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3,118 results for “resources”
The effects of resource subsidy duration in a detritus-based stream ecosystem: a mesocosm experiment
<p>1. Most resource subsidies are temporally variable, dynamically affecting the consumer populations, community structures, and ecosystem functions of recipient ecosystems. Temporally variable resource subsidies are characterized by the duration, magnitude, timing, and frequency of resource subsidy inputs. These different characteristics may have different mechanisms by which to affect recipient ecosystems.</p> <p>2. Few studies have examined the duration of resource subsidy inputs on recipient ecosystems, although there exist previous studies focusing on magnitude, timing, and frequency.</p> <p>3. We provide the first experimental test of the effects of subsidy duration on a stream ecosystem by using an outdoor mesocosm experiment, in which we directly manipulated the subsidy duration (pulsed vs. prolonged) of terrestrial invertebrate input into the mesocosm.</p> <p>4. Given the same overall amount of terrestrial invertebrate subsidy were added, a prolonged subsidy allowed large-stage fish to effectively monopolize the subsidy over small-stage fish, which led small-stage fish to maintain their predation pressure on in-situ prey, i.e., benthic invertebrates. On the other hand, a pulsed subsidy allowed small-stage fish to increase their feeding rate of the subsidy and to become away from foraging in-situ prey. Consequently, weaker indirect positive effects on in-situ benthic prey and leaf breakdown rate were found with the prolonged versus pulsed subsidy. However, these indirect effects varied by the dominant benthic prey species, which differed in edibility for fish. Such predator-specific vulnerability of benthic prey can be important in mediating trophic cascades in detritus-based stream food webs.</p> <p>5. Phenological events that generate temporal subsidies (e.g., salmon spawning run and arthropod emergence) can be synchronized (pulsed) or desynchronized (prolonged) within and among species, depending on the degree of spatial and temporal environmental heterogeneity. The effects of subsidy duration would thus be important to better understand ecological processes in spatially and temporally coupled ecosystems.</p>
Contribution of males to brood care can compensate for their food consumption from a shared resource
<p>The sharing of the same food source among parents and offspring can be a driver of the evolution of family life and parental care. However, if all family members desire the same meal, competitive situations can arise, especially if resource depletion is likely. When food is shared for reproduction and the raising of offspring, parents have to decide whether they should invest in self-maintenance or in their offspring and it is not entirely clear how these two strategies are balanced. In the burying beetle <i>Nicrophorus vespilloides</i>, parents care for their offspring either bi- or uniparentally at a vertebrate carcass as the sole food source. The question of whether biparental care in this species offers the offspring a better environment for development compared with uniparental care has been the subject of some debate. We tested the hypothesis that male contribution to biparental brood care has a beneficial effect on offspring fitness but that this effect can be masked because the male also feeds from the shared resource. We show that a mouse carcass prepared by two <i>Nicrophorus</i> beetles is lighter compared with a carcass prepared by a single female beetle at the start of larval hatching and provisioning. This difference in carcass mass can influence offspring fitness when food availability is limited, supporting our hypothesis. Our results provide new insights into the possible evolutionary pathway of biparental care in this species of burying beetles.</p>
Data from: A resource on latitudinal and altitudinal clines of ecologically relevant phenotypes of the Indian Drosophila
The unique geography of the Indian subcontinent has provided diverse natural environments for a variety of organisms. In this region, many ecological indices such as temperature and humidity vary predictably as a function of both latitude and altitude; these environmental parameters significantly affect fundamental dynamics of natural populations. Indian drosophilids are diverse in their geographic distribution and climate tolerance, possibly as a result of climatic adaptation. These associations with environmental parameters are further reflected in a large number of clines that have been reported for various fitness traits along these geographical ranges. This unique amalgamation of environmental variability and genetic diversity make the subcontinent an ecological laboratory for studying evolution in action. We assembled data collected over the last 20 years on the geographical clines for various phenotypic traits in several species of drosophilids and present a web-resource on Indian-Drosophila ( http://www.indian-drosophila.org/). The clinal data on ecologically relevant phenotypes of Indian drosophilids will be useful in addressing questions related to future challenges in biodiversity and ecosystems in this region.
Data from: A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans
Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic–Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.
Data from: "Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
This paper reports on SNP discovery in the Atlantic mackerel transcriptome, using next generation sequencing technologies and applying developed methodology already proven successful for the European anchovy. A total of 9,966 high quality transcriptome contigs were assembled, from which 951 putative SNPs were discovered. In all, 479 putative SNPs and 1,624 simple sequence repeats (SSRs) suitable for genotyping were identified. A subset of 96 was selected for genotyping; from these, 80 SNPs were considered polymorphic and reliably scored after genotyping of 105 individuals from three locations in the Eastern Atlantic Ocean. These markers will be valuable for future studies on population genetic structure assessment and for product tracing.
Data from: Environmental conditions alter successional trajectories on an ephemeral resource: a field experiment with beetles in dead wood
<p>Successional processes can be observed for many organisms and resources, but most studies of succession have focused on plants. A general framework has been proposed, advocating that successional patterns in species turnover are predominantly driven by competition, dispersal or abiotic limitation, and that the patterning of species accumulation over time gives clues to which process is most influential in a given system. We applied this framework to succession in communities of wood-living beetles, utilizing ephemeral resources in the form of 60 experimentally created dead aspen high stumps. High stumps were created at sun-exposed sites (high ambient temperature; favorable abiotic conditions) and shaded sites (low ambient temperature; abiotically limiting conditions). The sites were intermixed, ensuring similar dispersal opportunities. Beetle species richness and abundance were monitored with flight interception traps over four consecutive years. Consistent with predictions from the tested framework, several beetle functional groups accumulated species more slowly at the unfavorable shaded sites than at the favorable exposed sites. Species richness at the exposed sites increased rapidly to a plateau, consistent with a limiting effect of competition on community development. Similar results were obtained for beetle abundance and community structure. Part of the variance in beetle community structure was jointly explained by habitat and fungal community composition, suggesting that differences in the composition and developmental rate of fungal communities in the two habitats contributed to the observed patterns. Targeted experimental studies are now required to decisively establish what processes underlie the contrasting successional trajectories in the two environments.</p>
Data from: Developmental constraints and resource environment shape early emergence and investment in spines in saplings
Abstract <p> Background and Aims </p><p>Herbivory by large mammals imposes a critical recruitment bottleneck on plants in many systems. Spines defend plants against large herbivores and how early they emerge in saplings may be one of the strongest predictors of sapling survival in herbivore-rich environments. Yet little effort has been directed at understanding the variability in spine emergence across saplings.</p> Methods <p>We present a multi-species study examining whether and how sapling size,spine type and species' environmental niche (light and precipitation environment) influence early emergence and biomass investment in spines. A phylogenetically diverse pool of 45 species possessing different spine types (spines, prickles and thorns; that are derived from distinct plant organs: leaf, epidermis or cortex, and branch, respectively), were grown under common garden conditions, and patterns of spine emergence and biomass allocation to spines at 5 and 15 weeks after transplanting were characterized.</p> Key Results <p>Spine type and species' resource niche were the main factors driving early emergence and investment patterns. Spines emerged earliest in leaf spine-bearing species, and latest in thorn-bearing species. The probability of early spine emergence increased with decreasing precipitation, and was greater in species from open than closed habitats. Sapling investment in spines changed with plant mass but was contingent on spine type and habitat type.</p> Conclusions <p>Different spine types have strikingly different timing of expression, suggesting that developmental origins of spines play a critical role in sapling defences. Furthermore, species from different precipitation and light environments (open vs. closed habitats) showed contrasting patterns of early spine expression suggesting that resource limitation in their native range may have driven divergent evolution of early defence expression.</p> <p></p>
Data from: Diet variability among insular populations of Podarcis lizards reveals diverse strategies to face resource-limited environments
Access to resources is a dynamic and multi-causal process that determines the success and survival of a population. It is therefore often challenging to disentangle the factors affecting ecological traits like diet. Insular habitats provide a good opportunity to study how variation in diet originates, in particular in populations of mesopredators such as lizards. Indeed, high levels of population density associated with low food abundance and low predation are selection pressures typically observed on islands. In the present study, the diet of eighteen insular populations of two closely related species of lacertid lizards (Podarcis sicula and Podarcis melisellensis) was assessed. Our results reveal that despite dietary variability among populations, diet taxonomic diversity is not impacted by island area. In contrast, however, diet disparity metrics, based on the variability in the physical (hardness) and behavioral (evasiveness) properties of ingested food items, are correlated with island size. These findings suggest that an increase in intraspecific competition for access to resources may induce shifts in functional components of the diet. Additionally, the two species differed in the relation between diet disparity and island area suggesting that different strategies exist to deal with low food abundance in these two species. Finally, sexual dimorphism in diet and head dimensions is not greater on smaller islands, in contrast to our predictions.
Data from: Selfish partners: resource partitioning in male coalitions of Asiatic lions
Behavioral plasticity within species is adaptive which directs survival traits to take multiple pathways under varying conditions. Male-male cooperation is an evolutionary strategy often exhibiting an array of alternatives between and within species. African male lions coalesce to safeguard territories and mate-acquisition. Unique to these coalitions is lack of strict hierarchies between partners, who have similar resource-securities possibly because of many mating-opportunities within large female-groups. Skewed mating and feeding rights have only been documented in large coalitions where males were related. However, smaller modal prey coupled with less simultaneous mating-opportunities for male Asiatic lions in Gir forests, India would likely result in a different coalition-structure. Observations on mating-events (n=127) and feeding-incidents (n=44) were made on 11 male-coalitions and 9 female-prides in Gir, to assess resource distribution within- and among- different sized male-coalitions. Information from 39 males were used to estimate annual tenure-holding probabilities. Single-males had smaller tenures and appropriated fewer matings than coalition-males. Pronounced dominance-hierarchies were observed within coalitions, with one partner getting >70% of all matings and 47% more food. Competition between coalition-partners at kills increased with decline in prey-size, increase in coalition-size and the appetite-states of the males. However, immediate subordinates in coalitions had higher reproductive fitness than single-males. Declining benefits to partners with increasing coalition-size, with individuals below the immediate subordinates having fitness comparable to single-males, suggest to an optimal coalition-size of two lions. Lions under higher competitive selection in Gir show behavioral plasticity to form hierarchical-coalitions, wherein partners utilize resources asymmetrically, yet coalesce for personal gains.
Data from: Contrasting per-gram competitive and soil resource effects in grasses and woody plants
1. Plant species differ in their competitive effects by decreasing resource availability via uptake, but in some cases may increase resource availability via non-uptake pathways. Here we explore differences between grasses and woody plants in their competitive effects, and relate these to differences in resource effects. 2. We grew five species each of grasses and woody plants in monocultures for eight years. In the final two growing seasons, competitive effects were measured by growing transplants in all monocultures and in plots without neighbours. 3. Total competitive effects were significantly greater for woody plants than grasses. In contrast, the competitive effect per gram of grasses was about 17 times greater than that of woody plants. 4. For grasses, soil water and soil available N decreased significantly with increasing biomass. In contrast, for woody plants, soil water and soil available N increased significantly with increasing biomass. The results suggest that the intense per-gram competitive effects in grasses is related to the uptake of soil resources, and that the significantly lower per-gram competitive effects of woody plants may be related to their positive effects on soil resources. 5. Synthesis. The results link differences in competitive effects between grasses and woody plants to differences in the direction of their effects on soil resources. These differences may contribute to the entrainment of negative feedback in grasslands, excluding trees by means of strong competition, and the entrainment of positive feedback beneath woody plants establishing in grasslands, resulting in a state change from grassland to woody vegetation.
Dryness, wetness and temporary flooding reduce floral resources of plant communities with adverse consequences for pollinator attraction
1. Climate change alters precipitation regimes worldwide and is regarded as a major threat for pollinators and pollination services. Yet, not much is known on how wetter as well as drier conditions affect food resources for pollinators and pollinator attraction in a multi-species community context. It is unclear how community shifts under changed hydrological conditions might affect pollinators. 2. This mesocosm study addresses existing research gaps by investigating effects of drought, wetness and temporary flooding on floral resources and pollinator attraction within a plant community, initially including nine insect- and six wind-pollinated species. Floral resources were assessed over three growing seasons monitoring community descriptors (percentage of herbs and herbaceous species richness, presence of flowering insect-pollinated individuals), floral traits (flower height, size and weight, floral sugar content of one key species) and proxies for plant fitness (pollinator attraction, seed and flower weight of one key species). 3. Wetness and especially dryness decreased the species richness and biomass proportion of insect-pollinated herbaceous species and flowering herbaceous plant individuals occurred less frequently. Permanent wetness decreased the floral sugar content of the key species Trifolium pratense. Consequently, wet, temporary flooded and especially dry communities were visited by pollinators less often, and active pollinators spent less time within wet and flooded communities, while not at all visiting dry communities. Seed and flower weight of the obligate xenogamous T. pratense in flooded and dry communities was decreased, indicating negative consequences for plant fitness caused by a lack of pollination. 4. Synthesis: While dryness had negative effects for floral resources when looking at both, community descriptors and floral traits, negative effects of wetness and temporary flooding were mostly caused by a decrease of insect-pollinated herbaceous species. The study thus indicates that shifts in plant community composition are decisive for a predictive understanding of plant-pollinator interactions under environmental change, but have been neglected in past research. Changing precipitation patterns will adversely affect floral resources and pollinator attraction in agriculturally used temperate grassland, which might have widespread negative consequences for pollination services and food security in coming decades.
Dissecting the genetic basis of variation in Drosophila sleep using a multiparental QTL mapping resource
There is considerable variation in sleep duration, timing and quality in human populations, and sleep dysregulation has been implicated as a risk factor for a range of health problems. Human sleep traits are known to be regulated by genetic factors, but also by an array of environmental and social factors. These uncontrolled, non-genetic effects complicate powerful identification of the loci contributing to sleep directly in humans. The model system, Drosophila melanogaster, exhibits a behavior that shows the hallmarks of mammalian sleep, and here we use a multitiered approach, encompassing high-resolution QTL mapping, expression QTL data, and functional validation with RNAi to investigate the genetic basis of sleep under highly controlled environmental conditions. We measured a battery of sleep phenotypes in >750 genotypes derived from a multiparental mapping panel and identified several, modest-effect QTL contributing to natural variation for sleep. Merging sleep QTL data with a large head transcriptome eQTL mapping dataset from the same population allowed us to refine the list of plausible candidate causative sleep loci. This set includes genes with previously characterized effects on sleep and circadian rhythms, in addition to novel candidates. Finally, we employed adult, nervous system-specific RNAi on the Dopa decarboxylase, dyschronic, and timeless genes, finding significant effects on sleep phenotypes for all three. The genes we resolve are strong candidates to harbor causative, regulatory variation contributing to sleep.
Data from: Isotopic niches support the resource breadth hypothesis
Because a broad spectrum of resource use allows species to persist in a wide range of habitat types, and thus permits them to occupy large geographical areas, and because broadly distributed species have access to more diverse resource bases, the resource breadth hypothesis posits that the diversity of resources used by organisms should be positively related with the extent of their geographic ranges. We investigated isotopic niche width in a small radiation of South American birds in the genus Cinclodes. We analysed feathers of 12 species of Cinclodes to test the isotopic version of the resource breadth hypothesis and to examine the correlation between isotopic niche breadth and morphology. We found a positive correlation between the widths of hydrogen and oxygen isotopic niches (which estimate breadth of elevational range) and widths of the carbon and nitrogen isotopic niches (which estimates the diversity of resources consumed, and hence of habitats used). We also found a positive correlation between broad isotopic niches and wing morphology. Our study not only supports the resource breadth hypothesis but it also highlights the usefulness of stable isotope analyses as tools in the exploration of ecological niches. It is an example of a macroecological application of stable isotopes. It also illustrates the importance of scientific collections in ecological studies.
Competition for resources can promote the divergence of social learning phenotypes
<p>Social learning occurs when animals acquire knowledge or skills by observing or interacting with others, and is the fundamental building block of culture. Within populations, some individuals use social learning more frequently than others, but why social learning phenotypes differ among individuals is poorly understood. We modelled the evolution of social learning frequency in a system where foragers compete for resources and there are many different foraging options to learn about. Social learning phenotypes diverged when some options offered much better rewards than others and expected rewards changed moderately quickly over time. When options offered similar rewards or when rewards changed slowly, a single social learning phenotype evolved. This held for fixed and simple conditional social learning rules. Sufficiently complex conditional social learning rules prevented the divergence of social learning phenotypes under all conditions. Our results explain how competition can promote the divergence of social learning phenotypes.</p>
Data from: Contrasting leaf trait responses of conifer and broadleaved seedlings to altered resource availability are linked to resource strategies
<p>(1) Understanding tree seedling responses to water, nutrient and light availability is crucial to precisely predict potential shifts in composition and structure of forest communities under future climatic conditions.</p> <p>(2) We exposed seedlings of widespread central European tree species with contrasting leaf habit, deciduous broadleaves (DB) and evergreen conifers (EC), to factorial combinations of manipulated precipitation (100% and 50% of ambient), shade (40% and 60% of full sunlight) and nutrient availability (low and high NPK), and measured specific leaf area, C/N ratio, soluble sugars, starch and non-structural carbohydrate concentration, and δ<sup>13</sup>C of the leaves.</p> <p>(3) We found contrasting effects of water and nutrient availability on foliar traits of the two species groups: EC exhibited higher tolerance to low resource availability but also less plasticity in foliar traits, which is congruent with a "slow" resource strategy. In contrast, foliage of DB reacted particularly to altered nutrient availability, corresponding to a "fast" resource strategy with high foliar plasticity and rapid adjustments to resource fluctuations, commonly adopted by species with high growth rates.</p> <p>(4) We conclude that DB will respond to environmental change with foliar acclimation, while EC will either tolerate, to some extent, or shift their distribution range in response to environmental change.</p>
Data from: Dietary resource overlap among three species of frugivorous bat in Costa Rica
The maintenance of biodiversity in tropical forests is thought to be dependent on fine-scale mechanisms of niche partitioning that allow species to coexist. This study examined whether three species of short-tailed fruit bat that co-occur at a lowland tropical forest site in Costa Rica (Carollia castanea, C. perspicillata, C. sowelli) avoid inter- and intraspecific competition through dietary specialization on species in the genus Piper. First, dietary composition was examined using faecal samples (n = 210), which yielded three main findings: (1) bat species and sexes vary in overall reliance on fruits of Piper, with a higher percentage of seeds of Piper detected in the diets of C. castanea (98.2%) and females (91.5%); (2) adults and juveniles partition species of Piper by habitat, with a lower percentage of mid- to late-successional species of Piper detected in adults (20.8%); and (3) overall, there is a strong dietary overlap among and within the three species of Carollia. Second, controlled choice experiments were conducted with individual bats (n = 123) to examine preferences for different species of Piper. These results indicated few differences in Piper preference based on bat species, sex, age class or reproductive status, suggesting preference is not the primary mechanism shaping the observed differences in dietary composition. Overall, the dietary composition and preference similarities suggest there is strong competition both among and within the three species of Carollia for food resources.
Data from: Context-dependent defences in turtle ants: resource defensibility and threat level induce dynamic shifts in soldier deployment
1. Induced defences involve the dynamic deployment of limited and specialized defensive resources across multiple locations, to maximize organismal defensive function and fitness. They have been studied intensively in plants and solitary animals, but the induced defences of complex animal societies are poorly understood by comparison, despite the coordinated defensive actions of these taxa. 2. Here, we ask whether the level of environmental danger induces shifts in the deployment of limited and morphologically specialized soldiers across multiple nests in colonies of the turtle ant Cephalotes rohweri. Specifically, we test whether less defensible nests induce greater soldier deployment, and whether elevated enemy threat induced further increases in deployment, or reduced deployment consistent with a risk-limiting strategy. 3. We used colony-collection data to provide natural ecological context to our experiments, a field experiment to address how nest-entrance defensibility and soldier number impact defensive performance, and laboratory experiments to test whether differences in nest defensibility and threat level induce dynamic shifts in soldier deployment to new nests. 4. Less defensible nests were lost rapidly in our field experiment, irrespective of soldier number, but soldier deployment significantly increased survivorship of more defensible nests. Concordantly, less defensible nests induced the deployment of more soldiers per nest under low threat in laboratory experiments. Nevertheless, high-threat conditions revealed a risk-limiting soldier deployment strategy: with more danger, the number of soldiers per nest was significantly reduced in less defensible nests, as was the overall number of new soldier-defended nests. Total deployment to new nests was also consistently lower under high threat, dropping from 40% to 30% across colonies. 5. Induced soldier-based defences in turtle ants are therefore context-dependent, and dynamically scaled back at multiple levels when the environment is more dangerous. This dynamic, risk-limiting strategy is in strong contrast to stable patterns of soldier production in ants, and to typical task-allocation dynamics in members of the worker caste. Moreover, these findings establish that the evolution of specialized defensive agents can be coupled with sophisticated and inducible deployment strategies in complex social taxa, as we see for organisms at other levels of biological complexity.
Data from: The demography of a resource specialist in the tropics: Cecropia trees and the fitness of three-toed sloths
Resource specialists persist on a narrow range of resources. Consequently, the abundance of key resources should drive vital rates, individual fitness and population viability. While Neotropical forests feature both high levels of biodiversity and numbers of specialist species, no studies have directly evaluated how the variation of key resources affects the fitness of a tropical specialist. Here, we quantified the effect of key tree species density and forest cover on the fitness of three-toed sloths (Bradypus variegatus), an arboreal folivore strongly associated with Cecropia trees, in Costa Rica using a multi-year demographic, genetic and space use dataset. We found that the density of Cecropia trees was strongly and positively related to both adult survival and reproductive output. A matrix model parameterized with Cecropia-demography relationships suggested positive growth of sloth populations, even at low densities of Cecropia (0.7 trees/ha). Our study shows the first direct link between the density of a key resource to demographic consequences of a tropical specialist, underscoring the sensitivity of tropical specialists to the loss of a single key resource, but also point to targeted conservation measures to increase that resource. Finally, our study reveals that previously disturbed and regenerating environments can support viable populations of tropical specialists.
Data from: The greenscape shapes surfing of resource waves in a large migratory herbivore
The Green Wave Hypothesis posits that herbivore migration manifests in response to waves of spring green-up (i.e. green-wave surfing). Nonetheless, empirical support for the Green Wave Hypothesis is mixed, and a framework for understanding variation in surfing is lacking. In a population of migratory mule deer (Odocoileus hemionus), 31% surfed plant phenology in spring as well as a theoretically perfect surfer, and 98% surfed better than random. Green-wave surfing varied among individuals and was unrelated to age or energetic state. Instead, the greenscape, which we define as the order, rate and duration of green-up along migratory routes, was the primary factor influencing surfing. Our results indicate that migratory routes are more than a link between seasonal ranges, and they provide an important, but often overlooked, foraging habitat. In addition, the spatiotemporal configuration of forage resources that propagate along migratory routes shape animal movement and presumably, energy gains during migration.
Data from: An R package and online resource for macroevolutionary studies using the ray-finned fish tree of life
1. Comprehensive, time-scaled phylogenies provide a critical resource for many questions in ecology, evolution, and biodiversity. Methodological advances have increased the breadth of taxonomic coverage in phylogenetic data; however, accessing and reusing these data remain challenging. 2. We introduce the Fish Tree of Life website and associated R package fishtree to provide convenient access to sequences, phylogenies, fossil calibrations, and diversification rate estimates for the most diverse group of vertebrate organisms, the ray-finned fishes. The Fish Tree of Life website presents subsets and visual summaries of phylogenetic and comparative data, and is complemented by the R package, which provides flexible programmatic access to the same underlying data source for advanced users wishing to extend or reanalyze the data. 3. We demonstrate functionality with an overview of the website, and show three examples of advanced usage through the R package. First, we test for the presence of long branch attraction artifacts across the fish tree of life. The second example examines the effects of habitat on diversification rate in the pufferfishes. The final example demonstrates how a community phylogenetic analysis could be conducted with the package. 4. This resource makes a large comparative vertebrate dataset easily accessible via the website, while the R package enables the rapid reuse and reproducibility of research results via its ability to easily integrate with other R packages and software for molecular biology and comparative methods.
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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.