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Data from: Yellowstone bison—should we preserve artificial population substructure or rely on ecological processes?
Halbert et al. (2012) analyzed microsatellite genotypes collected from 661 Yellowstone bison sampled during winters from 1999 through 2003 and identified 2 genetically distinct subpopulations (central, northern) based on genotypic diversity and allelic distributions. Based on these findings, they raised concerns about the management and long-term conservation of Yellowstone bison due to disproportionate culling of the 2 subpopulations in some winters. The data and findings of Halbert et al. (2012) are significant and useful for managers charged with conserving these iconic wildlife. However, their article provides information regarding the behavior and management of Yellowstone bison that does not accurately portray historic or current conditions. This response clarifies those conditions and challenges some of their apparent deductions and recommendations.
Data from: Biogeophysical and physiological processes drive movement patterns in a marine predator
Background: Blue sharks (Prionace glauca) are among the most abundant and widely distributed of oceanic elasmobranchs. Millions are taken annually in pelagic longline fisheries and comprise the highest component of auctioned fin weight in the international shark fin trade. Though studies of blue sharks outnumber those of other large pelagic sharks, the species' complicated and sexually segregated life history still confound current understanding of Atlantic movement patterns. Lack of detailed information regarding movement and vertical behavior continues to limit management efforts that require such data for stock assessment and sustainable catch modeling. Therefore, this study aims to describe behavioral and ecological patterns distinct to aggregating and migrating blue sharks, and compare the findings to existing Atlantic movement models. Results: Data collected from 23 blue sharks instrumented with pop-up satellite archival tags were used in statistical predictive regression models to investigate habitat use during a localized aggregation in the northwest Atlantic, while undergoing seasonal migrations, and with respect to environmental variables. Deployment durations ranged from 4 to 273 days, with sharks inhabiting both productive coastal waters and the open ocean, and exhibiting long-distance seasonal movements exceeding 3700 km. While aggregating on the continental shelf of the northwest Atlantic, blue sharks displayed consistent depth use independent of sex and life stage, and exhibited varied response to environmental (temperature and chlorophyll a) factors. As sharks dispersed from the aggregation site, depth use was influenced by bathymetry, latitude, demography, and presence in the Gulf Stream. Mature females were not observed at the New England tagging site, however, two mature females with recent mating wounds were captured and tagged opportunistically in The Bahamas, one of which migrated to the Mid-Atlantic Ridge. Conclusions: Vertical behaviors displayed by blue sharks varied greatly among locales; depth use off the continental shelf was significantly greater, and individuals exhibited a greater frequency of deep-diving behavior, compared to periods of aggregation on the continental shelf. Sexual segregation was evident, suggesting mature and immature males, and immature females may be subjected to high levels of anthropogenic exploitation in this region during periods of aggregation. Analysis of the spatio-temporal tracks revealed that nine individuals traveled beyond the United States EEZ, including a mature female captured in The Bahamas that migrated to the Mid-Atlantic Ridge. These results reflect and augment existing Atlantic migration models, and highlight the complex, synergistic nature of factors affecting blue shark ecology and the need for a cooperative management approach in the North Atlantic.
Data from: Comparison of solar-induced chlorophyll fluorescence, light-use efficiency, and process-based GPP models in maize
Accurately quantifying cropland gross primary production (GPP) is of great importance to monitor cropland status and carbon budgets. Satellite-based light-use efficiency (LUE) models and process-based terrestrial biosphere models (TBMs) have been widely used to quantify cropland GPP at different scales in past decades. However, model estimates of GPP are still subject to large uncertainties, especially for croplands. More recently, space-borne solar-induced chlorophyll fluorescence (SIF) has shown the ability to monitor photosynthesis from space, providing new insights into actual photosynthesis monitoring. In this study, we examined the potential of SIF data to describe maize phenology and evaluated three GPP modeling approaches (space-borne SIF retrievals, a LUE-based Vegetation Photosynthesis Model (VPM), and a process-based Soil Canopy Observation of Photochemistry and Energy flux (SCOPE) model constrained by SIF) at a maize (Zea mays L.) site in Mead, Nebraska, USA. The result shows that SIF captured the seasonal variations (particularly during the early and late growing season) of tower-derived GPP (GPP_EC) much better than did satellite-based vegetation indices (enhanced vegetation index, EVI and land surface water index, LSWI). Consequently, SIF was strongly correlated with GPP_EC than were EVI and LSWI. Evaluation of GPP estimates against GPP_EC during the growing season demonstrated that all three modeling approaches provided reasonable estimates of maize GPP, with Pearson's correlation coefficients (r) of 0.97, 0.94, and 0.93 for the SCOPE, VPM, and SIF models, respectively. The SCOPE model provided the best simulation of maize GPP when SIF observations were incorporated through optimizing the key parameter of maximum carboxylation capacity (Vcmax). Our results illustrate the potential of SIF data to offer an additional way to investigate the seasonality of photosynthetic activity, to constrain process-based models for improving GPP estimates, and to reasonably estimate GPP by integrating SIF and GPP_EC data without dependency on climate inputs and satellite-based vegetation indices.
Data from: Regulation of reproductive processes with Dynamic Energy Budgets
1. Linking organismal level processes to underlying suborganismal mechanisms at the molecular, cellular and organ level constitutes a major challenge for predictive ecological risk assessments. This challenge can be addressed with the simple bioenergetic models in the family of Dynamic Energy Budget (DEB), which consist of a small number of state equations quantifying universal processes, such as feeding, maintenance, development, reproduction and growth. 2. Motivated by the need for process-based models to evaluate the impact of endocrine disruptors on ecologically relevant endpoints, this paper develops and evaluates two general modeling modules describing demand-driven feedback mechanisms within the DEB modeling framework exerted by gonads on the allocation of resources to production of reproductive matter. 3. These modules describe iteroparous, semelparous and batch-mode reproductive strategies. The modules have a generic form with both positive and negative feedback components; species and sex specific attributes of endocrine regulation can be added without changing the core of the modules. 4. We demonstrate that these modules successfully describe time-resolved measurements of wet weight of body, ovaries and liver, egg diameter and plasma content of vitellogenin and estradiol in rainbow trout (Oncorynchus mykiss) by fitting these models to published and new data, which require the estimation of less than two parameters per data type. 5. We illustrate the general applicability of the concept of demand-driven allocation of resources to reproduction by evaluating one of the modules with data on growth and seed production of an annual plant, the common bean (Phaseolis vulgaris).
Data from: The variation of grain size distribution in rock granular material in seepage process considering the mechanical-hydrological-chemical coupling effect: An experimental research
<p>As a common solid waste in geotechnical engineering, rock granular material should be properly treated and recycled. Rock granular material often coexists with water when it is used as the filling material in geotechnical engineering. Water flowing in rock granular materials is a complex progress with the mechanical-hydrological-chemical (MHC) coupling effect, i. e. the water scours in the gaps and spaces in the rock granular material structure, produces chemical reactions with rock grains, rock grains squeeze each other under the water pressure and compression leading re-breakage and producing secondary rock grains, the fine rock grains are migrated with water and rushed out. In this process, rock grain size distribution (GSD) changes, it affects the physical and mechanical characteristics of the rock granular materials, and even influences the seepage stability of the rock granular materials. To study the variation of GSD in the rock granular material considering the MHC coupling effect after the seepage process, seepage experiments of rock grain samples are carried out and analyzed in this paper. The result is expected to have a positive impact on further studies of the properties of the rock granular material.</p>
Data from: The multiple roles of β–diversity help untangle community assembly processes affecting recovery of temperate rocky shores
Metacommunity theory highlights the potential of β–diversity as a useful link to empirical research, especially in diverse systems where species exhibit a range of stage-dependent dispersal characteristics. To investigate the importance of different components and scales of β–diversity in community assembly we conducted a large-scale disturbance experiment and compared relative recovery across multiple sites and among plots within sites on the rocky shore. Six sites were spread along 80 km of coastline and, at each site, 5 plots were established, matching disturbed and undisturbed quadrats. Recovery was not complete at any of the sites after 1 year for either epibenthos (mostly composed of macroalgae and, locally, mussels) or infauna. Significant differences in recovery among sites were observed for epibenthos but not for infauna suggesting different community assembly processes were operating. This was supported by epibenthos in the recovering plots having higher species turnover than in undisturbed sediment, and recovery well predicted by local diversity, while infaunal recovery was strongly influenced by the epibenthic community's habitat complexity. However, infaunal community recovery did not simply track formation of habitat by recovering epibenthos, but appeared to be overlain by within-site and among-site aspects of infaunal -diversity. These results suggest that documenting changes in the large plants and animals alone will be a poor surrogate for rocky shore community assembly processes. No role for ecological connectivity (negative effect of among-site β–diversity) in driving recovery was observed, suggesting a low risk of effects from multiple disturbances propagating along the coast, but a limited resilience at the site scale to large-scale disturbances such as landslides or oil spills.
Data from: Inferring processes of coevolutionary diversification in a community of Panamanian strangler figs and associated pollinating wasps
The fig and pollinator wasp obligate mutualism is diverse (~750 described species), ecologically important, and ancient (~80 Ma). Once thought to be an example of strict one-to-one cospeciation, current thinking suggests genera of pollinator wasps codiversify with corresponding sections of figs, but the degree to which cospeciation or other processes contribute to the association at finer scales is unclear. Here we use genome-wide sequence data from a community of Panamanian strangler figs and associated wasp pollinators to estimate the relative contributions of four evolutionary processes generating cophylogenetic patterns in this mutualism: cospeciation, host switching, pollinator speciation, and pollinator extinction. Using a model-based approach adapted from the study of gene family evolution, our results demonstrate the importance of host switching of pollinator wasps at this fine phylogenetic and regional scale. Although we estimate a modest amount of cospeciation, simulations reveal the number of putative cospeciation events to be consistent with what would be expected by chance. Additionally, model selection tests identify host switching as a critical parameter for explaining cophylogenetic patterns in this system. Our study demonstrates a promising approach through which the history of evolutionary association between interacting lineages can be rigorously modeled and tested in a probabilistic phylogenetic framework.
Data from: Below-ground processes control the success of an invasive seaweed
1. Whilst the successful establishment and spread of invasive species can be determined by above ground processes, results are often equivocal. Emergent research, mostly from terrestrial ecosystems, demonstrates that below-ground processes (nutrient cycling, chemical properties) under microbial control can mediate interactions between native and invasive plants. Because microbes can control similar sediment properties in marine ecosystem that influence plant fitness, we argue that below-ground properties should also exert strong control interactions between native and invasive marine macrophytes. 2. We coupled surveys of microbial communities and chemistry of sediments collected from an invasive alga (Caulerpa cylindracea), a native competitor (the seagrass Posidonia oceanica) and unvegetated sediments with a large field experiment, in which we manipulated the presence/absence of the canopies of both species to determine the effects of above- and below-ground processes on the success of C. cylindracea. 3. P. oceanica and C. cylindracea sediments have microbial communities and predicted metabolic process that reflect aerobic and anaerobic conditions, respectively. Moreover, the nutritional quantity of organic matter was higher, but quality was lower in C. cylindracea sediments compared to the two native habitats. The growth of C. cylindracea fragments was equally low in the presence or absence of a P. oceanica canopy, whereas the growth of C. cylindracea was higher in the canopy removed vs. present treatment, possibly because, in the absence of a C. cylindracea canopy, fragments are released from intra-specific competition for resources. 4. Synthesis: Sediment/soil processes are increasingly recognised as important drivers of the success and hence impacts of invasive plants. We extended this theory to marine ecosystems and suggest biotic resistance to invasion may not always be attributable to intact canopies, but may also result from indirect effects of native macrophytes on sediment quality and microbial processes. This information may, in part, resolve why above-ground interactions don't always explain invasive plant success and thus can be used to develop better informed management strategies.
Data from: Exploring neutral and adaptive processes in expanding populations of gilthead sea bream, Sparus aurata L., in the North-East Atlantic
Recent studies in empirical population genetics have highlighted the importance of taking into account both neutral and adaptive genetic variation in characterizing microevolutionary dynamics. Here we explore the genetic population structure and the footprints of selection in four populations of the warm-temperate coastal fish, the gilthead sea bream (Sparus aurata), whose recent northward expansion has been linked to climate change. Samples were collected at four Atlantic locations, including Spain, Portugal, France and the South of Ireland, and genetically assayed using a suite of species-specific markers, including 15 putatively neutral microsatellites and 23 Expressed Sequence Tag-linked (ESTs) markers, as well as a portion of the mitochondrial DNA (mtDNA) Control Region. Two of the putatively neutral markers, Bld-10 and Ad-10, bore signatures of strong directional selection, particularly in the newly established Irish population, though the potential 'surfing effect' of rare alleles at the edge of the expansion front was also considered. Analyses after the removal of these loci suggest low but significant population structure likely affected by some degree of gene flow counteracting random genetic drift. No signal of historic divergence was detected at mtDNA. BLAST searches conducted with all 38 markers used failed to identify specific genomic regions associated to adaptive functions. However, the availability of genomic resources for this commercially valuable species is rapidly increasing, bringing us closer to the understanding of the interplay between selective and neutral evolutionary forces, shaping population divergence of an expanding species in a heterogeneous milieu.
Data from: Dispersal, niche, and isolation processes jointly explain species turnover patterns of nonvolant small mammals in a large mountainous region of China
Understanding the mechanisms that govern the spatial patterns of species turnover (beta diversity) has been one of the fundamental issues in biogeography. Species turnover is generally recognized as strong in mountainous regions, but the way in which different processes (dispersal, niche, and isolation) have shaped the spatial turnover patterns in mountainous regions remains largely unexplored. Here, we explore the directional and elevational patterns of species turnover for nonvolant small mammals in the Hengduan Mountains of southwest China and distinguish the relative roles of geographic distance, environmental distance, and geographic isolation on the patterns. The spatial turnover was assessed using the halving distance (km), which was the geographic distance that halved the similarity (Jaccard similarity) from its initial value. The halving distance was calculated for the linear, logarithmic, and exponential regression models between Jaccard similarity and geographic distance. We found that the east–west turnover is generally faster than the south–north turnover for high-latitudinal regions in the Hengduan Mountains and that this pattern corresponds to the geographic structure of the major mountain ranges and rivers that mainly extend in a south–north direction. There is an increasing trend of turnover toward the higher-elevation zones. Most of the variation in the Jaccard similarity could be explained by the pure effect of geographic distance and the joint effects of geographic distance, environmental distance, and average elevation difference. Our study indicates that dispersal, niche, and isolation processes are all important determinants of the spatial turnover patterns of nonvolant small mammals in the Hengduan Mountains. The spatial configuration of the landscape and geographic isolation can strongly influence the rate of species turnover in mountainous regions at multiple spatial scales.
Data from: Quantifying species contributions to ecosystem processes: a global assessment of functional trait and phylogenetic metrics across avian seed-dispersal networks
Quantifying the role of biodiversity in ecosystems not only requires understanding the links between species and the ecological functions and services they provide, but also how these factors relate to measurable indices, such as functional traits and phylogenetic diversity. However, these relationships remain poorly understood, especially for heterotrophic organisms within complex ecological networks. Here, we assemble data on avian traits across a global sample of mutualistic plant–frugivore networks to critically assess how the functional roles of frugivores are associated with their intrinsic traits, as well as their evolutionary and functional distinctiveness. We find strong evidence for niche complementarity, with phenotypically and phylogenetically distinct birds interacting with more unique sets of plants. However, interaction strengths—the number of plant species dependent on a frugivore—were unrelated to evolutionary or functional distinctiveness, largely because distinct frugivores tend to be locally rare, and thus have fewer connections across the network. Instead, interaction strengths were better predicted by intrinsic traits, including body size, gape width and dietary specialization. Our analysis provides general support for the use of traits in quantifying species ecological functions, but also highlights the need to go beyond simple metrics of functional or phylogenetic diversity to consider the multiple pathways through which traits may determine ecological processes.
Data from: Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae)
Phylogenetic niche conservatism and convergence are contrasting evolutionary patterns that describe phenotypic similarity across independent lineages. Assessing whether and how adaptive processes give origin to these patterns represent a fundamental step toward understanding phenotypic evolution. Phylogenetic model-based approaches offer the opportunity not only to distinguish between phylogenetic niche conservatism and convergence, but also to determine the extent that adaptive processes explain phenotypic similarity. The Myrmotherula complex in the Neotropical family Thamnophilidae is a polyphyletic group of sexually dimorphic small insectivorous forest birds that are relatively homogeneous in size and shape. Here, we integrate a comprehensive species-level molecular phylogeny of the Myrmotherula complex with morphometric and ecological data within a comparative framework to test whether phenotypic similarity is described by a pattern of phylogenetic niche conservatism or convergence, and to identify evolutionary mechanisms underlying body size and shape evolution. We show that antwrens in the Myrmotherula complex represent distantly related clades that exhibit adaptive convergent evolution in body size and divergent evolution in body shape. Phenotypic similarity in the group is primarily driven by their tendency to converge toward smaller body sizes. Differences in body size and shape across lineages are associated to ecological and behavioral factors.
Data from: Hierarchical structure of ecological and non-ecological processes of differentiation shaped ongoing gastropod radiation in the Malawi Basin
Ecological processes, non-ecological processes or a combination of both may cause reproductive isolation and speciation, but their specific roles and potentially complex interactions in evolutionary radiations remain poorly understood, which defines a central knowledge gap at the interface of microevolution and macroevolution. Here I examine genome scans in combination with phenotypic and environmental data to disentangle how ecological and non-ecological processes contributed to population differentiation and speciation in an ongoing radiation of Lanistes gastropods from the Malawi Basin. I found a remarkable hierarchical structure of differentiation mechanisms in space and time: neutral and mutation-order processes are older and occur mainly between regions, whereas more recent adaptive processes are the main driver of genetic differentiation and reproductive isolation within regions. The strongest differentiation occurs between habitats and between regions, i.e. when ecological and non-ecological processes act synergistically. The structured occurrence of these processes based on the specific geographic setting and ecological opportunities strongly influenced the potential for evolutionary radiation. The results highlight the importance of interactions between various mechanisms of differentiation in evolutionary radiations, and suggest that non-ecological processes are important in adaptive radiations, including those of cichlids. Insight into such interactions is critical to understanding large-scale patterns of organismal diversity.
Data from: Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities
Environmental degradation may have strong effects on community assembly processes. We examined the assembly of bacterial and fungal communities in anthropogenically altered and near-pristine streams. Using pyrosequencing of bacterial and fungal DNA from decomposed alder Alnus incana leaves, we specifically examined if environmental degradation deterministically decreases or increases the compositional turnover of bacterial and fungal communities. Our results showed that near-pristine streams and anthropogenically altered streams supported distinct fungal and bacterial communities. The mechanisms assembling these communities were different in near-pristine and altered environments. Environmental disturbance homogenized bacterial communities, whereas fungal communities were more dissimilar in disturbed sites than in near-pristine sites. Compositional variation of both bacteria and fungi was related to water chemistry variables in disturbed sites, further implying the influence of environmental degradation on community assembly. Bacterial and fungal communities in near-pristine streams were weakly controlled by environmental factors, suggesting that the relative importance of niche-based versus neutral processes in assembling microbial communities may strongly depend on the spatial scale and local environmental context. Our results thus suggest that environmental degradation may strongly affect the composition and β-diversity of stream microbial communities colonizing leaf litter, and that the direction of the change can be different between bacteria and fungi. A better understanding of the environmental tolerances of microbes and the mechanisms assembling microbial communities in natural environmental settings is needed to predict how environmental alteration is likely to affect microbial communities.
Data from: Belowground-mediated and phase-dependent processes drive nitrogen-evoked community changes in grasslands
<ol> <li>Enhanced deposition of atmospheric nitrogen (N) leads to loss of plant diversity in grassland ecosystems. Numerous theories have provided potential explanations for the negative effects of N enrichment on plant diversity. However, the relative importance of each mechanism and the time scales of responses for the different functional groups remain unclear.</li> <li>We investigated the temporal responses of plant community in a temperate steppe to N enrichment by linking aboveground to belowground processes using a series of field N-addition and greenhouse experiments.</li> <li>The N enrichment-induced declines in plant diversity of grasslands were phase-based, functional group-dependent, and driven by three belowground processes. The rapid accumulation of NH<sub>4</sub><sup>+</sup>-N by N addition inhibited photosynthetic rates of broad-leaf-non-rhizomatous forbs, contributing to loss of these N-sensitive species during early phase of N enrichment (≤3 years). The N-induced changes in this phase were independent of soil pH as evidenced by results from application lime to mitigate N-evoked soil acidification. With progression of N addition, manganese (Mn) toxicity to narrow-leaf-non-rhizomatous forbs due to soil acidification-induced Mn<sup>2+</sup> mobilization in soil accounted for their loss in the second phase of N enrichment (~ 4-9 years). When N addition proceeded longer than ~10 years, N enrichment stimulated belowground meristem differentiation and rhizome growth of the rhizomatous species, leading to the dominance by rhizomatous sedges/grasses in the community at later phase of N enrichment.</li> </ol> <p>Synthesis: The hierarchical mechanisms not only provide a comprehensive explanation for the N enrichment-induced diversity decline in grasslands, but can also facilitate us to understand the differential sensitivities of ecosystems to chronic N enrichment, and predict future ecosystem dynamics.</p>
Data from: Evolutionary processes and its environmental correlates in the cranial morphology of western chipmunks (Tamias)
The importance of the environment in shaping phenotypic evolution lies at the core of evolutionary biology. Chipmunks of the genus Tamias (subgenus Neotamias) are part of a very recent radiation, occupying a wide range of environments with marked niche partitioning among species. One open question is if and how those differences in environments affected phenotypic evolution in this lineage. Herein we examine the relative importance of genetic drift versus natural selection in the origin of cranial diversity exhibited by clade members. We also explore the degree to which variation in potential selective agents (environmental variables) are correlated with the patterns of morphological variation presented. We found that genetic drift cannot explain morphological diversification in the group, thus supporting the potential role of natural selection as the predominant evolutionary force during Neotamias cranial diversification, although the strength of selection varied greatly among species. This morphological diversification, in turn, was correlated with environmental conditions, suggesting a possible causal relationship. These results underscore that extant Neotamias represent a radiation in which aspects of the environment might have acted as the selective force driving species' divergence.
Data from: Inferring contemporary dispersal processes in plant metapopulations: comparison of direct and indirect estimates of dispersal for the annual species Crepis sancta
Analyzing population dynamics in changing habitats is a prerequisite for population dynamics forecasting. The recent development of metapopulation modeling allows the estimation of dispersal kernels based on the colonization pattern but the accuracy of these estimates compared with direct estimates of the seed dispersal kernel has rarely been assessed. In this study, we used recent genetic methods based on parentage analysis (spatially explicit mating models) to estimate seed and pollen dispersal kernels as well as seed and pollen immigration in fragmented urban populations of the plant species Crepis sancta with contrasting patch dynamics. Using two independent networks, we documented substantial seed immigration and a highly restricted dispersal kernel. Moreover, immigration heterogeneity among networks was consistent with previously reported metapopulation dynamics, showing that colonization was mainly due to external colonization in the first network (propagule rain) and local colonization in the second network. We concluded that the differences in urban patch dynamics are mainly due to seed immigration heterogeneity, highlighting the importance of external population source in the spatio-temporal dynamics of plants in a fragmented landscape. The results show that indirect and direct methods were qualitatively consistent, providing a proper interpretation of indirect estimates. This study provides attempts to link genetic and demographic methods and show that patch occupancy models may provide simple methods for analyzing population dynamics in heterogeneous landscapes in the context of global change.
Data from: Subordinate plants mitigate drought effects on soil ecosystem processes by stimulating fungi
The subordinate insurance hypothesis suggests that highly diverse communities contain greater numbers of subordinate species than less diverse communities. It has previously been reported that subordinate species can improve grassland productivity during drought, but the underlying mechanisms remain undetermined. Using a combination of subordinate species removal and summer drought, we show that soil processes play a critical role in community resistance to drought. Interestingly, subordinate species drive soil microbial community structure and largely mitigate the effect of drought on grassland soil functioning. Our results highlight subordinate species in shifting the balance within the phospholipid fatty acid (PLFA) microbial community towards more fungal dominance. Fungal communities promoted by subordinate species were more resistant to drought and maintained higher rates of litter decomposition and soil respiration. These results emphasize the important role of subordinate species in mitigating drought effects on soil ecosystem functions. Reciprocal effects between fungi and subordinate species explain also how subordinate species better resisted to drought conditions. Our results point to a delayed plant–soil feedback following environmental perturbation. Additionally, they extend the diversity insurance hypothesis by showing that more diverse communities not only contain species well adapted to perturbations, but also species with higher impacts on soil microbial communities and related ecosystem functions.
Data from: Influence of introgression and geological processes on phylogenetic relationships of western North American mountain suckers (Pantosteus, Catostomidae)
Intense geological activity caused major topographic changes in Western North America over the past 15 million years. Major rivers here are composites of different ancient rivers, resulting in isolation and mixing episodes between river basins over time. This history influenced the diversification of most of the aquatic fauna. The genus Pantosteus is one of several clades centered in this tectonically active region. The eight recognized Pantosteus species are widespread and common across southwestern Canada, western USA and into northern Mexico. They are typically found in medium gradient, middle-elevation reaches of rivers over rocky substrates. This study (1) compares molecular data with morphological and paleontological data for proposed species of Pantosteus, (2) tests hypotheses of their monophyly, (3) uses these data for phylogenetic inferences of sister-group relationships, and (4) estimates timing of divergence events of identified lineages. Using 8055 base pairs from mitochondrial DNA protein coding genes, Pantosteus and Catostomus are reciprocally monophyletic, in contrast with morphological data. The only exception to a monophyletic Pantosteus is P. columbianus whose mtDNA is closely aligned with C. tahoensis because of introgression. Within Pantosteus, several species have deep genetic divergences among allopatric sister lineages, several of which are diagnosed and elevated to species, bringing the total diversity in the group to 11 species. Conflicting molecular and morphological data may be resolved when patterns of divergence are shown to be correlated with sympatry and evidence of introgression.
Data from: Medical-device recalls in the UK and the device-regulation process: retrospective review of safety notices and alerts
Background: Medical devices are used widely for virtually every disease and condition. Although devices are subject to regulation, the number of recalls, the clinical data requirements for regulation and the impact on patient safety are poorly understood. Methods: The authors defined a device using European directives and used publicly available information on the Medicines and Health Regulatory Authority website to determine the number of devices recalled from January 2006 to December 2010. Two reviewers independently assessed Field Safety Notices and Medical Device Alerts. The authors wrote to manufacturers to obtain further information and clinical data, and summarised data by year, Conformité Européenne classification, indication, and Food and Drug Administration recall system of severity. Results: In total, 2124 field safety notices were issued over the 5-year period, an increase of 1220% (62 in 2006 to 757 in 2010). 447 Medical Device Alerts were issued in the same period, and 44% were assessed as a reasonable probability of causing serious adverse health consequences or death. The authors wrote to 192 manufacturers of withdrawn devices and received 101 (53%) replies; only four (2.1%) provided the clinical data the authors requested. A lack of available transparent data prevented full analyses of the safety impact. Of the highest-risk recalled devices, more than half were related to the cardiovascular system (25%) or musculoskeletal system (33%), and 88% (95% CI 80% to 97%) were assessed as a reasonable probability of causing serious adverse health consequences or death. For low-risk devices, the figure was 34% (95% CI 26% to 42%). Conclusion: The number of medical devices subject to recalls or warnings in the UK has risen dramatically. A substantial number of these devices may have caused serious adverse effects in patients and contributed to healthcare costs. Significant problems exist in the UK with a lack of access to transparent data and a registry of the highest-risk devices.
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.