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Data from: Collective dispersal leads to variance in fitness and maintains offspring size variation within marine populations
Variance in fitness is well known to influence the outcome of evolution but is rarely considered in the theory of marine reproductive strategies. In coastal environments, turbulent mesoscale eddies can collect larvae into 'packets' resulting in collective dispersal. Larvae in packets return to the coast or are lost offshore in groups, producing variance in fitness. Using a Markov process to calculate fixation probabilities for competing phenotypes, we examine the evolution of offspring size and spawning duration in species with benthic adults and pelagic offspring. The offspring size that provides mothers with the highest mean fitness also generates the greatest variance in fitness, but pairwise invasion plots show that bet-hedging strategies are not evolutionarily stable: maximizing expected fitness correctly predicts the unique evolutionarily stable strategy. Nonetheless, fixation can take a long time. We find that selection to increase spawning duration as a risk-avoidance strategy to reduce the negative impacts of stochastic recruitment success can allow multiple offspring sizes to coexist in a population for extended periods. This has two important consequences for offspring size: 1) coexistence occurs over a broader range of sizes and is longer when spawning duration is longer, because longer spawning durations reduce variation in fitness and increase the time to fixation, and 2) longer spawning durations can compensate for having a non-optimal size and even allow less optimal sizes to reach fixation. Collective dispersal and longer spawning durations could effectively maintain offspring size variation even in the absence of good and bad years or locations. Empirical comparisons of offspring size would, therefore, not always reflect environment-specific differences in the optimal size.
Data from: The complex net effect of reciprocal interactions and recruitment facilitation maintains an intertidal kelp community
1.Theoretical and empirical ecology has transitioned from a focus on the role of negative interactions in species coexistence to a more pluralistic view that acknowledges that coexistence in natural communities is more complex, and depends on species interactions that vary in strength, sign, and reciprocity, and such contexts as the environment and life history stage. 2. We used a whole-community approach to examine how species interactions contribute to the maintenance of a rocky intertidal macroalgal canopy-understorey assemblage. We determined both the types of interactions in this network, and whether interactions were sensitive to environmental gradients. 3. Focusing on a structurally dominant canopy kelp Saccharina sessilis, and its diverse co-occurring understorey assemblage, we evaluated the role of the understorey in controlling S. sessilis recruitment and quantified the reciprocal effect of the S. sessilis canopy and understorey on one another using a removal experiment replicated across 600 km of coastline. We determined the sensitivity of interactions to natural variation in light and nutrient availability (replicated among four regions on the N.E. Pacific coast), and under different wave conditions (three wave regimes). 4. Surprisingly, species interactions were similar across sites and thus not context-dependent. Unexpectedly, the understorey community had a strong positive effect on the S. sessilis canopy, whereby the adult canopy decreased dramatically following understorey removal. Additionally, S. sessilis recruitment depended on the presence of understorey coralline algal turf. In turn, the canopy had a neutral effect on the coralline understorey, but a negative effect on non-calcifying algal turfs, likely eventually generating positive indirect canopy effects on the coralline understorey. Density-dependent intra-specific competition between S. sessilis adults and recruits may moderate this positive feedback between the S. sessilis canopy and coralline understorey. 5. Synthesis. Our research highlights the importance of positive interactions for coexistence in natural communities, and the necessity of studying multiple life-history stages and reciprocal species interactions in order to elucidate the mechanisms that maintain diversity.
Data from: Deployment of organic farming at a landscape scale maintains low pest infestation and high crop productivity in vineyards
Organic farming is a promising way to reduce pesticide use but increasing the area under organic farming at the landscape scale could increase pest infestations and reduce crop productivity. Examining the effects of organic farming at multiple spatial scales and in different landscape contexts on pest communities and crop productivity is a major step in the ecological intensification of agricultural systems. We quantified the infestation levels of two pathogens and five arthropod pests, the intensity of pesticide use and crop productivity in 42 vineyards. Using a multi-scale hierarchical design, we unravelled the relative effects of organic farming at both field and landscape scales from the effects of semi-natural habitats in the landscape. At the field scale, pest communities did not differ between organic and conventional farming systems. At the landscape scale, increasing the area under organic farming did not increase pest infestation levels. Three out of seven pest taxa were affected both by local farming systems and the proportion of semi-natural habitats in the landscape. Our findings revealed that the proportion of semi-natural habitats reduced pest infestation for two out of seven pest taxa. Organic vineyards had much lower treatment intensities, very similar levels of pest control and equal crop productivity levels. Synthesis and Applications. Our results clearly indicate that policies promoting the development of organic farming in conventional vineyard landscapes will not lead to greater pest and disease infestations but will reduce the pesticide treatment intensity and maintain crop productivity. Moreover, the interactions between semi-natural habitats in landscape and local farming practices suggest that the deployment of organic farming should be adapted to landscape contexts.
Data from: Genetic composition of the Warm Springs River Chinook Salmon population maintained following eight generations of hatchery production
Balancing the disparate objectives of fishery augmentation and conservation of an endemic population presents a substantial challenge. In the case of Warm Springs National Fish Hatchery (Warm Springs Hatchery), strategies for achieving both objectives included incorporation of natural fish into the hatchery broodstock and restricting proportions of hatchery fish on the spawning grounds. The hatchery has been more successful in implementing the latter, however, than the former. We analyzed seventy-six SNP markers in Spring Chinook Salmon O. tshawytscha collected from the Warm Springs River in 1976 – 1977 (prior to hatchery produciton) and 2001-2011 (post-hatchery) to examine whether the genetic characteristics of the endemic population had changed during that time. Pre- and post- hatchery collections clustered together when compared to Round Butte Hatchery (a nearby segregated program) and other Columbia River populations. The difference between pre- and post- hatchery collections was non-significant (AMOVA), but post hatchery samples exhibited significantly lower He. We observed some evidence of reduced effective size (Ne) and increased genetic drift in fish produced at Warm Springs Hatchery (relative to natural-origin fish), and even stronger evidence in fish produced at Round Butte Hatchery. We conclude that natural-origin fish returning to the Warm Springs River form a distinct group within the Interior Columbia Basin Spring-run lineage and have changed very little over the past eight generations. We further speculate that differences between hatchery- and natural- origin fish at Warm Springs Hatchery are expected to increase if hatchery operations remain static (little integration of natural-origin fish and incorporation of Round Butte Hatchery fish in broodstock).
Data from: Genetic diversity maintained among fragmented populations of a tree undergoing range contraction
Dwarf birch (Betula nana) has a widespread boreal distribution but has declined significantly in Britain where populations are now highly fragmented. We analysed the genetic diversity of these fragmented populations using markers that differ in mutation rate: conventional microsatellites markers (PCR-SSRs), RADseq generated transition and transversion SNPs (RAD-SNPs), and microsatellite markers mined from RADseq reads (RAD-SSRs). We estimated the current population sizes by census and indirectly, from the linkage disequilibrium found in the genetic surveys. The two types of estimate were highly correlated. Overall we found genetic diversity to be only slightly lower in Britain than across a comparable area in Scandinavia where populations are large and continuous. Whilst the ensemble of British fragments maintain diversity levels close to Scandinavian populations, individually they have drifted apart and lost diversity; particularly the smaller populations. An ABC analysis, based on coalescent models, favours demographic scenarios in which Britain maintained high levels of genetic diversity through post-glacial recolonisation. This diversity has subsequently been partitioned into population fragments that have recently lost diversity at a rate corresponding to the current population-size estimates. We conclude that the British population fragments retain sufficient genetic resources to be the basis of conservation and re-planting programmes. Use of markers with different mutation rates gives us greater confidence and insight than one marker set could have alone, and we suggest that RAD-SSRs are particularly useful as high mutation rate marker set with a well-specified ascertainment bias, which are widely available yet often neglected in existing RAD datasets.
Data from: The effects of recent changes in breeding preferences on maintaining traditional Dutch chicken genomic diversity
Traditional Dutch chicken breeds are marginalised breeds of ornamental and cultural-historical importance. In the last decades, miniaturising of existing breeds (so called neo-bantam) has become popular and resulted in alternatives to original large breeds. However, while backcrossing is increasing the neo-bantams homozygosity, genetic exchange between breeders may increase their genetic diversity. We use the 60K SNP array to characterise the genetic diversity, demographic history, and level of inbreeding of Dutch heritage breeds, and particularly of neo-bantams. Commercial white layers are used to contrast the impact of management strategy on genetic diversity and demography. A high proportion of alleles was found to be shared between large fowls and neo-bantams, suggesting gene flow during neo-bantams development. Population admixture analysis supports these findings, in addition to revealing introgression from neo-bantams of the same breed and of phenotypically similar breeds. The prevalence of long runs of homozygosity (ROH) confirms the importance of recent inbreeding. A high diversity in management, carried out in small breeding units explains the high heterogeneity in diversity and ROH profile displayed by traditional breeds compared to commercial lines. Population bottlenecks may explain the long ROHs in large fowls, while repetitive backcrossing for phenotype selection may account for them in neo-bantams. Our results highlight the importance of using markers to inform breeding programmes on potentially harmful homozygosity to prevent loss of genetic diversity. We conclude that bantamisation has generated unique and identifiable genetic diversity. However, this diversity can only be preserved in the near future through structured breeding programmes.
Data from: Lizards at the peak: physiological plasticity does not maintain performance in lizards transplanted to high altitude
Warming climates are facilitating the range expansion of many taxa to habitats that were formerly thermally inhospitable, including to higher latitudes and elevations. The potential for such colonization, however, varies widely among taxa. Since environmental factors may interact to affect colonization potential, an understanding of underlying physiological and behavioural mechanisms is necessary to predict how species will respond to potentially suitable habitats. For example, temperature and oxygen availability will interact to shape physiological and performance traits. Our model species, the wall lizard Podarcis muralis, is a widely distributed ectotherm that continues to expand its range in Europe despite being limited by cold temperatures at high elevations and latitudes. To test the potential for organisms to expand to warming high-altitude environments, we conducted a transplant experiment to quantify the within-individual effects of high-altitude hypoxia on physiological and performance traits. Transplanted lizards maintained individual differences in physiological traits related to oxygen capacity and metabolism (haemoglobin concentration, haematocrit, and peak post-exhaustion metabolic rate) as well as performance traits tied to fitness (sprint speed and running endurance). Although lizards altered blood biochemistry to increase oxygen-carrying capacity, their performance was reduced at high altitude. Furthermore, lizards at high altitude suffered a rapid loss of body condition over the six-week experiment, potentially indicating an energetic cost to hypoxia. Taken together, this demonstrates a limited potential for within-individual plasticity to facilitate colonization of novel high-altitude environments.
Data from: Behavioral diversity is maintained by a conditional strategy in a freshwater zooplankton
Many populations have intraspecific diversity in phenotype and ecological strategy, but the mechanisms maintaining such diversity are not fully understood. Multiple behaviors can be maintained either as a conditional strategy, where fitness depends on an individual's phenotype, or as a mixed strategy where alternative behaviors have similar fitness independent of phenotype. Using high-resolution depth and time sampling, we characterize two distinct diel vertical migration behaviors in a population of freshwater zooplankton (Daphnia pulicaria). Individuals in this population differ in their color phenotype and migratory behavior with red morphs upregulating hemoglobin and undergoing a deep migration, and pale morphs not producing hemoglobin and undergoing a shallow migration. We experimentally manipulated the behavior of each phenotype in the field, and measured population growth in their natural migration behavior as well as population growth in their alternative behaviors. Experimental populations of pale and red morphs under their natural migrations had roughly equal fitness, despite vast differences in environmental conditions. When forced to switch behaviors, pale morphs suffered reduced fitness, whereas red morphs had similar fitness compared to their natural migration. Our results suggest that while behavioral diversity may be promoted by the opportunity for alternative behaviors of equal fitness, the distinct physiological conditions required for survival in alternative behaviors limit the capacity for individual behavioral switching and likely maintain behavioral diversity as a conditional strategy.
Data from: Conservation of old individual trees and small populations is integral to maintain species' genetic diversity of a historically fragmented woody perennial
Historically fragmented and specialised habitats such as granite outcrops are understudied globally unique hotspots of plant evolution. In contrast to predictions based on mainstream population genetics theory, some granite outcrop plants appear to have persisted as very small populations despite prolonged geographic and genetic isolation. Eucalyptus caesia Benth. is a long-lived lignotuberous tree endemic with a naturally fragmented distribution on granite outcrops in south-western Australia. To quantify population to landscape level genetic structure we employed microsatellite genotyping at 14 loci of all plants in 18 stands of E. caesia. Sampled stands were characterised by low levels of genetic diversity, small absolute population sizes, localised clonality and strong fine-scale genetic sub-division. There was no significant relationship between population size and levels of heterozygosity. At the landscape scale, high levels of population genetic differentiation were most pronounced among representatives of the two subspecies in E. caesia as originally circumscribed. Past genetic interconnection was evident between some geographical neighbours separated by up to 20 kilometres. Paradoxically, other pairs of neighbouring stands as little as 7 kilometres apart were genetically distinct. There was no consistent pattern of isolation by distance across the 280 km range of E. caesia. Low levels of gene flow, together with strong drift within stands, provides some explanation of the patterns of genetic differentiation we observed. Individual genet longevity via the ability to repeatedly re-sprout and expand from a lignotuber may enhance the persistence of some woody perennial endemic plants despite small population size, minimal genetic interconnection and low heterozygosity.
Maintaining historic disturbance regimes increases species' resilience to catastrophic hurricanes
<p>As habitat loss and fragmentation, urbanization, and global climate change accelerate, conservation of rare ecosystems increasingly relies on human intervention. However, any conservation strategy is vulnerable to unpredictable, catastrophic events. Whether active management increases or decreases a system's resilience to these events remains unknown. Following Hurricane Irma's landfall in our habitat restoration study sites, we found that rare ecosystems with active, human-imposed management suffered less damage in a hurricane's path than unmanaged systems. At the center of Irma's landfall, we found Croton linearis' (a locally rare plant that is the sole host for two endangered butterfly species) survival and population growth rates in the year of the hurricane were higher in previously managed plots than in un-managed controls. In the periphery of Irma's circulation, the effect of prior management was stronger than that of the hurricane. Maintaining the historical disturbance regime thus increased the resilience of the population to major hurricane disturbance. As climate change increases the probability and intensity of severe hurricanes, human management of disturbance-adapted landscapes will become increasingly important for maintaining populations of threatened species in a storm's path. Doing nothing will accelerate extinction.</p>
Does Co-Development with AI Assistants Lead to More Maintainable Code? Replication Package
<p>This is the replication package for the study "Echoes of AI: Investigating the Downstream Effects of AI Assistants on Software Maintainability" preregistered aat ICSME 2024 as “Does Co-Development with AI Assistants Lead to More Maintainable Code?”</p> <p>Abstract from the registered report:</p> <p>[Background/Context] AI assistants like GitHub Copilot are transforming software engineering, with several studies highlighting productivity improvements. However, their impact on code quality, particularly in terms of maintainability, requires further investigation.<br>[Objective/Aim] This study aims to examine the influence of AI assistants on software maintainability, specifically assessing how these tools affect the ability of developers to evolve code.<br>[Method] We will conduct a two-phased controlled experiment involving professional developers. In Phase 1, developers will add a new feature to a Java project, with or without the aid of an AI assistant. Phase 2, a randomized controlled trial, will involve a different set of developers evolving random Phase 1 projects - working without AI assistants. We will employ Bayesian analysis to evaluate differences in completion time, perceived productivity, code quality, and test coverage.</p> <p>Note: To maintain the integrity of the study, i.e., preventing any leakage to AI assistants' training data, we choose not to host the code in a public git repository. Instead, all relevant documents and code are shared through a replication package on Zenodo, available as PDF documents generated by repo2pdf (https://github.com/BankkRoll/repo2pdf). We have deliberately used settings to obfuscate the code (e.g., line numbers) to ensure it will not be scraped by any large language models before the study has been completed.</p> <p>Contents:</p> <ul> <li>Task 1 instructions.</li> <li>Task 2 instructions.</li> <li>The source code that the participants received.</li> <li>A causal graph with analysis details.</li> <li>Archives containing anonymized experimental data and analysis scripts (in .zip and .tar.gz for convenience). </li> </ul>
High parasite diversity maintained after an alga-virus coevolutionary arms race
<p>Data and analysis files accompanying the paper 'High parasite diversity maintained after an alga-virus coevolutionary arms race' (Lievens, Kühn et al. 2024, <em>J Evol Biol</em>). Includes data and code for the phenotypes (host clone range, survival, growth) and genotypes (SNPs, copy number variation) of the virus isolates form the post-arms race phase of an experimental coevolution between <em>Chlorella variabilis</em> algae and PBCV-1 viruses.</p>
Autophagy regulator ATG5 maintains cerebellar function by preventing its excessive glycolytic activity.
Open the record for dataset details and reuse information.
Evidence that metapopulation dynamics maintain a species' range limit
<p>This zip folder includes both raw data from a multi-year (2019 and 2022) survey of coastal dune habitat and occupancy by <em>Camissoniopsis cheiranthifolia</em>, as well as an R project and associated scripts for an analysis of variation in metapopulation dynamics towards a species' range limit.</p>
Woodpeckers and other excavators maintain the diversity of cavity-nesting vertebrates
<p>Woodpeckers and other excavators create most of the holes used by secondary tree-cavity nesting vertebrates (SCNs) in North American temperate mixedwood forests, but the degree to which excavators release SCNs from nest-site limitation is debated. Our goal was to quantify how excavators maintain the diversity and abundance of secondary cavity nesters in a temperate forest through the creation of tree cavities. We examined the short- and long-term (legacy) effects of excavators (principally woodpeckers, but also red-breasted nuthatches and black-capped chickadees) on forest biodiversity using longitudinal monitoring data (1732 nest cavities, 25 sites, 16 years) in British Columbia, Canada. Sites with higher densities of excavator nests had more cavities available, higher species richness of SCNs, and higher nest density of SCNs, indicating the importance of a standing stock of cavities. Years with higher nesting densities of excavators were followed by years with higher SCN diversity, indicating that the creation of nesting opportunities through fresh excavation releases SCNs from community-wide nest-site limitation. We also show that excavators leave a "legacy" of biodiversity (species richness and abundance) at a site by accumulating cavities at rates faster than they become unusable by decay or destruction. By quantifying site-level effects of cavity excavation on the SCN community, our study highlights the key role of excavators as ecosystem engineers that maintain forest wildlife biodiversity. 01-Nov-2021</p>
Distribution. Balabac, Ramos, and Bugsuk Is, Palawan region, Phillipines. In the late 1990s, a small stock of eight Balabac Chevrotains escaped from their enclosures on Calauit Island, a small island off the coast of Busuanga Island, north of Palawan, where the species had been maintained and bred since 1982. These animals were reported to have increased to at least 21 free-living individuals by 2006. Apparently the species was also introduced to the larger island of Palawan. No recent records confirm that it is still extant there, although unconfirmed reports suggest that it may survive in southern Palawan. in Tragulidae
Distribution. Balabac, Ramos, and Bugsuk Is, Palawan region, Phillipines. In the late 1990s, a small stock of eight Balabac Chevrotains escaped from their enclosures on Calauit Island, a small island off the coast of Busuanga Island, north of Palawan, where the species had been maintained and bred since 1982. These animals were reported to have increased to at least 21 free-living individuals by 2006. Apparently the species was also introduced to the larger island of Palawan. No recent records confirm that it is still extant there, although unconfirmed reports suggest that it may survive in southern Palawan.
Figure 2 in Flowers are essential to maintain high beetle diversity (Coleoptera) in a Neotropical rainforest canopy
Figure 2. Small white flowers of the generalist pollination syndrome in a lowland rainforest canopy, Venezuela. (a) Flowers of Hymenopus heteromorphus (Benth.) Sothers and Prance var. heteromorphus (Chrysobalanaceae), March 1999. (b) Macraspis festiva Burmeister (Scarabaeidae) mating on flowering Matayba guianensis Aubl. (Sapindaceae), September 1997.
Figure 3 in Flowers are essential to maintain high beetle diversity (Coleoptera) in a Neotropical rainforest canopy
Figure 3. Diversity of Chrysomelidae beetles visiting flowers of Hymenopus heteromorphus (Benth.) Sothers and Prance var. heteromorphus (Chrysobalanaceae), March 1999. (a) Colaspis Fabricius (Eumolpinae). (b) Coroicona danieli Bechyné (Alticini). (c) Griburius auricapillus (Suffrian) (Cryptocephalinae). (d) Hecataeus Jacoby (Galerucinae).
Figure 1 in Flowers are essential to maintain high beetle diversity (Coleoptera) in a Neotropical rainforest canopy
Figure 1. Specialised flower-visiting beetles often have mouth parts adapted to feed effectively on pollen and nectar. Adaptations can include prolonged mouthparts and dense brushes on the maxillae as in (a) Mecometopus Thomson sp. (Cerambycidae), or enlarged and securiform maxillary palpomeres as in (b) Mordellistena Costa sp. 3 (Mordellidae).
Global camera trap synthesis highlights the importance of protected areas in maintaining mammal diversity
<p>The establishment of protected areas (PAs) is a central strategy for global biodiversity conservation. While the role of PAs in protecting habitat has been highlighted, their effectiveness at protecting mammal communities remains unclear. We analyzed a global dataset from over 8,671 camera traps in 23 countries on four continents that detected 321 medium- to large-bodied mammal species. We found a strong positive correlation between mammal taxonomic diversity and the proportion of a surveyed area covered by PAs at a global scale (b = 0.39, 95% CI = 0.19, 0.60) and in Indomalaya (b = 0.69, 95% CI = 0.19,1.2), as well as between functional diversity and PA coverage in the Nearctic (b = 0.47, 95% CI = 0.09, 0.85), after controlling for human disturbances and environmental variation. Functional diversity was only weakly (and insignificantly) correlated with PA coverage at the global scale (b =0.22, 95% CI = -0.02, 0.46), pointing to a need to better understand the functional response of mammal communities to protection. Our study provides important evidence of the global effectiveness of PAs in conserving terrestrial mammals and emphasizes the critical role of area-based conservation in a post-2020 biodiversity framework.</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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.