title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1477 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A new tyrannosaurid (Dinosauria: Theropoda) from the Upper Cretaceous Menefee Formation of New Mexico link: https://peerj.com/articles/5749 last-modified: 2018-10-09 description: The giant tyrannosaurids were the apex predators of western North America and Asia during the close of the Cretaceous Period. Although many tyrannosaurid species are known from numerous skeletons representing multiple growth stages, the early evolution of Tyrannosauridae remains poorly known, with the well-known species temporally restricted to the middle Campanian-latest Maastrichtian (∼77–66 Ma). The recent discovery of a new tyrannosaurid, Lythronax argestes, from the Wahweap Formation of Utah provided new data on early Campanian (∼80 Ma) tyrannosaurids. Nevertheless, the early evolution of Tyrannosauridae is still largely unsampled. We report a new tyrannosaurid represented by an associated skeleton from the lower Campanian Allison Member of the Menefee Formation of New Mexico. Despite fragmentation of much of the axial and appendicular skeleton prior to discovery, the frontals, a metacarpal, and two pedal phalanges are well-preserved. The frontals exhibit an unambiguous autapomorphy and a second potential autapomorphy that distinguish this specimen from all other tyrannosaurids. Therefore, the specimen is made the holotype of the new genus and species Dynamoterror dynastes. A phylogenetic analysis places Dynamoterror dynastes in the tyrannosaurid subclade Tyrannosaurinae. Laser-scanning the frontals and creation of a composite 3-D digital model allows the frontal region of the skull roof of Dynamoterror to be reconstructed. creator: Andrew T. McDonald creator: Douglas G. Wolfe creator: Alton C. Dooley uri: https://doi.org/10.7717/peerj.5749 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 McDonald et al. title: Effects of wine-cap Stropharia cultivation on soil nutrients and bacterial communities in forestlands of northern China link: https://peerj.com/articles/5741 last-modified: 2018-10-09 description: BackgroundCultivating the wine-cap mushroom (Stropharia rugosoannulata) on forestland has become popular in China. However, the effects of wine-cap Stropharia cultivation on soil nutrients and bacterial communities are poorly understood.MethodsWe employed chemical analyses and high-throughput sequencing to determine the impact of cultivating the wine-cap Stropharia on soil nutrients and bacterial communities of forestland.ResultsCultivation regimes of Stropharia on forestland resulted in consistent increases of soil organic matter (OM) and available phosphorus (AP) content. Among the cultivation regimes, the greatest soil nutrient contents were found in the one-year interval cultivation regime, and the lowest total N and alkaline hydrolysable N contents were observed in the current-year cultivation regime. No significant differences were observed in alpha diversity among all cultivation regimes. Specific soil bacterial groups, such as Acidobacteria, increased in abundance after cultivation of Stropharia rugosoannulata.DiscussionGiven the numerous positive effects exerted by OM on soil physical and chemical properties, and the consistent increase in OM content for all cultivation regimes, we suggest that mushroom cultivation is beneficial to forest soil nutrient conditions through increasing OM content. Based on the fact that the one-year interval cultivation regime had the highest soil nutrient content as compared with other cultivation regimes, we recommend this regime for application in farming practice. The spent mushroom compost appeared to be more influential than the hyphae of S. rugosoannulata on the soil nutrients and bacterial communities; however, this requires further study. This research provides insight into understanding the effects of mushroom cultivation on the forest soil ecosystem and suggests a relevant cultivation strategy that reduces its negative impacts. creator: Sai Gong creator: Chen Chen creator: Jingxian Zhu creator: Guangyao Qi creator: Shuxia Jiang uri: https://doi.org/10.7717/peerj.5741 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gong et al. title: Comparing shade tolerance measures of woody forest species link: https://peerj.com/articles/5736 last-modified: 2018-10-09 description: Shade tolerance, the minimum light requirement for plant survival, is a key trait for understanding community assembly and forest dynamics. However, it is poorly defined for tree species to date. Current methods of measuring shade tolerance vary considerably in their performance. For instance, some measures of shade tolerance are unreliable except under some specific conditions. Therefore, it is necessary to compare the performance of these methods to provide guidance of choosing appropriate shade tolerance measures in future studies. We collected a large dataset of light traits and other life history traits for 137 understory wood species in a subtropical forest and tested the performance of five commonly used shade-tolerance indices. Results showed that all the shade-tolerance measures, except the low-light abundance index, performed poorly in distinguishing and ranking shade tolerance of the tested species. The shade tolerance quantified by the low-light abundance was consistent with empirical classification of shade-tolerance/intolerance groups and successional seral stages of species. Comparison of the shade tolerance between trees of different diameter at breast height (DBH) or height classes further confirmed the reliability of low-light abundance. We conclude that low-light abundance is the most objective and practical of the five most commonly-used methods for measuring and ranking shade tolerance of understory wood species in our study forest, and likely in other forests as well. The simplicity of the method should greatly facilitate the assessment of light niche differentiation between species and thus contribute to understanding coexistence of tree species in forests. creator: Jiayi Feng creator: Kangning Zhao creator: Dong He creator: Suqin Fang creator: TienMing Lee creator: Chengjin Chu creator: Fangliang He uri: https://doi.org/10.7717/peerj.5736 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Feng et al. title: A late surviving Pliocene seal from high latitudes of the North Atlantic realm: the latest monachine seal on the southern margin of the North Sea link: https://peerj.com/articles/5734 last-modified: 2018-10-09 description: BackgroundThe family of true seals, the Phocidae, is subdivided into two subfamilies: the southern Monachinae, and the northern Phocinae, following the subfamilies’ current distribution: extant Monachinae are largely restricted to the (sub-)Antarctic and the eastern Pacific, with historical distributions of the monk seals of the genus Monachus in the Caribbean, the Mediterranean and around Hawaii; and Phocinae to the northern temperate and Arctic zones. However, the fossil record shows that Monachinae were common in the North Atlantic realm during the late Miocene and early Pliocene. Until now, only one late Pliocene record is known from the Mediterranean, Pliophoca etrusca from Tuscany, Italy, but none from farther north in the North Atlantic.MethodsWe present the description of one partial phocid humerus collected in the early 20th century from the Antwerp area (Belgium), with an assessment of its stratigraphic origin using data from the literature.ResultsThe studied humerus was recovered during construction works at the former Lefèvre dock in the Antwerp harbour (currently part of the America dock). Combining the information associated to the specimen with data from the literature and from local boreholes, the upper Pliocene Lillo Formation is ascertained as the lithological unit from which the specimen originates. Morphologically, among other features the shape of the deltopectoral crest and the poor development of the supinator crest indicates a monachine attribution for this specimen. The development of the deltopectoral crest is closer to the condition in extant Monachinae than in extinct Monachinae.DiscussionThe presented specimen most likely represents a monachine seal and a literature study clearly shows that it came from the latest early to late Pliocene Lillo Formation. This would be the first known monachine specimen from the latest early to late Pliocene of the North Sea, and more broadly from the northern part of the North Atlantic realm. This humerus differs from the humerus of P. etrusca and suggests a higher diversity of Monachinae in the latest early to late Pliocene than previously assumed. creator: Leonard Dewaele creator: Olivier Lambert creator: Stephen Louwye uri: https://doi.org/10.7717/peerj.5734 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Dewaele et al. title: Raritas: a program for counting high diversity categorical data with highly unequal abundances link: https://peerj.com/articles/5453 last-modified: 2018-10-09 description: Acquiring data on the occurrences of many types of difficult to identify objects are often still made by human observation, for example, in biodiversity and paleontologic research. Existing computer counting programs used to record such data have various limitations, including inflexibility and cost. We describe a new open-source program for this purpose—Raritas. Raritas is written in Python and can be run as a standalone app for recent versions of either MacOS or Windows, or from the command line as easily customized source code. The program explicitly supports a rare category count mode which makes it easier to collect quantitative data on rare categories, for example, rare species which are important in biodiversity surveys. Lastly, we describe the file format used by Raritas and propose it as a standard for storing geologic biodiversity data. ‘Stratigraphic occurrence data’ file format combines extensive sample metadata and a flexible structure for recording occurrence data of species or other categories in a series of samples. creator: David B. Lazarus creator: Johan Renaudie creator: Dorina Lenz creator: Patrick Diver creator: Jens Klump uri: https://doi.org/10.7717/peerj.5453 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lazarus et al. title: strandCet: R package for estimating natural and non-natural mortality-at-age of cetaceans from age-structured strandings link: https://peerj.com/articles/5768 last-modified: 2018-10-09 description: 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. creator: Camilo Saavedra uri: https://doi.org/10.7717/peerj.5768 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Saavedra title: 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 link: https://peerj.com/articles/5718 last-modified: 2018-10-09 description: BackgroundThe 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.MethodsFor 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).ResultsThe 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.DiscussionIn 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. creator: Marion Leiberich creator: Hendrik Johannes Marais creator: Vinny Naidoo uri: https://doi.org/10.7717/peerj.5718 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Leiberich et al. title: 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 link: https://peerj.com/articles/5612 last-modified: 2018-10-09 description: BackgroundEcosystem 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.MethodsWe 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?ResultsWe 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. creator: Alan N. Costa creator: Emilio M. Bruna creator: Heraldo L. Vasconcelos uri: https://doi.org/10.7717/peerj.5612 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Costa et al. title: Artificial light at night alters life history in a nocturnal orb-web spider link: https://peerj.com/articles/5599 last-modified: 2018-10-09 description: 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. creator: Nikolas J. Willmott creator: Jessica Henneken creator: Caitlin J. Selleck creator: Therésa M. Jones uri: https://doi.org/10.7717/peerj.5599 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Willmott et al. title: Young, American Indian or Alaskan Native, and born in the USA: at excess risk of starting extra-medical prescription pain reliever use? link: https://peerj.com/articles/5713 last-modified: 2018-10-08 description: BackgroundPrescription 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.MethodsBetween 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.ResultsEach 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’).DiscussionEach 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). creator: Maria A. Parker creator: Catalina Lopez-Quintero creator: James C. Anthony uri: https://doi.org/10.7717/peerj.5713 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Parker et al.