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376 results for “local scales”
Local-scale climatic refugia offer sanctuary for a habitat-forming species during a marine heatwave
<p><b>1. </b>Gradual climate change and discrete extreme climatic events have driven shifts in the structure of populations and the distribution of species in many marine ecosystems. The most profound impacts of recent warming trends have been generally observed at species' warm edges and on large conspicuous species. However, given that <span>different species and populations exhibit different responses to warming, and that responses are highly variable at regional scales, </span>there is a need <span>to broaden the evidence to include less conspicuous species and to focus on both local and regional scale processes.</span></p> <p><b>2. </b>We examined the population dynamics of canopy-forming seaweed populations situated at the core range of their distribution during a regional marine heatwave (MHW) event that occurred in the Mediterranean Sea in 2015, to determine between-site variability in relation to the intensity of the MHW. We combined field observations with a thermo-tolerance experiment to elucidate mechanisms underlying observed responses.</p> <p><b>3.</b> Despite our study populations are located in the species core range, the MHW was concomitant with a high mortality and structural shifts in only one of the two surveyed populations, most likely due to differences in habitat characteristics between sites (e.g. degree of shelter and seawater transfer). The experiment showed high mortalities at temperatures of 28 ºC, having the most severe implications for early life stages and fertility, which is consistent with warming being the cause of population changes in the field. Crucially, the regional-scale quantification of the MHW (as described by satellite-derived SSTs) did not capture local-scale variation in MHW conditions at the study sites, which likely explained variation in population-level responses to warming.</p> <p><b>4. </b><i>Synthesis.</i> Enclosed and semi-enclosed seas, such as the Mediterranean Sea, often highly impacted by human perturbations, are also global hotspots for ocean warming and are highly susceptible to future MHWs. Our findings highlight that local-scale variability in the magnitude of extreme climatic events can lead to local extinctions of already fragmented populations of habitat-forming seaweeds, even towards the species' core range. However, our results highlight the potential for local-scale climatic refugia, which could be identified and managed to safeguard the persistence of canopy-forming seaweeds.</p>
Data from: Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis, and immune defence‐related genes
Elucidating the genetic basis of adaptation to the local environment can improve our understanding of how the diversity of life has evolved. In this study we used a dense SNP array to identify candidate loci potentially underlying fine-scale local adaptation within a large Atlantic salmon (Salmo salar) population. By combining outlier, gene–environment association, and haplotype homozygosity analyses, we identified multiple regions of the genome with strong evidence for diversifying selection. Several of these candidate regions had previously been identified in other studies, demonstrating that the same loci could be adaptively important in Atlantic salmon at sub-drainage, regional and continental scales. Notably, we identified signals consistent with local selection around genes associated with variation in sexual maturation, energy homeostasis, and immune defence. These included the large-effect age-at-maturity gene vgll3, the known obesity gene mc4r, and major histocompatibility complex II. Most strikingly, we confirmed a genomic region on Ssa09 that was extremely differentiated among subpopulations, and that is also a candidate for local selection over the global range of Atlantic salmon. This region co-localized with a haplotype strongly associated with spawning ecotype in sockeye salmon (Oncorhynchus nerka), with circumstantial evidence that the same gene (six6) may be the selective target in both cases. The phenotypic effect of this region in Atlantic salmon remains cryptic, although allelic variation is related to upstream catchment area and co-varies with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research.
Data from: Scaling up effects of measures mitigating pollinator loss from local- to landscape-level population responses
1. Declining pollinator populations have caused concern about consequences for food production, and have initiated an increasing number of initiatives that aim to mitigate pollinator loss through enhancement of floral resources. Studies evaluating effects of mitigation measures generally demonstrate positive responses of pollinators to floral resource enhancement. However, it remains unclear whether this represents landscape-level population effects or results from a spatial redistribution of individuals from otherwise unaffected populations. 2. Here we present a method for estimating landscape-level population effects using data from commonly used standardized pollinator transect surveys. The approach links local density responses of pollinators in both mitigation sites and surrounding landscape elements to the area these habitats occupy in mitigation landscapes as well as control landscapes to obtain landscape-level population estimates. 3. We demonstrate the method using data from a two-year study examining the effects of experimental wildflower enhancements on wild bumble bees and solitary bees in Dutch agricultural landscapes. The results show that conclusions based on local responses may differ significantly from those based on landscape-level responses. 4. Wildflower enhancements significantly enhanced landscape-level abundance of both bumble bees and solitary bees. Bumble bees showed a pronounced positive local density response in mitigation sites and the surrounding landscape that was in line with significant landscape-level increases in abundance. However, solitary bees showed no local response to mitigation sites, and the landscape-level increases in abundance only became apparent when the area of bee habitat was taken into account. 5. Incorporating the area of both newly created and pre-existing pollinator habitats into effect estimates accounts for density-dependent processes such as dilution, spill-over and local concentration of individuals. It therefore results in more reliable estimates of the response to mitigation measures of pollinators, as well as other mobile arthropod groups that are often being surveyed using transect surveys.
Data from: Local and landscape-scale heterogeneity shape spotted wing drosophila (Drosophila suzukii) activity and natural enemy abundance: implications for trophic interactions
Like natural enemies, invasive polyphagous pests may respond positively to local and landscape-scale diversity, making them more serious challenges to sustainable management than specialists. Yet the current view of landscape effects on pests rarely considers perennial systems or polyphagous pests. We investigated Drosophila suzukii (SWD) and natural enemy distributions and trophic interactions in blueberry systems of the southeast US in relation to local management and landscape structure. Fields were nested in 1-km landscapes along gradients of crop and forest heterogeneity (landscape compositional diversity) and field border and crop border lengths (landscape configurational diversity). Yeast-sugar bait traps were used to collect SWD and canopy suction sampling for natural enemies. Management practices at the local scale did not influence SWD abundance, but natural enemy abundance was higher in organic systems and fields with vegetation present between rows. Landscape configurational diversity and greater proportion of non-cropping habitat promoted higher SWD populations. Natural enemy communities were composed of highly generalized species, and contrary to our predictions, we observed lower abundances in landscapes with higher proportion of non-cropping area. Few predators were detected to have fed on SWD, and communities were dominated by predators with low specialization on prey in blueberry. Our results indicate that local and landscape features in blueberry landscapes have differential effects on a polyphagous pest and generalist natural enemies. Our initial analysis of predator diets, using a metabarcoding approach, suggests spatial structure in specialization on prey with high diversity of prey in predators collected in forested margins.
Data from: Outlier loci detect intraspecific biodiversity amongst spring and autumn spawning herring across local scales
Herring, Clupea harengus, is one of the ecologically and commercially most important species in European northern seas, where two distinct ecotypes have been described based on spawning time; spring and autumn. To date, it is unknown if these spring and autumn spawning herring constitute genetically distinct units. We assessed levels of genetic divergence between spring and autumn spawning herring in the Baltic Sea using two types of DNA markers, microsatellites and Single Nucleotide Polymorphisms, and compared the results with data for autumn spawning North Sea herring. Temporally replicated analyses reveal clear genetic differences between ecotypes and hence support reproductive isolation. Loci showing non-neutral behaviour, so-called outlier loci, show convergence between autumn spawning herring from demographically disjoint populations, potentially reflecting selective processes associated with autumn spawning ecotypes. The abundance and exploitation of the two ecotypes have varied strongly over space and time in the Baltic Sea, where autumn spawners have faced strong depression for decades. The results therefore have practical implications by highlighting the need for specific management of these co-occurring ecotypes to meet requirements for sustainable exploitation and ensure optimal livelihood for coastal communities.
Local and landscape scale variables shape insect diversity in an urban biodiversity hotspot.
<p>Local community structure is shaped by processes acting at local and landscape scales. The relative importance of drivers operating across different spatial scales are difficult to test without observations across regional or latitudinal gradients. Cities exhibit strong but predictable environmental gradients overlaying a mosaic of highly variable but repeated habitat types within a constrained area. Thus, cities present a unique opportunity to explore how both local and landscape factors influence local biotic communities. We used insect communities to examine the interactions among local environmental variables (such as temperature and relative humidity), local habitat characteristics (such as plant community composition), and broad-scale patterns of urbanization (including biophysical, human-built, and socio-economic variables) on local insect abundance, species richness, and species composition in Los Angeles, a hot, dry, near-desert city. After accounting for seasonal trends, insect species richness and abundance were highest in drier and hotter sites, but the magnitude of local environmental effects varied with the degree of urbanization. In contrast, insect species composition was best predicted by broad-scale urbanization trends, with the more native communities occurring in less urbanized sites and more cosmopolitan insects occurring in highly urbanized sites. However, insect species richness and abundance were >30% higher and insect composition was similar across sites that hosted either native or drought-tolerant plants, regardless of the degree of urbanization. These results demonstrate that urban insect biodiversity is a product of interacting mechanisms working at both local and landscape scales. However, local scale changes to urban habitats, such as cultivating plants that are adapted to the natural environment nearest the city, can positively impact urban biodiversity regardless of location.</p>
Above- and below-ground biodiversity jointly regulate temperate forest multifunctionality along a local-scale environmental gradient
<p><span>1. Tree diversity has been shown to promote a broad range of ecosystem functions in forests. However, how important these effects are in driving ecosystem multifunctionality in natural forests, relative to other drivers, such as below-ground biodiversity (e.g., soil microbial diversity), community-level functional traits and environmental conditions, remains poorly understood. Here, we hypothesise that tree species or phylogenetic diversity, stand structure, functional traits and soil microbial diversity jointly regulate temperate forest multifunctionality along a local-scale environmental gradient.</span></p> <p><span>2. Using repeated census data from a 25-ha old-growth temperate forest, we first quantified eight ecosystem functions and properties related to above- and below-ground nutrient cycling. We then used these to estimate ecosystem multifunctionality using both an averaging and multiple thresholds (50, 75, and 95%) approaches. Finally, we used structural equation models to explore how different facets of tree (tree species, functional and phylogenetic diversity) and soil (bacteria, fungi, and nematode diversity) biodiversity influence ecosystem multifunctionality, as well as how these relationships are modulated by stand structural attributes and environmental conditions (topography and soil nutrients).</span></p> <p><span>3. Forest multifunctionality was positively related to stand structural complexity but negatively related to acquisitive traits (i.e. community-weighted mean of specific leaf area). Plant phylogenetic diversity had no significant direct effect on forest multifunctionality, but it had a significant indirect effect via increased stand structural complexity. The effect of soil microbial diversity on forest multifunctionality increased with increasing threshold levels of forest multifunctionality and outperformed tree diversity and environmental conditions at the highest threshold level (i.e. 95%). Forests on steep slopes had lower levels of ecosystem multifunctionality due to decreased stand structural complexity. Soil nutrients were responsible for regulating forest multifunctionality via plant trait composition and, to a lesser extent, via tree diversity, stand structure and soil microbial diversity.</span></p> <p><span>4. <i>Synthesis</i>: Plant phylogenetic diversity, stand structure and soil microbial diversity jointly regulated forest multifunctionality, and these effects were influenced by local-scale changes in environmental conditions. Soil microbial diversity was a key driver of highly multifunctional forests, whereas conservation of complex stand structure and conservative trait dominance could enhance mean values of multiple functions.</span></p> <p><span>1. Tree diversity has been shown to promote a broad range of ecosystem functions in forests. However, how important these effects are in driving ecosystem multifunctionality in natural forests, relative to other drivers, such as below-ground biodiversity (e.g., soil microbial diversity), community-level functional traits and environmental conditions, remains poorly understood. Here, we hypothesise that tree species or phylogenetic diversity, stand structure, functional traits and soil microbial diversity jointly regulate temperate forest multifunctionality along a local-scale environmental gradient.</span></p> <p><span>2. Using repeated census data from a 25-ha old-growth temperate forest, we first quantified eight ecosystem functions and properties related to above- and below-ground nutrient cycling. We then used these to estimate ecosystem multifunctionality using both an averaging and multiple thresholds (50, 75, and 95%) approaches. Finally, we used structural equation models to explore how different facets of tree (tree species, functional and phylogenetic diversity) and soil (bacteria, fungi, and nematode diversity) biodiversity influence ecosystem multifunctionality, as well as how these relationships are modulated by stand structural attributes and environmental conditions (topography and soil nutrients).</span></p> <p><span>3. Forest multifunctionality was positively related to stand structural complexity but negatively related to acquisitive traits (i.e. community-weighted mean of specific leaf area). Plant phylogenetic diversity had no significant direct effect on forest multifunctionality, but it had a significant indirect effect via increased stand structural complexity. The effect of soil microbial diversity on forest multifunctionality increased with increasing threshold levels of forest multifunctionality and outperformed tree diversity and environmental conditions at the highest threshold level (i.e. 95%). Forests on steep slopes had lower levels of ecosystem multifunctionality due to decreased stand structural complexity. Soil nutrients were responsible for regulating forest multifunctionality via plant trait composition and, to a lesser extent, via tree diversity, stand structure and soil microbial diversity.</span></p> <p><span>4. <i>Synthesis</i>: Plant phylogenetic diversity, stand structure and soil microbial diversity jointly regulated forest multifunctionality, and these effects were influenced by local-scale changes in environmental conditions. Soil microbial diversity was a key driver of highly multifunctional forests, whereas conservation of complex stand structure and conservative trait dominance could enhance mean values of multiple functions.</span></p> <p><span>1. Tree diversity has been shown to promote a broad range of ecosystem functions in forests. However, how important these effects are in driving ecosystem multifunctionality in natural forests, relative to other drivers, such as below-ground biodiversity (e.g., soil microbial diversity), community-level functional traits and environmental conditions, remains poorly understood. Here, we hypothesise that tree species or phylogenetic diversity, stand structure, functional traits and soil microbial diversity jointly regulate temperate forest multifunctionality along a local-scale environmental gradient.</span></p> <p><span>2. Using repeated census data from a 25-ha old-growth temperate forest, we first quantified eight ecosystem functions and properties related to above- and below-ground nutrient cycling. We then used these to estimate ecosystem multifunctionality using both an averaging and multiple thresholds (50, 75, and 95%) approaches. Finally, we used structural equation models to explore how different facets of tree (tree species, functional and phylogenetic diversity) and soil (bacteria, fungi, and nematode diversity) biodiversity influence ecosystem multifunctionality, as well as how these relationships are modulated by stand structural attributes and environmental conditions (topography and soil nutrients).</span></p> <p><span>3. Forest multifunctionality was positively related to stand structural complexity but negatively related to acquisitive traits (i.e. community-weighted mean of specific leaf area). Plant phylogenetic diversity had no significant direct effect on forest multifunctionality, but it had a significant indirect effect via increased stand structural complexity. The effect of soil microbial diversity on forest multifunctionality increased with increasing threshold levels of forest multifunctionality and outperformed tree diversity and environmental conditions at the highest threshold level (i.e. 95%). Forests on steep slopes had lower levels of ecosystem multifunctionality due to decreased stand structural complexity. Soil nutrients were responsible for regulating forest multifunctionality via plant trait composition and, to a lesser extent, via tree diversity, stand structure and soil microbial diversity.</span></p> <p><span>4. <i>Synthesis</i>: Plant phylogenetic diversity, stand structure and soil microbial diversity jointly regulated forest multifunctionality, and these effects were influenced by local-scale changes in environmental conditions. Soil microbial diversity was a key driver of highly multifunctional forests, whereas conservation of complex stand structure and conservative trait dominance could enhance mean values of multiple functions.</span></p>
Data from: Variation in fine-scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird
The distribution of suitable habitat influences natal and breeding dispersal at small spatial scales, resulting in strong micro-geographic genetic structure. Although environmental variation can promote inter-population differences in dispersal behavior and local spatial patterns, the effects of distinct ecological conditions on within-species variation in dispersal strategies and in fine-scale genetic structure remain poorly understood. We studied local dispersal and fine-scale genetic structure in the thorn-tailed rayadito (Aphrastura spinicauda), a South American bird that breeds along a wide latitudinal gradient. We combine capture-mark-recapture data from eight breeding seasons and molecular genetics to compare two peripheral populations with contrasting environments in Chile: Navarino Island, a continuous and low density habitat, and Fray Jorge National Park, a fragmented, densely populated and more stressful environment. Natal dispersal showed no sex bias in Navarino, but was female-biased in the more dense population in Fray Jorge. In the latter, male movements were restricted and some birds seemed to skip breeding in their first year, suggesting habitat saturation. Breeding dispersal was limited in both populations, with males being more philopatric than females. Spatial genetic autocorrelation analyses using 13 polymorphic microsatellite loci confirmed the observed dispersal patterns: a fine-scale genetic structure was only detectable for males in Fray Jorge for distances up to 450 m. Furthermore, two-dimensional autocorrelation analyses and estimates of genetic relatedness indicated that related males tended to be spatially clustered in this population. Our study shows evidence for context-dependent variation in natal dispersal and corresponding local genetic structure in peripheral populations of this bird. It seems likely that the costs of dispersal are higher in the fragmented and higher density environment in Fray Jorge, particularly for males. The observed differences in micro-geographic genetic structure for rayaditos might reflect the genetic consequences of population-specific responses to contrasting environmental pressures near the range limits of its distribution.
Data from: Patterns of local community composition are linked to large-scale diversification and dispersal of clades
At any location, a group of organisms may be represented by several clades. What determines which clades will dominate local communities in terms of their species richness? Here, this relatively neglected question is addressed by analyzing 166 local assemblages of snakes distributed globally. For most regions, local assemblages are dominated by clades with higher global-scale diversification rates and more frequent dispersal into each region, and not by clades that have been present in that region longer. This result contrasts with many other studies of local richness (in other organisms), which show strong impacts of regional colonization time on overall local species richness of clades. Furthermore, even though local assemblages are assembled independently on different continents, most regions have converged on similar patterns of proportional richness. Specifically, a few rapidly diversifying clades dominate most communities around the world. The high diversification rates of these clades are then linked to their high dispersal rates. Similar patterns may occur in many groups, such as plants, frogs, salamanders, birds, and mammals.
Data from: Diversity dynamics of Phanerozoic terrestrial tetrapods at the local-community scale
The fossil record provides one of the strongest tests of the hypothesis that diversity within local communities is constrained over geological timescales. Constraints to diversity are particularly controversial in modern terrestrial ecosystems, yet long-term patterns are poorly understood. Here we document patterns of local richness in Phanerozoic terrestrial tetrapods using a global data set comprising 145,332 taxon occurrences from 27,531 collections. We show that the local richness of non-flying terrestrial tetrapods has risen asymptotically since their initial colonization of land, increasing at most threefold over the last 300 million years. Statistical comparisons support phase-shift models, with most increases in local richness occurring: (1) during the colonization of land by vertebrates, concluding by the late Carboniferous; and (2) across the Cretaceous/Paleogene boundary. Individual groups, such as mammals, lepidosaurs and dinosaurs also experienced early increases followed by periods of stasis often lasting tens of millions of years. Mammal local richness abruptly tripled across the Cretaceous/Paleogene boundary, but did not increase over the next 66 million years. These patterns are consistent with the hypothesis that diversity is constrained at the local-community scale.
Data from: On the relative importance of CSR ecological strategies and integrative traits to explain species dominance at local scales
PLEASE NOTE, PART OF THESE DATA ARE ALSO REFERRED TO ANOTHER ARTICLE. PLEASE SEE http://dx.doi.org/10.1111/j.1654-1103.2009.01119.x FOR MORE INFORMATION. 1. Identifying ecological strategies based on functional traits has been one of the main focuses of studies on plant community assembly. Recently, an important and timely tool, "StrateFy", has been proposed for detecting plant strategies across the globe according to the CSR scheme. The CSR scheme is undeniably efficient across scales, and distinct CSR strategies among species have been proposed to explain differing degrees of dominance among species. However, in a previous study we showed that dominance ranking of woody species in a resource-poor habitat (coastal sandy plain) was not explained by morphological traits commonly measured in functional approaches (such as those used to estimate CSR strategies), but by integrative traits (i.e. traits that are the result of different combinations of functional traits) more related to plant performance. 2. Here, we used CSR analysis and StrateFy on a dataset collected on a coastal sandy plain to test the hypothesis that the dominance ranking would be compatible with the CSR strategies; i.e., that dominant species would show a greater proportion of the stress-tolerance (S%) strategy than subordinate species. 3. Contrary to our hypothesis, all species exhibited an S/CS strategy, and the most-dominant species had neither similar values nor the highest S%. The inability of CSR analysis (as applied using StrateFy) to predict dominance ranking suggests that it can explain relative dominance when different strategies co-occur, but not in cases where dominant and subordinate plants share the same strategy. 4. We argue that the relative importance of CSR and integrative traits for describing dominance ranking may depend on how CSR strategies are filtered in each environment. In environments where only a narrow range of strategy classes are viable, integrative traits may be more important for explaining variation in degrees of dominance. Thus, the ability of a given species to achieve dominance may depend on integrative traits resulting from multiple trait arrays, not necessarily captured by the SLA, LDMC and LA measurements that are used to calculate the relative proportions of strategies in StrateFy.
Data from: Shared and non-shared genomic divergence in parallel ecotypes of Littorina saxatilis at a local scale
Parallel speciation occurs when selection drives repeated, independent adaptive divergence that reduces gene flow between ecotypes. Classical examples show parallel speciation originating from shared genomic variation, but this does not seem to be the case in the rough periwinkle (Littorina saxatilis) that has evolved considerable phenotypic diversity across Europe, including several distinct ecotypes. Small 'wave' ecotype snails inhabit exposed rocks and experience strong wave action, while thick-shelled, 'crab' ecotype snails are larger and experience crab predation on less exposed shores. Crab and wave ecotypes appear to have arisen in parallel and recent evidence suggests only marginal sharing of molecular variation linked to evolution of similar ecotypes in different parts of Europe. However the extent of genomic sharing is expected to increase with gene flow and more recent common ancestry. To test this we used de novo RAD-sequencing to quantify the extent of shared genomic divergence associated with phenotypic similarities among ecotype-pairs on three close islands (< 10 km distance) connected by weak gene flow (Nm~0.03) and with recent common ancestry (< 10,000 years). After accounting for technical issues, including a large proportion of null alleles due to a large effective population size, we found ~8-28% of positive outliers were shared between two islands and ~2-9% were shared among all three islands. This low level of sharing suggests that parallel phenotypic divergence in this system is not matched by shared genomic divergence despite a high probability of gene flow and standing genetic variation.
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.
Data from: The impact of spatial scale and habitat configuration on patterns of trait variation and local adaptation in a wild plant parasite
Theory indicates that spatial scale and habitat configuration are fundamental for coevolutionary dynamics and how diversity is maintained in host–pathogen interactions. Yet, we lack empirical data to translate the theory to natural host–parasite systems. In this study, we conduct a multiscale cross-inoculation study using the specialist wild plant pathogen Podosphaera plantaginis on its host plant Plantago lanceolata. We apply the same sampling scheme to a region with highly fragmented (Åland) and continuous (Saaremaa) host populations. Although theory predicts higher parasite virulence in continuous regions, we did not detect differences in traits conferring virulence among the regions. Patterns of adaptation were highly scale dependent. We detected parasite maladaptation among regions, and among populations separated by intermediate distances (6.0–40.0 km) within the fragmented region. In contrast, parasite performance did not vary significantly according to host origin in the continuous landscape. For both regions, differentiation among populations was much larger for genetic variation than for phenotypic variation, indicating balancing selection maintaining phenotypic variation within populations. Our findings illustrate the critical role of spatial scale and habitat configuration in driving host–parasite coevolution. The absence of more aggressive strains in the continuous landscape, in contrast to theoretical predictions, has major implications for long-term decision making in conservation, agriculture, and public health.
Data from: Species richness-productivity relationships of tropical terrestrial ferns at regional and local scales
1. The species richness-productivity relationship (SRPR), by which the species richness of habitats or ecosystems is related to the productivity of the ecosystem or the taxon, has been documented both on regional and local scales, but its generality, biological meaning, and underlying mechanisms remain debated. 2. We evaluated the SRPR and 3 mechanistic hypotheses using terrestrial ferns in 18 study plots along an elevational gradient (500-4000 m) in Ecuador. We measured annual increases in above-ground biomass of 6175 fern individuals from 91 species over 2 years, and estimated plot-level tree productivity from increases in above-ground woody biomass of 560 trees. Analyses were conducted by (a) comparing plots along the elevational gradient (regional scale) and (b) comparing plots within each elevational belt (local scale). 3. Fern diversity was related to the productivity of the fern assemblages, but not to above-ground productivity of the trees. At the regional scale, we found a positive relationship of fern species richness to fern productivity that appeared to be determined by an increase in the number of fern individuals and niche availability. In contrast, at the local scale this relationship was negative and likely driven by interspecific competition. 4. Synthesis: Plot diversity of ferns appears to be limited by the number of available niches and competition to occupy these niches. At the local scale, this is reflected in a negative SRPR probably driven by competition, whereas with increasing scale the positive influence of productivity emerges. This represents the first evidence that productivity and competition affect the diversity of tropical herb assemblages at the plot scale.
Data from: Kicking Triturus arntzeni when it's down: large-scale nuclear genetic data confirm that newts from the type locality are genetically admixed
We collected nuclear DNA data (52 markers) with next-generation sequencing for nine Triturus newt specimens, including the holotype and two of the paratypes of T. arntzeni, from the type locality at Vrtovać in eastern Serbia. We compare these data to a reference set composed of the four crested newt species distributed in eastern Serbia namely T. cristatus, T. dobrogicus, T. ivanbureschi and T. macedonicus to determine to which of these species the newts from the type locality of T. arntzeni should be attributed. The majority of alleles in individuals from Vrtovać is derived from T. macedonicus, but a considerable number of T. ivanbureschi alleles is also present; alleles typical for T. cristatus and T. dobrogicus are found at low frequency. Accordingly, we interpret Vrtovać as a T. macedonicus – T. ivanbureschi hybrid population, albeit not composed of F1 hybrids but of genetically admixed individuals derived through multiple generations of backcrossing. The data support the notion that the name T. arntzeni should not be applied to a species newly distinguished in T. karelinii sensu lato (to which the name T. ivanbureschi has been given). We conclude that because of the hybrid nature of the individuals from Vrtovać, the name T. arntzeni should be placed not only in the synonymy of T. macedonicus but also in the synonymy of T. ivanbureschi. In this study we demonstrate that next-generation sequencing can provide high quality data for type material with degraded DNA and therefore can play an important role in taxonomy.
Brazil (MZSP 122065). Fig. 1: ventral, lateral & dorsal views; Fig. 2: enlarged view of protoconch (not to scale); Fig. 3: apical view, V = varix, L = edge of outer lip. Fig. 4: paratype from the type locality, ventral view. in Taxonomic review of tropical western Atlantic shallow water Drilliidae (Mollusca: Gastropoda: Conoidea) including descriptions of 100 new species
Brazil (MZSP 122065). Fig. 1: ventral, lateral & dorsal views; Fig. 2: enlarged view of protoconch (not to scale); Fig. 3: apical view, V = varix, L = edge of outer lip. Fig. 4: paratype from the type locality, ventral view.
(MZSP 122062). Fig. 1: ventral, lateral & dorsal views; Fig. 3: apical view, V = varix, L = edge of outer lip. Fig 2: enlarged view of protoconch of specimen in Fig. 10 (not to scale). Lower panel, paratypes from the type locality. Figs. 4–5: MNRJ 34635; Figs. 6–7: USNM 1291334; Figs. 8–10: P. Stahlschmidt coll. in Taxonomic review of tropical western Atlantic shallow water Drilliidae (Mollusca: Gastropoda: Conoidea) including descriptions of 100 new species
(MZSP 122062). Fig. 1: ventral, lateral & dorsal views; Fig. 3: apical view, V = varix, L = edge of outer lip. Fig 2: enlarged view of protoconch of specimen in Fig. 10 (not to scale). Lower panel, paratypes from the type locality. Figs. 4–5: MNRJ 34635; Figs. 6–7: USNM 1291334; Figs. 8–10: P. Stahlschmidt coll.
Online repository for Paper "AgentFL: Scaling LLM-based Fault Localization to Project-Level Context"
<h3>Summary</h3> <p>This is the online repository for the arXiv paper "AgentFL: Scaling LLM-based Fault Localization to Project-Level Context".</p> <p>We also provide the results for the TSE'25 paper "SOAPFL: A Standard Operating Procedure for LLM-based Method-Level Fault Localization".</p> <h3>Environment</h3> <ul> <li><a href="https://github.com/rjust/defects4j/tree/v1.4.0">Defects4J-V1.4.0</a> (Note that the buggy items in V1.4.0 is identical with V1.2.0, we use V1.4.0 to avoid some problems in V1.2.0)</li> <li><a href="https://github.com/rjust/defects4j/tree/v2.0.0">Defects4J-V2.0.0</a></li> <li>Python version >= 3.8.5</li> </ul> <h3>Defects4J Mod</h3> <p>Before running AgentFL, please apply the files under the <code>AgentFL/Defects4J_mod</code> directory to modify your Defects4J V1.4.0/V2.0.0.</p> <h3>Run AgentFL</h3> <p>Set your own OpenAI API key in <code>AgentFL/camel/model_backend.py</code></p> <p>It's easy to run AgentFL for localizing a bug with the following command:</p> <p><code>python3 run.py --config <CONFIG_DIR> --version <D4J_VERSION> --project <PROJECT> --bugID <BUG_ID> --model <GPT_MODEL_NAME></code></p> <p>For example:</p> <p><code>python3 run.py --config Default --version 1.4.0 --project Closure --bugID 26 --model GPT_3_5_TURBO</code></p> <p>More configs can be seen under the directory <code>AgentFL/Config</code></p> <h3>Results</h3> <p>We release all of the results of AgentFL in the <code>AgentFL/Results</code> directory, including the evaluation results on Defects4J V1.4.0/V2.0.0 and the ablation study result.</p> <p>For each bug, we record all of the prompts, responses, and intermediate outputs.</p> <blockquote> <p>NEW: We have released the newest results for TSE'25 paper "SOAPFL: A Standard Operating Procedure for LLM-based Method-Level Fault Localization". The results can be found in the `<a href="https://zenodo.org/api/records/16938304/draft/files/SoapFL_results.zip/content" target="_blank" rel="noopener noreferrer">SoapFL_results.zip</a>` file!</p> </blockquote> <h3>Human Evaluation Results</h3> <p>The human evaluation results can be found in the file <code>AgentFL/EvaluationResult/DebugResult_d4j140_GPT35_human.xlsx</code></p> <h3>System Messages for Agents</h3> <ul> <li>Test Code Reviewer:</li> </ul> <blockquote> <p>You are a Test Code Reviewer. We share a common interest in collaborating to successfully locate the buggy code that cause the test suite to fail. You can examine the test code and the initialized classes to analyze the similar behavior of the failed tests within the test suite. To locate the bug, you must write a response that appropriately solves the requested instruction based on your expertise.</p> </blockquote> <ul> <li>Source Code Reviewer</li> </ul> <blockquote> <p>You are a Source Code Reviewer. we are both working at DebugDev. We share a common interest in collaborating to successfully locate the buggy code that cause the test suite to fail. Your main responsibilities is to generate a comment for each covered method base on the method call relationship. To locate the bug, you must write a response that appropriately solves the requested instruction based on your expertise.</p> </blockquote> <ul> <li>Software Test Engineer</li> </ul> <blockquote> <p>You are a Software Test Engineer. We share a common interest in collaborating to successfully locate the buggy code that cause the test suite to fail. You main responsibilities include examining the information of the failed tests to analyze the possible causes of the test failures, and determining the method that need to be fixed. To locate the bug, you must write a response that appropriately solves the requested instruction based on your expertise.</p> </blockquote> <ul> <li>Software Architect</li> </ul> <blockquote> <p>You are a Software Architect. We share a common interest in collaborating to successfully locate the buggy code that cause the test suite to fail. You are very familiar with the architecture of the software, the functions of each class and method in the software. You main responsibilities include examining the given information to locate the possible buggy classes and buggy methods. To locate the bug, you must write a response that appropriately solves the requested instruction based on your expertise.</p> </blockquote>
Codes and data: Community size predicts temporal β-diversity at local but not regional scales
<p>UPDATED VERSION 2025-08-30 (models were updated)</p> <p>This zip file contains the codes demonstrating how I analyzed and selected publicly available and globally extensive data on fish composition and environmental variables to test the hypothesis that random fluctuations caused by demographic stochasticity in small populations might extend to communities and metacommunities, potentially affecting stability propagation across biological levels and spatial scales. The READ_ME file contains additional details about the steps I took to develop this analysis.</p> <p>This study was financed by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brasil (CAPES) - Finance Code 001.</p>
ScienceDex guides
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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)
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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.