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.
34
datasets available to search
ShareScore release 0.9.0
Dataset results
34 results for “metapopulation structure”
Simulated genetic data in a hierarchical metapopulation structure
<p>The data are linked to a research article entitled: “<em>Interactions between microenvironment, selection and genetic architecture drive multiscale adaptation in a simulation experiment” </em>in<em> Journal of Evolutionary Biology</em> (see References).</p> <p>In this research on multiscale adaptation, we simulated a hierarchical metapopulation structure with four populations, two environments per population and three patches per environment, in a two-step procedure:</p> <ul> <li>an initialization step without selection, with eight combinations of mutation type, selfing rate and QTL number parameters (2 modes each); out of 200,000 simulated generations in each case, we chose one with appropriate characteristics as a starting point for the next step;</li> <li>a selection step with all possible combinations of the following parameters: environmental pattern (4 modes), environmental range (5 modes), selection intensity (4 modes), fecundity (3 modes).</li> </ul> <p>This resulted in 240 scenarios for each initialized metapopulation, i.e. 1,920 scenarios in total. Each scenario was replicated 10 times, i.e. 19,200 simulation runs.</p> <p>The archive includes all data needed to reproduce the simulations and analyses, or to re-use the simulated metapopulations for other analyses. It has the following structure (further detailed below):</p> <ol> <li><strong>NemoScripts directory </strong>contains the <em>Nemo </em>input files used to perform simulations for the initialization step and the selection step;</li> <li><strong>RScripts directory </strong>contains the <em>R</em> scripts to read the <em>Nemo </em>output files, compute synthetic variables(*), and produce the figures as they appear in the publication and supplementary material (*: long computations, therefore we also directly provide those synthetic variables in the Data directory);</li> <li><strong>Data directory </strong>contains the <em>Nemo </em>output files, the synthetic variables, and other data needed to reproduce the figures; this directory can be used as a working directory for the <em>R</em> scripts (recommended).</li> </ol> <p>Running the following command in a terminal <strong><em>tar –xzvf Archive_PC_SOM_IS_FL.tar</em></strong> will create a directory named <strong><em>Archive_PC_SOM_IS_FL</em></strong>, which detailed content is described in the <strong><em>README.pdf</em></strong> file.<br> Warning: the extracted archive is large (460Go, >40,000 files) and extraction may take some time.</p>
Data for the manuscript: Demographic basis of spatially structured fluctuations in a threespine stickleback metapopulation
<p>Uncovering the demographic basis of population fluctuations is a central goal of population biology. This is particularly challenging for spatially structured populations, which require disentangling synchrony in demographic rates from coupling via immigration. In this study, we fit a stage-structured metapopulation model to a 29-year times series of threespine stickleback abundance in the heterogeneous and productive Lake Myvatn, Iceland. The lake comprises two basins (North and South) connected by a channel through which the stickleback disperse. The model includes time-varying demographic rates, allowing us to assess the potential contributions of recruitment and survival, spatial coupling via immigration, and demographic transience to the population's large fluctuations in abundance. Our analyses indicate that recruitment was only modestly synchronized between the two basins, whereas survival probabilities of adults were more strongly synchronized, contributing to cyclic fluctuations in the lake-wide population size with a period of approximately six years. The analyses further show that the two basins are coupled through immigration, with the North Basin subsidizing the South Basin and playing a dominant role in driving the lake-wide dynamics. Our results show that cyclic fluctuations of a metapopulation can be explained in terms of the combined effects of synchronized demographic rates and spatial coupling.</p>
Data for the manuscript: Demographic basis of spatially structured fluctuations in a threespine stickleback metapopulation
Open the record for dataset details and reuse information.
SGS-LTER Genetic Structure of Metapopulation of Black-Tailed Prairie Dogs on the Central Plains Experimental Range and Pawnee National Grassland in Nunn, Colorado, USA 1997-1998
This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. Additional information and referenced materials can be found: http://hdl.handle.net/10217/83465. Thirteen colonies of black-tailed prairie dogs were studied within a 264-km2 area of the Central Plains Experimental Range and the Pawnee National Grasslands in Weld County, Colorado. Tissue Collection, DNA Extraction, and microsatellite genotype scoring was performed.
Data from: Unraveling hierarchical genetic structure in a marine metapopulation: a comparison of three high-throughput genotyping approaches
<p>Marine metapopulations often exhibit subtle population structure that can be difficult to detect. Given recent advances in high-throughput sequencing, an emerging question is whether various genetic approaches, in concert with improved sampling designs, will substantially improve our understanding of genetic structure in the sea. To address this question, we explored hierarchical patterns of structure in the coral reef fish <i>Elacatinus lori</i> using a high-resolution approach with respect to both genetic and geographic sampling. Previously, we identified three putative <i>E. lori</i> populations within Belize using traditional genetic markers and sparse geographic sampling: barrier reef and Turneffe Atoll; Glover's Atoll; and Lighthouse Atoll. Here, we systematically sampled individuals at ~10 km intervals throughout these reefs (1,129 individuals from 35 sites) and sequenced all individuals at three sets of markers: 2,418 SNPs; 89 microsatellites; and 57 non-repetitive nuclear loci. At broad spatial scales, the markers were consistent with each other and with previous findings. At finer spatial scales, there was new evidence of genetic substructure, but our three marker sets differed slightly in their ability to detect these patterns. Specifically, we found subtle structure between the barrier reef and Turneffe Atoll, with SNPs resolving this pattern most effectively. We also documented isolation by distance within the barrier reef. Sensitivity analyses revealed that the number of loci (and alleles) had a strong effect on the detection of structure for all three marker sets, particularly at small spatial scales. Taken together, these results illustrate empirically that high-throughput genotyping data can elucidate subtle genetic structure at previously-undetected scales in a dispersive marine fish.</p>
Data from: Characterizing morphological (co)variation using structural equation models: body size, allometric relationships and evolvability in a house sparrow metapopulation
Body size plays a key role in the ecology and evolution of all organisms. Therefore, quantifying the sources of morphological (co)variation, dependent and independent of body size, is of key importance when trying to understand and predict responses to selection. We combine structural equation modeling with quantitative genetics analyses to study morphological (co)variation in a meta-population of house sparrows (Passer domesticus). As expected, we found evidence of a latent variable 'body size', causing genetic and environmental covariation between morphological traits. Estimates of conditional evolvability show that allometric relationships constrain the independent evolution of house sparrow morphology. We also found spatial differences in general body size and its allometric relationships. On islands where birds are more dispersive and mobile, individuals were smaller and had proportionally longer wings for their body size. While in islands where sparrows are more sedentary and nest in dense colonies, individuals were larger and had proportionally longer tarsi for their body size. We corroborated these results using simulations and show that our analyses produce unbiased allometric slope estimates. This study highlights that in the short term allometric relationships may constrain phenotypic evolution, but that in the long term selection pressures can also shape allometric relationships.
Data from: Unraveling hierarchical genetic structure in a marine metapopulation: a comparison of three high-throughput genotyping approaches
Open the record for dataset details and reuse information.
Metapopulation structure modulates sexual antagonism
Open the record for dataset details and reuse information.
Data from: Characterizing morphological (co)variation using structural equation models: body size, allometric relationships and evolvability in a house sparrow metapopulation
Open the record for dataset details and reuse information.
Data from: Stay at home aphids: comparative spatial and seasonal metapopulation structure and dynamics of two specialist tansy aphid species studied using microsatellite markers
Two tansy-feeding aphids – Macrosiphoniella tanacetaria (MA) and Metopeurum fuscoviride (ME) – were studied at a small spatial scale in and around Jena (< 80 km2) using polymorphic microsatellite markers. Both species were found in ~ 60% of sites formerly known to harbour the aphids, although generally when they did occur, they occurred singly (MA ~ 50%; ME ~60%) and rarely together on the same plant at the same time (~10%) and then usually only in the early part of the growing season. This difference may be due to quasi-apparent competition effects elicited to ants farming ME aphids, and preferentially actively eliminating or disturbing MA aphids. In terms of population genetics, both aphids showed extreme genetic heterogeneity within a metapopulation structure, ME more than MA, i.e. higher FST values, ~ 0.4 vs. 0.15, respectively, and limited levels of interpopulation gene flow. Subpopulations often deviated from Hardy-Weinberg equilibrium and showed linkage disequilibria, as expected in animals with extended parthenogenetic reproduction, and had positive FIS values for most large samples, suggesting inbreeding, and possibly philopatry, certainly in ME. Hierarchical analysis (allele range and number per locus, analysis of molecular variance and FST) strongly suggested that the plant rather than site governs the level of genetic variation. Bayesian clustering analysis revealed that both species had heterogeneous historical genetic patterning, with K (number of subgroups) ranging from 3-7. Evidence is also provided from isolation by distance (IBD) and private allele analyses, that in MA, the presence of winged autumn males, absent in ME where males are wingless, influences comparative population genetic structuring, such that ME subpopulations are comparatively more inbred and genetically differentiated than MA subpopulations. Lastly, additional spatial arrangement (ALLELES-IN-SPACE) analysis showed that in both species, certain subpopulations were genetically isolated from the remainder, probably due to geographical barriers, including intervening buildings and woods. As such, the biology of these tansy aphids living in semi-natural habitats is very different from many pest aphid species examined within agro-ecosystems and infesting ephemeral crops, since the former seem much more reluctant to fly and hence show contrastingly much higher levels of interpopulation divergence, even at small spatial scales as here investigated. Indeed, the number of genotypic clusters found for tansy aphids found using Bayesian approaches is similar to that for the major pest the peach-potato aphid, Myzus persicae, globally.
Data from: Conservation of a domestic metapopulation structured into related and partly admixed strains
Preservation of genetic diversity is one of the most pressing challenges in the planetary boundaries concept. Within this context, we focused on genetic diversity in a native, unselected and highly admixed domesticated metapopulation. A set of 1828 individuals from 60 different cattle breeds was analysed using a medium density SNP chip. Among these breeds, 14 Buša strains formed a metapopulation represented by 350 individuals, while the remaining 46 breeds represented the global cattle population. Genetic analyses showed that the scarcely selected and less differentiated Buša metapopulation contributed a substantial proportion (52.6%) of the neutral allelic diversity to this global taurine population. Consequently, there is an urgent need for synchronised maintenance of this highly fragmented domestic metapopulation, which is distributed over several countries without sophisticated infrastructure and highly endangered by continuous replacement crossing as part of the global genetic homogenisation process. This study collected and evaluated samples, data and genome-wide information and developed genome-assisted cross-border conservation concepts. To detect and maintain genetic integrity of the metapopulation strains, we designed and applied a composite test that combines six metrics based on additive genetic relationships, a nearest neighbour graph and the distribution of semi-private alleles. Each metric provides distinct information components about past admixture events and offers an objective and powerful tool for the detection of admixed outliers. The here developed conservation methods and presented experiences could easily be adapted to comparable conservation programmes of domesticated or other metapopulations bred and kept in captivity or under some other sort of human control.
Data from: Initial genetic diversity enhances population establishment and alters genetic structuring of a newly established Daphnia metapopulation
When newly created habitats are initially colonized by genotypes with rapid population growth rates, later arriving colonists may be prevented from establishing. Although these priority effects have been documented in multiple systems, their duration may be influenced by the diversity of the founding population. We conducted a large-scale field manipulation to investigate how initial clonal diversity influences temporal and landscape patterns of genetic structure in a developing metapopulation. Six genotypes of obligately asexual Daphnia pulex were stocked alone (no clonal diversity) or in combination ('high' clonal diversity) into newly created experimental woodland ponds. We also measured the population growth rate of all clones in the laboratory when raised on higher-quality and lower-quality resources. Our predictions were that in the 3 years following stocking, clonally diverse populations would be more likely to persist than nonclonally diverse populations and exhibit evidence for persistent founder effects. We expected that faster growing clones would be found in more pools and comprise a greater proportion of individuals genotyped from the landscape. Genetic composition, both locally and regionally, changed significantly following stocking. Six of 27 populations exhibited evidence for persistent founder effects, and populations stocked with 'high' clonal diversity were more likely to exhibit these effects than nonclonally diverse populations. Performance in the laboratory was not predictive of clonal persistence or overall dominance in the field. Hence, we conclude that although laboratory estimates of fitness did not fully explain metapopulation genetic structure, initial clonal diversity did enhance D. pulex population establishment and persistence in this system.
Data from: Applying the multistate capture-recapture robust design to characterize metapopulation structure
1. Population structure must be considered when developing mark-recapture (MR) study designs as the sampling of individuals from multiple populations (or subpopulations) may increase heterogeneity in individual capture probability. Conversely, the use of an appropriate MR study design which accommodates heterogeneity associated with capture-occasion varying covariates due to animals moving between 'states' (i.e. geographic sites) can provide insight into how animals are distributed in a particular environment and the status and connectivity of subpopulations. 2. The Multistate Closed Robust Design was chosen to investigate: 1) the demographic parameters of Indo-Pacific bottlenose dolphins (Tursiops aduncus) subpopulations in coastal and estuarine waters of Perth, Western Australia; and 2) how they are related to each other in a metapopulation. Using four years of year-round photo-identification surveys across three geographic sites, we accounted for heterogeneity of capture probability based on how individuals distributed themselves across geographic sites and characterized the status of subpopulations based on their abundance, survival and interconnection. 3. MSCRD models highlighted high heterogeneity in capture probabilities and demographic parameters between sites. High capture probabilities, high survival and constant abundances described a subpopulation with high fidelity in an estuary. In contrast, low captures, permanent and temporary emigration and fluctuating abundances suggested transient use and low fidelity in an open coastline site. 4. Estimates of transition probabilities also varied between sites, with estuarine dolphins visiting sheltered coastal embayments more regularly than coastal dolphins visited the estuary, highlighting some dynamics within the metapopulation. 6. Synthesis and applications. To date, bottlenose dolphin studies using mark-recapture approach have focussed on investigating single subpopulations. Here, in a heterogeneous coastal-estuarine environment, we demonstrated that spatially structured bottlenose dolphin subpopulations contained distinct suites of individuals and differed in size, demographics and connectivity. Such insights into the dynamics of a metapopulation can assist in local-scale species conservation. The MSCRD approach is applicable to species/populations consisting of recognizable individuals and is particularly useful for characterizing wildlife subpopulations that vary in their vulnerability to human activities, climate change or invasive species.
Are metapopulation species drivers of metacommunity structure in sandstone outcrop communities?
<p><strong><em>Questions </em></strong>The extent to which metacommunities exhibit species with metapopulation dynamics is poorly understood. We investigate this issue within sandstone glade plant communities scattered across an upland hardwood forest. We investigate the life forms of metapopulation species and relationships between taxonomic, phylogenetic, and functional diversity, composition, and environmental factors.</p> <p><strong><em>Locations </em></strong>Twenty-three sandstone outcrop communities in southern Illinois, USA.</p> <p><strong><em>Methods </em></strong>Following vegetation surveys, species exhibiting metapopulations dynamics were identified and compared to all species based on origin, growth form, and lifecycle. Cohesion, turnover, and boundary clumping were utilized to determine metacommunity structure. Correlations evaluated associations between site-based variables, and regressions evaluated associations between diversity indices. Multivariate analyses compared sites to determine which variables contributed to compositional differences.</p> <p><strong><em>Results </em></strong>Twenty of 130 species exhibited metapopulations dynamics and were usually annual or biennial exotics. Metacommunity elements indicated a Clementsian metacommunity, where metapopulation species were subordinate as opposed to dominant or transient. The largest sites were the most regularly shaped, but not the most diverse. Species richness and metapopulation species determined phylogenetic and functional diversity, but largely non-standardized measures of diversity, indicating independence between types of diversity. Multivariate analyses showed that diversity metrics explained community composition differences, where more species-rich sites with more metapopulation species were also more phylogenetically and functional diverse.</p> <p><strong><em>Conclusions: </em></strong> Sandstone glade communities exhibited diverse plant communities, where phylogenetic and functional diversity were driven by both total and metapopulation species independently. The metapopulation species were usually short-lived and exotic species with their low number likely constrained via dispersal limitations. The communities exhibited Clementsian metacommunity structure indicating predictable community assemblages. Functional traits indicated that these communities include species adapted to xeric, substrate-poor conditions.</p>
Experimental evolution reveals differential evolutionary trajectories in male and female activity levels in response to sexual selection and metapopulation structure
<p>Behavior is central to interactions with the environment and thus has significant consequences for individual fitness. Sexual selection and demographic processes have been shown to independently shape behavioral evolution. However, while some studies have tested the simultaneous effects of these forces, no studies have investigated their interplay in behavioral evolution. We applied experimental evolution in the seed beetle <i>Callosobruchus maculatus</i> to investigate, for the first time, the interactive effects of sexual selection intensity (high (polygamy) vs. minimal (enforced monogamy)) and metapopulation structure (yes/no) on the evolution of movement activity, a crucial behavior involved in multiples functions (e.g., dispersal, predator avoidance or resource acquisition) and thus, closely related to <a>fitne</a>ss. We found that the interactive effects of the selection regimes did not affect individual activity, which was assayed under two different environments (absence vs. presence of conspecific cues from both sexes). However, contrasting selection regimes led to sex- and context-dependent divergence in activity. The relaxation of sexual selection favored an increase in female, but not male, movement activity that was consistent between environmental contexts. In contrast, selection associated with the presence/absence of metapopulation structure led to context-dependent responses only in male activity. In environments containing cues from conspecifics, males from selection lines under population subdivision showed increased levels of activity compared to those assayed in an environment devoid of conspecifics cues, while the opposite was true for males from panmictic lines. These results underscore that both the effects of sexual selection and population spatial structure may be crucial in shaping sex-specific behavioral evolution.</p>
Larval dispersal in three coral reef decapod species: influence of larval duration on the metapopulation structure
<p>Database on larval dispersal contains three files in excel format. The name of the files indicates the species and its PLD (pelagic larval duration)</p>
Data from: Metapopulation structure of a seed-predator weevil and its host plants in arms race coevolution
Although the importance of gene flow in the geographic structuring of host–parasite interactions has been well discussed, little is known about how dispersal drives the spatial dynamics of other types of coevolutionary interactions in nature. We evaluated the roles of gene flow in the geographically structured processes of a predator–prey arms race involving a seed-predatory weevil with a long mouthpart and its host camellia plant with a thick fruit coat. Molecular genetic analyses showed that both weevil and camellia populations were structured at a spatial scale of several kilometers. Importantly, the spatial pattern of the migration of weevils, but not that of camellias, imposed significant effects on the geographic configuration of the levels of coevolutionary escalation. This result suggests that even if migration is limited in one species (camellia), local coevolution with the other species that migrates between neighboring localities (weevil) can reduce the inter-population difference in the local adaptive optima of the former species. Thus, gene flow of a species potentially homogenizes local biological environments provided by the species and thereby promotes the evolutionary convergence of its coevolving counterparts. Consequently, by focusing on coevolutionary interactions in natural communities, "indirect" effects of gene flow on the adaptive divergence of organisms could be identified.
Spatial structure and dispersal dynamics in a house sparrow metapopulation
<p>1. The effects of spatial structure on metapopulation dynamics depend upon the interaction between local population dynamics and dispersal, and how this relationship is affected by the geographical isolation and spatial heterogeneity in habitat characteristics.</p> <p>2. Our aim is to examine how emigration and immigration of house sparrows, <i>Passer domesticus</i>, in a Norwegian archipelagic metapopulation are affected by key factors predicted by classic metapopulation models to affect dispersal: spatial and temporal variation in population size, inter-island distance, local demography and habitat characteristics.</p> <p>3. This metapopulation can be divided into two major habitat types: (1) islands closer to the mainland where sparrows breed in colonies on farms, and (2) islands without farms, situated farther away from the mainland where sparrows are exposed to harsher environmental conditions.</p> <p>4. Dispersal was spatially structured within the metapopulation; there was proportionally and numerically less emigration and immigration involving farm islands, as compared to non-farm islands. Furthermore, emigration and immigration occurred mostly between nearby islands. Moreover, emigration in response to spatial differences in mean population size differed between the habitat types, but populations with large mean received more immigrants in both habitat types. The number of emigrants and immigrants was negatively related to long-term recruit production, which was not the case in non-farm islands. The proportion and number of emigrants was positively related to temporal increases in recruit production on farm islands, however, not on non-farm islands.</p> <p>5. Our results demonstrate that spatial heterogeneity in environmental conditions influences how spatial variation in long-term mean population size, and temporal and spatial variation in recruit production, affects dispersal dynamics. The spatial structure of this metapopulation is therefore best described by a spatially explicit model in which the exchange of individuals within each habitat type is strongly affected by the degree of geographical isolation, population size and recruit production. However, these relationships differed between the two habitat types, with the non-farm islands showing similarities to a mainland-island model type of structure, whereas dispersal on the farm islands showed features more associated with source-sink or balanced dispersal models. Such differential dispersal dynamics between habitat types is expected to have important consequences for the ecological and evolutionary dynamics within this metapopulation.</p>
Data from: Initial genetic diversity enhances population establishment and alters genetic structuring of a newly established Daphnia metapopulation
Open the record for dataset details and reuse information.
Data from: Applying the multistate capture-recapture robust design to characterize metapopulation structure
Open the record for dataset details and reuse information.
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.