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.
1,659
datasets available to search
ShareScore release 0.9.0
Dataset results
1,659 results for “structured population”
Population structure shapes copy number variation in malaria parasites
GEO Series GSE75137. Plasmodium falciparum. 175 samples. Type: Genome variation profiling by genome tiling array.
Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia
GEO Series GSE33489. Homo sapiens. 142 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Genome-wide Patterns of Population Structure and Admixture among Hispanic/Latino Populations
GEO Series GSE21248. Homo sapiens. 100 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Multi-layered population structure in Island Southeast Asians
GEO Series GSE77508. Homo sapiens. 196 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array.
Spatial genetic structure to identify populations at risk
<p>Microsatellite genotypes, locality information, and raster data for Miller et al</p>
Meta-population structure and the evolutionary transition to multicellularity
<p>The evolutionary transition to multicellularity has occurred on numerous occasions, but transitions to complex life forms are rare. While the reasons are unclear, relevant factors include the intensity of within- versus between-group selection that are likely to shape the course of life cycle evolution. A highly structured environment eliminates the possibility of mixing between evolving lineages, thus ensuring strong competition between groups. Less structure intensifies competition within groups, decreasing opportunity for group-level evolution. Here, using populations of the bacterium <em>Pseudomonas fluorescens</em>, we report the results of experiments that explore the effect of lineage mixing on the evolution of nascent multicellular groups. Groups were propagated under regimes requiring reproduction via a life cycle replete with developmental and dispersal (propagule) phases, but in one treatment lineages never mixed, whereas in a second treatment, cells from different lineages experienced intense competition during the dispersal phase. The latter treatment favoured traits promoting cell growth at the expense of traits underlying group fitness, a finding that is supported by results from a mathematical model. Together our results show that the transition to multicellularity benefits from ecological conditions that maintain discreteness not just of the group (soma) phase, but also of the dispersal (germline) phase.</p>
Genomic structure of the Sicklefin Barb, Puntioplites falcifer (Cyprinidae), in the lower Mekong River basin reveals patterns of both migration and population partitioning
<p>Effective management of the Sicklefin Barb, <i>Puntioplites falcifer</i>, with the planned construction of several dams in the Mekong River Basin depends upon disentangling conflicting reports of isolated populations and highly migratory behavior. We investigated patterns of population genomic structure, relatedness, and inferred connectivity among three locations on the Mekong and a fourth at Attapeu on the Sekong tributary. The results supported both isolation of populations and migratory behavior. STRUCTURE, AMOVA, and PCA revealed three distinct nDNA clusters. The most divergent nDNA cluster (pairwise <i>F</i><sub>ST</sub> ≥ 0.43, <i>p < </i>0.0001) exhibited negligible inferred relative migration rates with the other samples (<i>m</i> ≤ 0.02), including those from common sampling locations, and was likely a different species - putatively <i>P. proctozysron </i>(Ppr). However, mtDNA barcoding suggested differentiation between Ppr and a published mtDNA genome for this species. Most of the fish from the Sekong tributary belonged to a second distinct nDNA cluster and the sample from that location was differentiated from the Mekong sites (pairwise <i>F</i><sub>ST</sub> = 0.02 - 0.03, <i>p</i> < 0.0001). Supporting migration, a third nDNA cluster exhibited high rates of migration among the Mekong locations (<i>m</i> = 0.6 - 1) and was found in small numbers at the Sekong location which was characterized by intermediate migration rates with the Mekong (<i>m</i> = 0.3 - 0.4). Mitochondrial DNA barcoding indicated that the fish comprising the Mekong and Sekong nDNA clusters were differentiated from a <i>P. falcifer </i>mtDNA genome sampled well upstream of the Mekong locations in this study. Estimates of <i>N</i><sub>e</sub> by both location and nDNA cluster were near or below the minimal sustainable size (173-1651), suggesting susceptibility to over-exploitation or population fragmentation. Together, these results suggest that proposed hydropower dams could subdivide connected Mekong populations, isolate and split the Sekong population, and further drive down <i>N</i><sub>e</sub> if accommodations are not made to facilitate connectivity. Additionally, the combined pattern of nDNA and mtDNA diversity is consistent with substantial cryptic diversity and a <i>P. falcifer</i> – <i>P. proctozysron</i> species complex that could be further described with rigorous population genomic surveys and expanded geographic sampling.</p>
SNP data: Population genetic structure in bull sharks (Carcharhinus leucas)
<p><span>The bull shark (<em>Carcharhinus leucas</em>) is a large, mobile, circumglobally distributed high trophic level predator that inhabits a variety of remote islands and continental coastal habitats, including freshwater environments. </span>Here, we hypothesise that the barriers to dispersal created by large oceanic expanses and deep-water trenches result in a heterogeneous distribution of the neutral genetic diversity between island bull shark populations compared to populations sampled in continental locations connected through continuous coastlines of continental shelves. <span>We analysed 1,494 high-quality neutral Single Nucleotide Polymorphism (SNP) markers in 215 individual bull sharks from widespread locations across the Indian and Pacific Oceans (South Africa, Indonesia, Western Australia, Papua New Guinea, eastern Australia, New Caledonia and Fiji). Genomic analyses revealed partitioning between remote insular and continental populations, with the Fiji population being genetically different from all other locations sampled (<i>F</i><sub>ST</sub> 0.034-0.044, <i>P </i>< 0.001), and </span>New Caledonia showing marginal isolation (<i>F</i><sub>ST</sub> 0.016-0.024, <i>P </i>< 0.001; albeit based on a small sample size) from most sampled sites<span>.</span> Discriminant Analysis of Principal Components (DAPC) identified samples from Fiji as a distinct cluster with all other sites as one large cluster. Genetic structure analyses (Admixture, STRUCTURE & AssignPOP) further supported the genetic isolation of bull sharks from Fiji, with the analyses in agreement. The observed differentiation in bull sharks from Fiji makes this site of special interest, as it indicates a lack of migration through dispersal across deep-water trenches and large ocean expanses.</p>
Data from: Population structure of a global agricultural invasive pest, Bactrocera dorsalis (Diptera: Tephritidae)
Bactrocera dorsalis, the Oriental fruit fly, is one of the world's most destructive agricultural insect pests and a major impediment to international fresh commodity trade. The genetic structuring of the species across its entire geographic range has never been undertaken, because under a former taxonomy B. dorsalis was divided into four distinct taxonomic entities, each with their own, largely non-overlapping, distributions. Based on the extensive sampling of six a priori groups from 63 locations, genetic and geometric morphometric datasets were generated to detect macrogeographic population structure, and to determine prior and current invasion pathways of this species. Weak population structure and high genetic diversity were detected among Asian populations. Invasive populations in Africa and Hawaii are inferred to be the result of separate, single invasions from South Asia; while South Asia is also the likely source of other Asian populations. The current northward invasion of B. dorsalis into central China is the result of multiple, repeated dispersal events, most likely related to fruit trade. Results are discussed in the context of global quarantine, trade and management of this pest. The recent expansion of the fly into temperate China, with very few associated genetic changes, clearly demonstrates the threat posed by this pest to ecologically similar areas in Europe and North America.
Data from: Population genetic structure of Picea engelmannii, P. glauca and their previously unrecognized hybrids in the central Rocky Mountains
Areas of geographic overlap between potentially hybridizing species provide the opportunity to study interspecific gene flow and reproductive barriers. Here we identified hybrids between Picea engelmannii and P. glauca by their genetic composition at 17 microsatellite markers, and determined the broad-scale geographic distribution of hybrids in the central Rocky Mountains of North America, a geographic region where hybrids and isolation between species had not previously been studied. Parameter estimates from admixture models revealed considerable variation in ancestry within and among collection sites, suggesting that within this area of geographic overlap, the interaction of the two species varies extensively. The results document a previously unrecognized patchy distribution of hybrids between P. engelmannii and P. glauca, including locations where hybrids were not known or expected to exist. Further, the ancestry of many hybrids was consistent with multiple generations of hybridization, with probable directional backcrossing to P. engelmannii, suggesting a relatively porous species boundary. The identification and characterization of hybridization between these spruce in this region raises the question of what factors maintain barriers to gene flow in these long-lived forest trees. The current research lays the groundwork for future study of the ecological and evolutionary contexts of their hybridization, as well as of differential introgression and permeability of species boundaries.
Data from: Genetic diversity and population structure of Urochloa grass accessions from Tanzania using simple sequence repeat (SSR) markers
Urochloa (syn.—Brachiaria s.s.) is one of the most important tropical forages that transformed livestock industries in Australia and South America. Farmers in Africa are increasingly interested in growing Urochloa to support the burgeoning livestock business, but the lack of cultivars adapted to African environments has been a major challenge. Therefore, this study examines genetic diversity of Tanzanian Urochloa accessions to provide essential information for establishing a Urochloa breeding program in Africa. A total of 36 historical Urochloa accessions initially collected from Tanzania in 1985 were analyzed for genetic variation using 24 SSR markers along with six South American commercial cultivars. These markers detected 407 alleles in the 36 Tanzania accessions and 6 commercial cultivars. Markers were highly informative with an average polymorphic information content of 0.79. The analysis of molecular variance revealed high genetic variation within individual accessions in a species (92%), fixation index of 0.05 and gene flow estimate of 4.77 showed a low genetic differentiation and a high level of gene flow among populations. An unweighted neighbor-joining tree grouped the 36 accessions and six commercial cultivars into three main clusters. The clustering of test accessions did not follow geographical origin. Similarly, population structure analysis grouped the 42 tested genotypes into three major gene pools. The results showed the Urochloa brizantha (A. Rich.) Stapf population has the highest genetic diversity (I = 0.94) with high utility in the Urochloa breeding and conservation program. As the Urochloa accessions analyzed in this study represented only 3 of 31 regions of Tanzania, further collection and characterization of materials from wider geographical areas are necessary to comprehend the whole Urochloa diversity in Tanzania.
Data from: A genome-wide assessment of genetic diversity and population structure of Korean native cattle breeds
Background: The native cattle breeds are an important genetic resource for meat and milk production throughout Asia. In Asia cattle were domesticated around 10,000 years ago and in Korea cattle are being raised since 2000 B.C. There are three native breeds of cattle in Korea viz. Brown Hanwoo, Brindle Hanwoo and Jeju Black. While one of these breeds, Brown Hanwoo, is a part of a Food and Agricultural Organization and national genetic evaluation plans, others get little attention. This study is an effort to understand and provide a detailed insight into the population structure and genetic variability of the Korean cattle breeds along with other Asian breeds using various methods. In this study we report the genetic variation and structure of the Korean cattle breeds and their comparison with five other Asian cattle breeds along with a panel of animals from European taurine, African taurine and indicine cattle breeds. Results: Asian cattle were found to be least differentiated which reflects their recent history. Amongst the Asian breeds Hainan, which is an indicine breed, had the lowest gene diversity while Yanbian had the highest followed by Mongolian and Korean cattle. Amongst the Korean breeds Brown Hanwoo had the highest diversity followed by Brindle Hanwoo and Jeju Black. The genetic diversity in Asian cattle breeds was found comparable to the European taurines and more than the African taurines and Zebu cattle. Korean cattle breed, Brown Hanwoo was consistently found to be closer to Yanbian, a Chinese cattle breed. We found low divergence and moderate levels of genetic diversity among the native Korean breeds. Indicine introgression from Hainan was seen in other Asian breeds. From Europe, Limousin, Holstein and Hereford introgression was found in Asian breeds. Conclusions: In this study we provide a genome-wide insight into the genetic history of the native cattle breeds of Korea. The outcomes of this study will help in prioritization and designing of the conservation plans.
Data from: Population genetic structure of the Pocillopora damicornis morphospecies along Ningaloo Reef, Western Australia
The effective management of a coral reef system relies on a detailed understanding of the population structure of dominant habitat-forming species. For some corals, however, high levels of phenotypic plasticity have made species delineation based on morphological characteristics alone unreliable, suggesting that previous studies of population genetic structure may have been influenced by the inclusion of multiple genetic lineages in the analyses. We examined the population structure of the Pocillopora damicornis morphospecies along the World Heritage Ningaloo Coast, Western Australia, and recovered 2 mitochondrial haplotypes from sympatrically occurring colonies possessing morphological characteristics consistent with taxonomic classification of P. damicornis. Despite a high degree of genetic differentiation between these lineages, we detected low levels of unidirectional admixture between them, suggesting that reproductive barriers are not fully developed. We found dual modes of reproduction for both lineages with considerable variation in the contribution of sexual reproduction among sample sites. Lastly, we identified a high dispersal potential of sexually produced propagules in the most common lineage with positive spatial autocorrelation detected over distances up to 60 km. Based on these results, it appears that populations of P. damicornis have a high capacity to recover from environmental perturbations as long as the effects of disturbances are patchy across Ningaloo Reef.
Data from: The role of ecological factors in determining phylogeographic and population genetic structure of two sympatric island skinks (Plestiodon kishinouyei and P. stimpsonii)
We conducted comparative phylogeographic and population genetic analyses of Plestiodon kishinouyei and P. stimpsonii, two sympatric skinks endemic to islands in the southern Ryukyus, to explore different factors that have influenced population structure. Previous phylogenetic studies using partial mitochondrial DNA (mtDNA) indicate similar divergence times from their respective closest relatives, suggesting that differences in population structure are driven by intrinsic attributes of either species rather than the common set of extrinsic factors that both presumably have been exposed to throughout their history. In this study, analysis of mtDNA sequences and microsatellite polymorphism demonstrate contrasting patterns of phylogeography and population structure: P. kishinouyei exhibits a lower genetic variability and lower genetic differentiation among islands than P. stimpsonii, consistent with recent population expansion. However, historical demographic analyses indicate that the relatively high genetic uniformity in P. kishinouyei is not attributable to recent expansion. We detected significant isolation-by-distance patterns among P. kishinouyei populations on the land bridge islands, but not among P. stimpsonii populations occurring on those same islands. Our results suggest that P. kishinouyei populations have maintained gene flows across islands until recently, probably via ephemeral Quaternary land bridges. The lower genetic variability in P. kishinouyei may also indicate smaller effective population sizes on average than that of P. stimpsonii. We interpret these differences as a consequence of ecological divergence between the two species, primarily in trophic level and habitat preference.
Data from: Evaluation of genetic diversity and population structure of five Chinese indigenous donkey breeds using microsatellite markers
China had the largest population of raising donkeys in the world, however the number of Chinese indigenous donkey decreased dramatically due to the increase of agriculture mechanization in the last century. The species has still been important in China because of its edible and medical value, therefore the survey on its genetic diversity in China is necessary for its conservation and utilization. In this study, 15 microsatellite markers were used to evaluate genetic diversity and population structure of five Chinese indigenous donkey breeds. The mean values of expected heterozygosity, allelic richness, and total number of alleles for all the tested Chinese donkeys were 0.70, 6.04, and 6.28 respectively, suggesting that the genetic diversity of Chinese indigenous donkeys is rich. The Bayesian analysis and principal component analysis plot yielded the same clustering result, which revealed that Guanzhong donkey was the most differentiated breed in all detected samples, and Jinnan (JN) and Guangling (GL) were genetically closed together. Additionally, our results indicated that the heterozygote deficit was severe in two Chinese indigenous donkey breeds (GL and JN), and it warned us that animal conservation activities on this species should be considered carefully in near future.
Figure 3 from: Zhao L, Wang S, Qu F, Liu Z, Gao T (2022) A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific. ZooKeys 1088: 1-15. https://doi.org/10.3897/zookeys.1088.70860
Figure 3 Phylogenetic network of all haplotypes.
Figure 1 from: Zhao L, Wang S, Qu F, Liu Z, Gao T (2022) A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific. ZooKeys 1088: 1-15. https://doi.org/10.3897/zookeys.1088.70860
Figure 1 Sampling locations of Odontamblyopus lacepedii in the present study.
Fig. 3 in Effect Of Farming And Rainfall On The Species Diversity, Population Density And Community Structure Of Birds Breeding In The Kalahari Woodland, Ne Namibia
Fig. 3. Percentage of main feeding guilds in 2014 and 2015.
Figure 1 from: Zhao L, Yi D, Li C, Sun D, Xu H, Gao T (2017) Phylogeography and population structure of - grypotus (Richardson, 1846) as revealed by mitochondrial control region sequences. ZooKeys 705: 143-158. https://doi.org/10.3897/zookeys.705.13001
Figure 1 - Sampling sites of J. grypotus
Figure 3 in The effect of insularity on the seasonal population structure of Mesobuthus gibbosus (Scorpiones: Buthidae)
Figure 3: The number of monthly captures in Crete and Volos.
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.