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258 results for “metapopulation”
Code and initial metapopulation data for model construction and simulation analyses for: Genetic rescue from protected areas is modulated by migration, hunting rate and timing of harvest
<p>Migrants from protected areas may buffer the risk of harvest-induced evolutionary changes in exploited populations that face strong selective harvest pressures in both terrestrial and marine ecosystems. Understanding the mechanisms favouring genetic rescue through migration could help ensure sustainable harvest outside protected areas and conserve genetic diversity inside those areas. We developed a stochastic individual-based metapopulation model to evaluate the potential for migration from protected areas to mitigate the evolutionary consequences of selective harvest. We parameterized the model with detailed data from individual monitoring of two populations of bighorn sheep subjected to trophy hunting. We tracked horn length through time in a metapopulation including large protected and trophy-hunted populations connected through male breeding migrations. We quantified and compared declines in horn length and rescue potential under various combinations of migration rate, hunting rate in hunted areas and temporal overlap in timing of harvest and migrations, which affects the migrants' survival and chances to breed within exploited areas. Our simulations suggest that the effects of size-selective harvest on male horn length in hunted populations can be dampened or avoided if harvest pressure is low, migration rate is substantial, and migrants have a low risk of being shot. Intense size-selective harvest impacts the phenotypic and genetic diversity in horn length, and population structure through changes in proportions of large-horned males, sex ratio and age structure. When hunting pressure is high and overlaps with male migrations, effects of selective removal also emerge in the protected population, so that instead of a genetic rescue of hunted populations, our model predicts undesirable effects inside protected areas. Our results stress the importance of a metapopulational approach to management, to promote genetic rescue from protected areas and limit ecological and evolutionary impacts of harvest on both harvested and protected populations.</p>
Data and code: Assessing fish-fishery dynamics from a spatially explicit metapopulation perspective reveals winners and losers in fisheries management
<ol> <li><span>Sustainable management of living resources must reconcile biodiversity conservation and socioeconomic viability of human activities. In the case of fisheries, sustainable management design is made challenging by the complex spatiotemporal interactions between fish and fisheries.</span></li> <li><span>We develop a comprehensive metapopulation framework integrating data on species life-history traits, connectivity and habitat distribution to identify priority areas for fishing regulation and assess how management impacts are spatially distributed. We trial this approach on European hake fisheries in the north-western Mediterranean, where we assess area-based management scenarios in terms of stock status and fishery productivity to prioritize areas for protection. </span></li> <li><span>Model simulations show that local fishery closures have the potential to enhance both spawning stock biomass and landings on a regional scale compared to a status quo scenario, but that improving protection is easier than increasing productivity. Moreover, the interaction between metapopulation dynamics and the redistribution of fishing effort following local closures implies that benefits and drawbacks are heterogeneously distributed in space, the former being concentrated in the proximity of the protected site. </span></li> <li><span>A network analysis shows that priority areas for protection are those with the highest connectivity (as expressed by network metrics) if the objective is to improve the spawning stock, while no significant relationship emerges between connectivity and potential for increased landings.</span></li> <li> <span><em>Synthesis and applications</em> – </span><span>Our framework provides a tool for 1) assessing area-based management measures aimed at improving fisheries outcomes in terms of both conservation and socioeconomic viability and 2) describing the spatial distribution of costs and benefits, which can help guide effective management and gain stakeholder support. Adult dispersal remains the main source of uncertainty that needs to be investigated to effectively apply our model to fisheries regulation.</span> </li> </ol>
Data for the manuscript: Demographic basis of spatially structured fluctuations in a threespine stickleback metapopulation
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Data from: A shift to metapopulation genetic management for persistence of a species threatened by fragmentation: the case of an endangered Australian freshwater fish
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Patch quality and genotype-by-environment interactions shape dispersal and post-settlement survival in a butterfly metapopulation
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Data from: Next-generation matrices for marine metapopulations: the case of sea lice and salmon farms
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Code and initial metapopulation data for model construction and simulation analyses for: Genetic rescue from protected areas is modulated by migration, hunting rate and timing of harvest
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Data and code: Assessing fish-fishery dynamics from a spatially explicit metapopulation perspective reveals winners and losers in fisheries management
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Data from: Dispersal in a house sparrow metapopulation: an integrative case study of genetic assignment calibrated with ecological data and pedigree information
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Stability of patch-turnover relationships under equilibrium and nonequilibrium metapopulation dynamics driven by biogeography
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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: Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation
<p>Inbreeding may increase the extinction risk of small populations. Yet, studies using modern genomic tools to investigate inbreeding depression in nature have been limited to single populations, and little is known about the dynamics of inbreeding depression in subdivided populations over time. Natural populations often experience different environmental conditions and differ in demographic history and genetic composition; characteristics that can affect the severity of inbreeding depression. We utilised extensive long-term data on more than 3100 individuals from eight islands in an insular house sparrow metapopulation to examine the generality of inbreeding effects. Using genomic<sub> </sub>estimates of realised inbreeding, we discovered that inbred individuals had lower survival probabilities and produced fewer recruiting offspring than non-inbred individuals. Inbreeding depression, measured as the decline in fitness related traits per unit inbreeding, did not vary appreciably among populations or with time. As a consequence, populations with more resident inbreeding (due to their demographic history) paid a higher total fitness cost, evidenced by a larger variance in fitness explained by inbreeding within these populations. Our results are in contrast to the idea that effects of inbreeding generally depend on ecological factors and genetic differences among populations, and expand the understanding of inbreeding depression in natural subdivided populations.</p>
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.
Metapopulation dynamics and foraging plasticity in a highly vagile seabird, the southern rockhopper penguin
<p>Population connectivity is driven by individual dispersal potential and modulated by natal philopatry. In seabirds, high vagility facilitates dispersal yet philopatry is also common, with foraging area overlap often correlated with population connectivity. We assess the interplay between these processes by studying past and current connectivity and foraging niche overlap among southern rockhopper penguin colonies of the coast of southern South America using genomic and stable isotope analyses. We found two distinct genetic clusters and detected low admixture between northern and southern colonies. Stable isotope analysis indicated niche variability between colonies, with Malvinas/Falklands colonies encompassing the species entire isotopic foraging niche, while the remaining colonies had smaller, nonoverlapping niches. A recently founded colony in continental Patagonia differed in isotopic niche width and position with Malvinas/Falklands colonies, its genetically identified founder population, suggesting the exploitation of novel foraging areas and/or prey items. Additionally, dispersing individuals found dead across the Patagonian shore in an unusual mortality event were also assigned to the northern cluster, suggesting northern individuals reach southern localities, but do not breed in these colonies. Facilitated by variability in foraging strategies, and especially during unfavorable conditions, the number of dispersing individuals may increase and enhance the probability of founding new colonies. Metapopulation demographic dynamics in seabirds should account for interannual variability in dispersal behavior and pay special attention to extreme climatic events, classically related to negative effects on population trends.</p>
Data from: Multi-generational genetic consequences of reinforcement in a bird metapopulation
<p>Translocation of conspecific individuals to reduce extinction risk of small, isolated populations and prevent genetic depletion is a powerful tool in conservation biology. An important question is how the translocated individuals influence the long-term genetic composition of the recipient population. Here, we experimentally reinforced a house sparrow (<i>Passer domesticus</i>) population, and examined the impact of this translocation on allele frequencies, levels of heterozygosity and genetic differentiation over six cohorts. We found no permanent increase in the mean number of alleles across loci or levels of observed heterozygosity, but a few alleles private to the translocated individuals remained in the population and we found a short-term increase in heterozygosity. Consequently, genetic differentiation of the recipient population compared to the genetic composition prior to reinforcement was small. The limited genetic impact was due to combined effects of a small probability of establishment and low mating success for the translocated individuals, together with increased genetic drift in the recipient population. Our findings emphasize the importance of selection and genetic drift as forces that may decrease the genetic contribution of reinforcement, especially in small populations. Conservation managers should aim to improve habitat quality in the recipient population to reduce genetic drift following translocation and thereby avoid the need for continued reinforcement. Furthermore, by facilitating establishment success and selecting individuals expected to have high mating success, possibly indicated by sexually selected traits, genetic contribution of released individuals is increased which in turn will decrease reproductive skew and genetic drift.</p>
Multitrophic metacommunity dataset, with metapopulation level butterfly data, in addition to predation pressure and floral abundance
<p>This dataset includes metapopulation level butterfly data within a butterfly metacommunity sampled across 15 sites at Burnt Lands Provincial Park in Ontario, Canada, during the summer of 2019. It includes floral abundance at each site for each sampling round. It also includes information on the number of predator attacks on experimental clay butterfly models at each site. It contains data on site size and connectivity for the 15 sites, as well as the length of butterfly survey transects sampled in each site.</p>
Data from: The genetic basis of dispersal in a vertebrate metapopulation
<p>Dispersal affects evolutionary processes by changing population size and genetic composition, influencing the viability and persistence of populations. Investigating which mechanisms underlie variation in dispersal phenotypes and whether populations harbor adaptive potential for dispersal is crucial to understanding the eco-evolutionary dynamics of this important trait. Here, we investigate the genetic architecture of dispersal among successfully recruited individuals in an insular metapopulation of house sparrows. We use an extensive long-term individual-based ecological data set and high-density single nucleotide polymorphism (SNP) genotypes for over 2500 individuals. We conducted a genome-wide association study (GWAS), finding a relationship between dispersal probability and an SNP located near genes known to regulate circadian rhythmic, glycogenesis and exercise performance, among other functions. However, this SNP only explained 3.8% of variance, suggesting that dispersal is a polygenic trait. We then used an animal model to estimate heritable genetic variation (<em>σ</em><sub><em>A</em></sub><sup><em>2 </em></sup>), which composes 10% of the total variation in dispersal probability. Finally, we investigated differences in <em>σ</em><sub><em>A</em></sub><sup><em>2 </em></sup> across populations occupying ecologically relevant habitat types (farm vs. non-farm) using a genetic-groups animal model. We found different adaptive potentials across habitats, with higher mean breeding value, <em>σ</em><sub><em>A</em></sub><sup><em>2 </em></sup>, and heritability for the habitat presenting lower dispersal rates, suggesting also different roles of environmental variation. Our results suggest a complex genetic architecture of dispersal, and demonstrate that adaptive potential may be environment-dependent in key eco-evolutionary traits. The eco-evolutionary implications of such environment-dependence and consequent spatial variation are likely to become ever more important with the increased fragmentation and loss of suitable habitats for many natural populations.</p>
Demography and environment modulate the effects of genetic diversity on extinction risk in a butterfly metapopulation
<p>Linking genetic diversity to extinction is a common goal in genomic studies. Recently, a debate has arisen regarding the importance of genetic variation in conservation as some studies have failed to find associations between genome-wide genetic diversity and extinction risk. However, only rarely are genetic diversity and fitness measured together in the wild, and typically variation in demographic history or environment are ignored. It is therefore difficult to infer whether a lack of an association is real or obscured by confounding factors. To address these shortcomings, we analysed genetic data from 7,501 individuals with extinction data from 279 meadows and mortality of 1,742 larval nests in a butterfly metapopulation. We found strong negative associations between genetic diversity and extinction when heterozygosity was included alone in models. However, this association was no longer present when ecological covariates were included. Interactions between heterozygosity and demographic variables revealed that associations are context-dependent or only detectable when confounding factors are controlled. For example, extinction declined with increasing heterozygosity in large but not currently small populations, although negative associations between heterozygosity, extinction, and mortality were detected in populations with a recent history of decline. We conclude that low genetic diversity is an important predictor of extinction, predicting >25% increase in extinction beyond ecological factors in certain contexts. This highlights that inferences about the importance of genetic diversity should not rely on genomic data alone but requires investments in obtaining demographic and environmental data from natural populations to jointly assess their impact on population extinction risk.</p>
A domesticated phage suppresses competitors in historical and modern metapopulations of pathogenic bacteria
<p>Bacteria have repeatedly repurposed the machinery of their viruses (bacteriophage) to kill strains of neighboring bacteria. These bacteriophage (phage)-derived elements are strain-specific in their killing activity, and this specificity has been proposed to drive bacterial population dynamics. Direct evidence of the impact of phage-derived elements on natural populations over time is limited. Here we identified viral sequences in a metapopulation of wild plant-associated <em>Pseudomonas</em> spp. genomes. We discovered that the most abundant viral cluster does not encode an intact phage but instead encodes a tailocin: a phage-derived element that bacteria use to kill bacterial competitors. Each pathogenic <em>Pseudomonas</em> sp. strain carries one of a few distinct tailocin variants, which target variable polysaccharides in the outer membrane of co-occurring pathogenic strains. Analysis of historic herbarium samples from the past 170 years revealed that the same tailocin and receptor variants have persisted in the <em>Pseudomonas</em> populations for at least two centuries, suggesting the continued use of a defined set of tailocin haplotypes and receptors. These results indicate that tailocin genetic diversity can be mined to develop targeted "tailocin cocktails" for microbial control.</p>
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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.