title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1481 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Growth and feeding of deep-sea coral Lophelia pertusa from the California margin under simulated ocean acidification conditions link: https://peerj.com/articles/5671 last-modified: 2018-09-27 description: The global decrease in seawater pH known as ocean acidification has important ecological consequences and is an imminent threat for numerous marine organisms. Even though the deep sea is generally considered to be a stable environment, it can be dynamic and vulnerable to anthropogenic disturbances including increasing temperature, deoxygenation, ocean acidification and pollution. Lophelia pertusa is among the better-studied cold-water corals but was only recently documented along the US West Coast, growing in acidified conditions. In the present study, coral fragments were collected at ∼300 m depth along the southern California margin and kept in recirculating tanks simulating conditions normally found in the natural environment for this species. At the collection site, waters exhibited persistently low pH and aragonite saturation states (Ωarag) with average values for pH of 7.66 ± 0.01 and Ωarag of 0.81 ± 0.07. In the laboratory, fragments were grown for three weeks in “favorable” pH/Ωarag of 7.9/1.47 (aragonite saturated) and “unfavorable” pH/Ωarag of 7.6/0.84 (aragonite undersaturated) conditions. There was a highly significant treatment effect (P < 0.001) with an average% net calcification for favorable conditions of 0.023 ± 0.009% d−1 and net dissolution of −0.010 ± 0.014% d-1 for unfavorable conditions. We did not find any treatment effect on feeding rates, which suggests that corals did not depress feeding in low pH/ Ωarag in an attempt to conserve energy. However, these results suggest that the suboptimal conditions for L. pertusa from the California margin could potentially threaten the persistence of this cold-water coral with negative consequences for the future stability of this already fragile ecosystem. creator: Carlos E. Gómez creator: Leslie Wickes creator: Dan Deegan creator: Peter J. Etnoyer creator: Erik E. Cordes uri: https://doi.org/10.7717/peerj.5671 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Gómez et al. title: Distribution, habitat associations, and conservation status updates for the pilose crayfish Pacifastacus gambelii (Girard, 1852) and Snake River pilose crayfish Pacifastacus connectens (Faxon, 1914) of the western United States link: https://peerj.com/articles/5668 last-modified: 2018-09-27 description: Our study evaluates the distribution, habitat associations, and current conservation status of the Snake River pilose crayfish Pacifastacus connectens (Faxon, 1914) and pilose crayfish Pacifastacus gambelii (Girard, 1852), two little-studied and data-deficient species endemic to the western United States. We first developed a species distribution model (SDM) for the pilose crayfishes based on their historical occurrence records using boosted regression trees and freshwater GIS data layers. We then sampled 163 sites in the summers of 2016 and 2017 within the distribution of these crayfishes, including 50 where these species were observed historically. We next compared our field results to modeled predictions of suitable habitat from the SDM. Our SDM predicted 73 sites (45%) we sampled as suitable for the pilose crayfishes, with a moderate AUC value of 0.824. The pilose crayfishes were generally predicted to occur in larger streams and rivers with less extreme upstream temperature and precipitation seasonality. We found the pilose crayfishes at only 20 (12%) of the 163 total sites we sampled, 14 (20%) of the 73 sites predicted as suitable for them by our SDM, and 12 (24%) of 50 historical sites that we sampled. We found the invasive virile crayfish Faxonius virilis (Hagen, 1870) at 22 sites total and 12 (24%) historical sites for the pilose crayfishes, and we found the “native invader” signal crayfish Pacifastacus leniusculus (Dana, 1852) at 29 sites total and 6 (12%) historical sites for the pilose crayfishes. We subsequently used a single classification tree to identify factors associated with our high rate of false positives for contemporary pilose crayfish distributions relative to our SDM. This classification tree identified the presence of invasive crayfishes, impairment of the benthic community, and sampling method as some of the factors differentiating false positives relative to true positives for the pilose crayfishes. Our study identified the historical distribution and habitat associations for P. connectens and P. gambelii using an SDM and contrasted this prediction to results of contemporary field sampling. We found that the pilose crayfishes have seemingly experienced substantial range declines, attributable to apparent displacement by invasive crayfishes and impairment or change to stream communities and habitat. We recommend increased conservation and management attention to P. connectens and P. gambelii in response to these findings. creator: Rachel M. Egly creator: Eric R. Larson uri: https://doi.org/10.7717/peerj.5668 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Egly and Larson title: Assessing the role of dispersed floral resources for managed bees in providing supporting ecosystem services for crop pollination link: https://peerj.com/articles/5654 last-modified: 2018-09-27 description: Most pollination ecosystem services studies have focussed on wild pollinators and their dependence on natural floral resources adjacent to crop fields. However, managed pollinators depend on a mixture of floral resources that are spatially separated from the crop field. Here, we consider the supporting role these resources play as an ecosystem services provider to quantify the use and availability of floral resources, and to estimate their relative contribution to support pollination services of managed honeybees. Beekeepers supplying pollination services to the Western Cape deciduous fruit industry were interviewed to obtain information on their use of floral resources. For 120 apiary sites, we also analysed floral resources within a two km radius of each site based on geographic data. The relative availability of floral resources at sites was compared to regional availability. The relative contribution of floral resources-types to sustain managed honeybees was estimated. Beekeepers showed a strong preference for eucalypts and canola. Beekeepers selectively placed more hives at sites with eucalypt and canola and less with natural vegetation. However, at the landscape-scale, eucalypt was the least available resource, whereas natural vegetation was most common. Based on analysis of apiary sites, we estimated that 700,818 ha of natural vegetation, 73,910 ha of canola fields, and 10,485 ha of eucalypt are used to support the managed honeybee industry in the Western Cape. Whereas the Cape managed honeybee system uses a bee native to the region, alien plant species appear disproportionately important among the floral resources being exploited. We suggest that an integrated approach, including evidence from interview and landscape data, and fine-scale biological data is needed to study floral resources supporting managed honeybees. creator: Annalie Melin creator: Mathieu Rouget creator: Jonathan F. Colville creator: Jeremy J. Midgley creator: John S. Donaldson uri: https://doi.org/10.7717/peerj.5654 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Melin et al. title: Analysis of relative abundances with zeros on environmental gradients: a multinomial regression model link: https://peerj.com/articles/5643 last-modified: 2018-09-27 description: Ecologists often analyze relative abundances, which are an example of compositional data. However, they have made surprisingly little use of recent advances in the field of compositional data analysis. Compositions form a vector space in which addition and scalar multiplication are replaced by operations known as perturbation and powering. This algebraic structure makes it easy to understand how relative abundances change along environmental gradients. We illustrate this with an analysis of changes in hard-substrate marine communities along a depth gradient. We fit a quadratic multivariate regression model with multinomial observations to point count data obtained from video transects. As well as being an appropriate observation model in this case, the multinomial deals with the problem of zeros, which often makes compositional data analysis difficult. We show how the algebra of compositions can be used to understand patterns in dissimilarity. We use the calculus of simplex-valued functions to estimate rates of change, and to summarize the structure of the community over a vertical slice. We discuss the benefits of the compositional approach in the interpretation and visualization of relative abundance data. creator: Fiona Chong creator: Matthew Spencer uri: https://doi.org/10.7717/peerj.5643 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Chong and Spencer title: Geopolitical species revisited: genomic and morphological data indicate that the roundtail chub Gila robusta species complex (Teleostei, Cyprinidae) is a single species link: https://peerj.com/articles/5605 last-modified: 2018-09-27 description: The Gila robusta species complex in the Lower Colorado River Basin has a complicated taxonomic history. Recent authors have separated this group into three nominal taxa, G. robusta, G. intermedia, and G. nigra, however aside from location, no reliable method of distinguishing individuals of these species currently exists. To assess relationships within this group, we examined morphology of type specimens and fresh material, and used RADseq methods to assess phylogenetic relationship among these nominal species. Maximum likelihood and Bayesian inference tree building methods reveal high concordance between tree topologies based on the mitochondrial and nuclear datasets. Coalescent SNAPP analysis resolved a similar tree topology. Neither morphological nor molecular data reveal diagnostic differences between these species as currently defined. As such, G. intermedia and G. nigra should be considered synonyms of the senior G. robusta. We hypothesize that climate driven wet and dry cycles have led to periodic isolation of population subunits and subsequent local divergence followed by reestablished connectivity and mixing. Management plans should therefore focus on retaining genetic variability and viability of geographic populations to preserve adaptability to changing climate conditions. creator: Joshua M. Copus creator: W. L. Montgomery creator: Zac H. Forsman creator: Brian W. Bowen creator: Robert J. Toonen uri: https://doi.org/10.7717/peerj.5605 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Copus et al. title: Pre-imaginal conditioning alters adult sex pheromone response in Drosophila link: https://peerj.com/articles/5585 last-modified: 2018-09-27 description: Pheromones are chemical signals that induce innate responses in individuals of the same species that may vary with physiological and developmental state. In Drosophila melanogaster, the most intensively studied pheromone is 11-cis-vaccenyl acetate (cVA), which is synthezised in the male ejaculatory bulb and is transferred to the female during copulation. Among other effects, cVA inhibits male courtship of mated females. We found that male courtship inhibition depends on the amount of cVA and this effect is reduced in male flies derived from eggs covered with low to zero levels of cVA. This effect is not observed if the eggs are washed, or if the eggs are laid several days after copulation. This suggests that courtship suppression involves a form of pre-imaginal conditioning, which we show occurs during the early larval stage. The conditioning effect could not be rescued by synthetic cVA, indicating that it largely depends on conditioning by cVA and other maternally-transmitted factor(s). These experiments suggest that one of the primary behavioral effects of cVA is more plastic and less stereotypical than had hitherto been realised. creator: Claude Everaerts creator: Laurie Cazalé-Debat creator: Alexis Louis creator: Emilie Pereira creator: Jean-Pierre Farine creator: Matthew Cobb creator: Jean-François Ferveur uri: https://doi.org/10.7717/peerj.5585 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Everaerts et al. title: Assessing bird avoidance of high-contrast lights using a choice test approach: implications for reducing human-induced avian mortality link: https://peerj.com/articles/5404 last-modified: 2018-09-26 description: BackgroundAvian collisions with man-made objects and vehicles (e.g., buildings, cars, airplanes, power lines) have increased recently. Lights have been proposed to alert birds and minimize the chances of collisions, but it is challenging to choose lights that are tuned to the avian eye and can also lead to avoidance given the differences between human and avian vision. We propose a choice test to address this problem by first identifying wavelengths of light that would over-stimulate the retina using species-specific perceptual models and by then assessing the avoidance/attraction responses of brown-headed cowbirds to these lights during daytime using a behavioral assay.MethodsWe used perceptual models to estimate wavelength-specific light emitting diode (LED) lights with high chromatic contrast. The behavioral assay consisted of an arena where the bird moved in a single direction and was forced to make a choice (right/left) using a single-choice design (one side with the light on, the other with the light off) under diurnal light conditions.ResultsFirst, we identified lights with high saliency from the cowbird visual perspective: LED lights with peaks at 380 nm (ultraviolet), 470 nm (blue), 525 nm (green), 630 nm (red), and broad-spectrum (white) LED lights. Second, we found that cowbirds significantly avoided LED lights with peaks at 470 and 630 nm, but did not avoid or prefer LED lights with peaks at 380 and 525 nm or white lights.DiscussionThe two lights avoided had the highest chromatic contrast but relatively lower levels of achromatic contrast. Our approach can optimize limited resources to narrow down wavelengths of light with high visual saliency for a target species leading to avoidance. These lights can be used as candidates for visual deterrents to reduce collisions with man-made objects and vehicles. creator: Benjamin Goller creator: Bradley F. Blackwell creator: Travis L. DeVault creator: Patrice E. Baumhardt creator: Esteban Fernández-Juricic uri: https://doi.org/10.7717/peerj.5404 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Goller et al. title: De novo transcriptome sequencing and analysis of genes related to salt stress response in Glehnia littoralis link: https://peerj.com/articles/5681 last-modified: 2018-09-26 description: Soil salinity is one of the major environmental stresses affecting plant growth, development, and reproduction. Salt stress also affects the accumulation of some secondary metabolites in plants. Glehnia littoralis is an endangered medicinal halophyte that grows in coastal habitats. Peeled and dried Glehnia littoralis roots, named Radix Glehniae, have been used traditionally as a Chinese herbal medicine. Although Glehnia littoralis has great ecological and commercial value, salt-related mechanisms in Glehnia littoralis remain largely unknown. In this study, we analysed the transcriptome of Glehnia littoralis in response to salt stress by RNA-sequencing to identify potential salt tolerance gene networks. After de novo assembly, we obtained 105,875 unigenes, of which 75,559 were annotated in public databases. We identified 10,335 differentially expressed genes (DEGs; false discovery rate <0.05 and |log2 fold-change| ≥ 1) between NaCl treatment (GL2) and control (GL1), with 5,018 upregulated and 5,317 downregulated DEGs. To further this investigation, we performed Gene Ontology (GO) analysis and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. DEGs involved in secondary metabolite biosynthetic pathways, plant signal transduction pathways, and transcription factors in response to salt stress were analysed. In addition, we tested the gene expression of 15 unigenes by quantitative real-time PCR (qRT-PCR) to confirm the RNA-sequencing results. Our findings represent a large-scale assessment of the Glehnia littoralis gene resource, and provide useful information for exploring its molecular mechanisms of salt tolerance. Moreover, genes enriched in metabolic pathways could be used to investigate potential biosynthetic pathways of active compounds by Glehnia littoralis. creator: Li Li creator: Mimi Li creator: Xiwu Qi creator: Xingli Tang creator: Yifeng Zhou uri: https://doi.org/10.7717/peerj.5681 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Li et al. title: Population history of deep-sea vent and seep Provanna snails (Mollusca: Abyssochrysoidea) in the northwestern Pacific link: https://peerj.com/articles/5673 last-modified: 2018-09-26 description: BackgroundGastropods of the genus Provanna are abundant and widely distributed in deep-sea chemosynthetic environments with seven extant species described in the northwestern Pacific.MethodsWe investigated the population history and connectivity of five Provanna species in the northwestern Pacific through population genetic analyses using partial sequences of the cytochrome c oxidase subunit I gene.ResultsWe found that P. subglabra, the most abundant and genetically diverse species, is genetically segregated by depth. Among the five species, the three comparatively shallower species (P. lucida, P. kuroshimensis, P. glabra) had a more constant demographic history compared to the deeper species (P. subglabra, P.  clathrata).DiscussionEnvironmental differences, especially depth, appears to have a role in the segregation of Provanna snails. The population of P. clathrata in the Irabu Knoll appears to have expanded after P. subglabra population. The remaining three species, P. lucida, P. kuroshimensis, and P. glabra, are only known from a single site each, all of which were shallower than 1,000 m. These data indicate that Provanna gastropods are vertically segregated, and that their population characteristics likely depend on hydrothermal activities. creator: Tomomi Ogura creator: Hiromi Kayama Watanabe creator: Chong Chen creator: Takenori Sasaki creator: Shigeaki Kojima creator: Jun-ichiro Ishibashi creator: Katsunori Fujikura uri: https://doi.org/10.7717/peerj.5673 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ogura et al. title: Tumor-preventing activity of aspirin in multiple cancers based on bioinformatic analyses link: https://peerj.com/articles/5667 last-modified: 2018-09-26 description: BackgroundAcetylsalicylic acid was renamed aspirin in 1899, and it has been widely used for its multiple biological actions. Because of the diversity of the cellular processes and diseases that aspirin reportedly affects and benefits, uncertainty remains regarding its mechanism in different biological systems.MethodsThe Drugbank and STITCH databases were used to find direct protein targets (DPTs) of aspirin. The Mentha database was used to analyze protein–protein interactions (PPIs) to find DPT-associated genes. DAVID was used for the GO and KEGG enrichment analyses. The cBio Cancer Genomics Portal database was used to mine genetic alterations and networks of aspirin-associated genes in cancer.ResultsEighteen direct protein targets (DPT) and 961 DPT-associated genes were identified for aspirin. This enrichment analysis resulted in eight identified KEGG pathways that were associated with cancers. Analysis using the cBio portal indicated that aspirin might have effects on multiple tumor suppressors, such as TP53, PTEN, and RB1 and that TP53 might play a central role in aspirin-associated genes.DiscussionThe results not only suggest that aspirin might have anti-tumor actions against multiple cancers but could also provide new directions for further research on aspirin using a bioinformatics analysis approach. creator: Diangeng Li creator: Peng Wang creator: Yi Yu creator: Bing Huang creator: Xuelin Zhang creator: Chou Xu creator: Xian Zhao creator: Zhiwei Yin creator: Zheng He creator: Meiling Jin creator: Changting Liu uri: https://doi.org/10.7717/peerj.5667 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Li et al.