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Data from: The nutritional balancing act of a large herbivore: an experiment with captive moose (Alces alces L)
The nutrient balancing hypothesis proposes that, when sufficient food is available, the primary goal of animal diet selection is to obtain a nutritionally balanced diet. This hypothesis can be tested using the Geometric Framework for nutrition (GF). The GF enables researchers to study patterns of nutrient intake (e.g. macronutrients; protein, carbohydrates, fat), interactions between the different nutrients, and how an animal resolves the potential conflict between over-eating one or more nutrients and under-eating others during periods of dietary imbalance. Using the moose (Alces alces L.), a model species in the development of herbivore foraging theory, we conducted a feeding experiment guided by the GF, combining continuous observations of six captive moose with analysis of the macronutritional composition of foods. We identified the moose's self-selected macronutrient target by allowing them to compose a diet by mixing two nutritionally complementary pellet types plus limited access to Salix browse. Such periods of free choice were intermixed with periods when they were restricted to one of the two pellet types plus Salix browse. Our observations of food intake by moose given free choice lend support to the nutrient balancing hypothesis, as the moose combined the foods in specific proportions that provided a particular ratio and amount of macronutrients. When restricted to either of two diets comprising a single pellet type, the moose i) maintained a relatively stable intake of non-protein energy while allowing protein intakes to vary with food composition, and ii) increased their intake of the food item that most closely resembled the self-selected macronutrient intake from the free choice periods, namely Salix browse. We place our results in the context of the nutritional strategy of the moose, ruminant physiology and the categorization of food quality.
Data from: Herbivores alter plant-wind interactions by acting as a point mass on leaves and by removing leaf tissue
In nature, plants regularly interact with herbivores and with wind. Herbivores can wound and alter the structure of plants, whereas wind can exert aerodynamic forces that cause the plants to flutter or sway. While herbivory has many negative consequences for plants, fluttering in wind can be beneficial for plants by facilitating gas exchange and loss of excess heat. Little is known about how herbivores affect plant motion in wind. We tested how the mass of an herbivore resting on a broad leaf of the tulip tree Liriodendron tulipifera, and the damage caused by herbivores, affected the motion of the leaf in wind. For this, we placed mimics of herbivores on the leaves, varying each herbivore's mass or position, and used high-speed video to measure how the herbivore mimics affected leaf movement and reconfiguration at two wind speeds inside a laboratory wind tunnel. In a similar setup, we tested how naturally occurring herbivore damage on the leaves affected leaf movement and reconfiguration. We found that the mass of an herbivore resting on a leaf can change that leaf's orientation relative to the wind and interfere with the ability of the leaf to reconfigure into a smaller, more streamlined shape. A large herbivore load slowed the leaf's fluttering frequency, while naturally occurring damage from herbivores increased the leaf's fluttering frequency. We conclude that herbivores can alter the physical interactions between wind and plants by two methods: (1) acting as a point mass on the plant while it is feeding and (2) removing tissue from the plant. Altering a plant's interaction with wind can have physical and physiological consequences for the plant. Thus, future studies of plants in nature should consider the effect of herbivory on plant–wind interactions, and vice versa.
Data from: Taxa, petitioning agency, and lawsuits affect time spent awaiting listing under the US Endangered Species Act
The United States' Endangered Species Act (ESA) is the world's foremost law for protecting species at risk of extinction; however, species must first be listed as threatened or endangered before receiving protection under the Act. We used an information theoretic approach to assess whether listing budget, policy phase (which was correlated with presidential administration), or both factors were associated with the number of species listed annually between 1983 and 2014. Annual listing rates were positively affected by larger listing budgets; policy phase also had a significant impact on annual listing rates after accounting for the effects of budget. However, the listing process for any one species spans multiple years, thus we also evaluated how taxonomic affiliation, the initiating organization, and lawsuits affected the amount of time 1338 listed species spent in review between 1973 and 2014. Species waited a median of 12.1 years to receive protection, with plants and invertebrates experiencing longer wait times than vertebrates. These process times exceed ESA deadlines, which are two years when initiated from a third party; this may perpetuate population declines and hinder recovery efforts. We observed that at the time of a lawsuit filling for either a proposed or final rule, species had waited, respectively, 4.19 and 0.70 years longer than species for which no lawsuits were filed, indicating lawsuits targeted species that experienced longer delays. We discuss how changes in ESA implementation over time interacted to produce high variability and often long wait times in the listing process. Our results indicated a positive role for both citizen petitions and budget increases to advance the listing process, thus hastening biodiversity protection.
Data from: Discovery and information-theoretic characterization of transcription factor binding sites that act cooperatively
Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein–DNA interactions at the sequence level is through position weight matrices (PWMs) that estimate the joint probability of a DNA binding site sequence by assuming positional independence within the DNA sequence. Here we construct conditional PWMs that depend on the motif signatures in the flanking DNA sequence, by conditioning known binding site loci on the presence or absence of additional binding sites in the flanking sequence of each siteʼs locus. Pooling known sites with similar flanking sequence patterns allows for the estimation of the conditional distribution function over the binding site sequences. We apply our model to the Dorsal transcription factor binding sites active in patterning the Dorsal–Ventral axis of Drosophila development. We find that those binding sites that cooperate with nearby Twist sites on average contain about 0.5 bits of information about the presence of Twist transcription factor binding sites in the flanking sequence. We also find that Dorsal binding site detectors conditioned on flanking sequence information make better predictions about what is a Dorsal site relative to background DNA than detection without information about flanking sequence features.
Data from: Improving rational use of ACTs through diagnosis-dependent subsidies: evidence from a cluster-randomized controlled trial in western Kenya
Background: More than half of artemisinin combination therapies (ACTs) consumed globally are dispensed in the retail sector where diagnostic testing is uncommon, leading to overconsumption and poor targeting. In many malaria-endemic countries, ACTs sold over-the-counter are available at heavily subsidized prices, further contributing to their misuse. Inappropriate use of ACTs can have serious implications for the spread of drug resistance and leads to poor outcomes for non-malaria patients treated with incorrect drugs. We evaluated the public health impact of an innovative strategy that targets ACT subsidies to confirmed malaria cases by coupling free diagnostic testing with a diagnosis-dependent ACT subsidy. Methods and Findings: We conducted a cluster-randomized controlled trial in 32 community clusters in western Kenya (population ~160,000). Eligible clusters had retail outlets selling ACTs and existing community health worker (CHW) programs and were randomly assigned 1:1 to control and intervention arms. In intervention areas, CHWs were available in their villages to perform malaria rapid diagnostic tests on demand for any individual >1 year of age experiencing a malaria-like illness. Malaria RDT positive individuals received a voucher for a discount on a quality-assured ACT, redeemable at a participating retail medicine outlet. In control areas, CHWs offered a standard package of health education, prevention and referral services. We conducted four population-based surveys, at baseline, 6 months, 12 months and 18 months, of a random sample of households with fever in the last 4 weeks to evaluate predefined, individual-level outcomes. The primary outcome was uptake of malaria diagnostic testing at 12 months. The main secondary outcome was rational ACT use, defined as the proportion of ACTs used by test-positive individuals. Analyses followed the intention-to-treat principle using generalized estimating equations to account for clustering with pre-specified adjustment for gender, age, education and wealth. All descriptive statistics and regressions were weighted to account for sampling design. Between July 2015 and May 2017, 32,404 participants were tested for malaria and 10,870 vouchers were issued. 7416 randomly-selected participants with recent fever from all 32 clusters were surveyed. The majority of recent fevers were in children under 18 years (62.9%, n=4653). The gender of enrolled participants was balanced in children (50.0%, n=2318 v 50.2%, n=2335), but more adult women were enrolled than men (78.0%, n=2139 v 22.0%, n=604). At baseline, 67.6% (n=1362) of participants took an ACT for their illness and 40.3% (n=810) of all participants took an ACT purchased from a retail outlet. At 12 months, 50.5% (n=454) in the intervention arm and 43.4% (n=389) in the control arm had a malaria diagnostic test for their recent fever (Adjusted Risk Difference=9 percentage points [pp], 95%CI: 2-15pp, p=0.015; Adjusted Risk Ratio=1.20, 95%CI:1.05-1.38, p=0.015). By 18-months, the ARR had increased to 1.25 (95%CI:1.09-1.44, p=0.005). Rational use of ACTs in the intervention area increased from 41.7% (n=279) at baseline to 59.6% (n=403) and was 40% higher in the intervention arm at 18 months (Adj RR 1.40, 95%CI: 1.19-1.64). While intervention effects increased between 12 and 18 months, we were not able to estimate longer-term impact of the intervention and could not independently evaluate the effects of the free testing and the voucher on uptake of testing. Conclusions: Diagnosis-dependent ACT subsidies and community-based interventions that include the private sector can have an important impact on diagnostic testing and population-wide rational use of ACTs. Targeting of the ACT subsidy itself to those with a positive malaria diagnostic test may also improve sustainability and reduce the cost of retail sector ACT subsidies.
Data from: Do secondary forests act as refuges for old growth forest animals? Recovery of ant diversity in the Atlantic forest of Brazil
The extent to which secondary forests occupying degraded and abandoned lands provide suitable habitat for forest-adapted species is an important conservation issue in times of vanishing old growth forests. We used ants (Hymenoptera: Formicidae), a functionally important and diverse group of invertebrates, to investigate the recovery of soil taxa during secondary forest succession in the Atlantic Forest of Southern Brazil. We compared the resilience of epigeic vs. hypogeic ant assemblages. For this purpose we established 27 sites that encompassed a chronosequence from pastures to old growth forests on two contrasting soil types. Our results are based on a collection of 35 508 individuals in 40 genera. Richness and composition of ant assemblages in secondary forests have recovered slowly and have not approached conditions typical of old growth forests. The distribution of genera along the successional stages was arranged in a nested pattern where ant genera of younger successional stages were a subset of genera present in older stages. Edaphic conditions had no influence on the recovery process. Overall, richness of ants was lower at study sites with water-logged soils than at sites where soils did not exhibit hydromorphic properties. The hypogeic ant assemblage recovered more slowly than the epigeic assemblage. Our results show that secondary forests do not act as refuges for many forest-adapted animals which are currently restricted to discontinuous patches of old growth forest in the highly endangered Atlantic Forest of Brazil. Moreover, estimated recovery times of 50 to several hundred years suggest it would take much longer than previously presumed for complete recolonization.
Data from: Do an ecosystem engineer and environmental gradient act independently or in concert to shape juvenile plant communities? Tests with the leaf-cutter ant Atta laevigata in a Neotropical savanna
Background. Ecosystem Engineers are species that transform habitats in ways that influence other species. While the impacts of many engineers have been well described, our understanding of how their impact varies along environmental gradients remains limited. Although disentangling the effects of gradients and engineers on biodiversity is complicated – the gradients themselves can be altered by engineers – doing so is necessary to advance conceptual and mathematical models of ecosystem engineering. We used leaf-cutter ants (Atta spp.) to investigate the relative influence of gradients and environmental engineers on the abundance and species richness of woody plants. Methods. We conducted our research in South America's Cerrado. With a survey of plant recruits along a canopy cover gradient, and data on environmental conditions that influence plant recruitment, we fit statistical models that addressed the following questions: (1) Does A. laevigata modify the gradient in canopy cover found in our Cerrado site? (2) Do environmental conditions that influence woody plant establishment in the Cerrado vary with canopy cover or proximity to A. laevigata nests? (3) Do A. laevigata and canopy cover act independently or in concert to influence recruit abundance and species richness? Results. We found that environmental conditions previously shown to influence plant establishment in the Cerrado varied in concert with canopy cover, but that ants are not modifying the cover gradient or cover over nests. However, ants are modifying other local environmental conditions, and the magnitude and spatial extent of these changes is consistent across the gradient. In contrast to prior studies, we found that ant-related factors (e.g., proximity to nests, ant changes in surface conditions), rather than canopy cover, had the strongest effect on the abundance of plant recruits. However, the diversity of plants was influenced by both the engineer and the canopy cover gradient. Discussion. Atta laevigata in the Cerrado modify local conditions in ways that have strong but spatially restricted consequences for plant communities. We hypothesize that ants indirectly reduce seedling establishment by clearing litter and reducing soil moisture, which leads to seed and seedling desiccation. Altering soil nutrients could also reduce juvenile growth and survivorship; if so these indirect negative effects of engineering could exacerbate their direct effects of harvesting plants. The effects of Atta appear restricted to nest mounds, but they could be long-lasting because mounds persist long after a colony has died or migrated. Our results support the hypothesis that leaf-cutter ants play a dominant role in Cerrado plant demography. We suggest the ecological and economic footprint of these engineers may increase dramatically in coming decades due to the transformation of the Cerrado by human activities.
Data from: Ant diversity in Neotropical savannas: hierarchical processes acting at multiple spatial scales
1. Understanding what creates and maintains macroscale biodiversity gradients is a central focus of ecological and evolutionary research. Spatial patterns in diversity are driven by a hierarchy of factors operating at multiple scales. Historical and climatic factors drive large-scale patterns of diversity by affecting the size of regional species pools, while habitat heterogeneity or microhabitat characteristics further influence species coexistence at small scales. 2. We tested the degree to which the species-energy, historical factors, habitat heterogeneity and local environment hypotheses explain observed patterns of ant diversity across hierarchical spatial scales. 3. We sampled ground-dwelling ants at 29 sites within a Neotropical savanna region, the Brazilian Cerrado. We measured species density – an abundance-dependent diversity metric – and rarefied species richness – an abundance-independent metric – at spatial scales with varying grain sizes. For each hypothesis, two correlates were used to predict ant diversity patterns: i) species-energy: rainfall and productivity; ii) historical factors: historical variation in rainfall and refugial areas; iii) habitat heterogeneity: heterogeneity in greenness and diversity of land cover; iv) local factors: contents of sand and coarse fragments in the soil. 4. Ant diversity patterns correlated to net primary productivity and to the proportion of coarse fragments in the soil, corroborating the species-energy and local environment hypotheses, respectively. Soil negatively influenced species density, but not rarefied species richness, which was positively influenced by productivity. We found scale dependencies in the effects of soil/productivity on species density; productivity best predicted species density patterns at large scales, since sampling completeness offset the abundance-driven effects of soil. 5. Considering abundance differences may help to discern the mechanisms underlying the relationship between macroscale diversity patterns and its ecological drivers. Plant productivity affected ant diversity independently of abundance, possibly by limiting the size of regional species pools. On the other hand, soil properties had an abundance-dependent effect on ant diversity, indicating a sampling mechanism. Our findings are consistent with predictions of the hierarchical theory of diversity. Large-scale patterns of productivity limit regional diversity, an effect that cascades down to finer spatial scales, where soil properties influence the number of coexisting species.
Data from: Polar lakes may act as ecological islands to aquatic protists
A fundamental question in ecology is whether microorganisms follow the same patterns as multicellular organisms when it comes to population structure and levels of genetic diversity. Enormous population sizes, predominately asexual reproduction, and presumably high dispersal due to small body size could have profound implications on their genetic diversity and population structure. Here, we have analyzed the population genetic structure in a lake-dwelling microbial eukaryote (dinoflagellate) and tested the hypothesis that there is population genetic differentiation among nearby lake subpopulations. This dinoflagellate occurs in the marine-derived saline lakes of the Vestfold Hills, Antarctica, which are ice-covered most of the year. Clonal strains were isolated from four different lakes, and were genotyped using AFLP (Amplified Fragment Length Polymorphism). Our results show high genetic differentiation among lake populations despite their close geographical proximity (< 9 km). Moreover, genotype diversity was high within populations. Gene flow in this system is clearly limited, either due to physical or biological barriers. Our results discard the null hypothesis that there is free gene flow among protist lake populations. Instead, limnetic protist populations may differentiate genetically, and lakes act as ecological islands even on the microbial scale.
Data from: Environmental conditions and biotic interactions acting together promote phylogenetic randomness in semi-arid plant communities: new methods help to avoid misleading conclusions
QUESTIONS: Molecular phylogenies are increasingly used to better understand the mechanisms structuring natural communities. The prevalent theory is that environmental factors and biotic interactions promote the phylogenetic clustering and over-dispersion of plant communities, respectively. However, both environmental filtering and biotic interactions are very likely to interact in most natural communities, jointly affecting community phylogenetic structure. How do environmental filters and biotic interactions jointly affect the phylogenetic structure of plant communities across environmental gradients? LOCATION: Eleven Stipa tenacissima L. grasslands located along an environmental gradient from central to southeast Spain, covering the core of the distribution area of this vegetation type in Europe. METHODS: We jointly evaluated the effects of environmental conditions and plant–plant interactions on the phylogenetic structure – measured with the mean phylogenetic distance index of the studied communities. As an indicator of environmental conditions, we used a PCA ordination including eight climatic variables. Different metrics were used to measure the following processes: (1) competition/facilitation shifts at the entire community level (species combination index), and (2) the effect of microclimatic amelioration provided by the two most important nurse plants on neighbour composition (similarity indices and comparison of the phylogenetic pattern between canopy patches and bare ground areas). RESULTS: Biotic interactions and, to a less extent, environmental conditions affected the phylogenetic pattern of the studied communities. While positive plant–plant interactions (both at community level and the scale of individual nurse plants) increased phylogenetic overdispersion, higher rainfall increased phylogenetic clustering. The opposing effects of environmental conditions and biotic interactions could be the main cause of the overall random phylogenetic structure found inmost of these communities. CONCLUSIONS: Our results illustrate, for the first time, how an overall random phylogenetic pattern may not only be promoted by the lack of influence of either environmental filtering or biotic interactions, but rather by their joint and opposing effects. They caution about making inferences on the underlying mechanisms shaping plant communities from the sole use of their phylogenetic pattern. We also provide a comprehensive set of easy-to-measure tools to avoid misleading conclusions when interpreting phylogenetic structure data obtained from observational studies.
Economic and financial barriers to delivering mental health services in Georgia: Informing policy and acting on evidence
<p>Dataset includes qualitative data for the manuscript entitled "Economic and financial barriers to delivering mental health services in Georgia: Informing policy and acting on evidence".</p>
FIGURES 21–24 in Study of a part of the A. G. Olivier Lixini collection (Coleoptera: Curculionidae): lectotype designations, new synonymies and nomenclatural acts
FIGURES 21–24. Labels of lectotypes. 21. Lixus iridis Olivier, 1807; 22. Lixus recurvus Olivier, 1807; 23. Lixus myagri Olivier, 1807; 24. Lixus cardui Olivier, 1807.
FIGURES 17–20 in Study of a part of the A. G. Olivier Lixini collection (Coleoptera: Curculionidae): lectotype designations, new synonymies and nomenclatural acts
FIGURES 17–20. Labels of lectotypes. 17. Larinus centaurii (Olivier, 1807); 18. Larinus cuniculus (Olivier, 1807); 19. Larinus gravidus (Olivier, 1807); 20. Larinus carthami (Olivier, 1807).
FIGURES 5–8. Lectotypes. 5–6 in Study of a part of the A. G. Olivier Lixini collection (Coleoptera: Curculionidae): lectotype designations, new synonymies and nomenclatural acts
FIGURES 5–8. Lectotypes. 5–6, Larinus gravidus (Olivier, 1807); 7–8, Larinus carthami (Olivier, 1807).
FIGURES 1–4. Lectotypes. 1–2 in Study of a part of the A. G. Olivier Lixini collection (Coleoptera: Curculionidae): lectotype designations, new synonymies and nomenclatural acts
FIGURES 1–4. Lectotypes. 1–2, Larinus centaurii (Olivier, 1807); 3–4, Larinus cuniculus (Olivier, 1807).
FIGURE 9 in <p><strong>Nomenclatural and taxonomic problems related to</strong> <strong>the electronic publication of new nomina and nomenclatural acts in zoology, with brief comments on optical discs and on the situation in botany</strong></p>
FIGURE 9. Three documents concerning Gingerich et al. (2009) downloaded from the PLoS website on 18 December 2012: (a) first web page devoted to this work on the website; (b) first page of PDF of work, dated 4 February 2009; (c) comment 2, dated 22 May 2009, accessed through the link "Comments: 2" on top of (a).
FIGURE 10 in <p><strong>Nomenclatural and taxonomic problems related to</strong> <strong>the electronic publication of new nomina and nomenclatural acts in zoology, with brief comments on optical discs and on the situation in botany</strong></p>
FIGURE 10. Three documents concerning Franzen et al. (2009) downloaded from the PLoS website on 18 December 2012: (a) first web page devoted to this work on the website; (b) comment 7, dated 21 May 2009, accessed through the link "Comments: 13" on top of (a); (c) "formal correction", dated 21 July 2009, accessed through the link "Formal correction: 1" on top of (a).
Figs. 25–33 in Colydiine Genera (Coleoptera: Zopheridae: Colydiinae) of the New World: A Key and Nomenclatural Acts 30 Years in the Making
Figs. 25–33. Dorsal habitus of New World colydiine genera, tribe Synchitini. 25) Endeitoma dentata; 26) Eucicones marginalis; 27) Eudesma undulata; 28) Globotrichus harti; 29) Helonoton ashei; 30) Holopleuridia sp., Panama; 31) Lasconotus complex; 32) Lobogestoria gibbicollis; 33) Lyreus alleni.
Figs. 1–2. Colydiinae anatomy. 1 in Colydiine Genera (Coleoptera: Zopheridae: Colydiinae) of the New World: A Key and Nomenclatural Acts 30 Years in the Making
Figs. 1–2. Colydiinae anatomy. 1) Antennal types. Club 1-segmented: a) Endeitoma sp., b) Synchita sp., c) Acolobicus sp. Club 2-segmented: d) Colobicus sp., e) Lobogestoria sp. Club 3-segmented: f) Lasconotus sp., g) Colydium sp., h) Rhagodera sp. Club gradual: i) Endestes sp.; 2) Tarsi, prothoracic leg. a) Nematidium sp., b) Lobogestoria sp., c) Pseudaulonium sp., d) Acropis sp., e) Monoedus sp.
Figs. 52–53 in Colydiine Genera (Coleoptera: Zopheridae: Colydiinae) of the New World: A Key and Nomenclatural Acts 30 Years in the Making
Figs. 52–53. Dorsal habitus of New World colydiine genera, tribe Synchitini and incertae sedis. 52) Synchita fuliginosa; 53) Phreatus rigidus.
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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.
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DANDI Archive for NWB datasets
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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.