Find research datasets worth reusing

Data from: Seasonal and spatial dynamics of gas ebullition in a temperate water-storage reservoir

Gas ebullition of river impoundments plays an increasingly significant role, particularly in transporting methane CH4 from their sediments to the atmosphere, and contributing to the global carbon budget and global warming. Quantifying stochastic and episodic nature of gas ebullition is complicated especially when conventionally conducted by using coverage-limited gas traps. Current knowledge of seasonality in a reservoir's gas ebullition is lacking in the literature. For this reason, advanced acoustic surveying was intensively applied to determine spatiotemporal distributions of gas ebullition in a European water-storage reservoir for two years. Additionally, the sampling was accompanied with gas collecting for analyzing gas composition. The gas released from the reservoir was primarily composed of CH4 (on average 52%, up to 94%). The longitudinal distribution of gas ebullition was mainly determined by a proximity to the river inflow as a source of organic matter. A magnitude of ebullitive fluxes within the reservoir varied up to 1,300 mL m-2 d-1(30 mmol CH4 m-2 d-1). The most significant period of ebullition has turned out to be in fall, on average reaching a sevenfold ebullitive flux (70 mL m-2 d-1, 1.6 mmol CH4 m-2 d-1) higher than in the rest of the season. A substantial contribution to the fall peak was induced by an expansion of gas ebullition into greater depths, covering two thirds of the reservoir in late fall. The study demonstrates that the ebullitive fluxes of the temperate water storage reservoir were correlated to season, depth, and inflow proximity.

opencc-zeroDec 2011View details →

Data from: On the spatial scale of dispersal in coral reef fishes

Marine biologists have gone through a paradigm shift, from the assumption that marine populations are largely 'open' due to extensive larval dispersal to the realization that marine dispersal is 'more restricted than previously thought'. Yet, population genetic studies often reveal low levels of genetic structure across large geographic areas. On the other side, more direct approaches such as mark-recapture provide evidence of localized dispersal. To what extent can direct and indirect studies of marine dispersal be reconciled? One approach consists in applying genetic methods that have been validated with direct estimates of dispersal. Here, we use such an approach - genetic isolation-by-distance between individuals in continuous populations - to estimate the spatial scale of dispersal in five species of coral reef fish presenting low levels of genetic structure across the Caribbean. Individuals were sampled continuously along a 220 km transect following the Mesoamerican Barrier Reef, population densities were estimated from surveys covering 17 200 m2 of reef, and samples were genotyped at a total of 58 microsatellite loci. A small but positive isolation-by-distance slope was observed in the five species, providing mean parent-offspring dispersal estimates ranging between 7 and 42 km (CI 1-113 km), and suggesting that there might be a correlation between minimum/maximum PLD and dispersal in coral reef fishes. Coalescent-based simulations indicate that these results are robust to a variety of dispersal distributions and sampling designs. We conclude that low levels of genetic structure across large geographic areas are not necessarily indicative of extensive dispersal at ecological timescales.

Data from: Mountain metacommunities: climate and spatial connectivity shape ant diversity in a complex landscape

Understanding what drives biodiversity patterns across scales is the central goal of ecology. Both environmental gradients and spatial landscape structure have been found to be important factors influencing species distributions and community composition, and partly reflect the balance of underlying deterministic and stochastic community processes. In some systems, environmental gradients and spatial connectivity are intertwined in that steep environmental gradients serve as boundaries on species movements and impose environment-derived complex spatial structure to metacommunities. Mountainous landscapes are prime examples of this, and recent theory has linked principles of geomorphology, environmental gradients, and spatial structure to make predictions for resulting community patterns. In this context, we examine variation in taxonomic and phylogenetic ant diversity patterns along a geographic transect spanning >5000 m in elevational range in the Hengduan mountains of southern China. We found that environmental gradients dominate variation in both alpha and beta diversity in this landscape, with alpha diversity strongly declining with elevation and beta diversity driven by elevational differences. However, within an elevational band spatial connectivity predicts beta diversity better than geographic distance. Our findings deviate from theoretical predictions in several ways, notably alpha diversity is monotonically declining and within-band beta diversity is invariant with increasing elevation. The discrepancies between theory and observation may be explained by differences in the Hengduan landscape from idealized fluvial landscapes, such as a lack of a mid-elevation peak in connectivity, as well as evolutionary limits on the source pool of species available to populate metacommunities at different elevations. The latter is supported by variation in phylogenetic community structure with elevation. Our results demonstrate the power of conceptual, statistical, and theoretical frameworks that integrate the roles of environment and spatial structure in metacommunities, but that additional work is needed to bridge the gap between abstract theory and real systems.

Data from: Spatial storage effect promotes biodiversity during adaptive radiation

Many ecological communities are enormously diverse. Variation in environmental conditions over time and space provides opportunities for temporal and spatial storage effects to operate, potentially promoting species coexistence and biodiversity. While several studies have provided empirical evidence supporting the significance of the temporal storage effect for coexistence, empirical tests of the role of the spatial storage effect are rare. In particular, we know little about how the spatial storage effect contributes to biodiversity over evolutionary timescales. Here, we report the first experimental study on the role of the spatial storage effect in the maintenance of biodiversity in evolving metacommunities, using the bacterium Pseudomonas fluorescens SBW25 as a laboratory model of adaptive radiation. We found that intercommunity spatial heterogeneity promoted phenotypic diversity of P. fluorescens in the presence of dispersal among local communities, by allowing the spatial storage effect to operate. Mechanistically, greater niche differences among P. fluorescens phenotypes arose in metacommunities with intercommunity spatial heterogeneity, facilitating negative frequency-dependent selection, and thus, the coexistence among P. fluorescens phenotypes. These results highlight the importance of the spatial storage effect for biodiversity over evolutionary timescales.

opencc-zeroDec 2018View details →

Data from: How does spatial resolution affect model performance? A case for ensemble approaches for marine benthic mesophotic communities

Aim: To investigate how changing grid size can alter model predictions of the distribution of mesophotic taxa and how it affects different modelling methods. Location: Ningaloo Marine Park, Western Australia. Taxon: Benthic mesophotic taxa: corals, macroalgae, and sponges. Methods: We determined the distributions of the major benthic taxonomic groups: corals, macroalgae, and sponges, using a number of modelling techniques and an ensemble using the 'sdm' R package. A range of grid sizes were used (10 m, 50 m, 100 m, and 250 m) to identify how model predictions were altered. Models were evaluated using the area under the curve of a receiver operator characteristic plot (AUC) and the true skill statistic (TSS) using a spatially independent dataset. Results: Grid size had a large effect on model performance across the taxonomic groups. Model outputs were compared to null surfaces and 88.8% of models performed significantly better than null. Distribution of corals was best predicted using the finest grid size (10 m) regardless of modelling method, although a model ensemble produced the best results (AUC = 0.80, TSS = 0.52). Macroalgae and sponges were better predicted at coaster grids sizes (250 m). Again, ensembles performed well for both macroalgae (AUC = 0.83, TSS = 0.63) and sponges (AUC = 0.88, TSS = 0.66). Model ensembles maintained high accuracy across grid sizes and were consistently the best, or second-best, performing method. Main Conclusions: This study has shown how grid size should be considered when producing distribution models. Identifying the most relevant grid size and being aware of the influence it may have will provide more accurate predictions of the distributions of taxa. Ensemble methods maintained good performance across scenarios and thus provide a useful tool for conservation and management especially where single modelling methods showed high levels of variability.

opencc-zeroSep 2019View details →

Data from: Network-scale effects of invasive species on spatially-structured amphibian populations

<p>Understanding the factors affecting the dynamics of spatially-structured populations (SSP) is a central topic of conservation and landscape ecology. Invasive alien species are increasingly important drivers of the dynamics of native species. However, the impacts of invasives are often assessed at the patch scale, while their effects on SSP dynamics are rarely considered. We used long-term abundance data to test whether the impact of invasive crayfish on subpopulations can also affect the whole SSP dynamics, through their influence on source populations. From 2010 to 2018, we surveyed a network of 58 ponds and recorded the abundance of Italian agile frog clutches, the occurrence of an invasive crayfish, and environmental features. Using Bayesian hierarchical models, we assessed relationships between frog abundance in ponds and a) environmental features; b) connectivity within the SSP; c) occurrence of invasive species at both the patch- and the SSP-levels. If spatial relationships between ponds were overlooked, we did not detect effects of crayfish presence on frog abundance or trends. When we jointly considered habitat, subpopulation, and SSP features, processes acting at all these levels affected frog abundance. At the subpopulation scale, frog abundance in a year was related to habitat features, but was unrelated to crayfish occurrence at that site during the previous year. However, when we considered the SSP level, we found a strong negative relationship between frog abundance in a given site and crayfish frequency in surrounding wetlands during the previous year. Hence, SSP-level analyses can identify effects that would remain unnoticed when focussing on single patches. Invasive species can affect population dynamics even in not invaded patches, through the degradation of subpopulation networks. Patch-scale assessments of the impact of invasive species can thus be insufficient: predicting the long-term interplay between invasive and native populations requires landscape-level approaches accounting for the complexity of spatial interactions.</p>

Data from: Low spatial genetic differentiation associated with rapid recolonization in the New Zealand fur seal Arctocephalus forsteri

Population declines resulting from anthropogenic activities are of major consequence for the long-term survival of species because the resulting loss of genetic diversity can lead to extinction via the effects of inbreeding depression, fixation of deleterious mutations, and loss of adaptive potential. Otariid pinnipeds have been exploited commercially to near extinction with some species showing higher demographic resilience and recolonization potential than others. The New Zealand fur seal (NZFS) was heavily impacted by commercial sealing between the late 18th and early 19th centuries, but has recolonized its former range in southern Australia. The species has also recolonized its former range in New Zealand, yet little is known about the pattern of recolonization. Here, we first used 11 microsatellite markers (n = 383) to investigate the contemporary population structure and dispersal patterns in the NZFS (Arctocephalus forsteri). Secondly, we model postsealing recolonization with 1 additional mtDNA cytochrome b (n = 261) marker. Our data identified 3 genetic clusters: an Australian, a subantarctic, and a New Zealand one, with a weak and probably transient subdivision within the latter cluster. Demographic history scenarios supported a recolonization of the New Zealand coastline from remote west coast colonies, which is consistent with contemporary gene flow and with the species' high resilience. The present data suggest the management of distinct genetic units in the North and South of New Zealand along a genetic gradient. Assignment of individuals to their colony of origin was limited (32%) with the present data indicating the current microsatellite markers are unlikely sufficient to assign fisheries bycatch of NZFSs to colonies.

Data from: Climatic conditions cause spatially dynamic polygyny thresholds in a large mammal

The polygyny threshold (PT) is a critical transition point in the sexual selection process for many organisms in natural populations, characterizing when females choose to mate with an already mated male over an unmated one to improve fitness. Understanding its causes and consequences is therefore of high interest. While both theoretical and empirical work suggest that the degree of polygyny within a species is plastic and a function of male inequality, the functional relationship between underlying availability of resources occupied by breeding males under variable climatic conditions and the dynamics of PTs across space and time has received less attention. Here, we use a standardized measure of male mating inequality as the culmination of female mate choices to analyse how spatially dynamic PTs in a naturally regulated feral horse (Equus ferus caballus) population emerge along a geographic gradient in a known, limiting resource (freshwater) each year from variable climatic conditions. Polygyny threshold distance from permanent freshwater increased with increasing precipitation during the breeding season of each year, suggesting a relationship between annual resource availability and female mate choice. The mechanism by which climatic conditions underpin the spatial dynamics of PTs was likely through precipitation providing ephemeral freshwater sources across the study area that effectively weakened the gradient in availability of permanent freshwater, thereby providing mating males that occupied home ranges far from permanent water with access to this limiting resource and enabling them to attract and retain females. Increased precipitation also coincided with a decreased proportion of males in the population that experienced sexual selection pressure attributed to female mate choice in relation to the acquisition and/or defence of freshwater sources. Climatic conditions caused spatial shifts in PTs annually along the geographic gradient in resource availability. Our findings reveal that such environmental gradients may either buffer or amplify impacts of climatic variation on selection pressure operating in natural populations, and emphasize the importance of integrating spatially explicit PTs with atmospheric fluctuations when predicting the effect of climatic change on selection processes within populations that occupy environmental gradients.

opencc-zeroDec 2012View details →

Data from: Spatial variation buffers temporal fluctuations in early juvenile survival for an endangered Pacific salmon

1. Spatial, phenotypic, and genetic diversity at relatively small scales can buffer species against large-scale processes such as climate change that tend to synchronize populations and increase temporal variability in overall abundance or production. This portfolio effect generally results in improved biological and economic outcomes for managed species. Previous evidence for the portfolio effect in salmonids has arisen from examinations of time series of adult abundance, but we lack evidence of spatial buffering of temporal variability in demographic rates such as survival of juveniles during their first year of life. 2. We therefore use density-dependent population models with multiple random effects to represent synchronous (similar among populations) and asynchronous (different among populations) temporal variability as well as spatial variability in survival. These are fitted to 25 years of survey data for breeding adults and surviving juveniles from 15 demographically distinct populations of Chinook salmon (Oncorhynchus tshawytscha) within a single metapopulation in the Snake River in Idaho, USA. 3. Model selection identifies the most support for the model that included both synchronous and asynchronous temporal variability, in addition to spatial variability. Asynchronous variability (log-SD = 0.55) is approximately equal in magnitude to synchronous temporal variability (log-SD = 0.67), but much lower than spatial variability (log-SD = 1.11). We also show that the pairwise correlation coefficient, a common measure of population synchrony, is approximated by the estimated ratio of shared and total variance, where both approaches yield a synchrony estimate of 0.59. We therefore find evidence for spatial buffering of temporal variability in early juvenile survival, although between-population variability that persists over time is also large. 4. We conclude that spatial variability decreases interannual changes in overall juvenile production, which suggests that conservation and restoration of spatial diversity will improve population persistence for this metapopulation. However, the exact magnitude of spatial buffering depends upon demographic parameters such as adult survival that may vary among populations, and is proposed as an area of future research using hierarchical life cycle models. We recommend that future sampling of this metapopulation employ a repeated-measure sampling design to improve estimation of early juvenile carrying capacity.

Data from: Effects of dispersal mode on the environmental and spatial correlates of nestedness and species turnover in pond communities

Advances in metacommunity theory have made a significant contribution to understanding the drivers of variation in biological communities. However, there has been limited empirical research exploring the expression of metacommunity theory for two fundamental components of beta diversity: nestedness and species turnover. In this paper, we examine the influence of local environmental and a range of spatial variables (hydrological connectivity, proximity and overall spatial structure) on total beta diversity and the nestedness and turnover components of beta diversity for the entire macroinvertebrate community and active and passively dispersing taxa within pond habitats. High beta diversity almost entirely reflects patterns of species turnover (replacement) rather than nestedness (differences in species richness) in our dataset. Local environmental variables were the main drivers of total beta diversity, nestedness and turnover when the entire community was considered and for both active and passively dispersing taxa. The influence of spatial processes on passively dispersing composition, total beta diversity and nestedness was significantly greater than for actively dispersing taxa. Our results suggest that species sorting (local environmental variables) operating through niche processes was the primary mechanism driving total beta diversity, nestedness and turnover for the entire community and active and passively dispersing taxa. In contrast, spatial factors (hydrological connectivity, proximity and spatial eigenvectors) only exerted a secondary influence on the nestedness and turnover components of beta diversity.

opencc-zeroDec 2011View details →

Data from: Parental frequencies and spatial configuration shape bumblebee behavior and floral isolation in hybridizing Rhinanthus

To shed light on the role played by pollinators in the diversification of angiosperms, focus is needed on how floral isolation varies locally in the early stages of plant divergence. The few studies performed so far have often used species pairs with distinct pollination syndromes and contrasting floral displays. Here, we focus on a hybridizing pair (Rhinanthus minor and R. angustifolius) with strong similarities in flower morphology and pollinators (bumblebees). We examined how ethological isolation changes locally in relation to relative Rhinanthus frequencies, spatial configurations, and pollinator assemblages. Interestingly, floral divergence based on adaptation to different pollinators is unlikely in Rhinanthus: no relationship was found between floral isolation and the local pollinator assemblage. In contrast, species frequency and spatial arrangement strongly influenced bumblebee behavior, ethological isolation, and thus potentially hybrid formation. When both Rhinanthus were present in equal proportions, bees generally preferred the more rewarding and conspicuous species. However, when the Rhinanthus frequencies were unbalanced, the more abundant species was preferred, although this was less pronounced when the less rewarding R. minor predominated. Ethological isolation is highly sensitive to site characteristics, and can be as high as in species with contrasting floral displays and pollinator suites, even though flowers are similar.

Data from: Drivers of the spatial scale that best predict primate responses to landscape structure

Understanding the effect of landscape structure on biodiversity is critically needed to improve management strategies. To accurately evaluate such effect, landscape metrics need to be assessed at the correct scale, i.e. considering the spatial extent at which species‐landscape relationship is strongest (scale of effect, SE). Although SE is highly variable, its drivers are poorly known, but of key relevance to understand the way species use the landscape. In this study, we evaluate whether and how species traits, biological responses, landscape variables and the regional context of the study drive SE in Mexican primates. We estimated the relative abundance and immature‐to‐female ratio (a proxy of reproductive success) of howler monkeys (Alouatta palliata and A. pigra) and spider monkeys (Ateles geoffroyi) in 48 forest patches from four rainforest regions (12 patches per region) with different land‐use intensity. We then assessed the composition (forest cover, matrix functionality) and configuration (forest patch density, connectors' density, forest edge density) of local landscapes considering 13 scales (100 to 1300‐m radius) to identify the spatial extent at which each landscape variable best predict each response variable in each species and region. We found that SE did not differ significantly among the drivers evaluated. However, it tended to be lower for connectors' density than for forest patch density and forest edge density, probably because connectors' density is associated with local‐scale processes such as supplementary dynamics. Surprisingly, SE also tended to be higher in the more disturbed region than in the rest of the regions, probably because primates in the more disturbed region used larger areas of the landscape. Our findings therefore suggest that SE depends more strongly on landscape variables and regional context than on species traits and biological responses, and hence, especial caution should be taken when attempting to generalize SE to different explanatory variables and regions.

opencc-zeroDec 2018View details →

Data from: Use of classical bird census transects as spatial replicates for hierarchical modeling of an avian community

New monitoring programs are often designed with some form of temporal replication to deal with imperfect detection by means of occupancy models. However, classical bird census data from earlier times often lack temporal replication, precluding detection-corrected inferences about occupancy. Historical data have a key role in many ecological studies intended to document range shifts, and so need to be made comparable with present‐day data by accounting for detection probability. We analyze a classical bird census conducted in the region of Murcia (SE Spain) in 1991 and 1992 and propose a solution to estimating detection probability for such historical data when used in a community occupancy model: the spatial replication of subplots nested within larger plots allows estimation of detection probability. In our study, the basic sample units were 1‐km transects, which were considered spatial replicates in two aggregation schemes. We fit two Bayesian multispecies occupancy models, one for each aggregation scheme, and evaluated the linear and quadratic effect of forest cover and temperature, and a linear effect of precipitation on species occupancy probabilities. Using spatial rather than temporal replicates allowed us to obtain individual species occupancy probabilities and species richness accounting for imperfect detection. Species‐specific occupancy and community size decreased with increasing annual mean temperature. Both aggregation schemes yielded estimates of occupancy and detectability that were highly correlated for each species, so in the design of future surveys ecological reasons and cost‐effective sampling designs should be considered to select the most suitable aggregation scheme. In conclusion, the use of spatial replication may often allow historical survey data to be applied formally hierarchical occupancy models and be compared with modern‐day data of the species community to analyze global change process.

Data from: Lions and leopards coexist without spatial, temporal or demographic effects of interspecific competition

1. Although interspecific competition plays a principle role in shaping species behaviour and demography, little is known about the population-level outcomes of competition between large carnivores, and the mechanisms that facilitate coexistence. 2. We conducted a multi-landscape analysis of two widely distributed, threatened large carnivore competitors to offer insight into coexistence strategies and assist with species-level conservation. 3. We evaluated how interference competition affects occupancy, temporal activity and population density of a dominant competitor, the lion (Panthera leo), and its subordinate competitor, the leopard (Panthera pardus). We collected camera-trap data over three years in ten study sites covering 5,070 km2. We used multispecies occupancy modelling to assess spatial responses in varying environmental and prey conditions and competitor presence, and examined temporal overlap and the relationship between lion and leopard densities across sites and years. 4. Results showed that both lion and leopard occupancy was independent of – rather than conditional on – their competitor's presence across all environmental covariates. Marginal occupancy probability for leopard was higher in areas with more bushy, 'hideable' habitat, human (tourist) activity and topographic ruggedness, whereas lion occupancy decreased with increasing hideable habitat and increased with higher abundance of very large prey. Temporal overlap was high between carnivores and there was no detectable relationship between species densities. 4. Lions pose a threat to the survival of individual leopards, but they exerted no tractable influence on leopard spatial or temporal dynamics. Furthermore, lions did not appear to suppress leopard populations, suggesting that intraguild competitors can coexist in the same areas without population decline. Aligned conservation strategies that promote functioning ecosystems, rather than target individual species, are therefore advised to achieve cost- and space-effective conservation.

Data from: Incorporating animal spatial memory in step selection functions

Memory is among the most important and neglected forces that shapes animal movement patterns. Research on the movement-memory interface is crucial to understand how animals use spatial learning to navigate across space because memory-biased navigation is directly linked to animals' space use and home range behaviour; however, because memory cannot be measured directly, it is difficult to account for. Here, we incorporated spatial memory into Step Selection Functions (SSF) to understand how resource selection and spatial memory affect space use of feral hogs (Sus scrofa). We used Biased Random Bridge kernel estimates linked to residence time as a surrogate for memory and tested four conceptually different dynamic maps of spatial memory. We applied this memory-based SSF to a data set of hog relocations to evaluate the importance of land cover type, time of day, and spatial memory on the animals' space use. Our approach has shown how the incorporation of spatial memory into animal movement models can improve estimates of habitat selection. Memory-based SSF provided a feasible way to gain insight into how animals use spatial learning to guide their movement decisions. We found that while hogs selected forested areas and water bodies and avoided grasslands during the day (primarily at noon), they had a strong tendency to select previously visited areas, mainly those held in recent memory. Beyond actively updating their memory with recent experiences, hogs were able to discriminate among spatial memories encoded at different circadian phases of their activity. Even though hogs are thought to have long memory retention, they likely relied on recent experiences because the local food resources are quickly depleted and slowly renewed, yielding an uncertain spatial distribution of resources.

Data from: Spatial variability in tree regeneration after wildfire delays and dampens future bark beetle outbreaks

Climate change is altering the frequency and severity of forest disturbances such as wildfires and bark beetle outbreaks, thereby increasing the potential for sequential disturbances to interact. Interactions can amplify or dampen disturbances, yet the direction and magnitude of future disturbance interactions are difficult to anticipate because underlying mechanisms remain poorly understood. We tested how variability in postfire forest development affects future susceptibility to bark beetle outbreaks, focusing on mountain pine beetle (Dendroctonus ponderosae) and Douglas-fir beetle (Dendroctonus pseudotsugae) in forests regenerating from the large high-severity fires that affected Yellowstone National Park in Wyoming in 1988. We combined extensive field data on postfire tree regeneration with a well-tested simulation model to assess susceptibility to bark beetle outbreaks over 130 y of stand development. Despite originating from the same fire event, among-stand variation in forest structure was very high and remained considerable for over a century. Thus, simulated emergence of stands susceptible to bark beetles was not temporally synchronized but was protracted by several decades, compared with stand development from spatially homogeneous regeneration. Furthermore, because of fire-mediated variability in forest structure, the habitat connectivity required to support broad-scale outbreaks and amplifying cross-scale feedbacks did not develop until well into the second century after the initial burn. We conclude that variability in tree regeneration after disturbance can dampen and delay future disturbance by breaking spatiotemporal synchrony on the landscape. This highlights the importance of fostering landscape variability in the context of ecosystem management given changing disturbance regimes.

Data from: Identifying drivers of spatial variation in occupancy with limited replication camera trap data

Occupancy models are widely used in camera trap studies to analyze species presence, abundance, and geographic distribution, among other important ecological quantities. These models account for imperfect detection using a latent variable to distinguish between true presence/absence and observed detection of a species. Under certain experimental setups, parameter estimation in a latent variable framework can be challenging. Several studies have issued guidelines on the number of independent replicated observations (surveys) needed for each unchanging occupancy field (season) to ensure reliable estimation. In this paper we present a spatio-temporal occupancy model, and show through a simulation study that it can be fit to data obtained from a \textit{single} survey per season, so long as the number of seasons is sufficiently large. We include an application using camera-trap data on the Thomson's gazelle in the Serengeti in Tanzania.

Data from: A local evaluation of the individual state-space to scale up Bayesian spatial capture recapture

1. Spatial capture-recapture models (SCR) are used to estimate animal density and to investigate a range of problems in spatial ecology that cannot be addressed with traditional non-spatial methods. Bayesian approaches in particular offer tremendous flexibility for SCR modelling. Increasingly, SCR data are being collected over very large spatial extents making analysis computational intensive, sometimes prohibitively so. 2. To mitigate the computational burden of large-scale SCR models, we developed an improved formulation of the Bayesian SCR model that uses local evaluation of the individual state-space (LESS). Based on prior knowledge about a species' home range size, we created square evaluation windows that restrict the spatial domain in which an individual's detection probability (detector window) and activity center location (AC window) are estimated. We used simulations and empirical data analyses to assess the performance and bias of SCR with LESS. 3. LESS produced unbiased estimates of SCR parameters when the AC window width was ≥5σ (σ: the scale parameter of the half-normal detection function), and when the detector window extended beyond the edge of the AC window by 2σ. Importantly, LESS considerably decreased the computation time needed for fitting SCR models. In our simulations, LESS increased the computation speed of SCR models up to 57 fold. We demonstrate the power of this new approach by mapping the density of an elusive large carnivore – the wolverine (Gulo gulo) – with an unprecedented resolution and across the species' entire range in Norway (more than 200 000 km2). 4. Our approach helps overcome a major computational obstacle to population and landscape-level SCR analyses. The LESS implementation in a Bayesian framework makes the customization and fitting of SCR accessible for practitioners that are working at scales that are relevant for conservation and management.

opencc-zeroDec 2018View details →

Data from: Dispersal syndromes can impact ecosystem functioning in spatially structured freshwater populations

Dispersal can strongly influence ecological and evolutionary dynamics. Besides the direct contribution of dispersal to population dynamics, dispersers often differ in their phenotypic attributes from non-dispersers, which leads to dispersal syndromes. The consequences of such dispersal syndromes have been widely explored at the population and community level, however, to date, ecosystem-level effects remain unclear. Here, we examine whether dispersing and resident individuals of two different aquatic keystone invertebrate species have different contributions to detrital processing, a key function in freshwater ecosystems. Using experimental two-patch systems, we found no difference in leaf consumption rates with dispersal status of the common native species Gammarus fossarum. In Dikerogammarus villosus, however, a Ponto-Caspian species now expanding throughout Europe, dispersers consumed leaf litter at roughly three times the rate of non-dispersers. Furthermore, this put the contribution of dispersing D. villosus to leaf litter processing on par with native G. fossarum, after adjusting for differences in organismal size. Given that leaf litter decomposition is a key function in aquatic ecosystems, and the rapid species turnover in freshwater habitats with range expansions of non-native species, this finding suggests that dispersal syndromes may have important consequences for ecosystem functioning.

Data from: Spatial population genetic structure of a bacterial parasite in close coevolution with its host

Knowledge of a species' population genetic structure can provide insight into fundamental ecological and evolutionary processes including gene flow, genetic drift, and adaptive evolution. Such inference is of particular importance for parasites, as an understanding of their population structure can illuminate epidemiological and coevolutionary dynamics. Here we describe the population genetic structure of the bacterium Pasteuria ramosa, a parasite that infects planktonic crustaceans of the genus Daphnia. This system has become a model for investigations of host-parasite interactions and represents an example of coevolution via negative frequency-dependent selection (a.k.a. 'Red Queen' dynamics). To sample P. ramosa, we experimentally infected a panel of Daphnia hosts with natural spore banks from the sediments of 25 ponds throughout much of the species range in Europe and Western Asia. Using 12 polymorphic VNTR loci, we identified substantial genetic diversity both within and among localities that was structured geographically among ponds. Genetic diversity was also structured among host genotypes within ponds, though this pattern varied by locality, with P. ramosa at some localities partitioned into distinct host-specific lineages, and other localities where recombination had shuffled genetic variation among different infection phenotypes. Across the sample range, there was a pattern of isolation-by-distance, and principal components analysis coupled with Procrustes rotation identified congruence between patterns of genetic variation and geography. Our findings support the hypothesis that Pasteuria is an endemic parasite coevolving closely with its host. These results provide important context for previous studies of this model system and inform hypotheses for future research.