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FIGURES 1–6 in Two new species of Balacha (Insecta: Hemiptera: Cicadellidae: Cicadellinae) from Brazil with comments on their phylogenetic position and biogeography
FIGURES 1–6. Balacha ancora sp. nov., male. (1) Head, pronotum, and mesonotum, dorsal view. (2–6) Terminalia: (2) pygofer, lateral view (most macrosetae are missing but their insertion points were illustrated); (3) style, connective, and subgenital plate, ventral view (only the insertion points of plate macrosetae were illustrated); (4) style and connective, dorsal view; (5) paraphyses, dorsal view; (6) aedeagus and anal tube, lateral view.
Data from: Dung beetle activity had no positive effect on nutrient concentration or performance of established rainforest seedlings
<p>All five datasets from this study correspond to field observations collected for seedlings of six tree species (<i>Brosimum alicastrum</i>, <i>Calophyllum brasiliense</i>, <i>Cymbopetalum baillonii</i>, <i>Diospyros digyna</i>, <i>Omphalea oleifera</i> and <i>Poulsenia armata</i>) in a tropical rainforest (Los Tuxtlas, Mexico). We estimated the concentrations of foliar nitrogen (N) and phosphorus (P), resource allocation (the ratio of biomass allocated to shoot vs root), seedling survival, and growth. Experimental seedlings were subject to three treatment levels: (a) feces added and beetles active, (b) feces added and beetles excluded, and (c) no feces added (and consequently no beetles active). We analyzed data at two levels: community (all plant species together) and individual species. For resource allocation (ESM_Dataset1_RootShoot) we weighed aerial parts (stem and leaves) and roots, separately, and calculated the root/shoot biomass ratio for each seedling. For foliar nutrients (ESM_Dataset2_FoliarNutrients) we obtained N and P concentrations using a Kjeldahl wet digestion and colorimetric analysis; for the analyses four outlier values were removed (for <em>Brosimum</em> one P value; for <i>Calophyllum</i> two P values and one N value). We analyzed foliar nutrients for all plant species. In the case of seedling survival (ESM_Dataset3_Survival) we registered seedling survival weekly during six weeks for <i>Cymbopetalum</i>, and during 26 weeks for the other five species. The response variable was the number of days elapsed until death; seedlings alive by the end of the experiment were included as right-censored data. For seedling growth in height (ESM_Dataset4_GrowthHeight; measured in all plant species except <i>Cymbopetalum</i>) we measured seedling height to the nearest centimeter every four or five weeks during 26 weeks. For this variable we calculated net growth in height (final height minus initial height). Finally, for the growth in the number of leaves (ESM_Dataset5_GrowthLeaves; measured in all plant species except <i>Cymbopetalum</i>) we counted the number of leaves lost and number of new leaves, every four or five weeks during 26 weeks; the response variable was the net growth in the number of leaves (final number of leaves minus initial number of leaves). All analyses were conducted in R. Detailed information about dataset structure and contents can be found in file ESM_Metadata.</p>
RNAseq raw counts FLCN positive vs. FLCN negative renal proximal tubular epithelial cells (RPTEC)
<p>Germline inactivating mutations in Folliculin (FLCN) cause Birt–Hogg–Dubé (BHD) syndrome, a rare autosomal dominant disorder predisposing to kidney tumors. FLCN is a conserved, essential gene linked to diverse cellular processes but the mechanisms by which FLCN prevents kidney cancer remain unknown. Here we show that deleting FLCN activates TFE3, upregulating its downstream E-box genes in human renal tubular epithelial cells (RPTEC/TERT1), including RRAGD and GPNMB, without modifying mTORC1 activity. Surprisingly, deletion of FLCN or its binding partners FNIP1/FNIP2 also induces interferon response genes, but independently of interferon. Mechanistically, FLCN loss promotes STAT2 recruitment to chromatin and slows cellular proliferation. Our integrated analysis identifies STAT1/2 signaling as a novel target of FLCN in renal cells and BHD tumors. STAT1/2 activation appears to counterbalance TFE3-directed hyper-proliferation and may influence the immune response. These findings shed light on unique roles of FLCN in human renal tumorigenesis and pinpoint candidate prognostic biomarkers.</p>
Data from: No biotic homogenisation across decades but consistent effects of landscape position and pH on macrophyte communities in boreal lakes
<p>It has been predicted that spatial beta diversity shows a decreasing trend in the Anthropocene due to increasing human impact, causing biotic homogenisation. We aimed to discover if vascular aquatic macrophyte communities show different spatial patterns in beta diversity in relation to land use and environmental characteristics in different decades from 1940s to 2010s. We aimed to discover if spatial structures differ between species-, phylogeny- and functional-based beta diversity. We used presence-absence data of aquatic macrophytes from five decades from small boreal lakes. We utilized generalised dissimilarity modelling to analyse spatial patterns in beta diversity in relation to environmental gradients. We found that lake elevation and pH were the most important variables in each decade, while land use was not particularly important in shaping beta diversity patterns. We did not find signs of a decreasing trend in spatial beta diversity in our study area during the past 70 years. We did not find signs of either biotic homogenisation or biotic differentiation (taxonomic, phylogenetic or functional). Vascular aquatic macrophyte communities showed only slightly different beta diversity patterns in relation to human impact across decades. The patterns of different facets of beta diversity diverged only slightly from each other. Lake position in the landscape, reflecting both natural connectivity and lake characteristics, explained the patterns found in beta diversity, probably because our study area has faced only modest changes in land use from 1940s to 2010s when compared globally. Our study highlights the fact that biotic homogenisation is not an unambiguous process acting similarly at all spatial and temporal scales or in different environments and different organism groups.</p>
Illustrating cases of horizontal head-shaking nystagmus (HSN) in posterior canal benign paroxysmal positional vertigo (PC-BPPV).
<p><strong>Supplementary video 1. </strong>Illustrating case of<strong> </strong>horizontal head-shaking nystagmus (HSN) in left posterior canal benign paroxysmal positional vertigo (PC-BPPV).</p> <p><strong>Supplementary video 2. </strong>Illustrating case of pure downbeat head-shaking nystagmus (HSN) in right posterior canal benign paroxysmal positional vertigo (PC-BPPV).</p> <p><strong>Supplementary video 3. </strong>Illustrating case of torsional downbeat head-shaking nystagmus (HSN) in right posterior canal benign paroxysmal positional vertigo (PC-BPPV).</p>
Data from: Positive relationship between genetic- and species diversity on limestone outcrops in the Carpathian Mountains
We asked if the genetic diversity of Saponaria bellidifolia (a habitat specialist plant) and the species diversity of its habitat are driven by parallel landscape-level processes in an island-like system of limestone outcrops in the Carpathian Mountains. We tested the relationship of these two diversity levels at local and regional geographic scales. Local genetic and species diversity showed parallel patterns influenced by the number of plant communities. Likewise, at regional level there was strong evidence for parallel equilibrial dynamics of genotypes and species. However, a superimposed matrix effect enhanced the regional species diversity only. Genetic diversity of habitat specialist organisms and species diversity of these limestone outcrop islands on mainland are modulated by parallel landscape-level processes at different geographic scales, and mechanisms may be identified at very high spatial resolutions.
Data from: Occupancy models for data with false positive and false negative errors and heterogeneity across sites and surveys
False positive detections, such as species misidentifications, occur in ecological data, although many models do not account for them. Consequently, these models are expected to generate biased inference. The main challenge in an analysis of data with false positives is to distinguish false positive and false negative processes while modeling realistic levels of heterogeneity in occupancy and detection probabilities without restrictive assumptions about parameter spaces. Building on previous attempts to account for false positive and false negative detections in occupancy models, we present hierarchical Bayesian models that utilize a subset of data with either confirmed detections of a species' presence (CP model) or both confirmed presences and confirmed absences (CACP model). We demonstrate that our models overcome the challenges associated with false positive data by evaluating model performance in Monte Carlo simulations of a variety of scenarios. Our models also have the ability to improve inference by incorporating previous knowledge through informative priors. We describe an example application of the CP model to quantify the relationship between songbird occupancy and residential development, plus we provide instructions for ecologists to use the CACP and CP models in their own research. Monte Carlo simulation results indicated that, when data contained false positive detections, the CACP and CP models generated more accurate and precise posterior probability distributions than a model that assumed data did not have false positive errors. For the scenarios we expect to be most generally applicable, those with heterogeneity in occupancy and detection, the CACP and CP models generated essentially unbiased posterior occupancy probabilities. The CACP model with vague priors generated unbiased posterior distributions for covariate coefficients. The CP model generated unbiased posterior distributions for covariate coefficients with vague or informative priors, depending on the function relating covariates to occupancy probabilities. We conclude that the CACP and CP models generate accurate inference in situations with false positive data for which previous models were not suitable.
Data from: A giant spurrey on a tiny island: on the phylogenetic position of Sanctambrosia manicata (Caryophyllaceae) and the generic circumscriptions of Spergula, Spergularia and Rhodalsine
The only member of the generally herbaceous family Caryophyllaceae that may grow to a small tree is Sanctambrosia manicata, endemic to remote San Ambrosio Island, off the coast of Chile. The monospecific Sanctambrosia has been suggested to be closely related to Spergula and Spergularia (spurreys) on the basis of morphology, despite its treelike habit and gynodioecy. A plastid DNA dataset (ndhF, rps16, trnL-F) is used to investigate the relationships of Sanctambrosia and other members of Sperguleae. Sanctambrosia manicata is shown to be nested in a clade of New World and Australian Spergularia and the new combination Spergularia manicata is proposed. The volcanic San Ambrosio has been estimated to be almost three million years old, and S. manicata presumably evolved its treelike habit and gynodioecy over a short period of time. Spergula and Spergularia are monophyletic and recognizable by their number of carpels, five in Spergula and three in Spergularia. Spergularia fallax, which resembles Spergula in leaf characters, is shown to be sister to all other species of Spergularia. Minuartia subg. Rhodalsine belongs in Sperguleae and is sister to Spergula and Spergularia together, which supports the recent resurrection of Rhodalsine at the generic level.
Data from: Trophic position determines functional and phylogenetic recovery after disturbance within a community
1. The roles that functional traits and/or evolutionary history of species from co-occuring trophic groups have in determining community recovery following disturbance are poorly understood. Functional traits help determine how species interact with their environment, thus functional traits are likely to change with time since logging. However, traits of species may also be phylogenetically constrained depending on their evolutionary history. Because beetles are trophically diverse, the effects of phylogenetic and functional aspects of community recovery can be compared between co-occuring trophic groups. 2. Using a chronosequence of forest ages following logging, we applied a novel combination of functional trait and phylogenetic approaches to assess the extent to which taxonomic, functional and phylogenetic composition recovered after logging, and if these dimensions of composition approached those characteristic of mature forests, for both predators and decomposers/primary consumers. We also examined to what extent functional traits of both trophic groups were phylogenetically conserved. 3. Predator functional compostion had recovered ~45 years after logging, and this recovery preceded taxonomic recovery. Neither taxonomic nor functional composition had recovered for the decomposer/primary consumer communites by this time. 4. In contrast to decomposers/primary consumers, predator community recovery had no distinct phylogenetic signature, yet predator functional traits were more phylogenetically conserved than decomposers/primary consumer functional traits. 5. Trait syndromes that characterise forest recovery stages are identified and provide a basis for future work on community re-assembly following disturbance. 6. We demonstrate differential recovery of co-occuring beetle trophic groups following disturbance. We show that functional and phylogenetic composition may be disconnected from taxonomic composition; highlighting the advantages of integrating understanding of these three potentially independent components of ecological diversity to enable deeper understanding of animal community composition.
Data from: Positive effects of non-native grasses on the growth of a native annual in a southern California ecosystem
Fire disturbance is considered a major factor in the promotion of non-native plant species. Non-native grasses are adapted to fire and can alter environmental conditions and reduce resource availability in native coastal sage scrub and chaparral communities of southern California. In these communities persistence of non-native grasses following fire can inhibit establishment and growth of woody species. This may allow certain native herbaceous species to colonize and persist beneath gaps in the canopy. A field manipulative experiment with control, litter, and bare ground treatments was used to examine the impact of non-native grasses on growth and establishment of a native herbaceous species, Cryptantha muricata. C. muricata seedling survival, growth, and reproduction were greatest in the control treatment where non-native grasses were present. C. muricata plants growing in the presence of non-native grasses produced more than twice the number of flowers and more than twice the reproductive biomass of plants growing in the treatments where non-native grasses were removed. Total biomass and number of fruits were also greater in the plants growing in the presence of non-native grasses. Total biomass and reproductive biomass was also greater in late germinants than early germinants growing in the presence of non-native grasses. This study suggests a potential positive effect of non-native grasses on the performance of a particular native annual in a southern California ecosystem.
Data from: Defoliation of a grass by reindeer is compensated by the positive effects of its soil legacy, dung deposition, and moss removal
Herbivory is one of the key drivers shaping plant community dynamics. Herbivores can strongly influence plant productivity directly through defoliation and the return of nutrients in the form of dung and urine, but also indirectly by reducing the abundance of neighbouring plants and inducing changes in soil processes. However, the relative importance of these processes is poorly understood. We, therefore, established a common garden experiment to study plant responses to defoliation, dung addition, moss cover, and the soil legacy of reindeer grazing. We used an arctic tundra grazed by reindeer as our study system, and Festuca ovina, a common grazing-tolerant grass species as the model species. The soil legacy of reindeer grazing had the strongest effect on plants, and resulted in higher growth in soils originating from previously heavily-grazed sites. Defoliation also had a strong effect and reduced shoot and root growth and nutrient uptake. Plants did not fully compensate for the tissue lost due to defoliation, even when nutrient availability was high. In contrast, defoliation enhanced plant nitrogen concentrations. Dung addition increased plant production, nitrogen concentrations and nutrient uptake, although the effect was fairly small. Mosses also had a positive effect on aboveground plant production as long as the plants were not defoliated. The presence of a thick moss layer reduced plant growth following defoliation. This study demonstrates that grasses, even though they suffer from defoliation, can tolerate high densities of herbivores when all aspects of herbivores on ecosystems are taken into account. Our results further show that the positive effect of herbivores on plant growth via changes in soil properties is essential for plants to cope with a high grazing pressure. The strong effect of the soil legacy of reindeer grazing reveals that herbivores can have long-lasting effects on plant productivity and ecosystem functioning after grazing has ceased.
Data from: A chromosome 5q31.1 locus associates with tuberculin skin test reactivity in HIV-positive individuals from tuberculosis hyper-endemic regions in east Africa
One in three people has been infected with Mycobacterium tuberculosis (MTB), and the risk for MTB infection in HIV-infected individuals is even higher. We hypothesized that HIV-positive individuals living in tuberculosis-endemic regions who do not get infected by Mycobacterium tuberculosis are genetically resistant. Using an "experiment of nature" design that proved successful in our previous work, we performed a genome-wide association study of tuberculin skin test positivity using 469 HIV-positive patients from prospective study cohorts of tuberculosis from Tanzania and Uganda to identify genetic loci associated with MTB infection in the context of HIV-infection. Among these individuals, 244 tested were tuberculin skin test (TST) positive either at enrollment or during the >8 year follow up, while 225 were not. We identified a genome-wide significant association between the dominant model of rs877356 and binary TST status in the combined cohort (OR=0.2671, p=1.22x10-8). Association was replicated with similar significance when examining TST induration as a continuous trait. The variant lies in the 5q31.1 region, 57kb downstream from IL9. Two-locus analyses of association of variants near rs877356 showed a haplotype comprised of rs877356 and an IL9 missense variant rs2069885 had the most significant association (p=1.59x10-12). We also replicated previously linked loci on chromosomes 2, 5, and 11. IL9 is a cytokine produced by mast cells and T¬H2 cells during inflammatory responses, providing a possible link between airway inflammation and protection from MTB infection. Our results indicate that studying uninfected participants with extensive exposure increases the power to detect associations in complex infectious disease.
Data from: Resolving the phylogenetic position of Darwin's extinct ground sloth (Mylodon darwinii) using mitogenomic and nuclear exon data
Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first discovered its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12,880 year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that this sample was exceptionally well preserved for an ancient sub-fossil, likely the result of the dry and cold conditions prevailing within the cave. Accordingly, taxonomic assessment of our shotgun metagenomic data showed a very high percentage of endogenous DNA with 22% of the assembled metagenomic contigs assigned to Xenarthra. Additionally, we enriched over 15 kilobases of sequence data from seven nuclear exons, using target sequence capture designed against a wide xenarthran dataset. Phylogenetic and dating analyses of the mitogenomic dataset including all extant species of xenarthrans and the assembled nuclear supermatrix unambiguously place Mylodon darwinii as the sister-group of modern two-fingered sloths from which it diverged around 22 million years ago. These congruent results from both the mitochondrial and nuclear data support the diphyly of the two modern sloths lineages, implying the convergent evolution of their unique suspensory behaviour as an adaption to arboreality. Our results offer promising perspectives for whole genome sequencing of this emblematic extinct taxon.
Data from: Sperm competition and the evolution of precopulatory weapons: testis size and amplexus position, but not arm strength, affect fertilization success in a chorusing frog
Trade-offs between pre- and postcopulatory traits influence their evolution, and male expenditure on such traits is predicted to depend on the number of competitors, the benefits from investing in weapons, and the risk and intensity of sperm competition. Males of the chorusing frog Crinia georgiana use their arms as weapons in contest competition. Previously, we showed that increased numbers of rivals elevated the risk and intensity of sperm competition due to multimale amplexus, and caused a reversal in the direction of precopulatory selection on arm girth. Here we focused on the factors affecting postcopulatory fertilization success during group spawning, using paternity data from natural choruses. Competitive fertilization success depended on the time spent amplexed and amplexus position. Relative testes size but not arm girth, contributed to fertilization success, but the effect of testes size depended on amplexus position. Our findings offer within species empirical support for recent sperm competition models that incorporate precopulatory male-male competition, and show why an understanding of the evolution of animal weapons requires a consideration of both pre- and postcopulatory episodes of sexual selection.
Data from: Testing macroecological abundance patterns: the relationship between local abundance and range size, range position and climatic suitability among European vascular plants
<p><strong>Aim: </strong>A fundamental question in macroecology centres around understanding the relationship between species' local abundance and their distribution in geographic and climatic space (i.e. the multi-dimensional climatic space or climatic niche). Here, we tested three macroecological hypotheses that link local abundance to the following range properties: (1) the abundance-range size relationship, (2) the abundance-range centre relationship, and (3) the abundance-suitability relationship.<br> <br> <strong>Location: </strong>Europe<br> <br> <strong>Taxon: </strong>Vascular plants<br> <br> <strong>Methods:</strong> Distribution range maps were extracted from the Chorological Database to derive information on the range and niche sizes of 517 European vascular plant species. To estimate local abundance, we assessed samples from 744,513 vegetation plots in the European Vegetation Archive, where local species' abundance is available as plant cover per plot. We then calculated the 'centrality', i.e. the distance between the location of the abundance observation and each species' range centre in geographic and climatic space. The climatic suitability of plot locations was estimated using coarse-grain species distribution models (SDMs). The relationships between centrality or climatic suitability with abundance were tested using linear models and quantile regression. We summarized the overall trend across species' regression slopes from linear models and quantile regression using a meta-analytical approach.<br> <br> <strong>Results: </strong>We did not detect any positive relationships between a species' mean local abundance and the size of its geographic range or climatic niche. Contrasting yet significant correlations were detected between abundance and centrality or climatic suitability among species.<br> <br> <strong>Main conclusions:</strong> Our results do not provide unequivocal support for any of the relationships tested, demonstrating that determining properties of species' distributions at large grains and extents might be of limited use for predicting local abundance, including current SDM approaches. We conclude that environmental factors influencing individual performance and local abundance are likely to differ from those factors driving plant species' distribution at coarse resolution and broad geographic extents.</p>
Data from: A meta-analysis reveals a positive correlation between genetic diversity metrics and environmental status in the long-lived seagrass Posidonia oceanica
The seagrass Posidonia oceanica is a key engineering species structuring coastal marine systems throughout much of the Mediterranean basin. Its decline is of concern, leading to the search for short- and long-term indicators of seagrass health. Using ArcGIS maps from a recent, high-resolution (1–4 km) modelling study of 18 disturbance factors affecting coastal marine systems across the Mediterranean (Micheli et al. 2013, http://globalmarine.nceas.ucsb.edu/mediterranean/), we tested for correlations with genetic diversity metrics (allelic diversity, genotypic/clonal diversity and heterozygosity) in a meta-analysis of 56 meadows. Contrary to initial predictions, weak but significantly positive correlations were found for commercial shipping, organic pollution (pesticides) and cumulative impact. This counterintuitive finding suggests greater resistance and resilience of individuals with higher genetic and genotypic diversity under disturbance (at least for a time) and/or increased sexual reproduction under an intermediate disturbance model. We interpret the absence of low and medium levels of genetic variation at impacted locations as probable local extinctions of individuals that already exceeded their resistance capacity. Alternatively, high diversity at high-impact sites is likely a temporal artefact, reflecting the mismatch with pre-environmental impact conditions, especially because flowering and sexual recruitment are seldom observed. While genetic diversity metrics are a valuable tool for restoration and mitigation, caution must be exercised in the interpretation of correlative patterns as found in this study, because the exceptional longevity of individuals creates a temporal mismatch that may falsely suggest good meadow health status, while gradual deterioration of allelic diversity might go unnoticed.
Positive and negative interactions jointly determine the structure of Müllerian mimetic communities
<p>Negative and positive ecological interactions have opposite effects on the structure of ecological communities, in particular in terms of ecological similarity among interacting species. In nature, species belonging to the same guild often interact in both negative and positive ways, yet the interplay between interactions of different kinds in intraguild community dynamics remains poorly understood. Müllerian mimetic communities are particularly suited for investigating this interplay because positive (mutualistic mimicry) and negative (competition for trophic resource and micro-habitat) interactions are relatively easy to identify. Empirical research has shown that the combination of competition and mutualistic mimicry does not necessarily drive convergence along all dimensions of the ecological niche, but the determinants of such mixed result are unknown. Here, we analyze the structure of Müllerian mimetic communities simulated with an agent-based model. We show that mutualistic mimicry favours ecological similarity on dimensions along which similarity favours fine-scale co-occurrence. Co-mimetic species use similar micro-habitats, but do not necessarily use similar resources. Heterogeneity of resources among micro-habitats is necessary for ecological similarity on resource use among co-mimetic species to occur. We therefore highlight the importance of fine-scale co-occurrence if we are to understand how positive and negative interactions structure ecological communities.</p> <p> </p>
Data from: Assessing the impacts of positive selection on coalescent-based species tree estimation and species delimitation.
The assumption of strictly neutral evolution is fundamental to the multispecies coalescent model and permits the derivation of gene tree distributions and coalescent times conditioned on a given species tree. In this study, we conduct computer simulations to explore the effects of violating this assumption in the form of species-specific positive selection when estimating species trees, species delimitations, and coalescent parameters under the model. We simulated datasets under an array of evolutionary scenarios that differ in both speciation parameters (i.e., divergence times, strength of selection) and experimental design (i.e., number of loci sampled) and incorporated species-specific positive selection occurring within branches of a species tree to identify the effects of selection on multispecies coalescent inferences. Our results highlight particular evolutionary scenarios and parameter combinations in which inferences may be more, or less, susceptible to the effects of positive selection. In some extreme cases, selection can decrease error in species delimitation and increase error in species tree estimation, yet these inferences appear to be largely robust to the effects of positive selection under many conditions likely to be encountered in empirical datasets.
Data from: Mitochondria and Wolbachia titers are positively correlated during maternal transmission
Mothers provide their offspring with symbionts. Maternally transmitted, intracellular symbionts must disperse from mother to offspring with other cytoplasmic elements, like mitochondria. Here, we investigated how the intracellular symbiont Wolbachia interacts with mitochondria during maternal transmission. Mitochondria and Wolbachia may interact antagonistically and compete as each population tries to ensure its own evolutionary success. Alternatively, mitochondria and Wolbachia may cooperate as both benefit from ensuring the fitness of the mother. We characterized the relationship between mitochondria and Wolbachia titers in ovaries of D. melanogaster. We found that mitochondria and Wolbachia titers are positively correlated in common laboratory genotypes of D. melanogaster. We attempted to perturb this covariation through the introduction of Wolbachia variants that colonize at different titers. We also attempted to perturb the covariation through manipulating the female reproductive tract to disrupt maternal transmission. Finally, we also attempted to disrupt the covariation by knocking down gene expression for two loci involved in mitochondrial metabolism: NADH dehydrogenase and a mitochondrial transporter. Overall, we find that mitochondria and Wolbachia titers are commonly positively correlated, but this positive covariation is disrupted at high titers of Wolbachia. Our results suggest that mitochondria and Wolbachia have likely evolved mechanisms to stably coexist, but the competitive dynamics change at high Wolbachia titers. We provide future directions to better understand how their interaction influences the maintenance of the symbiosis.
Occupancy in dynamic systems: accounting for multiple scales and false positives using environmental DNA to inform monitoring
<div class="page"> <div class="section"> <p>Occupancy is an important metric to understand current and future trends in populations that have declined globally. In addition, occupancy can be an efficient tool for conducting landscape-scale and long-term monitoring. A challenge for occupancy monitoring programs is to determine the appropriate spatial scale of analysis and to obtain precise occupancy estimates for elusive species. We used a multi-scale occupancy model to assess occupancy of Columbia spotted frogs in the Great Basin, USA, based on environmental DNA (eDNA) detections. We collected three replicate eDNA samples at 220 sites across the Great Basin. We estimated and modeled ecological factors that described watershed and site occupancy at multiple spatial scales simultaneously while accounting for imperfect detection. Additionally, we conducted visual and dipnet surveys at all sites and used our paired detections to estimate the probability of a false positive detection for our eDNA sampling. We applied the estimated false positive rate to our multi-scale occupancy dataset and assessed changes in model selection. We had higher naïve occupancy estimates for eDNA (0.37) than for traditional survey methods (0.20). We estimated our false positive detection rate per qPCR replicate at 0.023 (95% CI: 0.016-0.033). When the false positive rate was applied to the multi-scale dataset, we did not observe substantial changes in model selection or parameter estimates. Conservation and resource managers have an increasing need to understand species occupancy in highly variable landscapes where the spatial distribution of habitat changes significantly over time due to climate change and human impact. A multi-scale occupancy approach can be used to obtain regional occupancy estimates that can account for spatially dynamic differences in availability over time, especially when assessing potential declines. Additionally, this study demonstrates how eDNA can be used as an effective tool for improved occupancy estimates across broad geographic scales for long-term monitoring.</p> </div> </div>
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.