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Figure 4 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446

Figure 4 Image processing and indices of the radula of Chiton articulatus.

Figure 10 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446

Figure 10 List of collaborators in the project.

Figure 5 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446

Figure 5 Equipment used to take pictures of each chiton and example of some chitons photographed.

Figure 1 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446

Figure 1 Specimens of the mollusc Chiton articulatus in its habitat on the intertidal rocky shore.

opencc-zeroDec 2018View details →

Data from: Large scale plasma metabolome analysis reveals alterations in HDL metabolism in migraine

Objective: To identify a plasma metabolomic biomarker signature for migraine. Methods: Plasma samples from 8 Dutch cohorts (n = 10,153: 2,800 migraine patients and 7,353 controls) were profiled on a 1H-NMR-based metabolomics platform, to quantify 146 individual metabolites (e.g., lipids, fatty acids, and lipoproteins) and 79 metabolite ratios. Metabolite measures associated with migraine were obtained after single-metabolite logistic regression combined with a random-effects meta-analysis performed in a nonstratified and sex-stratified manner. Next, a global test analysis was performed to identify sets of related metabolites associated with migraine. The Holm procedure was applied to control the family-wise error rate at 5% in single-metabolite and global test analyses. Results: Decreases in the level of apolipoprotein A1 (β −0.10; 95% confidence interval [CI] −0.16, −0.05; adjusted p = 0.029) and free cholesterol to total lipid ratio present in small high-density lipoprotein subspecies (HDL) (β −0.10; 95% CI −0.15, −0.05; adjusted p = 0.029) were associated with migraine status. In addition, only in male participants, a decreased level of omega-3 fatty acids (β −0.24; 95% CI −0.36, −0.12; adjusted p = 0.033) was associated with migraine. Global test analysis further supported that HDL traits (but not other lipoproteins) were associated with migraine status. Conclusions: Metabolic profiling of plasma yielded alterations in HDL metabolism in migraine patients and decreased omega-3 fatty acids only in male migraineurs.

opencc-zeroDec 2012View details →

Data from: Mouth asymmetry in the textbook example of scale-eating cichlid fish is not a discrete dimorphism after all

Individuals of the scale-eating cichlid fish, Perissodus microlepis, from Lake Tanganyika tend to have remarkably asymmetric heads that are either left-bending or right-bending. The 'left' morph opens its mouth markedly towards the left and preferentially feeds on the scales from the right side of its victim fish and the 'right' morph bites scales from the victims' left side. This striking dimorphism made these fish a textbook example of their astonishing degree of ecological specialization and as one of the few known incidences of negative frequency-dependent selection acting on an asymmetric morphological trait, where left and right forms are equally frequent within a species. We investigated the degree and the shape of the frequency distribution of head asymmetry in P. microlepis to test whether the variation conforms to a discrete dimorphism, as generally assumed. In both adult and juvenile fish, mouth asymmetry appeared to be continuously and unimodally distributed with no clear evidence for a discrete dimorphism. Mixture analyses did not reveal evidence of a discrete or even strong dimorphism. These results raise doubts about previous claims, as reported in textbooks, that head variation in P. microlepis represents a discrete dimorphism of left- and right-bending forms. Based on extensive field sampling that excluded ambiguous (i.e. symmetric or weakly asymmetric) individual adults, we found that left and right morphs occur in equal abundance in five populations. Moreover, mate pairing for 51 wild caught pairs was random with regard to head laterality, calling into question reports that this laterality is maintained through disassortative mating.

Data from: Gigapixel big data movies provide cost‐effective seascape scale direct measurements of open‐access coastal human use such as recreational fisheries

Collecting data on unlicensed open‐access coastal activities, such as some types of recreational fishing, has often relied on telephone interviews selected from landline directories. However, this approach is becoming obsolete due to changes in communication technology such as a switch to unlisted mobile phones. Other methods, such as boat ramp interviews, are often impractical due to high labor cost. We trialed an autonomous, ultra‐high‐resolution photosampling method as a cost effect solution for direct measurements of a recreational fishery. Our sequential photosampling was batched processed using a novel software application to produce "big data" time series movies from a spatial subset of the fishery, and we validated this with a regional bus‐route survey and interviews with participants at access points. We also compared labor costs between these two methods. Most trailer boat users were recreational fishers targeting tuna spp. Our camera system closely matched trends in temporal variation from the larger scale regional survey, but as the camera data were at much higher frequency, we could additionally describe strong, daily variability in effort. Peaks were normally associated with weekends, but consecutive weekend tuna fishing competitions led to an anomaly of high effort across the normal weekday lulls. By reducing field time and batch processing imagery, Monthly labor costs for the camera sampling were a quarter of the bus‐route survey; and individual camera samples cost 2.5% of bus route samples to obtain. Gigapixel panoramic camera observations of fishing were representative of the temporal variability of regional fishing effort and could be used to develop a cost‐efficient index. High‐frequency sampling had the added benefit of being more likely to detect abnormal patterns of use. Combinations of remote sensing and on‐site interviews may provide a solution to describing highly variable effort in recreational fisheries while also validating activity and catch.

Data from: Strong effects of coral species on the diversity and structure of reef fish communities: a multi-scale analysis

While there is increasing evidence for habitat specialization in coral reef fishes, the extent to which different corals support different fish communities is not well understood. Here we quantitatively assess the relative importance of different coral species in structuring fish communities and evaluate whether sampling scale and coral colony size affect the perceived strength of fish-habitat relationships. Fish communities present on colonies of 8 coral species (Porites cylindrica, Echinopora horrida, Hydnophora rigida, Stylophora pistillata, Seriatopora hystrix, Acropora formosa, A. tenuis and A. millepora) were examined in the Lizard Island lagoon. Additionally, the differences in fish communities supported by 3 coral species (P. cylindrica, E. horrida, H. rigida) were investigated at 3 spatial scales of sampling (2x2 m, 1x1 m, 0.5x0.5 m). Substantial differences in fish communities were observed across the different coral species, with E. horrida and H. rigida supporting the most fish species and individuals. Coral species explained more of the variability in fish species richness (20.9-53.6%), than in fish abundance (0-15%). Most coral species supported distinctive fish communities, with dissimilarities ranging from 50 to 90%. For 3 focal coral species, a greater amount of total variation in fish species richness and fish abundance was evident at a larger scale of sampling. Together, these results indicate that the structure of reef fish communities is finely tuned to coral species. Loss of preferred coral species could have profound effects on reef fish biodiversity, more so than would be predicted on the basis of declining coral cover alone.

opencc-zeroDec 2013View details →

Data from: A large-scale field study examining effects of exposure to clothianidin seed-treated canola on honey bee colony health, development, and overwintering success

In summer 2012, we initiated a large-scale field experiment in southern Ontario, Canada, to determine whether exposure to clothianidin seed-treated canola (oil seed rape) has any adverse impacts on honey bees. Colonies were placed in clothianidin seed-treated or control canola fields during bloom, and thereafter were moved to an apiary with no surrounding crops grown from seeds treated with neonicotinoids. Colony weight gain, honey production, pest incidence, bee mortality, number of adults, and amount of sealed brood were assessed in each colony throughout summer and autumn. Samples of honey, beeswax, pollen, and nectar were regularly collected, and samples were analyzed for clothianidin residues. Several of these endpoints were also measured in spring 2013. Overall, colonies were vigorous during and after the exposure period, and we found no effects of exposure to clothianidin seed-treated canola on any endpoint measures. Bees foraged heavily on the test fields during peak bloom and residue analysis indicated that honey bees were exposed to low levels (0.5–2 ppb) of clothianidin in pollen. Low levels of clothianidin were detected in a few pollen samples collected toward the end of the bloom from control hives, illustrating the difficulty of conducting a perfectly controlled field study with free-ranging honey bees in agricultural landscapes. Overwintering success did not differ significantly between treatment and control hives, and was similar to overwintering colony loss rates reported for the winter of 2012–2013 for beekeepers in Ontario and Canada. Our results suggest that exposure to canola grown from seed treated with clothianidin poses low risk to honey bees.

Data from: Variation in three community features across habitat types and scales within a 15-ha subtropical evergreen-deciduous broadleaved mixed forest dynamics plot in China

The evergreen and deciduous broadleaved mixed forests (EDBMFs) belong to one of the ecosystems most sensitive to environmental change, however, little is known about the environmental determinants for their plant diversity and forest structure at different habitat types and spatial scales. Here, we used data from a 15-ha (300×500 m) forest dynamic plot (FDP) of an old-growth EDBMF to examine the patterns and determinants of the three community features (stem abundance, rarefied species richness and basal area) in three habitat types (ridge, hillside and foothill) and at three spatial scales (20×20 m, 50×50 m and 100×100 m). We found that the three community features significantly changed with habitat type, but only one of them (rarefied richness) changed with scale. Among spatial scales, the principle environmental factors that widely affected community features were pH, SOM and TP, while these effects only taken place at certain habitat. Variations in the three community features explained by soil conditions were generally greater than those explained by topographical conditions. With changes in habitat type, the proportion of variations explained by environmental conditions was 31-53%, 8-25%, and 18-26% for abundance, rarefied richness and basal area (BA), respectively. With increasing spatial scale, the variations explained by environmental conditions were 44-75% for abundance, 28-95% for rarefied richness, and 18-86% for BA. Our study demonstrated that environmental factors had great impacts on the plant diversity and forest structure in the EDBMFs, especially the soil factors such as pH. In addition, the importance of the environmental determinants on these community features was highly related to the spatial scale.

Data from: Scaling up DNA barcoding - primer sets for simple and cost efficient arthropod systematics by multiplex PCR and Illumina amplicon sequencing

1. The simplicity and cost efficiency of Illumina amplicon sequencing has greatly contributed to the advancement of DNA barcoding and metabarcoding applications. However, current amplicon sequencing based barcoding approaches are usually restricted to short, single-locus fragments, limiting their taxonomic and phylogenetic resolution. 2. Here, we establish a cost efficient and simple multiplex PCR protocol for arthropod systematics by Illumina amplicon sequencing. We introduce primer sets, including several new, generic primers, to reliably amplify nine loci across a wide range of arthropods. Using a diverse collection of arthropod species from 19 orders, we test loci for amplification efficiency and estimate the effect of cross-species amplification bias on taxon recovery from bulk community samples. We then explore the taxonomic and phylogenetic utility of the primer sets, focusing on a dataset of spiders that includes both deep and recent divergences. 3. The set of loci provides good phylogenetic support across a wide taxonomic spectrum, making it a useful addition to COI for resolving lineages within a comparative context. All loci recover sequences for the majority of arthropod taxa in separate PCRs. However, cross-species amplification bias in some primers prevents an exhaustive taxon recovery from bulk community samples. 4. Our protocol makes it possible to generate multilocus datasets for large numbers of arthropod taxa for a fraction of the price and workload of Sanger sequencing. This opens up the possibility for parallel phylogenetic and taxonomic analysis of large collections of arthropods, but also enables rapid exploratory analyses of target lineages. Primers for metabarcoding applications should be carefully evaluated for their performance in bulk community samples and chosen to minimize cross-species amplification bias.

Data from: Sensory deficiencies affect resources selection and associational effects at two spatial scales

Many insect species have limited sensory abilities and may not be able to perceive the quality of different types of resources while approaching patchily distributed resources. These restrictions may lead to differences in selection rates between separate patches and between different resource types within a patch, which may have consequences for associational effects between resources. In this study, we used an oviposition assay containing different frequencies of apple and banana substrates divided over two patches to compare resource selection rates of wild type Drosophila melanogaster at the between and within patch scales. Next, we compared the wild type behavior with that of the olfactory deficient strain Orco2, and the gustatory deficient strain PoxnΔM22-B5 and found comparable responses to patch heterogeneity and similarly strong selection rates for apple at both scales for the wild type and olfactory deficient flies. Their oviposition behavior translated into associational susceptibility for apple and associational resistance for banana. The gustatory deficient flies, on the other hand, no longer had a strong selection rate for apple, strongly differed in between and within patch selection rates from the wild type flies, and caused no associational effects between the resources. Our study suggests that differences in sensory capabilities can affect resource selection at different search behavior scales in different ways, and in turn underlie associational effects between resources at different spatial scales.

opencc-zeroDec 2018View details →

Data from: Grizzly bear response to fine spatial and temporal scale spring snow cover in Western Alberta

Snow dynamics influence seasonal behaviors of wildlife, such as denning patterns and habitat selection related to the availability of food resources. Under a changing climate, characteristics of the temporal and spatial patterns of snow are predicted to change, and as a result, there is a need to better understand how species interact with snow dynamics. This study examines grizzly bear (Ursus arctos) spring habitat selection and use across western Alberta, Canada. Made possible by newly available fine-scale snow cover data, this research tests a hypothesis that grizzly bears select for locations with less snow cover and areas where snow melts sooner during spring (den emergence to May 31st). Using Integrated Step Selection Analysis, a series of models were built to examine whether snow cover information such as fractional snow covered area and date of snow melt improved models constructed based on previous knowledge of grizzly bear selection during the spring. Comparing four different models fit to 62 individual bear-years, we found that the inclusion of fractional snow covered area improved model fit 60% of the time based on Akaike Information Criterion tallies. Probability of use was then used to evaluate grizzly bear habitat use in response to snow and environmental attributes, including fractional snow covered area, date since snow melt, elevation, and distance to road. Results indicate grizzly bears select for lower elevation, snow-free locations during spring, which has important implications for management of threatened grizzly bear populations in consideration of changing climatic conditions. This study is an example of how fine spatial and temporal scale remote sensing data can be used to improve our understanding of wildlife habitat selection and use in relation to key environmental attributes.

opencc-zeroSep 2019View details →

Data from: Social spider webs harbor largely consistent bacterial communities across broad spatial scales

Social animals that live in domiciles constructed from biomaterials may facilitate microbial growth. Spider webs are one of the most conspicuous biomaterials in nature, yet almost nothing is known about the potential for webs to harbor microbes, even in social spiders that live in dense, long-term aggregations. Here, we tested whether the dominant bacteria present in social spider webs vary across sampling localities and whether the more permanent retreat web harbors compositionally distinct microbes from the more ephemeral capture webs in the desert social spider Stegodyphus dumicola. We also sampled spider cuticles and prey items in a subset of colonies. We found that spider colonies across large spatial scales harbored similar web-associated bacterial communities. We also found substantial overlap in bacterial community composition between spider cuticle, prey, and web samples. These data suggest that social spider webs can harbor characteristic microbial communities and potentially facilitate microbial transmission among individuals, and this study serves as the first step towards understanding the microbial ecology of these peculiar animal societies.

opencc-zeroDec 2011View details →

Data from: Fine-scale genetic analysis of species-specific female preference in Drosophila simulans

Behavioral differences are thought to be the first components to contribute to species isolation, yet the precise genetic basis of behavioral isolation remains poorly understood. Here, we used a combination of behavior assays and genetic mapping to provide the first refined map locating candidate genes for interspecific female preference isolating Drosophila simulans from D. melanogaster. First, we tested whether two genes identified as affecting D. melanogaster female intraspecific mate choice also affect interspecific mate choice; neither of these genes was found to contribute to species-specific female preference. Next, we used deficiency mapping to locate genes on the right arm of the third chromosome for species-specific female preference and identified five small significant regions that contain candidate genes contributing to behavioral isolation. All five regions were located in areas that would have low interspecific recombination, which mirrors the results of other behavioral isolation studies that used quantitative trait locus (QTL) mapping, but without the potential concern of bias towards regions of low recombination that QTL mapping may have. Since this model system may be refined to the individual gene level using the same methodology, this initial map we provide may potentially serve as a ready template for the identification and characterization of the first behavioral isolation genes.

opencc-zeroDec 2018View details →

Data from: Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.

opencc-zeroDec 2016View details →

Data from: Big biology meets microclimatology: Defining thermal niches of ectotherms at landscape scales for conservation planning

Temperature profoundly affects ecology, a fact ever more evident as the ability to measure thermal environments increases and global changes alter these environments. The spatial structure of thermalscapes is especially relevant to the distribution and abundance of ectothermic organisms but the ability to describe biothermal relationships at extents and grains relevant to conservation planning has been limited by small or sparse datasets. Here, we combine a large occurrence database of >23,000 aquatic species surveys with stream microclimate scenarios supported by an equally large temperature database for a 149,000-km mountain stream network to describe thermal relationships for 14 fish and amphibian species. Species occurrence probabilities peaked across a wide range of temperatures (7.0–18.8 °C) but distinct warm- or cold-edge distribution boundaries were apparent for all species and represented environments where populations may be most sensitive to thermal changes. Warm-edge boundary temperatures for a native species of conservation concern were used with geospatial datasets and a habitat occupancy model to highlight subsets of the network where conservation measures could benefit local populations by maintaining cool temperatures. Linking that strategic approach to local estimates of habitat impairment remains a key challenge but is also an opportunity to build relationships and develop synergies between the research, management, and regulatory communities. As with any data mining or species distribution modeling exercise, care is required in analysis and interpretation of results, but the use of large biological datasets with accurate microclimate scenarios can provide valuable information about the thermal ecology of many ectotherms and a spatially-explicit way of guiding conservation investments.

opencc-zeroDec 2014View details →

Data from: Assembly mechanisms determining high species turnover in aquatic communities over regional and continental scales

Niche and neutral processes drive community assembly and metacommunity dynamics, but their relative importance might vary with the spatial scale. The contribution of niche processes is generally expected to increase with increasing spatial extent at a higher rate than that of neutral processes. However, the extent to what community composition is limited by dispersal (usually considered a neutral process) over increasing spatial scales might depend on the dispersal capacity of composing species. To investigate the mechanisms underlying the distribution and diversity of species known to have great powers of dispersal (hundreds of kilometres), we analysed the relative importance of niche processes and dispersal limitation in determining beta-diversity patterns of aquatic plants and cladocerans over regional (up to 300 km) and continental (up to 3300 km) scales. Both taxonomic groups were surveyed in five different European regions and presented extremely high levels of beta-diversity, both within and among regions. High beta-diversity was primarily explained by species replacement (turnover) rather than differences in species richness (i.e. nestedness). Abiotic and biotic variables were the main drivers of community composition. Within some regions, small-scale connectivity and the spatial configuration of sampled communities explained a significant, though smaller, fraction of compositional variation, particularly for aquatic plants. At continental scale (among regions), a significant fraction of compositional variation was explained by a combination of spatial effects (exclusive contribution of regions) and regionally-structured environmental variables. Our results suggest that, although dispersal limitation might affect species composition in some regions, aquatic plant and cladoceran communities are not generally limited by dispersal at the regional scale (up to 300 km). Species sorting mediated by environmental variation might explain the high species turnover of aquatic plants and cladocerans at regional scale, while biogeographic processes enhanced by dispersal limitation among regions might determine the composition of regional biotas.

opencc-zeroDec 2016View details →

Data from: Cophylogenetic signal is detectable in pollination interactions across ecological scales

That evolutionary history can influence the way that species interact is a basic tenet of evolutionary ecology. However, when the role of evolution in determining ecological interactions is investigated, focus typically centers on just one side of the interaction. A cophylogenetic signal, the congruence of evolutionary history across both sides of an ecological interaction, extends these previous explorations and provides a more complete picture of how evolutionary patterns influence the way species interact. To date, cophylogenetic signal has most typically been studied in interactions that occur between fine taxonomic clades that show high intimacy. In this study, we took an alternative approach and made an exhaustive assessment of cophylogeny in pollination interactions. To do so, we assessed the strength of cophylogenetic signal at four distinct scales of pollination interaction: (1) across plant–pollinator associations globally, (2) in local pollination communities, (3) within the modular structure of those communities, and (4) in individual modules. We did so using a globally distributed dataset comprised of 54 pollination networks, over 4000 species, and over 12,000 interactions. Within these data, we detected cophylogenetic signal at all four scales. Cophylogenetic signal was found at the level of plant–pollinator interactions on a global scale and in the majority of pollination communities. At the scale defined by the modular structure within those communities, however, we observed a much weaker cophylogenetic signal. Cophylogenetic signal was detectable in a significant proportion of individual modules and most typically when within-module phylogenetic diversity was low. In sum, the detection of cophylogenetic signal in pollination interactions across scales provides a new dimension to the story of how past evolution shapes extant pollinator–angiosperm interactions.

Data from: Video-fluoroscopic swallowing study scale for predicting aspiration pneumonia in Parkinson's disease

Introduction A number of video-fluoroscopic swallowing study (VFSS) abnormalities have been reported in patients with Parkinson's disease (PD). However, the most crucial finding of subsequent aspiration pneumonia has not been validated fully. We conducted a retrospective and case-control study to determine the clinically significant VFSS findings in this population, and to propose a practical scale for predicting aspiration pneumonia in patients with PD. Methods We enrolled 184 PD patients who underwent VFSS because of suspected dysphagia. The patients who developed aspiration pneumonia within six months of the VFSS were assigned as cases and the patients without aspiration pneumonia at six months were designated as controls. Logistic regression analysis was performed to determine the prognostic VFSS features based on the data of swallowing 3 mL of jelly, which were used to make a PD VFSS scale (PDVFS). The validity of the new PDVFS was evaluated by ROC analysis. Additionally, we used the survival time analysis to compare time to death between groups, stratified by the PDVFS score. Results Twenty-five patients developed aspiration pneumonia. Among the previously-proposed VFSS features, mastication, lingual motility prior to transfer, aspiration, and total swallow time were identified as significant prognostic factors. We combined these factors to form the PDVFS. The PDVFS score ranges from 0 to 12, with 12 being the worst. ROC analysis revealed 92% sensitivity and 82% specificity at a cutoff point of 3. The higher PDVFS group showed shorter time-to-death than the lower PDVFS group (log rank P = 0.001). Conclusion Our newly developed VFSS severity scale (based on jelly swallowing) for patients with PD was easy to rate and could predict subsequent aspiration pneumonia and poor prognosis in patients with PD.