography, selection, and migration were examined for 192 individuals from four populations of O. crassipes. From the sampled individuals, two populations (clusters) were identified via multiple methodologies and with both types of data. With SNP data, population substructure was further resolved among one of these populations to identify two distinct groups of individuals. Multiple individuals recognized as having mixed ancestry, along with Fst values and AMOVA results, provide evidence of genetic exchange among populations, which is less common for gypsophiles than non-gypsophiles, and the rate of migration among populations has been increasing recently. The Fst values for O. crassipes are more similar to those of other rare species than to other gypsophiles. Additionally, while distyly specifically does not necessarily impact the population genetics of the species, allogamy, which is facilitated by distyly, seems to have played a role in the genetic structure of O. crassipes.
Population genomics of flat-tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape
<p><em>Phrynosoma mcallii</em> (flat-tailed horned lizards) is a species of conservation concern in the Colorado Desert of the United States and Mexico. We analyzed ddRADseq data from 45 lizards to estimate population structure, infer phylogeny, identify migration barriers, map genetic diversity hotspots, and model demography. We identified the Colorado River as the main geographic feature contributing to population structure, with the populations west of this barrier further subdivided by the Salton Sea. Phylogenetic analysis confirms that northwestern populations are nested within southeastern populations. The best-fit demographic model indicates Pleistocene divergence across the Colorado River, with significant bidirectional gene flow, and a severe Holocene population bottleneck. These patterns suggest that management strategies should focus on maintaining genetic diversity on both sides of the Colorado River and Salton Sea. We recommend additional lands in the U.S. and Mexico that should be considered for similar conservation goals as those in the Rangewide Management Strategy (RMS). We also recommend periodic rangewide genomic sampling to monitor ongoing attrition of diversity, hybridization, and changing structure due to habitat fragmentation, climate change and other long-term impacts.</p>
Comparing genome-based estimates of relatedness for use in pedigree-based conservation management
<p>Researchers have long debated which estimator of relatedness best captures the degree of relationship between two individuals. In the genomics era, this debate continues, with relatedness estimates being sensitive to the methods used to generate markers, marker quality, and levels of diversity in sampled individuals. Here, we compare six commonly used genome-based relatedness estimators (kinship genetic distance (KGD), Wang Maximum Likelihood (TrioML), Queller and Goodnight (Rxy), Kinship INference for Genome-wide association studies (KING-robust), and Pairwise Relatedness (RAB), allele-sharing co-ancestry (AS)) across five species bred in captivity–including three birds and two mammals–with varying degrees of reliable pedigree data, using reduced-representation and whole genome resequencing data. Genome-based relatedness estimates varied widely across estimators, sequencing methods, and species, yet the most consistent results for known first order relationships were found using Rxy, RAB, and AS. However, AS was found to be less consistently correlated with known pedigree relatedness than either Rxy or RAB. Our combined results indicate there is not a single genome-based estimator that is ideal across different species and data types. To determine the most appropriate genome-based relatedness estimator for each new dataset, we recommend assessing the relative: (1) correlation of candidate estimators with known relationships in the pedigree and (2) precision of candidate estimators with known first-order relationships. These recommendations are broadly applicable to conservation breeding programs, particularly where genome-based estimates of relatedness can complement and complete poorly pedigreed populations. Given a growing interest in the application of wild pedigrees, our results are also applicable to in-situ wildlife management.</p>
Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus)
<p><span>We live in a world characterised by biodiversity loss and global environmental change. The extinction of large carnivores can have ramifying effects on ecosystems like an uncontrolled increase in wild herbivores, which in turn can have knock-on impacts on vegetation regeneration and communities. Cheetahs (</span><em><span>Acinonyx jubatus</span></em><span>) serve important ecosystem functions as apex predators; </span><span>yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-wildlife conflict, and illegal trafficking, there are only approximately 7,100 individuals remaining in nature. We present the most comprehensive genome-wide analysis of cheetah phylogeography and conservation genomics to date, assembling samples from nearly the entire current and past species' range. We show that their phylogeography is more complex than previously thought, and that East African cheetahs (<em>A. j. raineyi</em>) are genetically distinct from Southern African individuals (<em>A. j. jubatus</em>), warranting their recognition as a distinct subspecies. </span><span>We found strong genetic differentiation between all classically recognised subspecies, thus refuting earlier findings that cheetahs show only little differentiation. The strongest differentiation was </span><span>observed</span><span> between the Asiatic </span><span>and all the African subspecies.</span> <span>We detected high inbreeding in the Critically Endangered Iranian (<em>A. j. venaticus</em>) and North-western (<em>A. j. hecki</em>) subspecies, and show that overall cheetahs, along with snow leopards, have the lowest genome-wide heterozygosity of all the big cats. This further emphasizes the cheetah's perilous conservation status. Our results provide novel and important information on cheetah phylogeography that can support evidence-based conservation policy decisions to help protect this species. This is especially relevant in light of ongoing and proposed translocations across subspecies boundaries, and the increasing threats of illegal trafficking.</span></p>
ScienceDex guides
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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.