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Data from: Sexual conflict and interacting phenotypes: a quantitative genetic analysis of fecundity and copula duration in Drosophila melanogaster
Many reproductive traits that have evolved under sexual conflict may be influenced by both sexes. Investigation of the genetic architecture of such traits can yield important insight into their evolution, but this entails that the heritable component of variation is estimated for males and females – as an interacting phenotype. We address the lack of research in this area through an investigation of egg production and copula duration in the fruit fly, Drosophila melanogaster. Despite egg production rate being determined by both sexes, which may cause sexual conflict, an assessment of this trait as an interacting phenotype is lacking. It is currently unclear whether copula duration is determined by males and/or females. We found significant female, but not male, genetic variance for egg production rate which may indicate reduced potential for ongoing sexually antagonistic coevolution. In contrast, copula duration was determined by significant genetic variance in both sexes. We also identified genetic variation in egg retention among virgin females. Although previously identified in wild populations, it is unclear why this should be present in a laboratory stock. This study provides a novel insight into the shared genetic architecture of reproductive traits that are the subject of sexual conflict.
Data from: The influence of ecological and life history factors on ectothermic temperature-size responses: analysis of three Lycaenidae butterflies (Lepidoptera)
Body size has been shown to decrease with increasing temperature in many species, prompting the suggestion that it is a universal ecological response. However, species with complex life cycles, such as holometabolous insects, may have correspondingly complicated temperature-size responses. Recent research suggests that life history and ecological traits may be important for determining the direction and strength of temperature-size responses. Yet, these factors are rarely included in analyses. Here, we aim to determine if the size of the bivoltine butterfly, Polyommatus bellargus, and the univoltine butterflies, Plebejus argus and Polyommatus coridon, change in response to temperature and whether these responses differ between the sexes, and for P. bellargus, between generations. Forewing length was measured using digital specimens from the Natural History Museum, London (NHM), from one locality in the UK per species. The data were initially compared to annual and seasonal temperature values, without consideration of life history factors. Sex and generation of the individuals and mean monthly temperatures, which cover the growing period for each species, were then included in analyses. When compared to annual or seasonal temperatures only, size was not related to temperature for P. bellargus and P. argus, but there was a negative relationship between size and temperature for P. coridon. When sex, generation and monthly temperatures were included, male adult size decreased as temperature increased in the early larval stages, and increased as temperature increased during the late larval stages. Results were similar but less consistent for females, while second generation P. bellargus showed no temperature-size response. In P. coridon, size decreased as temperature increased during the pupal stage. These results highlight the importance of including life history factors, sex and monthly temperature data when studying temperature-size responses for species with complex life cycles.
Data from: Sensitivity analysis of conservation targets in systematic conservation planning
Systematic conservation planning has rapidly advanced in the past decade and has been increasingly incorporated in multiple studies and conservation projects. One of its requirements is a quantitative definition of conservation targets. While the Convention on Biological Diversity aims to expand the world's protected area network to 17% of the land surface, in many cases such uniform policy-driven targets may not be appropriate for achieving persistence of various species. Targets are often set arbitrarily, often because information required for the persistence of each species is unavailable or unknown in the focal region. Conservation planners therefore need to establish complementary novel approaches to address the gaps in setting targets. Here, we develop and present a novel method that aims to help guide the selection of conservation targets, providing support for decision makers, planners, and managers. This is achieved by examining the overall flexibility of the conservation network resulting from conservation prioritization, and aiming for greater flexibility. To test this approach we applied the decision support tool Marxan to determine marine conservation priority areas in the eastern Mediterranean Sea as a case study. We assessed the flexibility of the conservation network by comparing 80 different scenarios in which conservation targets were gradually increased and assessed by a range of calculated metrics (e.g., the percentage of the total area selected, the overall connectivity). We discovered that when conservation targets were set too low (i.e., below 10% of the distribution range of each species), very few areas were identified as irreplaceable and the conservation network was not well defined. Interestingly, when conservation targets were set too high (over 50% of the species' range), too many conservation priority areas were selected as irreplaceable, an outcome which is realistically infeasible to implement. As a general guideline, we found that flexibility in a conservation network is adequate when ~10−20% of the study area is considered irreplaceable (selection frequency values over 90%). This approach offers a useful sensitivity analysis when applying target-based systematic conservation planning tools, ensuring that the resulting protected area conservation network offers more choices for managers and decision makers.
Data from: Patterns of MHC-dependent mate selection in humans and non-human primates: a meta-analysis
Genes of the major histocompatibility complex (MHC) in vertebrates are integral for effective adaptive immune response and are associated with sexual selection. Evidence from a range of vertebrates supports MHC-based preference for diverse and dissimilar mating partners, but evidence from human mate choice studies has been disparate and controversial. Methodologies and sampling peculiarities specific to human studies make it difficult to know whether wide discrepancies in results among human populations are real or artefact. To better understand what processes may affect MHC-mediated mate choice across humans and nonhuman primates, we performed phylogenetically controlled meta-analyses using 58 effect sizes from 30 studies across seven primate species. Primates showed a general trend favouring more MHC-diverse mates, which was statistically significant for humans. In contrast, there was no tendency for MHC-dissimilar mate choice, and for humans, we observed effect sizes indicating selection of both MHC-dissimilar and MHC-similar mates. Focusing on MHC-similar effect sizes only, we found evidence that preference for MHC similarity was an artefact of population ethnic heterogeneity in observational studies but not among experimental studies with more control over sociocultural biases. This suggests that human assortative mating biases may be responsible for some patterns of MHC-based mate choice. Additionally, the overall effect sizes of primate MHC-based mating preferences are relatively weak (Fisher's Z correlation coefficient for dissimilarity Zr = 0.044, diversity Zr = 0.153), calling for careful sampling design in future studies. Overall, our results indicate that preference for more MHC-diverse mates is significant for humans and likely conserved across primates.
Data from: Point process models for presence-only analysis
1. Presence-only data are widely used for species distribution modelling, and point process regression models are a exible tool that has considerable potential for this problem, when data arise as point events. 2. In this paper we review point process models, some of their advantages, and some common methods of fitting them to presence-only data. 3. Advantages include (and are not limited to): clarification of what the response variable is that is modelled; a framework for choosing the number and location of quadrature points (commonly referred to as pseudoabsences or \background points") objectively; clarity of model assumptions and tools for checking them; models to handle spatial dependence between points when it is present; ways forward regarding difficult issues such as accounting for sampling bias. 4. Point process models are related to some common approaches to presenceonly species distribution modelling, which means that a variety of different software tools can be used to fit these models, including MAXENT or generalised linear modelling software.
Data from: A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change
Background: Grapes are one of the most economically important fruit crops. There are about 60 species in the genus Vitis. The phylogenetic relationships among these species are of keen interest for the conservation and use of this germplasm. We selected 309 accessions from 48 Vitis species,varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times based on fossil calibrations. Results: Vitis formed a strongly supported clade. There was substantial support for species and less for the higher-level groupings (series). As estimated from extant taxa, the crown age of Vitis was 28 Ma and the divergence of subgenera (Vitis and Muscadinia) occurred at ~18 Ma. Higher clades in subgenus Vitis diverged 16 -- 5 Ma with overlapping confidence intervals, and ongoing divergence formed extant species at 12 -- 1.3 Ma. Several species had species-specific SNPs. NeighborNet analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward. Fitch Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species. Conclusions: Phylogenetic patterns suggested origination of the genus in North America, fragmentation of an ancestral range during the Miocene, formation of extant species in the late Miocene-Pleistocene, and differentiation of species in the context of Pliocene-Quaternary tectonic and climatic change. Nuclear SNPs effectively resolved relationships at and below the species level in grapes and rectified several misclassifications of accessions in the repositories. Our results challenge current higher-level classifications, reveal the abundance of genetic diversity in the genus that is potentially available for crop improvement, and provide a valuable resource for species delineation, germplasm conservation and use.
Data from: Survival analysis and classification methods for forest fire size
Factors affecting wildland-fire size distribution include weather, fuels, and fire suppression activities. We present a novel application of survival analysis to quantify the effects of these factors on a sample of sizes of lightning-caused fires from Alberta, Canada. Two events were observed for each fire: the size at initial assessment (by the first fire fighters to arrive at the scene) and the size at "being held" (a state when no further increase in size is expected). We developed a statistical classifier to try to predict cases where there will be a growth in fire size (i.e., the size at "being held" exceeds the size at initial assessment). Logistic regression was preferred over two alternative classifiers, with covariates consistent with similar past analyses. We conducted survival analysis on the group of fires exhibiting a size increase. A screening process selected three covariates: an index of fire weather at the day the fire started, the fuel type burning at initial assessment, and a factor for the type and capabilities of the method of initial attack. The Cox proportional hazards model performed better than three accelerated failure time alternatives. Both fire weather and fuel type were highly significant, with effects consistent with known fire behaviour. The effects of initial attack method were not statistically significant, but did suggest a reverse causality that could arise if fire management agencies were to dispatch resources based on a-priori assessment of fire growth potentials. We discuss how a more sophisticated analysis of larger data sets could produce unbiased estimates of fire suppression effect under such circumstances.
Data from: Cluster analysis successfully identifies clinically meaningful knee valgus moment patterns: frequency of early peaks reflects sex-specific ACL injury incidence
Background: Biomechanical studies of ACL injury risk factors frequently analyze only a fraction of the relevant data, and typically not in accordance with the injury mechanism. Extracting a peak value within a time series of relevance to ACL injuries is challenging due to differences in the relative timing and size of the peak value of interest. Aims/hypotheses: The aim was to cluster analyze the knee valgus moment time series curve shape in the early stance phase. We hypothesized that 1a) There would be few discrete curve shapes, 1b) there would be a shape reflecting an early peak of the knee valgus moment, 2a) youth athletes of both sexes would show similar frequencies of early peaks, 2b) adolescent girls would have greater early peak frequencies. Methods: N = 213 (39% boys) youth soccer and team handball athletes (phase 1) and N = 35 (45% boys) with 5 year follow-up data (phase 2) were recorded performing a change of direction task with 3D motion analysis and a force plate. The time series of the first 30% of stance phase were cluster analyzed based on Euclidean distances in two steps; shape-based main clusters with a transformed time series, and magnitude based sub-clusters with body weight normalized time series. Group differences (sex, phase) in curve shape frequencies, and shape-magnitude frequencies were tested with chi-squared tests. Results: Six discrete shape-clusters and 14 magnitude based sub-clusters were formed. Phase 1 boys had greater frequency of early peaks than phase 1 girls (38% vs 25% respectively, P < 0.001 for full test). Phase 2 girls had greater frequency of early peaks than phase 2 boys (42% vs 21% respectively, P < 0.001 for full test). Conclusions: Cluster analysis can reveal different patterns of curve shapes in biomechanical data, which likely reflect different movement strategies. The early peak shape is relatable to the ACL injury mechanism as the timing of its peak moment is consistent with the timing of injury. Greater frequency of early peaks demonstrated by Phase 2 girls is consistent with their higher risk of ACL injury in sports.
Data from: Do deposit-feeders compete? Isotopic niche analysis of an invasion in a species-poor system
Successful establishment of invasive species is often related to the existence of vacant niches. Competition occurs when invaders use the same limiting resources as members of the recipient community, which will be reflected in some overlap of their trophic niches. The concept of isotopic niche has been used to study trophic niche partitioning among species. Here, we present a two-year field study comparing isotopic niches of the deposit-feeding community in a naturally species-poor system. The isotopic niche analyses showed no overlap between a recent polychaete invader and any of the native species suggesting that it has occupied a vacant niche. Its narrow isotopic niche suggests specialized feeding, however, the high d15N values compared to natives are most likely due to isotope fractionation effects related to nitrogen recycling and a mismatch between biological stoichiometry of the polychaete and the sediment nitrogen content. Notably, highly overlapping isotopic niches were inferred for the native species, which is surprising in a food-limited system. Therefore, our results demonstrate that invaders may broaden the community trophic diversity and enhance resource utilization, but also raise questions about the congruence between trophic and isotopic niche concepts and call for careful examination of assumptions underlying isotopic niche interpretation.
Data from: How do baleen whales stow their filter? A comparative biomechanical analysis of baleen bending
Bowhead and right whale (balaenid) baleen filtering plates, longer in vertical dimension (3-4+ m) than the closed mouth, presumably bend during gape closure. This has not been observed in live whales, even with scrutiny of videorecorded feeding sequences. To determine what happens to baleen as gape closes, we conducted an integrative, multifactorial study including materials testing, functional (flow tank and kinematic) testing, and histological examination. We measured baleen bending properties along the dorsoventral length of plates and anteroposterior location within a rack of plates via mechanical (axial bending, composite flexure, compression, and tension) tests of hydrated and air-dried tissue samples from balaenid and other whale baleen. Balaenid baleen is remarkably strong yet pliable, with ductile fringes and low stiffness and high elasticity when wet; it likely bends in the closed mouth when not used for filtration. Calculation of flexural modulus from stress/strain experiments shows baleen is slightly more flexible where it emerges from the gums and at its ventral terminus, but kinematic analysis indicates plates bend evenly along their whole length. Fin and humpback whale baleen has similar material properties but less flexibility, with no dorsoventral variation. Internal horn tubes have greater external and hollow luminal diameter but lower density in lateral relative to medial baleen of bowhead and fin whales, suggesting greater capacity for lateral bending. Baleen bending has major consequences not only for feeding morphology and energetics but also conservation given that entanglement in fishing gear is a leading cause of whale mortality.
Data from: Grow where you thrive, or where only you can survive? An analysis of performance curve evolution in a clade with diverse habitat affinities
Performance curves are valuable tools for quantifying the fundamental niches of organisms and testing hypotheses about evolution, life history trade-offs, and the drivers of variation in species' distribution patterns. Here, we present a novel Bayesian method for characterizing performance curves that facilitates comparisons among species. We then use this model to quantify and compare the hydrological performance curves of 14 different taxa in the genus Lasthenia, an ecologically diverse clade of plants that collectively occupy a variety of habitats with unique hydrological features, including seasonally flooded wetlands called vernal pools. We conducted a growth chamber experiment to measure each taxon's fitness across five hydrological treatments that ranged from severe drought to extended flooding, and identified differences in hydrological performance curves that explain their associations with vernal pool and terrestrial habitats. Our analysis revealed that the distribution of vernal pool taxa in the field do not reflect their optimal hydrological environments: all taxa, regardless of habitat affinity, have highest fitness under similar hydrological conditions of saturated soil without submergence. We also found that a taxon's relative position across flood gradients within vernal pools is best predicted by the height of its performance curve. These results demonstrate the utility of our approach for generating insights into when and how performance curves evolve among taxa as they diversify into distinct environments. To facilitate its use, the modeling framework has been developed into an R package (https://github.com/silastittes/performr).
Data from: Multivariate analysis of dopaminergic gene variants as risk factors of heroin dependence
BACKGROUND: Heroin dependence is a debilitating psychiatric disorder with complex inheritance. Since the dopaminergic system has a key role in rewarding mechanism of the brain, which is directly or indirectly targeted by most drugs of abuse, we focus on the effects and interactions among dopaminergic gene variants. OBJECTIVE: To study the potential association between allelic variants of dopamine D2 receptor (DRD2), ANKK1 (ankyrin repeat and kinase domain containing 1), dopamine D4 receptor (DRD4), Catechol-O-methyl transferase (COMT) and dopamine transporter (SLC6A3) genes and heroin dependence in Hungarian patients. METHODS: 303 heroin dependent subjects and 555 healthy controls were genotyped for 7 single nucleotide polymorphisms (SNPs): rs4680 of the COMT gene; rs1079597 and rs1800498 of the DRD2 gene; rs1800497 of the ANKK1 gene; rs1800955, rs936462 and rs747302 of the DRD4 gene. Four variable number of tandem repeats (VNTRs) were also genotyped: 120 bp duplication and 48 bp VNTR in exon 3 of DRD4 and 40 bp VNTR and intron 8 VNTR of SLC6A3. We also provide a multivariate model for the associations among them implying Bayesian networks in Bayesian multilevel analysis. FINDINGS AND CONCLUSIONS: In single marker analysis the TaqIA (rs1800497) and TaqIB (rs1079597) variants were associated with heroin dependence. Moreover, -521 C/T SNP (rs1800955) of the DRD4 gene showed nominal association with a possible protective effect of the C allele. After applying the Bonferroni correction TaqIB was still significant suggesting that the minor (A) allele of the TaqIB SNP is a risk component in the genetic background of heroin dependence. The findings of the additional multiple marker analysis are consistent with the results of the single marker analysis, but this method was able to reveal an indirect effect of a promoter polymorphism (rs936462) of the DRD4 gene and this effect is mediated through the -521 C/T (rs1800955) polymorphism in the promoter.
Data from: Environmental DNA analysis as a non-invasive quantitative tool for reproductive migration of a threatened endemic fish in rivers
Quantitative information regarding reproduction is essential for conserving endangered animals; however, some conventional quantitative methods can be damaging to the target population and their habitats. In the present study, the reproductive migration of a threatened endemic fish, three-lips (Opsariichthys uncirostris uncirostris), was non-invasively monitored by quantitative PCR of species-specific environmental DNA (eDNA), the usefulness of which has been under-studied. Water sampling and from-shore visual inspection were performed weekly along a tributary of Lake Biwa (Japan), where adult fish seasonally migrate upstream to reproduce as well as at lake sites near the river mouth. Species-specific eDNA was collected at all locations at times when the fish were visually observed and at certain sites where the fish were not observed. Log-transformed individual counts from visual inspection were positively correlated with log-transformed eDNA concentration in the river sites, indicating that eDNA analysis can be a reliable quantitative tool for fish abundance in rivers. Furthermore, distance from the lake did not influence eDNA concentration, suggesting that eDNA transport by river flow had a negligible effect on eDNA quantification. eDNA concentration and individual counts both gradually increased from May–July, then both decreased in August. Importantly, eDNA analysis showed that the fish occupied more habitats in the peak reproductive season and stayed for longer time at any given site. An additional underwater survey confirmed unexpected eDNA detections as true positives. eDNA analysis has great potential to quantitatively monitor reproductive fish migrations under certain conditions.
Data from: DNA metabarcoding diet analysis for species with parapatric versus sympatric distribution: a case study on subterranean rodents
Closely related sympatric species commonly develop different ecological strategies to avoid competition. Ctenomys minutus and C. flamarioni are subterranean rodents parapatrically distributed in the southern Brazilian coastal plain, showing a narrow sympatric zone. To gain understanding on food preferences and possible competition for food resources, we evaluated their diet composition performing DNA metabarcoding analyzes of 67 C. minutus and 100 C. flamarioni scat samples, collected along the species geographical ranges. Thirteen plant families, mainly represented by Poaceae, Araliaceae, Asteraceae and Fabaceae, were identified in the diet of C. minutus. For C. flamarioni, 10 families were recovered, with a predominance of Poaceae, Araliaceae and Asteraceae. A significant correlation between diet composition and geographical distance was detected in C. minutus, whereas the diet of C. flamarioni was quite homogeneous throughout its geographical distribution. No significant differences were observed between males and females of each species. However, differences in diet composition between species were evident according to multivariate analysis. Our results suggest some level of diet partitioning between C. flamarioni and C. minutus in the sympatric region. While the first species is more specialized on few plant items, the second showed a more varied and heterogeneous diet pattern among individuals. These differences might have been developed to avoid competition in the region of co-occurrence. Resource availability in the environment also seems to influence food choices. Our data indicate that C. minutus and C. flamarioni are generalist species, but that some preference for Poaceae, Asteraceae and Araliaceae families can be suggested for both rodents.
Data from: Estimation of a killer whale (Orcinus orca) population's diet using sequencing analysis of DNA from feces
Estimating diet composition is important for understanding interactions between predators and prey and thus illuminating ecosystem function. The diet of many species, however, is difficult to observe directly. Genetic analysis of fecal material collected in the field is therefore a useful tool for gaining insight into wild animal diets. In this study, we used high-throughput DNA sequencing to quantitatively estimate the diet composition of an endangered population of wild killer whales (Orcinus orca) in their summer range in the Salish Sea. We combined 175 fecal samples collected between May and September from five years between 2006 and 2011 into 13 sample groups. Two known DNA composition control groups were also created. Each group was sequenced at a ~330bp segment of the 16s gene in the mitochondrial genome using an Illumina MiSeq sequencing system. After several quality controls steps, 4,987,107 individual sequences were aligned to a custom sequence database containing 19 potential fish prey species and the most likely species of each fecal-derived sequence was determined. Based on these alignments, salmonids made up >98.6% of the total sequences and thus of the inferred diet. Of the six salmonid species, Chinook salmon made up 79.5% of the sequences, followed by coho salmon (15%). Over all years, a clear pattern emerged with Chinook salmon dominating the estimated diet early in the summer, and coho salmon contributing an average of >40% of the diet in late summer. Sockeye salmon appeared to be occasionally important, at >18% in some sample groups. Non-salmonids were rarely observed. Our results are consistent with earlier results based on surface prey remains, and confirm the importance of Chinook salmon in this population's summer diet.
Data from: Model-assisted analysis of sugar metabolism throughout tomato fruit development reveals enzyme and carrier properties in relation to vacuole expansion
A kinetic model combining enzyme activity measurements and subcellular compartmentation was parameterized to fit the sucrose, hexose, and glucose-6-P contents of pericarp throughout tomato (Solanum lycopersicum) fruit development. The model was further validated using independent data obtained from domesticated and wild tomato species and on transgenic lines. A hierarchical clustering analysis of the calculated fluxes and enzyme capacities together revealed stage-dependent features. Cell division was characterized by a high sucrolytic activity of the vacuole, whereas sucrose cleavage during expansion was sustained by both sucrose synthase and neutral invertase, associated with minimal futile cycling. Most importantly, a tight correlation between flux rate and enzyme capacity was found for fructokinase and PPi-dependent phosphofructokinase during cell division and for sucrose synthase, UDP-glucopyrophosphorylase, and phosphoglucomutase during expansion, thus suggesting an adaptation of enzyme abundance to metabolic needs. In contrast, for most enzymes, flux rates varied irrespectively of enzyme capacities, and most enzymes functioned at <5% of their maximal catalytic capacity. One of the major findings with the model was the high accumulation of soluble sugars within the vacuole together with organic acids, thus enabling the osmotic-driven vacuole expansion that was found during cell division.
Data from: Assessing the vulnerability of Africa's freshwater fishes to climate change: a continent-wide trait-based analysis
Climate change is a key driver of biodiversity loss across the globe, and freshwater fishes are predicted to be among the most vulnerable taxa. African freshwater ecosystems are home to one of the most unique and diverse ichthyo-faunas on the planet, and freshwater fish species provide essential livelihoods for millions of people living in riparian communities across the continent. Although nearly one sixth of African freshwater fishes have been designated as endangered or vulnerable to extinction by the IUCN Red List assessment, the effects of climate change on these species have not been explored on a continent-wide scale. In this study, we present the first trait-based climate change vulnerability assessment (CCVA) comprising the majority (85%) of Africa's currently described freshwater fishes. We assembled data relating to three dimensions of vulnerability including sensitivity, adaptive capacity, and exposure. In addition, we developed an index of 'conservation value' based on traditional conservation metrics including extinction risk, endemism, and provision of ecosystem services. We found that almost 40% of African freshwater fishes are vulnerable to climate change, mostly owing to the many species with highly specialized habitat and life-history requirements, and because of the numerous anthropogenic stressors they face. High proportions of species within the Nothobranchiidae and Cichlidae families were found to be vulnerable. Regions with high frequencies of vulnerable species included the African rift valley lakes, the Congo River drainage, and the coastal rivers of West Africa. Several important data deficiencies were identified relating to species' population sizes, genetic variability, and life history traits, and constitute priority research areas for the future. In addition, we highlighted some cases where traditional conservation approaches overlook species and regions that are predicted to be threatened by climate change.
Data from: Correlation of native and exotic species richness: a global meta-analysis finds no invasion paradox across scales
Support for the "biotic resistance hypothesis," that species-rich communities are more successful at resisting invasion by exotic species than are species-poor communities, has long been debated. It has been argued that native-exotic richness relationships (NERR) are negative at small spatial scales and positive at large scales, but evidence for the role of spatial scale on NERR has been contradictory. However, no formal quantitative synthesis has previously examined whether NERR is scale-dependent across multiple studies, and previous studies on NERR have not distinguished spatial grain and extent, which may drive very different ecological processes. We used a global systematic review and hierarchical mixed-effects meta-analysis to provide a comprehensive quantitative assessment of the patterns of NERR over a range of spatial grain sizes and spatial extents, based on 204 individual cases of observational (non-experimental) NERRs from 101 publications. We show that NERR was indeed highly scale-dependent across studies and increased with the log of grain size. However, mean NERR was not negative at any grain size, although there was high heterogeneity at small grain sizes. We found no clear patterns of NERR across different spatial extents, suggesting that extent plays a less important role in determining NERR than does grain, although there was a complex interaction between extent and grain size. Almost all studies on NERR were conducted in North America, western Europe, and a few other regions, with little information on tropical or Arctic regions. We did find that NERR increased northward in temperate regions and also varied with longitude. We discuss possible explanations for the patterns we found, and caution that our results do not show that invasive species are benign or have no negative consequences for biodiversity preservation. This study represents the first global quantitative analysis of scale-based NERR and casts doubt on the existence of an "invasion paradox" of negative NERR at small scales and positive correlations at large scales in non-experimental studies.
Data from: Differential gene expression analysis of symbiotic and aposymbiotic Exaiptasia anemones under immune challenge with Vibrio coralliilyticus
Anthozoans are a class of Cnidarians that includes scleractinian corals, anemones and their relatives. Despite a global rise in disease epizootics impacting scleractinian corals, little is known about the immune response of this key group of invertebrates. To better characterize the anthozoan immune response, we used the model anemone Exaiptasia pallida to explore the genetic links between the anthozoan-algal symbioses and immunity in a two-factor RNA-Seq experiment using both symbiotic and aposymbiotic(menthol-bleached) Exaiptasia pallida exposed to the bacterial pathogen Vibrio coralliilyticus. Multivariate and univariate analyses of Exaiptasia gene expression demonstrated that exposure to live Vibrio coralliilyticus had strong and significant impacts on transcriptome-wide gene expression for both symbiotic and aposymbiotic anemones, but we did not observe strong interactions between symbiotic state and Vibrio exposure. There were 4,164 significantly differentially expressed (DE) genes for Vibrio exposure, 1,114 DE genes for aposymbiosis, and 472 DE genes for the additive combinations of Vibrio and aposymbiosis. KEGG enrichment analyses identified 11 pathways - involved in immunity (5), transport and catabolism (4) and cell growth and death (2) - that were enriched due to both Vibrio and/or aposymbiosis. Immune pathways showing strongest differential expression included complement, coagulation, nucleotide-binding and oligomerization domain (NOD), and Toll for Vibrio exposure and coagulation and apoptosis for aposymbiosis.
Data from: Antennal transcriptome analysis and expression profiles of odorant binding proteins in Eogystia hippophaecolus (Lepidoptera: Cossidae)
Background: Eogystia hippophaecolus (Hua et al.) (Lepidoptera: Cossidae) is the major threat to seabuckthorn plantations in China. Specific and highly efficient artificial sex pheromone traps was developed and used to control it. However, the molecular basis for the pheromone recognition is not known. So we established the antennal transcriptome of E. hippophaecolus and characterized the expression profiles of odorant binding proteins. These results establish and improve the basis knowledge of the olfactory receptive system, furthermore provide a theoretical basis for the development of new pest control method. Results: We identified 29 transcripts encoding putative odorant-binding proteins (OBPs), 18 putative chemosensory proteins (CSPs), 63 odorant receptors (ORs), 13 gustatory receptors (GRs), 12 ionotropic receptors (IRs), and two sensory neuron membrane proteins (SNMPs). Based on phylogenetic analysis, we found one Orco and three pheromone receptors of E. hippophaecolus and found that EhipGR13 detects sugar, EhipGR11 and EhipGR3 detect bitter. Nine OBPs expression profile indicated that most were the highest expression in antennae, consistent with functions of OBPs in binding and transporting odors during the antennal recognition process. OBP6 was external expressed in male genital-biased in, and this locus may be responsible for pheromone binding and recognition as well as mating. OBP1 was the highest and biased expressed in the foot and may function as identification of host plant volatiles. Conclusions: One hundred thirty-seven chemosensory proteins were identified and the accurate functions and groups of part proteins were obtained by phylogenetic analysis. The most OBPs were antenna-biased expressed, which are involved in antennal recognition. However, few OBP was detected biased expression in the foot and external genitalia, and these loci may function in pheromone recognition, mating, and the recognition of plant volatiles.
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.