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637 results for “Population analysis”
Strong association between the 12q24 locus and sweet taste preference in the Japanese population revealed by genome-wide meta-analysis: Summary stats
<p>Summary stats of the genome-wide meta-analysis with METAL software in the article "Strong association between the 12q24 locus and sweet taste preference in the Japanese population revealed by genome-wide meta-analysis."</p>
ISSR analysis of Tulipa suaveolens (Liliaceae) populations in the European part of the species range
<p>Tulipa suaveolens Roth is a decorative bulbous, polycarpic species in the Liliaceae family. Currently, the species populations are declining due to the degradation of natural steppes. In the present article, we evaluated the genetic diversity of 216 specimens from 22 natural T. suaveolens localities in the European part of the species range using 10 inter simple sequence repeat (ISSR) markers. The polymerase chain reaction (PCR) yielded 250 unambiguous and reproducible polymorphic bands with a mean polymorphism information content (PIC) value of 0.27. Neither the principal component analysis nor the clustering method split the dataset. However, the Bayesian model-based STRUCTURE analysis detected two genetic clusters of T. suaveolens. The analysis of the biogeographical distributional pattern of the revealed genetic groups confirmed our hypothesis that the evolution and distribution of T. suaveolens were likely affected by the Early Khvalynian transgression of the Caspian Sea and the following Enotayevsk regression. Furthermore, this hypothesis was supported by the results of the NEW HYBRIDS analysis identifying the specimens from the populations located outside the Early Khvalynian flooding limit as pure parents, while the specimens of the populations within the flooding limit were classified as backcrosses and second generation hybrids.</p>
Transcriptome analysis of invasive Gypsophila paniculata (baby's breath) populations from Michigan and Washington, USA.
<p>Invasive species provide an opportune system to investigate how populations respond to new or changing environments. While the impacts of invasive species increase annually, many gaps in our understanding of how these species invade, adapt, and thrive in the areas they are introduced to remain. Using the perennial forb <i>Gypsophila paniculata</i> as a study system, we aimed to investigate how invasive species respond to different environments. Baby's breath (<i>Gypsophila paniculata</i>) was introduced to North America in the late 1800's and has since spread throughout the northwestern United States and western Canada. We used an RNA-seq approach to explore how molecular processes may be contributing to the success of invasive <i>G. paniculata</i> populations that are thought to share similar genetic backgrounds across distinct habitats. Transcription profiles were constructed for root, stem, and leaf tissue from seedlings collected from a sand dune ecosystem in Petoskey, MI (PSMI) and a sagebrush ecosystem in Chelan, WA (CHWA). Using these data we assessed differential gene expression between the two populations and identified SNPs within differentially expressed genes. We identified 1,146 transcripts that were differentially expressed across all tissues between the two populations. GO processes enriched by genes displaying higher expression in PSMI were associated with increased nutrient starvation, while enriched processes in CHWA were associated with abiotic stress. Only 7.4% of the differentially expressed genes across all three tissues contained SNPs differing in allele frequencies of at least 0.5 between the populations. In addition, common garden studies found the two populations differed in germination rate and seedling emergence success, but not in above- and below-ground tissue allocation. Our results suggest that the success of invasive <i>G. paniculata</i> across these two environments is likely the result of plasticity in molecular processes responding to different environmental conditions, although some genetic divergence may also be contributing to these differences.</p>
Mixed-stock analysis using Rapture genotyping to evaluate stock-specific exploitation of a walleye population despite weak genetic structure
<p>Mixed-stock analyses using genetic markers have informed fisheries management in cases where strong genetic differentiation occurs among local spawning populations, yet many fisheries are supported by multiple spawning stocks that are weakly differentiated. Freshwater fisheries exemplify this problem, with many harvested populations supported by multiple stocks of young evolutionary age and that are isolated across small spatial scales. As a result, attempts to conduct genetic mixed-stock analyses of inland fisheries have often been unsuccessful. Advances in genomic sequencing now offer the ability to discriminate among populations with weak population structure, by providing the necessary resolution to conduct mixed-stock assignment among previously indistinguishable stocks. We demonstrate the use of genomic data to conduct a mixed-stock analysis of Lake Erie's commercial and recreational walleye (<em>Sander vitreus</em>) fisheries and estimate the relative harvest of weakly differentiated stocks. We used RAD-capture (Rapture) to sequence and genotype individuals at 12,081 loci that had been previously determined to be capable of discriminating between western and eastern basin stocks (mean pairwise F<sub>ST</sub> = 0.001) with 95% reassignment accuracy. An outcome not possible in the past with microsatellite markers. Genetic assignment of 1,075 fish harvested from recreational and commercial fisheries in the eastern basin indicated that western basin stocks supported the majority of the harvest during peak harvest (July – September). Composition of harvest changed seasonally, with eastern basin fish comprising much of the early season harvest (May – June). Clear spatial structure in stock-specific harvest existed; more easterly sites contained more individuals of east basin origin than did westerly sites. Our study provides important stock contribution estimates for Lake Erie fishery management and demonstrates the power of genomic data to facilitate mixed-stock analysis in exploited fish populations with weak population structure or limited existing genetic resources.</p>
Does genetic diversity protect host populations from parasites? A meta-analysis across natural and agricultural systems
<p>If parasites transmit more readily between closely related hosts, then parasite burdens should decrease with increased genetic diversity of host populations. This important hypothesis is often accepted at face value - notorious epidemics of crop monocultures testify to the vulnerability of host populations that have been purged of diversity. Yet the relationship between genetic diversity and parasitism likely varies across contexts, differing between crop and non-crop hosts and between experimental and natural host populations. Here, we used a meta-analytic approach to ask if host diversity confers protection against parasites over the range of contexts in which it has been tested.</p> <p>We synthesized the results of 102 studies, comprising 2,004 effect sizes representing a diversity of approaches and host-parasite systems. Our results validate a protective effect of genetic diversity, while revealing significant variation in its strength across biological and empirical contexts. In experimental host populations, genetic diversity reduces parasitism by ~20% for non-crop hosts and by ~50% for crop hosts. In contrast, observational studies of natural host populations show no consistent relationship between genetic diversity and parasitism, with both strong negative and positive correlations reported. This result supports the idea that, if parasites preferentially attack close relatives, the correlation of genetic diversity with parasitism could be positive or negative depending upon the potential for host populations to evolve in response to parasite selection. Taken together, these results reinforce genetic diversity as a priority for both conservation and agriculture and emphasize the challenges inherent to drawing comparisons between controlled experimental populations and dynamic natural populations.</p>
Data from: Large-scale meta-analysis on rheumatoid arthritis across East Asian and European populations
<p><span><span><span><b>Objective:</b> Nearly 110 susceptibility loci for rheumatoid arthritis (RA) with modest effect sizes have been identified by population-based genetic association studies, suggesting a large number of undiscovered variants behind a highly polygenic genetic architecture of RA. Here, we performed the largest-ever trans-ancestral meta-analysis with the aim to identify new RA loci and to better understand RA biology underlying genetic associations.</span></span></span></p> <p><span><span><span><b>Methods:</b> Genome-wide RA association summary statistics in three large case-control collections consisting of 311,292 individuals of Korean, Japanese, and European populations were used in an inverse-variance-weighted fixed-effects meta-analysis. Several computational analyses using public omics resources were conducted to prioritize causal variants and genes, RA variant-implicating features (tissues, pathways, and transcription factors), and potentially repurposable drugs for RA treatment. </span></span></span></p> <p><span><span><span><b>Results:</b> We identified 11 new RA susceptibility loci that explained 6.9% and 1.8% of the SNP-based heritability in East Asians and Europeans, respectively, and confirmed 71 known non-HLA susceptibility loci, identifying 90 independent association signals. The RA variants were preferentially located in binding sites of various transcription factors and in cell type-specific transcription-activation histone marks that simultaneously highlighted the importance of CD4<sup>+</sup> T-cell activation and the potential role of non-immune organs in RA pathogenesis. A total of 615 plausible effector genes, based on gene-based associations, expression-associated variants, and chromatin interaction, included targets of drugs approved for RA treatments and potentially repurposable drugs approved for other indications.</span></span></span></p> <p><span><span><span><b>Conclusion:</b> Our findings provide useful insights regarding RA genetic etiology and variant-driven RA pathogenesis.</span></span></span></p>
Data from: Population genomic analysis of Brook Trout Salvelinus fontinalis in Pennsylvania's Appalachian region
Informed conservation of stream fishes requires detailed understanding of the effects of both natural processes and anthropogenic activities on genetic diversity. Brook Trout Salvelinus fontinalis, a salmonid native to eastern North America, typically resides in cold, high-quality stream ecosystems. The species has not only faced historical anthropogenic pressures, but also confronts current and future pressures. In a genetic analysis we used a reduced representation sequencing method (ddRADseq) to characterize 63 individuals from 23 streams where Brook Trout are native in the Appalachian region of Pennsylvania. A total of 2,590 loci passed filtering criteria, and 53% displayed significant association with a major stream drainage basin (Susquehanna or Allegheny; mean FST = 0.085). Mapping of the sequencing reads to the Atlantic Salmon Salmo salar genome revealed no clustering of high interdrainage FST values to specific genome regions. Evidence for genetic heterogeneity within each drainage basin was also detected. Stepwise regression of observed heterozygosity against geographic and environmental features revealed that drainage basin and effective area of watersheds were significant predictors of observed heterozygosity of Brook Trout within streams. Natural features such as waterfalls and major drainage basin, as well as the effects of dams and acid-mine drainage have fragmented habitat and shaped genetic diversity within Brook Trout populations in the Appalachian region of Pennsylvania, overall indicating the vulnerability of this species to increased industrialization.
Data from: Long-term population dynamics of dreissenid mussels (Dreissena polymorpha and D. rostriformis): a cross-system analysis
Dreissenid mussels (including the zebra mussel Dreissena polymorpha and the quagga mussel D. rostriformis) are among the world's most notorious invasive species, with large and widespread ecological and economic effects. However, their long‐term population dynamics are poorly known, even though these dynamics are critical to determining impacts and effective management. We gathered and analyzed 67 long‐term (>10 yr) data sets on dreissenid populations from lakes and rivers across Europe and North America. We addressed five questions: (1) How do Dreissena populations change through time? (2) Specifically, do Dreissena populations decline substantially after an initial outbreak phase? (3) Do different measures of population performance (biomass or density of settled animals, veliger density, recruitment of young) follow the same patterns through time? (4) How do the numbers or biomass of zebra mussels or of both species combined change after the quagga mussel arrives? (5) How does body size change over time? We also considered whether current data on long‐term dynamics of Dreissena populations are adequate for science and management. Individual Dreissena populations showed a wide range of temporal dynamics, but we could detect only two general patterns that applied across many populations: (1) Populations of both species increased rapidly in the first 1–2 yr after appearance, and (2) quagga mussels appeared later than zebra mussels and usually quickly caused large declines in zebra mussel populations. We found little evidence that combined Dreissena populations declined over the long term. Different measures of population performance were not congruent; the temporal dynamics of one life stage or population attribute cannot generally be accurately inferred from the dynamics of another. We found no consistent patterns in the long‐term dynamics of body size. The long‐term dynamics of Dreissena populations probably are driven by the ecological characteristics (e.g., predation, nutrient inputs, water temperature) and their temporal changes at individual sites rather than following a generalized time course that applies across many sites. Existing long‐term data sets on dreissenid populations, although clearly valuable, are inadequate to meet research and management needs. Data sets could be improved by standardizing sampling designs and methods, routinely collecting more variables, and increasing support.
Data from: Reticulate evolution within a spruce (Picea) species complex revealed by population genomic analysis
The role of reticulation in the rapid diversification of organisms is attracting greater attention in evolutionary biology. Here, we report a population genomics approach to test the role of hybridization and introgression in the evolution of the Picea likiangensis species complex. Based on 84,793 SNPs detected in transcriptomes of 82 trees collected from 35 localities, we identified 18 hybrids (including backcrosses) distributed within the range boundaries of the four taxa. Coalescent simulations, for each pair of taxa and for all taxa taken together, rejected several tree-like divergence models and supported instead a reticulate evolution model with secondary contacts occurring during Pleistocene glacial cycles after initial divergence in the late Pliocene. Significant gene flow occurred among some taxa after secondary contact according to an analysis based on modified ABBA-BABA statistics that accommodated a rapid diversification scenario. A novel finding was that introgression between certain taxa can contribute to increasing divergence (and possibly reproductive isolation) between those taxa and other taxa within a complex at some loci. These results illuminate the reticulate nature of evolution within the P. likiangensis complex and highlight the value of population genomic data in detecting the effects of introgression in the rapid diversification of related taxa.
Supplementary Material for Frontiers Plant Genetics and Genomics 'Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality'
<p>Authors</p> <p>Zhian N. Kamvar, Jonah C. Brooks, and Niklaus J. Grünwald</p>
Targeted DNA-seq analysis was performed on sorted population of CD45+/CD34+ HSPCs from control or FLI-1 modified mRNA treated mPB after co-culture with vascular niche cells
<p>Human mPB HSPCs were harvested isolated and transduced with either control or FLI-1 modified mRNA. HSPCs were introduced into co-culture with vascular niche ECs. Cultures were harvested and CD45+/CD34+ HSPCs were resoerted and processed for trageted DNA-seq analysis. Contains raw FASTQ sequencing files, unfiltered VCFs, and curated results in an excel.</p>
Population Genomics Analysis of 30 Samples from Each of Multiple Populations Reveals Signatures of Selection from Breeding for Rapid Growth and Apical Dominance in Paulownia fortunei
<p><i>Paulownia fortunei</i> is an ecologically and economically valuable tree cultivated for its rapid growth and high-quality timber. To enhance <i>Paulownia</i> germplasm, we have developed the elite variety QingT with patented advantages in growth rate and apical dominance. To illuminate the genetic basis of QingT's superior traits, here we harness comparative population genomics to analyze genomic variation patterns between QingT and common <i>Paulownia</i>. We performed whole-genome re-sequencing of 30 QingT and 30 common samples, detecting 15.6 million SNPs and 2.6 million indels. Phylogeny and population structure analyses robustly partitioned common and QingT into distinct groups which indicate robust genome stabilization. QingT exhibited reduced heterozygosity and linkage disequilibrium decay compared to common <i>Paulownia</i>, reflecting high recombination, indicating hybridizing effects with common white-flowered string is the source of its patented advantages. Genome selection scans uncovered 25 regions of 169 genes with elevated nucleotide diversity, indicating selection sweeps among groups. Functional analysis of sweep genes revealed upregulation of ribosomal, biosynthesis and growth pathways in QingT, implicating enhanced protein production and developmental processes in its rapid growth phenotype. This study's insights comprehensively chart genomic variation during <i>Paulownia</i> breeding, localizing candidate loci governing agronomic traits, and underpinnings of future molecular breeding efforts to boost productivity. </p>
Genomic analysis of population history for Hawaiian monk seals
<p>The Hawaiian monk seal, one of the world's most endangered pinnipeds, has faced decades of declines and been the focus of intensive conservation efforts. A myriad of conservation threats has led to range-wide population declines, but population trends among islands can vary widely in response to heterogeneous threats. Populations in the Northwestern Hawaiian Islands have been declining whereas Main Hawaiian Islands numbers are expanding. Molecular data can provide information to disentangle population structure and dynamics; however, previous studies have yielded insufficient resolution in such a genetically depauperate species. Advances in genomic technology and affordability offer a novel opportunity to revisit questions about Hawaiian monk seal trends with high resolution markers that provide better discrimination ability in low diversity species. Here, we investigated region- and island-level population structuring and connectivity. We used BestRAD sequencing on 169 seals from 14 islands that span the archipelago to estimate genetic diversity, genetic differentiation, population structure, and migration rates. We did not find robust evidence for island-level population structure. For the first time, our dataset provided resolution to differentiate regional populations with low but significant genetic differentiation. Further, DAPC analyses illustrated population structure with evidence for connectivity, which mirrored our migration rate estimates. Future conservation decisions will need to consider the balance of maintaining connectivity between regions while not homogenizing and losing valuable yet rare, regional unique variation.</p>
Data from: Range-wide genetic analysis of an endangered bumble bee (Bombus affinis) reveals population structure, isolation by distance, and low colony abundance
<p>Declines in bumblebee species ranges and abundances are documented across multiple continents and have prompted the need for research to aid species recovery and conservation. The rusty patched bumblebee (<em>Bombus affinis</em>) is the first federally-listed bumblebee species in North America. We conducted a range-wide population genetics study of <em>B. affinis</em> from across all extant conservation units to inform conservation efforts. To understand the species' vulnerability and help establish recovery targets, we examined population structure, patterns of genetic diversity, and population differentiation. Additionally, we conducted site-level analysis of colony abundance to inform prioritizing areas for conservation, translocation, and other recovery actions. We find substantial evidence of population structuring along an east-to-west gradient. Putative populations show evidence of isolation by distance, high inbreeding coefficients, and a range wide male diploidy rate of ~15%. Our results suggest the Appalachians represents a genetically distinct cluster with high levels of private alleles and substantial differentiation from the rest of the extant range. Site-level analyses suggest low colony abundance estimates for <em>B. affinis</em> compared to similar datasets of stable, co-occurring species. These results lend genetic support to trends from observational studies suggesting B. affinis has undergone a recent decline and exhibits substantial spatial structure. The low colony abundances observed here suggest caution in overinterpreting the stability of populations even where <em>B. affinis</em> is reliably detected interannually. These results help delineate informed management units, provide context for the potential risks of translocation programs, and can help set clear recovery targets for this and other threatened bumblebee species.</p>
Density of states and Crystal Orbital Hamilton Population Analysis of CO adsorbed on Co
<p>This dataset pertains to an extensive study of the electronic structure of CO adsorbed on various active site topologies on cobalt. The following cobalt active site configurations were explored:</p> <ul> <li>Co(0001) (fcc)</li> <li>Co(0001) (hcp)</li> <li>Co(11-21) 3f</li> <li>Co(11-21) B5</li> <li>Co(100)</li> <li>Co(110)</li> <li>Co55/Al2O3 (top)</li> <li>Co55/Al2O3 (interfacial site)</li> <li>Co52/Al2O3 (defect site)</li> <li>Co84/Al2O3 (nanorod)</li> <li>Co54/TiO2 (cluster)</li> <li>Co81/TiO2 (nanorod)</li> </ul> <p>For each adsorption site, a density of states and crystal orbital hamilton population analysis was performed by means of the <a href="http://www.cohp.de/">Lobster</a> program. The original electronic structure calculations are performed using <a href="https://www.vasp.at/">VASP</a>. The input and output files for all calculations as well as the Python scripts how these files were parsed are found in this repository.</p>
Data from: Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape - patterns of genetic diversity, population structure and gene flow
<p><span><span>Red deer (</span><span><em>Cervus elaphus</em></span><span>) throughout central Europe are</span> impacted by different anthropogenic activities including habitat fragmentation, selective hunting, and translocations<span>. This has substantial influences on genetic diversity and the long-term conservation of local populations of this species. Here we use genetic samples from 480 red deer individuals to assess the genetic diversity and differentiation of the 12 administrative management units located in Schleswig Holstein, the northernmost federal state in Germany. </span></span><span><span>We applied multiple analytical approaches and show that the history of local populations (i.e., translocations, culling of individuals outside of designated red deer zones, and anthropogenic infrastructures) has led to comparably low levels of genetic diversity. The mean expected heterozygosity was below 0.6 and we observed on average 4.2 alleles across 12 microsatellite loci. Effective population sizes below the recommended level of 50 were estimated for multiple local populations. </span></span><span><span>Our estimates of genetic structure and gene flow show that red deer in northern Germany are best described as a complex network of asymmetrically connected subpopulations, with high genetic exchange among some local populations and reduced connectivity of others. Genetic diversity was also correlated with population densities of neighboring management units. </span></span></p> <p><span><span>Based on these findings, we suggest that connectivity among existing management units needs to be considered in the practical management of the species, which means that some administrative management units should be managed together, while the effective isolation of other units needs to be mitigated.</span></span></p>
Dispersal increases spatial synchrony of populations but has weak effects on population variability: a meta-analysis
<p><span>The effects of dispersal on spatial synchrony and population variability have been well documented in theoretical research, and a growing number of empirical tests have been performed. Yet a synthesis is still lacking. Here, we conducted a meta-analysis of relevant experiments and examined how dispersal affected spatial synchrony and temporal population variability across scales. Our analyses showed that dispersal generally promoted spatial synchrony, and such effects </span><span>increased with dispersal rate and decreased with environmental correlation among patches. The synchronizing effect of dispersal, however, was only detected when spatial synchrony was measured using the correlation-based index, but not for the covariance-based index. In contrast to theoretical predictions, the effect of dispersal on local population variability was generally non-significant, except when environment correlation among patch was negative and/or experimental period was long. At the regional scale, while low dispersal stabilized metapopulation dynamics, high dispersal led to destabilization. </span><span>Overall, the sign and strength of dispersal effects on spatial synchrony and population variability were modulated by taxa, environmental heterogeneity, </span><span><span>type of perturbations, patch number, and experimental length. </span>Our synthesis demonstrates that dispersal can substantially affect the dynamics of spatially distributed populations, but its effects are context dependent on abiotic and biotic factors. </span></p>
Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae
<p>The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species. Results The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories. Conclusions The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.</p>
Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds
<p><strong>Summary</strong></p> <p>Uganda is endowed with a large population of goats from predominantly indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture of the exotic breed Boer is still limited. Using a medium density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six Ugandan goat breeds. Samples from five indigenous Ugandan goat breeds including Mubende (n=29), Kigezi (n=29), Small East African (n=29), Sebei (n=29) and Karamojong (n=15), and the exotic breed Boer (n=13) from different agro-ecological regions of Uganda were genotyped using the GoatSNP50 BeadChip. Analysis of genotype data revealed high levels of polymorphism with the proportion of polymorphic SNPs ranging from 0.885 in Kigezi to 0.928 in Sebei. The overall mean genetic diversity indices across breeds for <em>H<sub>O</sub></em> and <em>H<sub>E</sub></em> was 0.355±0.147 and 0.384±0.143 respectively. Principle components, genetic distances and ADMIXTURE analyses revealed weak population sub-structuring among the breeds. Principle components separate Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong are tightly entangled together while Mubende occupies a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. ADMIXTURE and four population test analyses further revealed gene-flow from Boer to Ugandan indigenous goat breeds and varying levels of admixture among the Ugandan indigenous breeds. Generally, moderate to high levels of genetic variability were observed in the Ugandan goat breeds. Our findings provide useful insight to devise strategies to maintain genetic diversity in local goat breeds from Uganda and to design appropriate breeding programs to exploit within breed diversity and heterozygote advantage in cross-breeding schemes.</p>
Correlation-based Analysis of the Influence of Bound Constraint Handling Methods on Population Dynamics in Differential Evolution
<p>The dataset is based on the average values collected over 5 independent runs, considering the largest common number of<br>iterations for LSHADE algorithm coupled with ’sat’, ’midT’, ’midB’, ’unif’, ’beta’, ’mir’, ’tor’, ’expC_R’, ’expC_T’, ’expC_B’, ’vectR’, ’vectT’, ’vectB’, ’mahalanobis’ correction methods, on BBOB function f3, 4, 5, 16, 23, instance 1</p> <p>Plots for the averaged values are included for measures 'pop_size', 'best', 'error', 'prob_infeas', 'genMutatedComponent', 'genSuccessMutants','meanImprovements', 'varPop', 'avgF', 'avgCR', 'extension', 'shape', 'eccentricity', 'kl_unif'</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.