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258 results for “metapopulation”
Metapopulation-level associations in positively interacting stream fishes
<p>Positive biotic interactions are recognized as important factors determining species distributions. Although effects of positive interactions have often been observed at local scales, much less is known about consequences at larger spatial scales. Here, we study nest associations of stream fishes - widespread reproductive facilitation between host (nest-builder) and beneficiary (nest associate) species in North America - as a model system to examine the role of positive interactions in determining the metapopulation-level relationship between host and beneficiary species. Using regional data of fish distribution in the Midwestern US, we found that watershed-level occupancy of host species (i.e., metapopulation occupancy) remarkably increased that of nest associates. Our results illustrated that the effects of positive biotic interactions at the metapopulation level were comparable or even stronger than environmental drivers, i.e., factors that have been studied most extensively in metapopulation studies. Further, our model supported the hypothesis that the metapopulation-level relationship between hosts and nest associates was mediated by a gradient of environmental conditions: strong associations occurred under stressful habitats. This study provides insightful evidence that positive biotic interactions have larger scale consequences for distributions of organisms than previously thought. Successful biodiversity conservation may need a broader framework that appreciates the role of positive biotic interactions at larger spatial scales.</p>
Cestode infection facilitates co-infection by other parasites in a metapopulation of threespine stickleback
<p><span><span><span><span><span><span><span><span><span><span><span>Parasitic infections are a global occurrence and impact the health of many species. Co-infections, where two or more species of parasite are present in a host, are a common phenomenon across species. Co-infecting parasites can interact directly or indirectly via their manipulation of (and susceptibility to) the immune system of their shared host. Helminths, such as the cestode <i>Schistocephalus solidus</i>, are well known to suppress immunity of their host (threespine stickleback), potentially facilitating other parasite species. Yet, hosts can evolve a more robust immune response (as seen in some stickleback populations), potentially turning facilitation into inhibition. Using wild-caught stickleback from 21 populations with non-zero <i>S. solidus</i> prevalence, we show there is an overall tendency towards facilitation: individuals with <i>S. solidus</i> infections have 28% higher diversity of other parasites, compared to <i>S. solidus</i>-uninfected individuals from the corresponding lakes. This facilitation effect, however, is stronger in lakes where <i>S. solidus</i> is particularly successful but tends towards inhibition in lakes with sparse and smaller cestodes (indicative of stronger host immune response). These results illustrate how even a single parasite species can vary geographically in their capacity for facilitation or inhibition of co-infections.</span></span></span></span></span></span></span></span></span></span></span></p>
Causes and consequences of variation in early‐life telomere length in a bird metapopulation
<p><span>Environmental conditions during early-life development can have lasting effects shaping individual heterogeneity in fitness and fitness-related traits. The length of telomeres, the DNA sequences protecting chromosome ends, may be affected by early-life conditions, and telomere length (TL) has been associated with individual performance within some wild animal populations. Thus, knowledge of the mechanisms that generate variation in TL, and the relationship between TL and fitness, is important in understanding the role of telomeres in ecology and life-history evolution. Here, we investigate how environmental conditions and morphological traits are associated with early-life blood TL and if TL predicts natal dispersal probability or components of fitness in 2746 wild house sparrow (<em>Passer domesticus</em>) nestlings from two populations sampled across 20 years (1994-2013). We retrieved weather data and we monitored population fluctuations, individual survival, and reproductive output using field observations and genetic pedigrees. We found a negative effect of population density on TL, but only in one of the populations. There was a curvilinear association between TL and the maximum daily North Atlantic Oscillation index during incubation, suggesting that there are optimal weather conditions that result in the longest TL. Dispersers tended to have shorter telomeres than non-dispersers. TL did not predict survival, but we found a tendency for individuals with short telomeres to have higher annual reproductive success. Our study showed how early-life TL is shaped by effects of growth, weather conditions, and population density, supporting that environmental stressors negatively affect TL in wild populations. In addition, shorter telomeres may be associated with a faster pace-of-life, as individuals with higher dispersal rates and annual reproduction tended to have shorter early-life TL.</span></p>
MetaSqueeze: A spatially-explicit metapopulation model for Banksia hookeriana in south-west Australia
<p>Climate change, with warming and drying weather conditions, is reducing the growth, seed production, and survival of fire-adapted plants in fire-prone regions such as Mediterranean-type ecosystems. These effects of climate change on local plant demographics have recently been shown to reduce the persistence time of local populations of the fire-killed shrub <em>Banksia hookeriana</em> dramatically. In principle, extinctions of local populations may be partly compensated by recolonization events through long-distance dispersal mechanisms of seeds, such as post-fire wind and bird-mediated dispersal, facilitating persistence in spatially structured metapopulations. However, to what degree and under which assumptions metapopulation dynamics might compensate for the drastically increased local extinction risk remains to be explored. Given the long timespans involved and the complexity of interwoven local and regional processes, mechanistic, process-based models are one of the most suitable approaches to systematically explore the potential role of metapopulation dynamics and its underlying ecological assumptions for fire-prone ecosystems. Here we extend a recent mechanistic, process-based, spatially implicit population model for the well-studied fire-killed and serotinous shrub species <em>B</em><em>.</em><em> hookeriana</em> to a spatially explicit metapopulation model. We systematically tested the effects of different ecological processes and assumptions on metapopulation dynamics under past (1988–2002) and current (2003–2017) climatic conditions, including (i) effects of different spatiotemporal fires, (ii) effects of (likely) reduced intraspecific plant competition under current conditions, and (iii) effects of variation in plant performance among and within patches. In general, metapopulation dynamics had the potential to increase the overall regional persistence of <em>B</em><em>.</em><em> hookeriana</em>. However, increased population persistence only occurred under specific optimistic assumptions. In both climate scenarios, the highest persistence occurred with larger fires and intermediate to long inter-fire intervals. The assumption of lower intraspecific plant competition caused by lower densities under current conditions alone was not sufficient to increase persistence significantly. To achieve long-term persistence (defined as > 400 years) it was necessary to additionally consider empirically observed variation in plant performance among and within patches, i.e., improved habitat quality in some large habitat patches (≥ seven) that could function as source patches and a higher survival rate and seed production for a subset of plants, specifically the top 25% of flower producers based on current climate conditions monitoring data. Our model results demonstrate that the impacts of ongoing climate change on plant demographics are so severe that even under optimistic assumptions, the existing metapopulation dynamics shift to an unstable source-sink dynamic state. Based on our findings, we recommend increased research efforts to understand the consequences of intraspecific trait variation on plant demographics, emphasizing the variation of individual traits both among and within populations. From a conservation perspective, we encourage fire and land managers to revise their prescribed fire plans, which are typically short interval, small fires, as they conflict with the ecologically appropriate spatio-temporal fire regime for <em>B. hookeriana</em>, and likely as well for many other fire-killed species.</p>
Vortex input files -- Linking habitat and population viability analysis models of a metapopulation of Florida scrub-jays
<p>Vortex input files for manuscript "<span>Linking </span><span><span>habitat and population viability analysis models to account for <span>vegetation dynamics, habitat fragmentation, and social behavior of a metapopulation of Florida scrub-jays</span></span></span>" by R. C. Lacy, D. B. Breininger, et al. </p>
Metapopulation connectivity retains genetic diversity following historical bottleneck in a federally endangered seabird
<p>Despite intensive management since the 1970s, recovery of the endangered northwestern Atlantic population of the Roseate Tern (<i>Sterna dougallii dougallii</i>) has not offset low productivity from a female-biased sex ratio, low adult survival, and habitat constriction. Now, >90% of individuals breed at three sites within 200 km from Long Island, NY to Buzzards Bay, MA (warm-water subregion). To characterize the impact of historical bottlenecks, metapopulation structure, and demographic fluctuations on genetic variation, Roseate Terns from the warm-water (1870s, 1970s, 1997, 2016) and cold-water (Nova Scotia, Canada; 2018) subregions were genotyped at 8-16 microsatellites and two-three mitochondrial regions. Diversity declined in the warm-water subregion from the 1870s (H<sub>E</sub>= 0.44, A<sub>R</sub>= 2.86) and 1970s (H<sub>E</sub> = 0.53, A<sub>R </sub>= 3.25) to 1997 (H<sub>E</sub> = 0.38, A<sub>R </sub>= 2.58). Genetic signatures of bottlenecks persisted in 1997 (<i>P</i> = 0.001 – 0.003) and 2016 (<i>P</i> = <0.001 – 0.005), but an increase in variation occurred by 2016 (H<sub>E</sub>= 0.50, A<sub>R</sub>= 2.85). Weak structure was detected between contemporary warm- and cold-water subregions (θ = 0.06) and within the warm-water subregion (θ = 0.04). Both demographic (<span><span></span></span>= 3439-3821) and genetic (<span><span></span></span>= 3040) estimates suggested effective population size stability over the last 100 years, despite large fluctuations in census size (4000 – 8662). Results suggest that 50 years of management (restoring habitat, preventing gull encroachment, controlling predators) at colony sites supported a small, stable <i>N<sub>e</sub></i> and maintained a hierarchical metapopulation that allowed gene flow to redistribute genetic variation throughout the NW Atlantic. The metapopulation remains highly vulnerable to stochastic events but harbors resiliency and redundancy through gene flow and a stable <i>Ne</i>. For long-term persistence from a genetic perspective, managers must maintain the major source colonies, increase availability of high-quality peripheral breeding sites, and protect concentrated non-breeding sites that facilitate gene flow.</p>
Individual fish infection data from metapopulation epidemics used to calculate resistance, tolerance and competence
<p>Host competence, defined as the likelihood that a host will transmit infection, may be affected by an individual's resistance to infection and its ability to withstand damage caused by infection (tolerance). Host competence may therefore be one of the most important factors to impact host-parasite dynamics, yet the relationships among resistance, tolerance, and competence are poorly understood. The objective of the present study was to determine whether individual host resistance (ability to resist or minimize infection) and/or tolerance (ability to withstand or minimize reduction in fitness due to infection) contributed to the competence (ability to spread infection) of hosts using guppies infected with the ectoparasite, <em>Gyrodactylus turnbulli.</em> This individual-fish level analysis used data collected from a previous metapopulation experiment that had tracked host-parasite dynamics at the metapopulation scale using individually marked guppies that were moved among experimental tanks within replicate metapopulations. Fish tolerance was measured as the residual from a fish's expected survival post-infection for a given parasite burden. Fish resistance was measured as the peak parasite load ( - log-transformed). Host competence was measured as the incidence (number of new infections over two days after the arrival of a fish to a tank) weighted by the density of available uninfected fish in the tank. In contrast to the assumption of a trade-off between resistance and tolerance, individual fish tolerance and resistance were both negatively associated with competence. Connectivity (the number of fish with which an individual came into contact) was not associated with competence. Our results indicate that resistance and tolerance are both important to disease spread. These findings highlight the importance of understanding how individual defence against parasites may contribute to its competence as a host, and therefore impact metapopulation-level dynamics.</p>
Data for: Are immigrants outbred and unrelated? Testing standard assumptions in a wild metapopulation
<p><span>Immigration into small recipient populations is expected to alleviate inbreeding and increase genetic variation, and hence facilitate population persistence through genetic and/or evolutionary rescue. Such expectations depend on three standard assumptions: that immigrants are outbred, unrelated to existing natives at arrival, and unrelated to each other. These assumptions are rarely explicitly verified, including in key field systems in evolutionary ecology. Yet, they could be violated due to non-random or repeated immigration from adjacent small populations. We combined molecular genetic marker data for 150-160 microsatellite loci with comprehensive pedigree data to test the three assumptions for a song sparrow (<i>Melospiza melodia)</i> population that is a model system for quantifying effects of inbreeding and immigration in the wild. Immigrants were less homozygous than existing natives on average, with mean homozygosity that closely resembled outbred natives. Immigrants can therefore be considered outbred on the focal population scale. Comparisons of homozygosity of real or hypothetical offspring of immigrant-native, native-native and immigrant-immigrant pairings implied that immigrants were typically unrelated to existing natives and to each other. Indeed, immigrants' offspring would be even less homozygous than outbred individuals on the focal population scale. The three standard assumptions of population genetic and evolutionary theory were consequently largely validated. Yet, our analyses revealed some deviations that should be accounted for in future analyses of heterosis and inbreeding depression, implying that the three assumptions should be verified in other systems to probe patterns of non-random or repeated dispersal and facilitate precise and unbiased estimation of key evolutionary parameters.</span></p>
Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation
<p>Please refer to the publication Shin et al. (2021): "Shin CR, Choi EH, Kim G. et al. (2021). Characterization of metapopulation of <em>Ellobium chinense</em> through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation. Scientific Reports 11: 12239.</p> <p><span>The land snail <i>Ellobium chinense</i> (Pulmonata, Ellobiida, Ellobiidae), which inhabits the salt marshes along the coastal areas of northwestern Pacific, is an endangered species on the IUCN Red List. Over recent decades, the population size of <i>E. chinense</i> has consistently decreased due to environmental interference caused by natural disasters and human activities. Here, we provide the first assessment of the genetic diversity and population genetic structures of northwestern Pacific <i>E. chinense </i>based on <i>COI</i> and 10 microsatellite markers. The analyses of 140 <i>COI </i>data from South Korea and Japan and 54 microsatellite data from South Korea revealed that <i>E. chinense</i> has high haplotype and low nucleotide diversity without showing any genetic structures that reflect geographical isolations. It strongly implies that the subfamily Ellobiinae may have first appeared around the Eocene Optimum immediately after the Paleocene–Eocene Thermal Maximum (PETM; ca. 55 mya) and the examined <i>E. chinense</i> populations in Northwestern Pacific may have been maintained in a metapopulation under the influence of the Kuroshio warm currents through the Late-Middle Pleistocene (0.350−0.126 mya) and Late Pleistocene (0.126−0.012 mya). We also found four phylogenetic groups, regardless of geographical distributions, which were easily distinguishable by four unidirectional and stepwise adenine-to-guanine transitions in <i>COI</i> (sites 207-282-354-420: A-A-A-A, A-A-G-A, G-A-G-A, and G-G-G-G). Additionally, the four <i>COI</i> hotspots were robustly connected with a high degree of covariance between them. We discuss the role of these covariate guanines which link to form four consecutive G-quadruplexes, and their possible beneficial effects under positive selection pressure. </span></p>
Alternative developmental and transcriptomic responses to host plant water limitation in a butterfly metapopulation
<p>The dataset is from a study examining the effects of host plant water stress on the developmental and transcriptomic responses of its specialist Lepidopteran herbivore. The study combines host plant metabolic profiling with development assays and full-transcriptome sequencing of herbivore larvae. First, we profiled metabolic differences between well-watered and water-limited ribwort plantain (<em>Plantago lanceolata</em>) using proton nuclear magnetic resonance spectroscopy (<sup>1</sup>H-NMR). Second, we tested how performance of developing Glanville fritillary (<em>Melitaea cinxia</em>) larvae was affected by host plant water limitation experienced at different larval developmental stages. Third, we examined larval gene regulatory responses to water limited host plants by sequencing full transcriptomes of 77 female larvae (RNA seq). Finally, to examine intrapopulation variation in the responses of the larvae, we compared the phenotypic and transcriptomic responses across full-sib families originating from different parts of the metapopulation. In this dataset, we provide data for the <em>P. lanceolata</em> metabolite responses to water limitation and developmental responses of the <em>M. cinxia</em> larvae to feeding on water limited <em>P. lanceolata</em>. The transcriptomic data are available from NCBI's Gene Expression Omnibus, with the accession number GSE159376.</p>
Coupled stochastic modelling of hierarchical channel network dynamics and metapopulation persistency - Dataset
<p>Dynamic changes in the active portion of stream networks represent a phenomenon common to diverse climates and geologic settings. However, the ecological implications of river network expansions/retractions remain poorly understood owing to operational difficulties in mechanistically describing these processes at the relevant spatio-temporal scales. Here we present a novel Bayesian framework for the simulation of event-based channel network dynamics capitalizing on the concept of "hierarchical structuring of temporary streams" - a general principle to identify the activation/deactivation order of network nodes. The framework incorporates a dynamic version of a stochastic occupancy metapopulation model, and is used to analyze the impact of pulsing river networks on species persistence in different scenarios. Climate strongly controls temporal variations of the active length, influencing the preferential configuration of the active channels and the speed of network retraction during drying. We also identify a climate-dependent detrimental effect of network dynamics on species spread and persistence. This effect is enhanced by dry climates, where flashy expansions and retractions of the flowing channels induce metapopulation extinction. Survival probabilities are particularly reduced in settings where the spatial heterogeneity of network connectivity is pronounced. The proposed framework provides novel insight on the multi-faced ecological legacies of channel network dynamics.</p>
Data from: Population connectivity patterns of genetic diversity, immune responses and exposure to infectious pneumonia in a metapopulation of desert bighorn sheep
<p>Habitat fragmentation is an important driver of biodiversity loss and can be remediated through management actions aimed at maintenance of natural connectivity in metapopulations. Connectivity may protect populations from infectious diseases by preserving immunogenetic diversity and disease resistance. However, connectivity could exacerbate the risk of infectious disease spread across vulnerable populations.</p> <p>We tracked the spread of a novel strain of <em>Mycoplasma ovipneumoniae</em> in a metapopulation of desert bighorn sheep (<em>Ovis canadensis nelsoni</em>) in the Mojave desert to investigate how variation in connectivity among populations influenced disease outcomes.</p> <p><em>M. ovipneumoniae</em> was detected throughout the metapopulation, indicating that the relative isolation of many of these populations did not protect them from pathogen invasion. However, we show that connectivity among bighorn sheep populations was correlated with higher immunogenetic diversity, a protective immune response and lower disease prevalence. Variation in protective immunity predicted infection risk in individual bighorn sheep and was associated with heterozygosity at genetic loci linked to adaptive and innate immune signalling.</p> <p>Together, these findings may indicate that population connectivity maintains immunogenetic diversity in bighorn sheep populations in this system and has direct effects on immune responses in individual bighorn sheep and their susceptibility to infection by a deadly pathogen.</p> <p>Our study suggests that the genetic benefits of population connectivity could outweigh the risk of infectious disease spread and supports conservation management that maintains natural connectivity in metapopulations.</p>
Life on the edge: a changing genetic landscape within an iconic American pika metapopulation over the last half century
<p>Declines and extirpations of American pika (<em>Ochotona princeps</em>) populations at historically occupied sites started being documented in the literature during the early 2000s. Commensurate with global climate change, many of these losses at peripheral and lower elevation sites have been associated with changes in ambient air temperature and precipitation regimes. Here, we report on a decline in available genetic resources for an iconic American pika metapopulation, located at the southwestern edge of the species distribution in the Bodie Hills of eastern California, USA. Composed of a highly fragmented habitat created by hard rock mining, the ore dumps at this site were likely colonized by pikas at the end of the 19th century from nearby natural talus outcrops. Genetic data extracted from both contemporary samples and archived natural history collections allowed us to track population and patch-level genetic diversity for Bodie pikas across three distinct sampling points during the last half-century (1948, 1988-1991, 2013-2015). In addition to declines in within-population allelic diversity and expected heterozygosity, we observed an increase in population structure and a reduction in effective population size from more extensive sampling of extant patches during 1988-1991 and 2013-2015, respectively. Furthermore, census records from the last 50 years as well as archived museum samples collected in 1947 from a nearby pika population in the Wassuk range (NV, USA) provide further support for the increasing isolation and genetic coalescence occurring in this region. This study highlights the importance of museum samples and long-term monitoring in contextualizing our understanding of population viability.</p>
Dataset: Corridor quality buffers extinction under extreme droughts in experimental metapopulations
<p>Corridors with good-quality habitats maintain the spatial dynamics of metapopulations by promoting dispersal between habitat patches, potentially buffering populations and communities against continued global change. However, this function is threatened by habitats becoming increasingly fragmented, and habitat matrices becoming increasingly inhospitable, potentially reducing the resilience and persistence of populations. Yet, we lack a clear understanding of how reduced corridor quality interacts with rates of environmental change to destabilise populations. Using laboratory microcosms containing metapopulations of the Collembola <em>Folsomia candida</em>, we investigate the impact of corridor quality on metapopulation persistence under a range of simulated droughts, a key stressor for this species. We manipulated both drought severity and the number of patches affected by drought across landscapes connected by either good or poor-quality corridors. We measured the time of metapopulation extinction, the maximum rate of metapopulation decline, and the variability of abundance among patches as criteria to evaluate the persistence ability of metapopulations. We show that whilst drought severity negatively influenced the time of metapopulation extinction and the increase in drought patches caused metapopulation decline, these results were mitigated by good quality corridors, which increased metapopulation persistence time and decreased both how fast metapopulations declined and the inter-patch variability in abundances. Our results suggest that enhancing corridor quality can increase the persistence of metapopulations, increasing the time available for conservation actions to take effect, and/or for species to adapt or move in the face of continued stress. Given that fragmentation increases the isolation of habitats, improving the quality of habitat corridors may provide a useful strategy to enhance the resistance of spatially structured populations.</p>
Coupled stochastic modelling of hierarchical channel network dynamics and metapopulation persistency - Dataset
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Selection on Sporulation Strategies in a Metapopulation Can Lead to Coexistence
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Data from: Inferring the timing of long-distance dispersal between Rail metapopulations using genetic and isotopic assignments
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Data from: Phylogenomics supports island contribution to metapopulation dynamics in a predominantly continental bird species
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Data for: Are immigrants outbred and unrelated? Testing standard assumptions in a wild metapopulation
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Life on the edge: a changing genetic landscape within an iconic American pika metapopulation over the last half century
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