Experimental evaluation of spatial capture–recapture study design

This research was funded by the National Institute of Food and Agriculture, accession 1009581. This is a contribution of the Salamander Population and Adaptation Network (SPARCnet) and contribution #767 of the U.S. Geological Survey’s Amphibian Research and Monitoring Initiative (ARMI).A principal challenge impeding strong inference in analyses of wild populations is the lack of robust and long-term data sets. Recent advancements in analytical tools used in wildlife science may increase our ability to integrate smaller data sets and enhance the statistical power of population estimates. One such advancement, the development of spatial capture-recapture (SCR) methods, explicitly accounts for differences in spatial study designs, making it possible to equate multiple study designs in one analysis. SCR has been shown to be robust to variation in design as long as minimal sampling guidance is adhered to. However, these expectations are based on simulation and have yet to be evaluated in wild populations. Here we conduct a rigorously designed field experiment by manipulating the arrangement of artificial cover objects (ACOs) used to collect data on red-backed salamanders (Plethodon cinereus) to empirically evaluate the effects of design configuration on inference made using SCR. Our results suggest that, using SCR, estimates of space use and detectability are sensitive to study design configuration, namely the spacing and extent of the array, and that caution is warranted when assigning biological interpretation to these parameters. However, estimates of population density remain robust to design except when the configuration of detectors grossly violates existing recommendations.Publisher PDFPeer reviewe

Ignoring species availability biases occupancy estimates in single-scale occupancy models

Most applications of single-scale occupancy models do not differentiate between availability and detectability, even though species availability is rarely equal to one. Species availability can be estimated using multi-scale occupancy models; however, for the practical application of multi-scale occupancy models, it can be unclear what a robust sampling design looks like and what the statistical properties of the multi-scale and single-scale occupancy models are when availability is less than one. Using simulations, we explore the following common questions asked by ecologists during the design phase of a field study: (Q1) what is a robust sampling design for the multi-scale occupancy model when there are a priori expectations of parameter estimates? (Q2) what is a robust sampling design when we have no expectations of parameter estimates? and (Q3) can a single-scale occupancy model with a random effects term adequately absorb the extra heterogeneity produced when availability is less than one and provide reliable estimates of occupancy probability? Our results show that there is a tradeoff between the number of sites and surveys needed to achieve a specified level of acceptable error for occupancy estimates using the multi-scale occupancy model. We also document that when species availability is low (\u3c0.40 on the probability scale), then single-scale occupancy models underestimate occupancy by as much as 0.40 on the probability scale, produce overly precise estimates, and provide poor parameter coverage. This pattern was observed when a random effects term was and was not included in the single-scale occupancy model, suggesting that adding a random-effects term does not adequately absorb the extra heterogeneity produced by the availability process. In contrast, when species availability was high (\u3e0.60), single-scale occupancy models performed similarly to the multi-scale occupancy model. Users can further explore our results and sampling designs across a number of different scenarios using the RShiny app https://gdire nzo.shiny apps.io/multiscale -occ/. Our results suggest that unaccounted for availability can lead to underestimating species distributions when using single-scale occupancy models

Interbasin Water Transfer, Riverine Connectivity, and Spatial Controls on Fish Biodiversity

BACKGROUND: Large-scale inter-basin water transfer (IBWT) projects are commonly proposed as solutions to water distribution and supply problems. These problems are likely to intensify under future population growth and climate change scenarios. Scarce data on the distribution of freshwater fishes frequently limits the ability to assess the potential implications of an IBWT project on freshwater fish communities. Because connectivity in habitat networks is expected to be critical to species' biogeography, consideration of changes in the relative isolation of riverine networks may provide a strategy for controlling impacts of IBWTs on freshwater fish communities. METHODS/PRINCIPAL FINDINGS: Using empirical data on the current patterns of freshwater fish biodiversity for rivers of peninsular India, we show here how the spatial changes alone under an archetypal IBWT project will (1) reduce freshwater fish biodiversity system-wide, (2) alter patterns of local species richness, (3) expand distributions of widespread species throughout peninsular rivers, and (4) decrease community richness by increasing inter-basin similarity (a mechanism for the observed decrease in biodiversity). Given the complexity of the IBWT, many paths to partial or full completion of the project are possible. We evaluate two strategies for step-wise implementation of the 11 canals, based on economic or ecological considerations. We find that for each step in the project, the impacts on freshwater fish communities are sensitive to which canal is added to the network. CONCLUSIONS/SIGNIFICANCE: Importantly, ecological impacts can be reduced by associating the sequence in which canals are added to characteristics of the links, except for the case when all 11 canals are implemented simultaneously (at which point the sequence of canal addition is inconsequential). By identifying the fundamental relationship between the geometry of riverine networks and freshwater fish biodiversity, our results will aid in assessing impacts of IBWT projects and balancing ecosystem and societal demands for freshwater, even in cases where biodiversity data are limited

Polar bears are inefficient predators of seabird eggs

Climate-mediated sea-ice loss is disrupting the foraging ecology of polar bears (Ursus maritimus) across much of their range. As a result, there have been increased reports of polar bears foraging on seabird eggs across parts of their range. Given that polar bears have evolved to hunt seals on ice, they may not be efficient predators of seabird eggs. We investigated polar bears\u27 foraging performance on common eider (Somateria mollissima) eggs on Mitivik Island, Nunavut, Canada to test whether bear decision-making heuristics are consistent with expectations of optimal foraging theory. Using aerial-drones, we recorded multiple foraging bouts over 11 days, and found that as clutches were depleted to completion, bears did not exhibit foraging behaviours matched to resource density. As the season progressed, bears visited fewer nests overall, but marginally increased their visitation to nests that were already empty. Bears did not display different movement modes related to nest density, but became less selective in their choice of clutches to consume. Lastly, bears that capitalized on visual cues of flushing eider hens significantly increased the number of clutches they consumed; however, they did not use this strategy consistently or universally. The foraging behaviours exhibited by polar bears in this study suggest they are inefficient predators of seabird eggs, particularly in the context of matching behaviours to resource density

PubChem3D: Diversity of shape

<p>Abstract</p> <p>Background</p> <p>The shape diversity of 16.4 million biologically relevant molecules from the PubChem Compound database and their 1.46 billion diverse conformers was explored as a function of molecular volume.</p> <p>Results</p> <p>The diversity of shape space was investigated by determining the shape similarity threshold to achieve a maximum on the count of reference shapes per unit of conformer volume. The rate of growth in shape space, as represented by a decreasing shape similarity threshold, was found to be remarkably smooth as a function of volume. There was no apparent correlation between the count of conformers per unit volume and their diversity, meaning that a single reference shape can describe the shape space of many chemical structures. The ability of a volume to describe the shape space of lesser volumes was also examined. It was shown that a given volume was able to describe 40-70% of the shape diversity of lesser volumes, for the majority of the volume range considered in this study.</p> <p>Conclusion</p> <p>The relative growth of shape diversity as a function of volume and shape similarity is surprisingly uniform. Given the distribution of chemicals in PubChem versus what is theoretically synthetically possible, the results from this analysis should be considered a conservative estimate to the true diversity of shape space.</p

Speciation with gene flow in a narrow endemic West Virginia cave salamander (\u3ci\u3eGyrinophilus subterraneus\u3c/i\u3e)

Due to their limited geographic distributions and specialized ecologies, cave species are often highly endemic and can be especially vulnerable to habitat degradation within and surrounding the cave systems they inhabit. We investigated the evolutionary history of the West Virginia Spring Salamander (Gyrinophilus subterraneus), estimated the population trend from historic and current survey data, and assessed the current potential for water quality threats to the cave habitat. Our genomic data (mtDNA sequence and ddRADseq-derived SNPs) reveal two, distinct evolutionary lineages within General Davis Cave corresponding to G. subterraneus and its widely distributed sister species, Gyrinophilus porphyriticus, that are also differentiable based on morphological traits. Genomic models of evolutionary history strongly support asymmetric and continuous gene flow between the two lineages, and hybrid classification analyses identify only parental and first generation cross (F1) progeny. Collectively, these results point to a rare case of sympatric speciation occurring within the cave, leading to strong support for continuing to recognize G. subterraneus as a distinct and unique species. Due to its specialized habitat requirements, the complete distribution of G. subterraneus is unresolved, but using survey data in its type locality (and currently the only known occupied site), we find that the population within General Davis Cave has possibly declined over the last 45 years. Finally, our measures of cave and surface stream water quality did not reveal evidence of water quality impairment and provide important baselines for future monitoring. In addition, our unexpected finding of a hybrid zone and partial reproductive isolation between G. subterraneus and G. porphyriticus warrants further attention to better understand the evolutionary and conservation implications of occasional hybridization between the species

Transparent, Open, and Reproducible Prevention Science

The field of prevention science aims to understand societal problems, identify effective interventions, and translate scientific evidence into policy and practice. There is growing interest among prevention scientists in the potential for transparency, openness, and reproducibility to facilitate this mission by providing opportunities to align scientific practice with scientific ideals, accelerate scientific discovery, and broaden access to scientific knowledge. The overarching goal of this manuscript is to serve as a primer introducing and providing an overview of open science for prevention researchers. In this paper, we discuss factors motivating interest in transparency and reproducibility, research practices associated with open science, and stakeholders engaged in and impacted by open science reform efforts. In addition, we discuss how and why different types of prevention research could incorporate open science practices, as well as ways that prevention science tools and methods could be leveraged to advance the wider open science movement. To promote further discussion, we conclude with potential reservations and challenges for the field of prevention science to address as it transitions to greater transparency, openness, and reproducibility. Throughout, we identify activities that aim to strengthen the reliability and efficiency of prevention science, facilitate access to its products and outputs, and promote collaborative and inclusive participation in research activities. By embracing principles of transparency, openness, and reproducibility, prevention science can better achieve its mission to advance evidence-based solutions to promote individual and collective well-being

Fast 3D shape screening of large chemical databases through alignment-recycling

<p>Abstract</p> <p>Background</p> <p>Large chemical databases require fast, efficient, and simple ways of looking for similar structures. Although such tasks are now fairly well resolved for graph-based similarity queries, they remain an issue for 3D approaches, particularly for those based on 3D shape overlays. Inspired by a recent technique developed to compare molecular shapes, we designed a hybrid methodology, alignment-recycling, that enables efficient retrieval and alignment of structures with similar 3D shapes.</p> <p>Results</p> <p>Using a dataset of more than one million PubChem compounds of limited size (< 28 heavy atoms) and flexibility (< 6 rotatable bonds), we obtained a set of a few thousand diverse structures covering entirely the 3D shape space of the conformers of the dataset. Transformation matrices gathered from the overlays between these diverse structures and the 3D conformer dataset allowed us to drastically (100-fold) reduce the CPU time required for shape overlay. The alignment-recycling heuristic produces results consistent with <it>de novo </it>alignment calculation, with better than 80% hit list overlap on average.</p> <p>Conclusion</p> <p>Overlay-based 3D methods are computationally demanding when searching large databases. Alignment-recycling reduces the CPU time to perform shape similarity searches by breaking the alignment problem into three steps: selection of diverse shapes to describe the database shape-space; overlay of the database conformers to the diverse shapes; and non-optimized overlay of query and database conformers using common reference shapes. The precomputation, required by the first two steps, is a significant cost of the method; however, once performed, querying is two orders of magnitude faster. Extensions and variations of this methodology, for example, to handle more flexible and larger small-molecules are discussed.</p

PubChem3D: Similar conformers

<p>Abstract</p> <p>Background</p> <p>PubChem is a free and open public resource for the biological activities of small molecules. With many tens of millions of both chemical structures and biological test results, PubChem is a sizeable system with an uneven degree of available information. Some chemical structures in PubChem include a great deal of biological annotation, while others have little to none. To help users, PubChem pre-computes "neighboring" relationships to relate similar chemical structures, which may have similar biological function. In this work, we introduce a "Similar Conformers" neighboring relationship to identify compounds with similar 3-D shape and similar 3-D orientation of functional groups typically used to define pharmacophore features.</p> <p>Results</p> <p>The first two diverse 3-D conformers of 26.1 million PubChem Compound records were compared to each other, using a shape Tanimoto (ST) of 0.8 or greater and a color Tanimoto (CT) of 0.5 or greater, yielding 8.16 billion conformer neighbor pairs and 6.62 billion compound neighbor pairs, with an average of 253 "Similar Conformers" compound neighbors per compound. Comparing the 3-D neighboring relationship to the corresponding 2-D neighboring relationship ("Similar Compounds") for molecules such as caffeine, aspirin, and morphine, one finds unique sets of related chemical structures, providing additional significant biological annotation. The PubChem 3-D neighboring relationship is also shown to be able to group a set of non-steroidal anti-inflammatory drugs (NSAIDs), despite limited PubChem 2-D similarity.</p> <p>In a study of 4,218 chemical structures of biomedical interest, consisting of many known drugs, using more diverse conformers per compound results in more 3-D compound neighbors per compound; however, the overlap of the compound neighbor lists per conformer also increasingly resemble each other, being 38% identical at three conformers and 68% at ten conformers. Perhaps surprising is that the average count of conformer neighbors per conformer increases rather slowly as a function of diverse conformers considered, with only a 70% increase for a ten times growth in conformers per compound (a 68-fold increase in the conformer pairs considered).</p> <p>Neighboring 3-D conformers on the scale performed, if implemented naively, is an intractable problem using a modest sized compute cluster. Methodology developed in this work relies on a series of filters to prevent performing 3-D superposition optimization, when it can be determined that two conformers cannot possibly be a neighbor. Most filters are based on Tanimoto equation volume constraints, avoiding incompatible conformers; however, others consider preliminary superposition between conformers using reference shapes.</p> <p>Conclusion</p> <p>The "Similar Conformers" 3-D neighboring relationship locates similar small molecules of biological interest that may go unnoticed when using traditional 2-D chemical structure graph-based methods, making it complementary to such methodologies. The computational cost of 3-D similarity methodology on a wide scale, such as PubChem contents, is a considerable issue to overcome. Using a series of efficient filters, an effective throughput rate of more than 150,000 conformers per second per processor core was achieved, more than two orders of magnitude faster than without filtering.</p

PubChem3D: a new resource for scientists

<p>Abstract</p> <p>Background</p> <p>PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse chemical structures with similar biological efficacies against targets available in PubChem that are difficult to interrelate using traditional 2-D similarity methods. A new layer called PubChem3D is added to PubChem to assist in this analysis.</p> <p>Description</p> <p>PubChem generates a 3-D conformer model description for 92.3% of all records in the PubChem Compound database (when considering the parent compound of salts). Each of these conformer models is sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) RMSD between conformers. A diverse conformer ordering gives a maximal description of the conformational diversity of a molecule when only a subset of available conformers is used. A pre-computed search per compound record gives immediate access to a set of 3-D similar compounds (called "Similar Conformers") in PubChem and their respective superpositions. Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data.</p> <p>A series of retrospective studies help to demonstrate important connections between chemical structures and their biological function that are not obvious using 2-D similarity but are readily apparent by 3-D similarity.</p> <p>Conclusions</p> <p>The addition of PubChem3D to the existing contents of PubChem is a considerable achievement, given the scope, scale, and the fact that the resource is publicly accessible and free. With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to exploit when exploring the biological annotations in PubChem.</p