strandCet: R package for estimating natural and non-natural mortality-at-age of cetaceans from age-structured strandings
Mortality is one of the most important parameters for the study of population dynamics. One of the main sources of information to calculate the mortality of cetaceans arises from the observed age-structure of stranded animals. A method based on an adaptation of a Heligman-Pollard model is proposed. A freely accessible package of functions (strandCet) has been created to apply this method in the statistical software R. Total, natural, and anthropogenic mortality-at-age is estimated using only data of stranded cetaceans whose age is known. Bayesian melding estimation with Incremental Mixture Importance Sampling is used for fitting this model. This characteristic, which accounts for uncertainty, further eases the estimation of credible intervals. The package also includes functions to perform life tables, Siler mortality models to calculate total mortality-at-age and Leslie matrices to derive population projections. Estimated mortalities can be tested under different scenarios. Population parameters as population growth, net production or generation time can be derived from population projections. The strandCet R package provides a new analytical framework to assess mortality in cetacean populations and to explore the consequences of management decisions using only stranding-derived data.
Saavedra (2018) strandCet: R package for estimating natural and non-natural mortality-at-age of cetaceans from age-structured strandings. PeerJ 6:e5768 https://doi.org/10.7717/peerj.5768
Phylogenetic analysis of the cytochrome P450 (CYP450) nucleotide sequences of the horse and predicted CYP450s of the white rhinoceros (Ceratotherium simum) and other mammalian species
Background The plight of the white rhinoceros (Ceratotherium simum) and the increasing need of treatment options for injured poaching victims led to the necessity to expand the knowledge on applicable drugs in this endangered species. With very little information available on drug pharmacokinetics in rhino, veterinarians have to rely on information generated from other species. The horse being a closely related species, has served as the model for dose extrapolations. However, from recent research on enrofloxacin and carprofen, the white rhino showed considerable differences in the pharmacokinetic properties of these drugs in comparison to the horse. While the reason for the differences is unknown, a likely cause may be a difference in present cytochrome P450 (CYP450), which may result in the rhino being genetically deficient in certain enzyme families. Methods For this paper we assess the degree of similarity of the CYP genome sequences across the different species, using BLAT (BLAST-like alignment tool) for the alignment of the nucleotide sequences of the equine CYP450 with potential homologous nucleotide sequences of the published database from white rhinos and other mammalian species (cow, pig, dog, sheep, elephant, mouse and human). Results The white rhino nucleotide sequences were 90.74% identical to the equine sequences. This was higher than the degree of similarity between any of the other evaluated species sequences. While no specific CYP family were found to be deficient in the published rhino genome, the horse genome contained additional genetic sequence for a larger number of iso-enzymes that were not present in the rhino. Discussion In pharmacokinetic study, it is well known that absence of a metabolic enzyme will result in constraints in drug metabolism and drug elimination. While this was our speculation, comparison to the horse and other mammalian species indicate that all the described CYP genes required for metabolism are present within the rhino genome. These results leave functional differences in enzyme activity and a lack of isoenzymes as the likely reason for the constraint in drug metabolism. Despite a more than 90% similarity of the equine and rhino gene sequences, seemingly small differences can have major effects on drug metabolism. Thus, in spite of the close anatomical relationship, the rhino should not simply be treated like a big horse.
Leiberich et al. (2018) Phylogenetic analysis of the cytochrome P450 (CYP450) nucleotide sequences of the horse and predicted CYP450s of the white rhinoceros (Ceratotherium simum) and other mammalian species. PeerJ 6:e5718 https://doi.org/10.7717/peerj.5718
Do an ecosystem engineer and environmental gradient act independently or in concert to shape juvenile plant communities? Tests with the leaf-cutter ant Atta laevigata in a Neotropical savanna
Background Ecosystem engineers are species that transform habitats in ways that influence other species.While the impacts of many engineers have been well described, our understanding of how their impact varies along environmental gradients remains limited. Although disentangling the effects of gradients and engineers on biodiversity is complicated—the gradients themselves can be altered by engineers—doing so is necessary to advance conceptual and mathematical models of ecosystem engineering. We used leaf-cutter ants (Atta spp.) to investigate the relative influence of gradients and environmental engineers on the abundance and species richness of woody plants. Methods We conducted our research in South America’s Cerrado. With a survey of plant recruits along a canopy cover gradient, and data on environmental conditions that influence plant recruitment, we fit statistical models that addressed the following questions: (1) Does A. laevigata modify the gradient in canopy cover found in our Cerrado site? (2) Do environmental conditions that influence woody plant establishment in the Cerrado vary with canopy cover or proximity to A. laevigata nests? (3) Do A. laevigata and canopy cover act independently or in concert to influence recruit abundance and species richness? Results We found that environmental conditions previously shown to influence plant establishment in the Cerrado varied in concert with canopy cover, but that ants are not modifying the cover gradient or cover over nests. However, ants are modifying other local environmental conditions, and the magnitude and spatial extent of these changes are consistent across the gradient. In contrast to prior studies, we found that ant-related factors (e.g., proximity to nests, ant changes in surface conditions), rather than canopy cover, had the strongest effect on the abundance of plant recruits. However, the diversity of plants was influenced by both the engineer and the canopy cover gradient. Discussion Atta laevigata in the Cerrado modify local conditions in ways that have strong but spatially restricted consequences for plant communities. We hypothesize that ants indirectly reduce seedling establishment by clearing litter and reducing soil moisture, which leads to seed and seedling desiccation. Altering soil nutrients could also reduce juvenile growth and survivorship; if so these indirect negative effects of engineering could exacerbate their direct effects of harvesting plants. The effects of Atta appear restricted to nest mounds, but they could be long-lasting because mounds persist long after a colony has died or migrated. Our results support the hypothesis that leaf-cutter ants play a dominant role in Cerrado plant demography. We suggest the ecological and economic footprint of these engineers may increase dramatically in coming decades due to the transformation of the Cerrado by human activities.
Costa et al. (2018) Do an ecosystem engineer and environmental gradient act independently or in concert to shape juvenile plant communities? Tests with the leaf-cutter ant Atta laevigata in a Neotropical savanna. PeerJ 6:e5612 https://doi.org/10.7717/peerj.5612
Artificial light at night alters life history in a nocturnal orb-web spider
The prevalence of artificial light at night (ALAN) is increasing rapidly around the world. The potential physiological costs of this night lighting are often evident in life history shifts. We investigated the effects of chronic night-time exposure to ecologically relevant levels of LED lighting on the life history traits of the nocturnal Australian garden orb-web spider (Eriophora biapicata). We reared spiders under a 12-h day and either a 12-h natural darkness (∼0 lux) or a 12-h dim light (∼20 lux) night and assessed juvenile development, growth and mortality, and adult reproductive success and survival. We found that exposure to ALAN accelerated juvenile development, resulting in spiders progressing through fewer moults, and maturing earlier and at a smaller size. There was a significant increase in daily juvenile mortality for spiders reared under 20 lux, but the earlier maturation resulted in a comparable number of 0 lux and 20 lux spiders reaching maturity. Exposure to ALAN also considerably reduced the number of eggs produced by females, and this was largely associated with ALAN-induced reductions in body size. Despite previous observations of increased fitness for some orb-web spiders in urban areas and near night lighting, it appears that exposure to artificial night lighting may lead to considerable developmental costs. Future research will need to consider the detrimental effects of ALAN combined with foraging benefits when studying nocturnal insectivores that forage around artificial lights.
Willmott et al. (2018) Artificial light at night alters life history in a nocturnal orb-web spider. PeerJ 6:e5599 https://doi.org/10.7717/peerj.5599
Young, American Indian or Alaskan Native, and born in the USA: at excess risk of starting extra-medical prescription pain reliever use?
Background Prescription pain reliever (PPR) overdoses differentially affect ‘American Indian/Alaskan Natives’ in the United States (US). Here, studying onset of extra-medical PPR use in 12-24-year-olds, we examine subgroup variations in rates of starting to use prescription pain relievers extra-medically (i.e., to get ‘high’ or for other reasons outside boundaries of prescriber’s intent). Risk differences (RD) are estimated for US-born versus non-US-born young people, stratified by American Indian/Alaskan Natives versus other ethnic self-identities. Methods Between 2002–2009, nationally representative cross-sectional samples of 12–24-year-old non-institutionalized civilians completed interviews for the US National Surveys of Drug Use and Health. Analysis-weighted annual incidence estimates, RD, and confidence intervals (CI) are from the Restricted-use Data Analysis System, an online software tool for US National Surveys of Drug Use and Health. Results Each year, an estimated 2.5% of 12-24-year-olds in the US start using PPR extra-medically (95% CI [2.1%–3.0%]). Estimates for the US-born (3.8%; 95% CI [3.7%–3.9%]) are larger (non-US-born: 1.8%; 95% CI [1.5%–2.0%]; RD = 2.0; p < 0.05). US-born American Indian/Alaskan Natives youths have the largest incidence rate (4.8%). Robust RD for US-born can be seen for ‘non-Hispanic White’ subgroups, and for others (e.g., ‘Cuban’, ‘Dominican’). Discussion Each year, one in 20 of US-born American Indian/Alaskan Natives starts using PPR extra-medically. Overdose prevention is important, but is no substitute for primary prevention initiatives for all young people. The observed epidemiological patterns can guide targeted prevention initiatives for the identified higher risk subgroups in complement with more universal prevention efforts intended to reduce incidence of first extra-medical PPR use, a crucial rate-limiting step on the path toward more serious drug involvement (i.e., progressing past initial use).
Parker et al. (2018) Young, American Indian or Alaskan Native, and born in the USA: at excess risk of starting extra-medical prescription pain reliever use?. PeerJ 6:e5713 https://doi.org/10.7717/peerj.5713
The CCB-ID approach to tree species mapping with airborne imaging spectroscopy
Background Biogeographers assess how species distributions and abundances affect the structure, function, and composition of ecosystems. Yet we face a major challenge: it is difficult to precisely map species across landscapes. Novel Earth observations could overcome this challenge for vegetation mapping. Airborne imaging spectrometers measure plant functional traits at high resolution, and these measurements can be used to identify tree species. In this paper, I describe a trait-based approach to species identification with imaging spectroscopy, the Center for Conservation Biology species identification (CCB-ID) method, which was developed as part of an ecological data science evaluation competition. Methods These methods were developed using airborne imaging spectroscopy data from the National Ecological Observatory Network (NEON). CCB-ID classified tree species using trait-based reflectance variation and decision tree-based machine learning models, approximating a morphological trait and dichotomous key method inspired by botanical classification. First, outliers were removed using a spectral variance threshold. The remaining samples were transformed using principal components analysis (PCA) and resampled to reduce common species biases. Gradient boosting and random forest classifiers were trained using the transformed and resampled feature data. Prediction probabilities were calibrated using sigmoid regression, and sample-scale predictions were averaged to the crown scale. Results CCB-ID received a rank-1 accuracy score of 0.919, and a cross-entropy cost score of 0.447 on the competition test data. Accuracy and specificity scores were high for all species, but precision and recall scores varied for rare species. PCA transformation improved accuracy scores compared to models trained using reflectance data, but outlier removal and data resampling exacerbated class imbalance problems. Discussion CCB-ID accurately classified tree species using NEON data, reporting the best scores among participants. However, it failed to overcome several species mapping challenges like precisely identifying rare species. Key takeaways include (1) selecting models using metrics beyond accuracy (e.g., recall) could improve rare species predictions, (2) within-genus trait variation may drive spectral separability, precluding efforts to distinguish between functionally convergent species, (3) outlier removal and data resampling can exacerbate class imbalance problems, and should be carefully implemented, (4) PCA transformation greatly improved model results, and (5) targeted feature selection could further improve species classification models. CCB-ID is open source, designed for use with NEON data, and available to support species mapping efforts.
Spatial and Geographic Information Science
Anderson (2018) The CCB-ID approach to tree species mapping with airborne imaging spectroscopy. PeerJ 6:e5666 https://doi.org/10.7717/peerj.5666
Patient-centered care interventions to reduce the inappropriate prescription and use of benzodiazepines and z-drugs: a systematic review
Background Benzodiazepines (BZDs) and z-drugs are effective drugs, but they are prescribed excessively worldwide. International guidelines recommend a maximum treatment duration of 4 weeks. Although these drugs are effective in the short-term, long-term BZD therapy is associated with considerable adverse effects, the development of tolerance and, finally, addiction. However, there are different interventions in terms of patient-centered care that aim to reduce the use of BZDs and z-drugs as well as assist health care professionals (HCPs) in preventing the inappropriate prescription of BZDs. Aim The aim of this systematic review was to identify interventions that promote patient-centered treatments for inappropriate BZD and z-drug use and to analyze their effectiveness in reducing the inappropriate use of these drugs. Methods To identify relevant studies, the PubMed, EMBASE, PsycINFO, Psyndex, and Cochrane Library databases were searched. Studies with controlled designs focusing on adult patients were included. Trials with chronically or mentally ill patients were excluded if long-term BZD and z-drug use was indicated. Study extraction was performed based on the Cochrane Form for study extraction. To assess the quality of the studies, we used a tool based on the Cochrane Collaboration’s tool for assessing the risk of bias in randomized trials. Results We identified 7,068 studies and selected 20 for systematic review. Nine interventions focused on patients, nine on HCPs, and two on both patients and HCPs. Intervention types ranged from simple to multifaceted. Patient-centered interventions that provided patient information effectively increased the appropriate use of BZDs. The educational approaches for HCPs that aimed to achieve appropriate prescription reported inconsistent results. The methods that combined informing patients and HCPs led to a significant reduction in BZD use. Conclusions This is the first review of studies focused on patient-centered approaches to reducing the inappropriate prescription and use of BZDs and z-drugs. The patient-centered dimension of patient information was responsible for a decrease in BZD and z-drug consumption. Further, in some studies, the patient-centered dimensions responsible for reducing the prescription and use of BZDs and z-drugs were the clinician’s essential characteristics and clinician-patient communication.
Mokhar et al. (2018) Patient-centered care interventions to reduce the inappropriate prescription and use of benzodiazepines and z-drugs: a systematic review. PeerJ 6:e5535 https://doi.org/10.7717/peerj.5535
Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event
Using a large, consistent set of loci shared by descent (orthologous) to study relationships among taxa would revolutionize among-lineage comparisons of divergence and speciation processes. Ultraconserved elements (UCEs), highly conserved regions of the genome, offer such genomic markers. The utility of UCEs for deep phylogenetics is clearly established and there are mature analytical frameworks available, but fewer studies apply UCEs to recent evolutionary events, creating a need for additional example datasets and analytical approaches. We used UCEs to study population genomics in snow and McKay’s buntings (Plectrophenax nivalis and P. hyperboreus). Prior work suggested divergence of these sister species during the last glacial maximum (∼18–74 Kya). With a sequencing depth of ∼30× from four individuals of each species, we used a series of analysis tools to genotype both alleles, obtaining a complete dataset of 2,635 variable loci (∼3.6 single nucleotide polymorphisms/locus) and 796 invariable loci. We found no fixed allelic differences between the lineages, and few loci had large allele frequency differences. Nevertheless, individuals were 100% diagnosable to species, and the two taxa were different genetically (FST = 0.034; P = 0.03). The demographic model best fitting the data was one of divergence with gene flow. Estimates of demographic parameters differed from published mtDNA research, with UCE data suggesting lower effective population sizes (∼92,500–240,500 individuals), a deeper divergence time (∼241,000 years), and lower gene flow (2.8–5.2 individuals per generation). Our methods provide a framework for future population studies using UCEs, and our results provide additional evidence that UCEs are useful for answering questions at shallow evolutionary depths.
Winker et al. (2018) Ultraconserved elements (UCEs) illuminate the population genomics of a recent, high-latitude avian speciation event. PeerJ 6:e5735 https://doi.org/10.7717/peerj.5735
Trophic state (TSISD) and mixing type significantly influence pelagic zooplankton biodiversity in temperate lakes (NW Poland)
Background Lake depth and the consequent mixing regime and thermal structure have profound effects on ecosystem functioning, because depth strongly affects the availability of nutrients, light, and oxygen. All these conditions influence patterns of zooplankton diversity. Zooplankton are a key component of the aquatic environment and are essential to maintaining natural processes in freshwater ecosystems. However, zooplankton biodiversity can be different regard to depth, mixing type and trophic state. Therefore, the aim of this study was to examine how depth and mixing regime affect zooplankton diversity in lakes. We also investigated the vertical distribution of diversity across a trophic gradient of lakes. Methods A total of 329 zooplankton samples from 79 temperate lakes (36 polymictic and 43 dimictic) were collected. The biodiversity of zooplankton was calculated using species richness (SR) and the Shannon index (SI). An index based on Secchi disc visibility was used to determine the trophic state index (TSISD) of lakes. The one-way ANOVA with Duncan’s post hoc test were used to determine differences in zooplankton biodiversity between mictic lake types and thermal layers. To find the best predictors for zooplankton biodiversity a multiple stepwise regression was used. The rarefaction method was used to evaluate the impact of mixing types, thermal layers, and the TSISDon zooplankton biodiversity indices. A Sørensen similarity analysis and nonmetric multidimensional scaling (NMDS) were performed to describe the similarity patterns in species composition among lakes. Results We identified a total of 151 taxa from 36 polymictic and 43 dimictic lakes. Lake depth and the TSISD were significantly correlated with the biodiversity of lake zooplankton. The results of ANOVA and Duncan tests show that mictic type and thermal zones had a significant effect on zooplankton biodiversity. The rarefaction curve showed significant differences in zooplankton biodiversity, which was greater in lakes with lower trophic state. Ordination by NMDS showed clustering of different mictic types, thermal layers, and composition changes throughout the TSISDprofile. Moreover, we determined that polymictic lakes are more heterogeneous than dimictic lakes in regard to zooplankton similarities. Discussion Both mictic lake types were characterized by varying levels of zooplankton biodiversity, which is shaped by the communities’ response to lake depth, thermal layers and TSISD values. The zooplankton SR and SI (during daylight hours) depends greatly on the mixing type. Lake type also indicates the importance of the metalimnion in shaping zooplankton biodiversity in dimictic lakes. In addition, data from NW Polish lakes indicated that the increase of the TSISD leads to taxonomic shifts and has a negative effect on the diversity of all groups of zooplankton.
Sługocki et al. (2018) Trophic state (TSISD) and mixing type significantly influence pelagic zooplankton biodiversity in temperate lakes (NW Poland). PeerJ 6:e5731 https://doi.org/10.7717/peerj.5731
Potential impacts of finfish aquaculture on eelgrass (Zostera marina) beds and possible monitoring metrics for management: a case study in Atlantic Canada
Eelgrass (Zostera marina) has been designated an Ecologically Significant Species in Atlantic Canada. The development and rapid expansion of netpen finfish aquaculture into sensitive coastal habitats has raised concerns about the impacts of finfish aquaculture on eelgrass habitats. To date, no studies have been done in Atlantic Canada to examine these impacts or to identify potential monitoring variables that would aid in the development of specific conservation and management objectives. As a first step in addressing this gap, we examined differences in environmental variables, eelgrass bed structure and macroinfauna communities at increasing distances from a finfish farm in Port Mouton Bay, a reference site in adjacent Port Joli Bay, and published survey results from other sites without finfish farms along the Atlantic Coast of Nova Scotia. Drawing on research done elsewhere and our results, we then identified possible metrics for assessing and monitoring local impacts of finfish aquaculture on eelgrass habitats. Our results suggest some nutrient and organic enrichment, higher epiphyte loads, lower eelgrass cover and biomass, and lower macroinfauna biomass closer to the farm. Moreover, community structure significantly differed between sites with some species increasing and others decreasing closer to the farm. Changes in the macroinfauna community could be linked to observed differences in environmental and eelgrass bed variables. These results provide new insights into the potential impacts of finfish aquaculture on eelgrass habitats in Atlantic Canada. We recommend a suite of measures for assessment and monitoring that take into account response time to disturbance and account for different levels of eelgrass organizational response (from physiological to community).
Cullain et al. (2018) Potential impacts of finfish aquaculture on eelgrass (Zostera marina) beds and possible monitoring metrics for management: a case study in Atlantic Canada. PeerJ 6:e5630 https://doi.org/10.7717/peerj.5630