title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1494 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Analyzing mixing systems using a new generation of Bayesian tracer mixing models link: https://peerj.com/articles/5096 last-modified: 2018-06-21 description: The ongoing evolution of tracer mixing models has resulted in a confusing array of software tools that differ in terms of data inputs, model assumptions, and associated analytic products. Here we introduce MixSIAR, an inclusive, rich, and flexible Bayesian tracer (e.g., stable isotope) mixing model framework implemented as an open-source R package. Using MixSIAR as a foundation, we provide guidance for the implementation of mixing model analyses. We begin by outlining the practical differences between mixture data error structure formulations and relate these error structures to common mixing model study designs in ecology. Because Bayesian mixing models afford the option to specify informative priors on source proportion contributions, we outline methods for establishing prior distributions and discuss the influence of prior specification on model outputs. We also discuss the options available for source data inputs (raw data versus summary statistics) and provide guidance for combining sources. We then describe a key advantage of MixSIAR over previous mixing model software—the ability to include fixed and random effects as covariates explaining variability in mixture proportions and calculate relative support for multiple models via information criteria. We present a case study of Alligator mississippiensis diet partitioning to demonstrate the power of this approach. Finally, we conclude with a discussion of limitations to mixing model applications. Through MixSIAR, we have consolidated the disparate array of mixing model tools into a single platform, diversified the set of available parameterizations, and provided developers a platform upon which to continue improving mixing model analyses in the future. creator: Brian C. Stock creator: Andrew L. Jackson creator: Eric J. Ward creator: Andrew C. Parnell creator: Donald L. Phillips creator: Brice X. Semmens uri: https://doi.org/10.7717/peerj.5096 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Stock et al. title: Effect of human recreation on bird anti-predatory response link: https://peerj.com/articles/5093 last-modified: 2018-06-21 description: Wildlife perceive humans as predators, and therefore normally flushes. Flight initiation distance (FID) is the distance a human can approach an animal at a steady pace until it flushes. Recently, several studies showed differences in within-species FID according to human presence by comparing urban and rural habitats, with urban birds showing reduced FIDs. However, urban and rural habitats also differ in structure, which might affect FID. Therefore, in order to understand the real effect of human presence, we investigated whether differences in FID are also present in natural habitats (forests), differing only in the intensity of human use for recreation. We found that human frequentation had a distinct effect on bird escape responses, with shorter FIDs in forests more-heavily frequented by humans than in forests rarely visited by humans. Whether this finding is driven by non-random spatial distribution of personalities (shy vs. bold) or phenotypic plasticity (habituation to humans) cannot be assessed with our data. Studies relying on FIDs should also incorporate human recreation intensity, as this affects the measurements strongly. creator: Yves Bötsch creator: Selina Gugelmann creator: Zulima Tablado creator: Lukas Jenni uri: https://doi.org/10.7717/peerj.5093 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Bötsch et al. title: Starch biotransformation into isomaltooligosaccharides using thermostable alpha-glucosidase from Geobacillus stearothermophilus link: https://peerj.com/articles/5086 last-modified: 2018-06-21 description: The present study first identified the biotransformation of starch as a novel preparation method was investigated using the alpha-transglucosidase-producing Geobacillus stearothermophilus U2. Subsequently, 5 L- and 20 L-scale fermentations were performed. After isolation and purification, liquid alpha-glucosidase preparations were obtained. Through covalent cross-linking and adsorption cross-linking using chitosan as the carrier and glutaraldehyde as the crosslinking agent, the conditions for immobilization of alpha-glucosidase on chitosan were determined. Moreover, Isomaltooligosaccharides (IMOs) were then prepared using chitosan membrane-immobilized alpha-glucosidase, beta-amylase, pullulanase, fungal alpha-amylase and starch as substrate. The mixed syrup that contained IMOs was evaluated and analyzed by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC). In addition, small-scale preparation of IMOs was performed. These results are a strong indication that the alpha-transglucosidase-producing G. stearothermophilus as a potential application technique can be successfully used to prepare industrial IMOs. creator: Peng Chen creator: Ruixiang Xu creator: Jianhui Wang creator: Zhengrong Wu creator: Lei Yan creator: Wenbin Zhao creator: Yuheng Liu creator: Wantong Ma creator: Xiaofeng Shi creator: Hongyu Li uri: https://doi.org/10.7717/peerj.5086 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chen et al. title: An integrative taxonomic analysis reveals a new species of lotic Hynobius salamander from Japan link: https://peerj.com/articles/5084 last-modified: 2018-06-21 description: We examine the phylogenetic structure and morphological differentiation within the Hynobius kimurae–H. boulengeri species complex—a widely-distributed group of stream-breeding hynobiid salamanders, inhabiting montane areas of western, central and eastern parts of Honshu Island, Japan. Phylogenetic relationships were assessed based on analyses of mitochondrial (mtDNA) and nuclear (nuDNA) gene fragments for a total of 51 samples representing 23 localities covering the entire range of the species complex. Morphological study included one-way analysis of variance (ANOVA) and principal components analysis (PCA) analyses of 26 morphometric and six meristic characters for 38 adult specimens of H. kimurae and three adult specimens of H. boulengeri. MtDNA genealogy supported monophyly of the H. kimurae–H. boulengeri complex, which is sister to all other Hynobius except H. retardatus. The complex is subdivided into three major clades, corresponding to the Eastern (Clade I) and Western (Clade II) populations of H. kimurae sensu lato, and to H. boulengeri (Clade III). Monophyly of H. kimurae sensu lato is only moderately supported by mtDNA, while nuDNA suggested that the Western form of H. kimurae is closer to H. boulengeri than to the eastern form. The time of the split of the H. kimurae–H. boulengeri complex is estimated as late Miocene and coincides with intensive crust movement in western Japan. Divergence between Clades I and II took place in early Pliocene and was likely influenced by the uplift of Central Japanese Highlands. All three clades were found to be different in a number of morphological characters, allowing us to describe the eastern form of H. kimurae as a new species, Hynobius fossigenussp. nov. creator: Hisanori Okamiya creator: Hirotaka Sugawara creator: Masahiro Nagano creator: Nikolay A. Poyarkov uri: https://doi.org/10.7717/peerj.5084 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Okamiya et al. title: Fish species richness is associated with the availability of landscape components across seasons in the Amazonian floodplain link: https://peerj.com/articles/5080 last-modified: 2018-06-21 description: Understanding environmental biodiversity drivers in freshwater systems continues to be a fundamental challenge in studies of their fish assemblages. The present study seeks to determine the degree to which landscape variables of Amazonian floodplain lakes influences fish assemblages in these environments. Fish species richness was estimated in 15 Amazonian floodplain lakes during the high and low-water phases and correlated with the areas of four inundated wetland classes: (i) open water, (ii) flooded herbaceous, (iii) flooded shrubs and (iv) flooded forest estimated in different radius circular areas around each sampling site. Data were analyzed using generalized linear models with fish species richness, total and guilds as the dependent variable and estimates of buffered landscape areas as explanatory variables. Our analysis identified the significance of landscape variables in determining the diversity of fish assemblages in Amazonian floodplain lakes. Spatial scale was also identified as a significant determinant of fish diversity as landscape effects were more evident at larger spatial scales. In particular, (1) total species richness was more sensitive to variations in the landscape areas than number of species within guilds and (2) the spatial extent of the wetland class of shrubs was consistently the more influential on fish species diversity. creator: Carlos Edwar Carvalho Freitas creator: Laurie Laurenson creator: Kedma Cristine Yamamoto creator: Bruce Rider Forsberg creator: Miguel Petrere creator: Caroline Arantes creator: Flavia Kelly Siqueira-Souza uri: https://doi.org/10.7717/peerj.5080 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Carvalho Freitas et al. title: Initial response of phenology and yield components of wheat (Triticum durum L., CIRNO C2008) under experimental warming field conditions in the Yaqui Valley link: https://peerj.com/articles/5064 last-modified: 2018-06-21 description: This work evaluates the experimental warming effects on phenology and grain yield components of wheat in the Yaqui Valley, Sonora, México, using CIRNO C2008 variety from Triticum durum L., as a model during the cropping cycle of 2016–2017 (December to April). Infrared radiators were deployed to induce experimental warming by 2 °C above ambient crop canopy temperature, in a temperature free-air controlled enhancement system. Temperature was controlled by infrared temperature sensors placed in eight plots which covered a circle of r = 1.5 m starting five days after germination until harvest. The warming treatment caused a reduction of phenophases occurrence starting at the stem extension phenophase. Such phenological responses generated a significant biological cycle reduction of 14 days. Despite this delay, CIRNO C2008 completed its biological cycle adequately. However, plant height under the warming treatment was reduced significantly and differences were particularly observed at the final phenophases of the vegetative cycle. Plant height correlated negatively with spikes length, spikes mass, and number of filled grains. Warming also reduced grain yield in 33%. The warming treatment caused a stress intensity (SI = 1-yield warming/yield control) of 39.4% and 33.2% in biomass and grain yield, respectively. The differences in stress intensities between biomass and grain yield were based on plant height reduction. Grain mass was not affected, demonstrating the crop capability for remobilization and adequate distribution of elaborated substances for the spikes under warming conditions. creator: Jaime Garatuza-Payan creator: Leandris Argentel-Martinez creator: Enrico A. Yepez creator: Tulio Arredondo uri: https://doi.org/10.7717/peerj.5064 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Garatuza-Payan et al. title: aaquetzalli is required for epithelial cell polarity and neural tissue formation in Drosophila link: https://peerj.com/articles/5042 last-modified: 2018-06-21 description: Morphogenetic movements during embryogenesis require dynamic changes in epithelial cell polarity and cytoskeletal reorganization. Such changes involve, among others, rearrangements of cell-cell contacts and protein traffic. In Drosophila melanogaster, neuroblast delamination during early neurogenesis is a well-characterized process requiring a polarized neuroepithelium, regulated by the Notch signaling pathway. Maintenance of epithelial cell polarity ensues proper Notch pathway activation during neurogenesis. We characterize here aaquetzalli (aqz), a gene whose mutations affect cell polarity and nervous system specification. The aqz locus encodes a protein that harbors a domain with significant homology to a proline-rich conserved domain of nuclear receptor co-activators. aqz expression occurs at all stages of the fly life cycle, and is dynamic. aqz mutants are lethal, showing a disruption of cell polarity during embryonic ventral neuroepithelium differentiation resulting in loss of epithelial integrity and mislocalization of membrane proteins (shown by mislocalization of Crumbs, DE-Cadherin, and Delta). As a consequence, aqz mutant embryos with compromised apical-basal cell polarity develop spotty changes of neuronal and epithelial numbers of cells. creator: Miguel A. Mendoza-Ortíz creator: Juan M. Murillo-Maldonado creator: Juan R. Riesgo-Escovar uri: https://doi.org/10.7717/peerj.5042 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mendoza-Ortíz et al. title: Biodegradation of Crystal Violet dye by bacteria isolated from textile industry effluents link: https://peerj.com/articles/5015 last-modified: 2018-06-21 description: Industrial effluent containing textile dyes is regarded as a major environmental concern in the present world. Crystal Violet is one of the vital textile dyes of the triphenylmethane group; it is widely used in textile industry and known for its mutagenic and mitotic poisoning nature. Bioremediation, especially through bacteria, is becoming an emerging and important sector in effluent treatment. This study aimed to isolate and identify Crystal Violet degrading bacteria from industrial effluents with potential use in bioremediation. The decolorizing activity of the bacteria was measured using a photo electric colorimeter after aerobic incubation in different time intervals of the isolates. Environmental parameters such as pH, temperature, initial dye concentration and inoculum size were optimized using mineral salt medium containing different concentration of Crystal Violet dye. Complete decolorizing efficiency was observed in a mineral salt medium containing up to 150 mg/l of Crystal Violet dye by 10% (v/v) inoculums of Enterobacter sp. CV–S1 tested under 72 h of shaking incubation at temperature 35 °C and pH 6.5. Newly identified bacteria Enterobacter sp. CV–S1, confirmed by 16S ribosomal RNA sequencing, was found as a potential bioremediation biocatalyst in the aerobic degradation/de-colorization of Crystal Violet dye. The efficiency of degrading triphenylmethane dye by this isolate, minus the supply of extra carbon or nitrogen sources in the media, highlights the significance of larger-scale treatment of textile effluent. creator: Dipankar Chandra Roy creator: Sudhangshu Kumar Biswas creator: Ananda Kumar Saha creator: Biswanath Sikdar creator: Mizanur Rahman creator: Apurba Kumar Roy creator: Zakaria Hossain Prodhan creator: Swee-Seong Tang uri: https://doi.org/10.7717/peerj.5015 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Roy et al. title: Effects of anthropogenic wildfire in low-elevation Pacific island vegetation communities in French Polynesia link: https://peerj.com/articles/5114 last-modified: 2018-06-20 description: Anthropogenic (or human-caused) wildfire is an increasingly important driver of ecological change on Pacific islands including southeastern Polynesia, but fire ecology studies are almost completely absent for this region. Where observations do exist, they mostly represent descriptions of fire effects on plant communities before the introduction of invasive species in the modern era. Understanding the effects of wildfire in southeastern Polynesian island vegetation communities can elucidate which species may become problematic invasives with continued wildfire activity. We investigate the effects of wildfire on vegetation in three low-elevation sites (45–379 m) on the island of Mo’orea in the Society Islands, French Polynesia, which are already heavily impacted by past human land use and invasive exotic plants, but retain some native flora. In six study areas (three burned and three unburned comparisons), we placed 30 transects across sites and collected species and abundance information at 390 points. We analyzed each local community of plants in three categories: natives, those introduced by Polynesians before European contact (1767 C.E.), and those introduced since European contact. Burned areas had the same or lower mean species richness than paired comparison sites. Although wildfire did not affect the proportions of native and introduced species, it may increase the abundance of introduced species on some sites. Non-metric multidimensional scaling indicates that (not recently modified) comparison plant communities are more distinct from one another than are those on burned sites. We discuss conservation concerns for particular native plants absent from burned sites, as well as invasive species (including Lantana camara and Paraserianthes falcataria) that may be promoted by fire in the Pacific. creator: Erica A. Newman creator: Carlea A. Winkler creator: David H. Hembry uri: https://doi.org/10.7717/peerj.5114 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Comparison of the toxic effects of different mycotoxins on porcine and mouse oocyte meiosis link: https://peerj.com/articles/5111 last-modified: 2018-06-20 description: BackgroundAflatoxin B1 (AFB1), deoxynivalenol (DON), HT-2, ochratoxin A (OTA), zearalenone (ZEA) are the most common mycotoxins that are found in corn-based animal feed which have multiple toxic effects on animals and humans. Previous studies reported that these mycotoxins impaired mammalian oocyte quality. However, the effective concentrations of mycotoxins to animal oocytes were different.MethodsIn this study we aimed to compare the sensitivity of mouse and porcine oocytes to AFB1, DON, HT-2, OTA, and ZEA for mycotoxin research. We adopted the polar body extrusion rate of mouse and porcine oocyte as the standard for the effects of mycotoxins on oocyte maturation.Results and DiscussionOur results showed that 10 μM AFB1 and 1 μM DON significantly affected porcine oocyte maturation compared with 50 μM AFB1 and 2 μM DON on mouse oocytes. However, 10 nM HT-2 significantly affected mouse oocyte maturation compared with 50 nM HT-2 on porcine oocytes. Moreover, 5 μM OTA and 10 μM ZEA significantly affected porcine oocyte maturation compared with 300 μM OTA and 50 μM ZEA on mouse oocytes. In summary, our results showed that porcine oocytes were more sensitive to AFB1, DON, OTA, and ZEA than mouse oocytes except HT-2 toxin. creator: Yujie Lu creator: Yue Zhang creator: Jia-Qian Liu creator: Peng Zou creator: Lu Jia creator: Yong-Teng Su creator: Yu-Rong Sun creator: Shao-Chen Sun uri: https://doi.org/10.7717/peerj.5111 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Lu et al.