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Data from: The bacterium Pseudomonas aeruginosa senses and gradually responds to inter-specific competition for iron
Phenotypic plasticity in response to competition is a well-described phenomenon in higher organisms. Here, we show that also bacteria have the ability to sense the presence of competitors and mount fine-tuned responses to match prevailing levels of competition. In our experiments, we studied inter-specific competition for iron between the bacterium Pseudomonas aeruginosa (PA) and its competitor Burkholderia cenocepacia (BC). We focused on the ability of PA to phenotypically adjust the production of pyoverdine, an iron-scavenging siderophore. We found that PA up-regulates pyoverdine production early on during competition under condition of low iron availability. This plastic upregulation was fine-tuned in response to the level of competition imposed by BC, and seems to confer a relative fitness benefit to PA in the form of an earlier initiation of growth. At later time points, however, PA showed reduced growth in mixed compared to monoculture, suggesting that competitive responses are costly. Altogether, our results demonstrate that phenotypic plasticity in siderophore production plays an important role in inter-specific competition for iron. Upregulating siderophore production may be a powerful strategy to lock iron away from competing species, and to reserve this nutrient for strain members possessing the compatible receptor for uptake.
Data from: Species-specific responses to habitat conversion across scales synergistically restructure Neotropical bird communities
Ecologists are increasingly exploring methods for preserving biodiversity in agricultural landscapes. Yet because species vary in how they respond to habitat conversion, ecological communities in agriculture and more natural habitats are often distinct. Unpacking the heterogeneity in species responses to habitat conversion will be essential for predicting and mitigating community shifts. Here, we analyze two years of bird censuses at 150 sites across gradients of local land cover, landscape forest amount and configuration, and regional precipitation in Costa Rica to holistically characterize species responses to habitat conversion. Specifically, we used Poisson-binomial mixture models to (1) delineate groups of species that respond similarly to environmental gradients, (2) explore the relative importance of local versus landscape-level habitat conversion, and (3) determine how landscape context influences species' local habitat preferences. We found that species fell into six groups: habitat generalists, abundant and rare forest specialists, and three groups of agricultural specialists that differed in their responses to landscape forest cover, fragmentation, and regional precipitation. Birds were most sensitive to local forest cover, but responses were contingent on landscape context. Specifically, forest specialists benefitted most when local forest cover increased in forested landscapes, while habitat generalists exhibited compensatory dynamics, peaking at sites with either local or landscape-level forest, but not both. Our study demonstrates that species responses to habitat conversion are complex but predictable. Characterizing species-level responses to environmental gradients represents a viable approach for forecasting the winners and losers of global change and designing interventions to minimize the ongoing restructuring of Earth's biota.
Data from: Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli
Ecological opportunities promote population divergence into coexisting lineages. However, the genetic mechanisms that enable new lineages to exploit these opportunities are poorly understood except in cases of single mutations. We examined how two Escherichia coli lineages diverged from their common ancestor at the outset of a long-term coexistence. By sequencing genomes and reconstructing the genetic history of one lineage, we showed that three mutations together were sufficient to produce the frequency-dependent fitness effects that allowed this lineage to invade and stably coexist with the other. These mutations all affected regulatory genes and collectively caused substantial metabolic changes. Moreover, the particular derived alleles were critical for the initial divergence and invasion, indicating that the establishment of this polymorphism depended on specific epistatic interactions.
Data from: Inbreeding effects on gene-specific DNA methylation among tissues of Chinook salmon
Inbreeding depression is the loss of fitness resulting from the mating of genetically related individuals. Traditionally, the study of inbreeding depression focused on genetic effects, although recent research has identified DNA methylation as also having a role in inbreeding effects. Since inbreeding depression and DNA methylation change with age and environmental stress, DNA methylation is a likely candidate for the regulation of genes associated with inbreeding depression. Here, we use a targeted, multigene approach to assess methylation at 22 growth-, metabolic-, immune- and stress-related genes. We developed PCR-based DNA methylation assays to test the effects of intense inbreeding on intragenic gene-specific methylation in inbred and outbred Chinook salmon. Inbred fish had altered methylation at three genes, CK-1, GTIIBS and hsp70, suggesting that methylation changes associated with inbreeding depression are targeted to specific genes and are not whole-genome effects. While we did not find a significant inbreeding by age interaction, we found that DNA methylation generally increases with age, although methylation decreased with age in five genes, CK-1, IFN-ɣ, HNRNPL, hsc71 and FSHb, potentially due to environmental context and sexual maturation. As expected, we found methylation patterns differed among tissue types, highlighting the need for careful selection of target tissue for methylation studies. This study provides insight into the role of epigenetic effects on ageing, environmental response and tissue function in Chinook salmon and shows that methylation is a targeted and regulated cellular process. We provide the first evidence of epigenetically based inbreeding depression in vertebrates.
Data from: Sex-specific maternal effects in a viviparous fish
Mothers vary in their effects on their offspring, but studies of variation in maternal effects rarely ask whether differences between mothers are consistent for sons and daughters. Here, we analysed maternal effects in the mosquitofish Gambusia holbrooki for development time and adult size of sons and daughters, and a primary male sexual character (gonopodium length). We found substantial maternal effects on all traits, most notably for gonopodium length. There were significant correlations within each sex for maternal effects on different traits, indicative of trade-offs between development rate and adult size. By contrast, there was no evidence of any consistency in maternal effects on sons and daughters. This suggests that the evolution of maternal effects will follow independent trajectories dependent on sex-specific selection on offspring. Importantly, failure to recognize the sex-specific nature of maternal effects in this population would have substantially underestimated the extent of their variation between mothers.
Data from: Fundamental activity constraints lead to specific interpretations of the connectome
The continuous integration of experimental data into coherent models of the brain is an increasing challenge of modern neuroscience. Such models provide a bridge between structure and activity, and identify the mechanisms giving rise to experimental observations. Nevertheless, structurally realistic network models of spiking neurons are necessarily underconstrained even if experimental data on brain connectivity are incorporated to the best of our knowledge. Guided by physiological observations, any model must therefore explore the parameter ranges within the uncertainty of the data. Based on simulation results alone, however, the mechanisms underlying stable and physiologically realistic activity often remain obscure. We here employ a mean-field reduction of the dynamics, which allows us to include activity constraints into the process of model construction. We shape the phase space of a multi-scale network model of the vision-related areas of macaque cortex by systematically refining its connectivity. Fundamental constraints on the activity, i.e., prohibiting quiescence and requiring global stability, prove sufficient to obtain realistic layer- and area-specific activity. Only small adaptations of the structure are required, showing that the network operates close to an instability. The procedure identifies components of the network critical to its collective dynamics and creates hypotheses for structural data and future experiments. The method can be applied to networks involving any neuron model with a known gain function.
Data from: Local inter-species introgression is the main cause of extreme levels of intra-specific differentiation in mussels
Structured populations, and replicated zones of contact between species, are an ideal opportunity to study regions of the genome with unusual levels of differentiation; and these can illuminate the genomic architecture of species isolation, and the spread of adaptive alleles across species ranges. Here, we investigated the effects of gene flow on divergence and adaptation in the Mytilus complex of species, including replicated parental populations in quite distant geographical locations. We used target enrichment sequencing of 1269 contigs of a few Kb each, including some genes of known function, to infer gene genealogies at a small chromosomal scale. We show that geography is an important determinant of the genome-wide patterns of introgression in Mytilus, and that gene flow between different species, with contiguous ranges, explained up to half of the intra-specific outliers. This suggests that local introgression is both widespread and tends to affect larger chromosomal regions than purely intraspecific processes. We argue that this situation might be common, and this implies that genome scans should always consider the possibility of introgression from sister species, unsampled differentiated backgrounds, or even extinct relatives, e.g. Neanderthals in humans. The hypothesis that reticulate evolution over long periods of time contributes widely to adaptation, and to the spatial and genomic reorganisation of genetic backgrounds, needs to be more widely considered in order to make better sense of genome scans.
Data from: Species-specific plant–soil feedbacks alter herbivore-induced gene expression and defense chemistry in Plantago lanceolata
Plants actively interact with antagonists and beneficial organisms occurring in the above- and belowground domains of terrestrial ecosystems. In the past decade, studies have focused on the role of plant–soil feedbacks (PSF) in a broad range of ecological processes. However, PSF and its legacy effects on plant defense traits, such as induction of defense-related genes and production of defensive secondary metabolites, have not received much attention. Here, we study soil legacy effects created by twelve common grassland plant species on the induction of four defense-related genes, involved in jasmonic acid signaling, related to chewing herbivore defense (LOX2, PPO7), and in salicylic acid signaling, related to pathogen defense (PR1 and PR2) in Plantago lanceolata in response to aboveground herbivory by Mamestra brassicae. We also assessed soil legacy and herbivory effects on the production of terpenoid defense compounds (the iridoid glycosides aucubin and catalpol) in P. lanceolata. Our results show that both soil legacy and herbivory influence phenotypes of P. lanceolata in terms of induction of Pl PPO7 and Pl LOX2, whereas the expression of Pl PR1 and Pl PR2-1 is not affected by soil legacies, nor by herbivory. We also find species-specific soil legacy effects on the production of aucubin. Moreover, P. lanceolata accumulates more catalpol when they are grown in soils conditioned by grass species. Our study highlights that PSF can influence aboveground plant–insect interactions through the impacts on plant defense traits and suggests that aboveground plant defense responses can be determined, at least partly, by plant-specific legacy effects induced by belowground organisms.
Data from: Sequence specificity despite intrinsic disorder: how a disease-associated Val/Met polymorphism rearranges tertiary interactions in a long disordered protein
The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) in precursor brain-derived neurotrophic factor (BDNF) is one of the earliest SNPs to be associated with neuropsychiatric disorders, and the underlying molecular mechanism is unknown. Here we report on over 250 μ s of fully-atomistic, explicit solvent, temperature replica exchange molecular dynamics (MD) simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence. The simulations were able to correctly reproduce the location of both local and non-local secondary changes due to the Val66Met mutation when compared with NMR spectroscopy. We find that the change in local structure is mediated via entropic and sequence specific effects. We developed a hierarchical sequence-based framework for analysis and conceptualization, which first identifies "blobs" of 5-15 residues representing local globular regions or linkers. We use this framework within a novel test for enrichment of higher-order (tertiary) structure in disordered proteins; the size and shape of each blob is extracted from MD simulation of the real protein (RP), and used to parameterize a self-avoiding heterogenous polymer (SAHP). The SAHP version of the BDNF prodomain suggested a protein segmented into three regions, with a central long, highly disordered polyampholyte linker separating two globular regions. This effective segmentation was also observed in full simulations of the RP, but the Val66Met substitution significantly increased interactions across the linker, as well as the number of participating residues. The Val66Met substitution replaces β -bridging between Val66 and Val94 (on either side of the linker) with specific side-chain interactions between Met66 and Met95.The protein backbone in the vicinity of Met95 is then free to form β -bridges with residues 31-41 near the N-terminus, which condenses the protein. A significant role for Met/Met interactions is consistent with previously-observed non-local effects of the Val66Met SNP, as well as established interactions between the Met66 sequence and a Met-rich receptor that initiates neuronal growth cone retraction.
Data from: Diabetes mellitus and the risk of fractures at specific sites: a meta-analysis
Objective: Diabetes mellitus (DM) is associated with an increased fracture risk; however, the impact of DM and subsequent fracture at different sites and the associations according to patient characteristics remain unknown. Design: Meta-analysis. Data Sources: The PubMed, EMBASE, and Cochrane Library databases were searched from inception to March 2018. Eligibility Criteria: We included prospective and retrospective cohort studies on the associations of DM and subsequent fracture risk at different sites. Data extraction and synthesis: Two authors independently extracted data and assessed the study quality. Relative risks (RRs) with 95% confidence intervals (CIs) were calculated using a random-effects model, and the heterogeneity across the included studies was evaluated using I2 and Q statistics. Results: Overall, DM was associated with an increased risk of total (RR: 1.32; 95% CI: 1.17–1.48; P<0.001), hip (RR: 1.77; 95% CI: 1.56–2.02; P<0.001), upper arm (RR: 1.47; 95% CI: 1.02–2.10; P=0.037), and ankle fractures (RR: 1.24; 95% CI: 1.10–1.40; P<0.001), whereas DM had no significant impact on the incidence of distal forearm (RR: 1.02; 95% CI: 0.88–1.19; P=0.809) and vertebral fractures (RR: 1.56; 95% CI: 0.78–3.12; P=0.209). RR ratios suggested that compared with type 2 DM (T2DM) patients, type 1 DM (T1DM) patients had greater risk of total (RR ratio: 1.24; 95% CI: 1.08–1.41; P=0.002), hip (RR ratio: 3.43; 95% CI: 2.27–5.17; P<0.001), and ankle fractures (RR ratio: 1.71; 95% CI: 1.06 –2.78; P=0.029). Although no other significant differences were observed between subgroups, the association of DM with upper arm or ankle, vertebrae, and total fracture differed according to sex, study design, and country, respectively. Conclusions: DM patients had greater risks of total, hip, upper arm, and ankle fractures, with T1DM having a more harmful effect than T2DM.
Data from: Finding flies in the mushroom soup: host specificity of fungus-associated communities revisited with a novel molecular method
Fruiting bodies of fungi constitute an important resource for thousands of other taxa. The structure of these diverse assemblages has traditionally been studied with labour-intensive methods involving cultivation and morphology-based species identification, to which molecular information might offer convenient complements. To overcome challenges in DNA extraction and PCR associated with the complex chemical properties fruiting bodies, we developed a pipeline applicable for extracting amplifiable total DNA from soft fungal samples of any size. Our protocol purifies DNA in two sequential steps: (1) initial salt-isopropanol extraction of all nucleic acids in the sample is followed by (2) an extra clean-up step using solid-phase reversible immobilization (SPRI) magnetic beads. The protocol proved highly efficient, with practically all of our samples — regardless of biomass or other properties — being successfully PCR amplified using metabarcoding primers and subsequently sequenced. As a proof-of-concept, we apply our methods to address a topical ecological question: is host specificity a major characteristic of fungus-associated communities, i.e., do different fungus species harbour different communities of associated organisms? Based on an analysis of 312 fungal fruiting bodies representing ten species in five genera from three orders, we show that molecular methods are suitable for studying this rich natural microcosm. Comparing to previous knowledge based on rearing and morphology-based identifications, we find a species-rich assemblage characterized by a low degree of host specialization. Our method opens up new horizons for molecular analyses of fungus-associated interaction webs and communities.
Data from: Sex-specific fitness consequences of nutrient intake and the evolvability of diet preferences
The acquisition of nutrients is fundamental for the maintenance of bodily functions, growth, and reproduction in animals. As a result, fitness can be maximized only when animals are able to direct their attention to foods that reflect their current nutritional needs. Despite significant literature documenting the fitness consequences of nutrient composition and preference, less is known about the underlying genetic architecture of the dietary preferences themselves, specifically, the degree to which they can respond to selection. We addressed this by integrating evolutionary quantitative genetics and nutritional geometry to examine the shape of the sex-specific fitness surfaces and the availability of genetic variance for macronutrient preferences in the fruit fly Drosophila melanogaster. Combining these analyses, we found that the microevolutionary potential of carbohydrate and protein preference was above average in this population, because the expected direction of selection was relatively well aligned with the major axis of the genetic variance-covariance matrix, G. We also found that potential exists for sexually antagonistic genetic constraint in this system; macronutrient blends maximizing fitness differed between the sexes, and cross-sex genetic correlations for their consumption were positive. However, both sexes were displaced from their feeding optima, generating similar directional selection on males and females, with the combined effect being that minimal sex-specific genetic constraints currently affect dietary preferences in this population.
Data from: Comparative genomics of chemosensory protein genes reveals rapid evolution and positive selection in ant-specific duplicates
Gene duplications can have a major role in adaptation, and gene families underlying chemosensation are particularly interesting due to their essential role in chemical recognition of mates, predators and food resources. Social insects add yet another dimension to the study of chemosensory genomics, as the key components of their social life rely on chemical communication. Still, chemosensory gene families are little studied in social insects. Here we annotated chemosensory protein (CSP) genes from seven ant genomes and studied their evolution. The number of functional CSP genes ranges from 11 to 21 depending on species, and the estimated rates of gene birth and death indicate high turnover of genes. Ant CSP genes include seven conservative orthologous groups present in all the ants, and a group of genes that has expanded independently in different ant lineages. Interestingly, the expanded group of genes has a differing mode of evolution from the orthologous groups. The expanded group shows rapid evolution as indicated by a high dN/dS (nonsynonymous to synonymous changes) ratio, several sites under positive selection and many pseudogenes, whereas the genes in the seven orthologous groups evolve slowly under purifying selection and include only one pseudogene. These results show that adaptive changes have played a role in ant CSP evolution. The expanded group of ant-specific genes is phylogenetically close to a conservative orthologous group CSP7, which includes genes known to be involved in ant nestmate recognition, raising an interesting possibility that the expanded CSPs function in ant chemical communication.
Data from: Wild dwarf mongooses produce general alert and predator-specific alarm calls
Many species produce alarm calls in response to predator threats. Whilst these can be general alert calls, some are urgency-based, indicating perceived threat level, some are predator-specific, indicating the predator type present, and some encode information about both urgency level and predator type. Predator-specific calls given to a narrow range of stimuli and which elicit a specific, adaptive, response from the receiver are termed functionally referential. Differing escape strategies, habitat structural complexity and sociality may favor the evolution of functionally referential calls. A study of one captive group of dwarf mongooses (Helogale parvula) suggested their alarm calls could transmit information about species, distance, and elevation of predators. Using recordings of natural predator encounters, predator presentations and audio playbacks, we investigated the alarm-call system in 7 wild dwarf mongoose groups. We recorded 11 different alarm-call types given to 9 stimulus categories. Of the 5 commonly emitted alarm-call types, 3 appeared to be non-specific and 2 predator-specific, given to aerial and terrestrial predators respectively. The remaining 6 call types were rarely produced. Furthermore, aerial alarms were given to a narrower range of stimuli than their terrestrial alarm calls, which were given to both visible terrestrial predators and secondary cues of predators. Unlike other mongoose species, dwarf mongoose seem to use the same alarm-call type for both physically present terrestrial predators and secondary cues of their presence. We argue that detailed knowledge of species' alarm-call systems under natural conditions can shed light on the evolutionary emergence of different types of alarm calls.
Data from: Herbivore-specific induction of defence metabolites in a grass-endophyte association
Plants have developed a variety of defence strategies against herbivores. One possible strategy is the induced production of metabolites following herbivore attack. Plant-associated micro-organisms can be the source of such defensive compounds. For example, cool-season grasses can be associated with systemic endophytic fungi of the genus Epichloё, which produce herbivore-toxic alkaloids. In a controlled common garden approach, we tested the hypothesis that different types of herbivory induce endophyte growth and increase the endophyte-mediated production of three bioactive alkaloids which can deter or toxify herbivores. During 18 weeks, we analysed biweekly endophyte and alkaloid concentrations in the grass Lolium perenne infected with the endophytic fungus Epichloё festucae var. lolii. The experiment was conducted throughout the field season and compared three different herbivore treatments to the control treatment (herbivory exclosure). We showed that the concentration of the vertebrate toxic alkaloid lolitrem B increased following clipping (a simulation of grazing herbivores), while the insect deterring alkaloid peramine increased following locust herbivory (biting–chewing herbivores). The endophyte concentration increased slightly following clipping (P = 0·09). Sap sucking aphids altered neither endophyte nor alkaloid concentrations. Our study provides evidence for an herbivore-specific induction of endophyte-mediated responses following herbivore attack on its host grass. Our results suggest that the grass–endophyte symbiosis involves a close chemical crosstalk between the interacting partners.
Data from: Genome-wide association study of a Varroa-specific defense behavior in honeybees (Apis mellifera)
Honey bees are exposed to many damaging pathogens and parasites. The most devastating is Varroa destructor, which mainly affects the brood. A promising approach for preventing its spread is to breed Varroa-resistant honey bees. One trait that has been shown to provide significant resistance against the Varroa mite is hygienic behavior, which is a behavioral response of honeybee workers to brood diseases in general. Here we report the use of an Affymetrix 44K SNP array to analyze SNPs associated with detection and uncapping of Varroa-parasitized brood by individual worker bees (Apis mellifera). For this study, 22,000 individually labeled bees were video-monitored and a sample of 122 cases and 122 controls was collected and analyzed to determine the dependence / independence of SNP genotypes from hygienic and non-hygienic behavior on a genome-wide scale. After false-discovery rate correction of the p-values, six SNP markers had highly significant associations with the trait investigated (alpha < 0.01). Inspection of the genomic regions around these SNPs led to the discovery of putative candidate genes.
Data from: Individual variation, population-specific behaviours, and stochastic processes shape marine migration phenologies
1. The phenology of long distance migrations can influence individual fitness, moderate population dynamics, and regulate the availability of ecosystem services to other trophic levels. Phenology varies within and among populations, and can be influenced by conditions individuals experience both prior to departure and encounter en route. 2. Assessing how intrinsic and extrinsic factors (e.g. individual physical condition vs. environmental conditions) interact to influence variation in migratory phenologies across ecological scales is often limited due to logistical constraints associated with tracking large numbers of individuals from multiple populations simultaneously. 3. We used two natural tags, DNA and otolith microstructure analysis, to estimate the relative influence of individual traits (life history strategy, body size at departure, and growth during migration), population-specific strategies, and interannual variability on the phenology of marine migrations in juvenile sockeye salmon Oncorhynchus nerka. 4. We show that the timing and duration of juvenile sockeye salmon migrations were correlated with both life history strategy and body size, while migration duration was also correlated with departure timing and growth rates during migration. Even after accounting for the effect of individual traits, several populations exhibited distinct migration phenologies. Finally, we observed substantial interannual and residual variation, suggesting stochastic environmental conditions moderate the influence of carry-over effects that develop prior to departure, as well as population-specific strategies. 5. Migratory phenologies are shaped by complex interactions between drivers acting at multiple ecological and temporal scales. Given evidence that intraspecific diversity can stabilize ecological systems, conservation efforts should seek to maintain migratory variation among populations and preserve locally adapted phenotypes; however, variation within populations, which may buffer systems from environmental stochasticity, should also be regularly assessed and preserved.
Data from: Sex-specific pace-of-life syndromes
The pace-of-life syndrome (POLS) hypothesis considers an animal's behavior, physiology, and life-history as non-independent components of a single integrated phenotype. However, frequent deviations from the expected correlations between POLS traits suggests that these relationships may be context, and potentially, sex-dependent. To determine whether the sexes express distinct POLS trait covariance structures, we observed the behavior (mobility, latency to emerge from a shelter), physiology (mass-specific metabolic rate) and life-history (lifespan, development time) of male and female Australian field crickets (Teleogryllus oceanicus). Path analysis modelling suggested that POLS trait covariation differed between the sexes. Although neither sex displayed the complete integration of traits predicted by the POLS hypothesis, females did display greater overall integration with a significant negative correlation between metabolic rate and risk-taking behavior but with life-history traits varying independently. In males, however, there was no clear association between traits. These results suggest that T. oceanicus do indeed display sex-specific trait covariance structures, emphasizing the importance of acknowledging sex in assessments of pace-of-life syndromes.
Data from: Sex-specific selection under environmental stress in seed beetles
Sexual selection can increase rates of adaptation by imposing stronger selection in males, thereby allowing efficient purging of the mutation load on population fitness at a low demographic cost. Indeed, sexual selection tends to be male-biased throughout the animal kingdom, but little empirical work has explored the ecological sensitivity of this sex difference. In this study, we generated theoretical predictions of sex-specific strengths of selection, environmental sensitivities and genotype-by-environment interactions, and tested them in seed beetles by manipulating either larval host plant or rearing temperature. Using fourteen isofemale lines, we measured sex-specific reductions in fitness components, genotype-by-environment interactions, and strength of selection (variance in fitness) in the juvenile and adult stage. As predicted, variance in fitness increased with stress, was consistently greater in males than females for adult reproductive success (implying strong sexual selection), but was similar in the sexes in terms of juvenile survival across all stress-levels. While genetic variance in fitness increased in magnitude under severe stress, heritability decreased, and particularly so in males. Moreover, genotype-by-environment interactions for fitness were common but specific to the type of stress and each sex and life stage, suggesting that new environments may change the relative alignment and strength of selection in males and females. Our study thus exemplifies how environmental stress can influence the relative forces of natural and sexual selection, as well as concomitant changes in genetic variance in fitness, which are predicted to have consequences for rates of adaptation in sexual populations.
Data from: From steps to home range formation: species-specific movement upscaling among sympatric ungulates
Animals move to interact with the environment in order to find food resources and cover. Intrinsic characteristics affecting feeding and antipredatory strategies likely shape variation in movement patterns and home range formation between individuals, populations and species. Browsing herbivores selectively forage on patchily distributed resources in areas with more canopy cover, whereas mixed feeders and grazers feed on more open grasslands and tend to aggregate as an antipredatory strategy. We therefore predicted that at small temporal scales, browsers will show greater net displacements (i.e. typical of searching patterns) than mixed feeders or grazers; but at larger temporal scales, we expect the opposite pattern, since gregarious species will need to use larger areas to feed the whole herd. We also predicted that the feeding/antipredatory strategy will determine the behavioural responses to other environmental factors. To test this, we compared spatial movement patterns at multiple scales (from 20-min intervals to annual home ranges) of three sympatric, similar-sized, alpine ungulates which differ in their feeding/antipredatory strategy: roe deer (solitary browsers), mouflon (gregarious grazers) and chamois (intermediate feeders in smaller groups). We used location data from GPS-collared females of the three species in the French Alps. As predicted, we found that multi-scale spatial patterns depended on the feeding/antipredatory strategy. Browsers foraged within smaller range areas, searching back and forth. Mixed feeders and, especially, grazers covered larger areas, presumably to satisfy herd needs. The feeding/antipredatory strategies also determined the interspecific variability in behavioural responses to factors such as maternal status, weather, habitat type or human disturbance, supporting our hypothesis. Exploring interspecific variability, we showed how movement behaviour and home range formation vary substantially, even among species within the same guild. This mechanism might be important to maintain intra-guild multi-species associations and increase biodiversity, through contributing to niche segregation and, thus, coexistence.
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.