title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1489 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Nitrous oxide variability at sub-kilometre resolution in the Atlantic sector of the Southern Ocean link: https://peerj.com/articles/5100 last-modified: 2018-07-06 description: The Southern Ocean is an important region for global nitrous oxide (N2O) cycling. The contribution of different source and sink mechanisms is, however, not very well constrained due to a scarcity of seawater data from the area. Here we present high-resolution surface N2O measurements from the Atlantic sector of the Southern Ocean, taking advantage of a relatively new underway setup allowing for collection of data during transit across mesoscale features such as frontal systems and eddies. Covering a range of different environments and biogeochemical settings, N2O saturations and sea-to-air fluxes were highly variable: Saturations ranged from 96.5% at the sea ice edge in the Weddell Sea to 126.1% across the Polar Frontal Zone during transit to South Georgia. Negative sea-to-air fluxes (N2O uptake) of up to −1.3 µmol m−2 d−1 were observed in the Subantarctic Zone and highest positive fluxes (N2O emission) of 14.5 µmol m−2 d−1 in Stromness Bay, coastal South Georgia. Although N2O saturations were high in areas of high productivity, no correlation between saturations and chlorophyll a (as a proxy for productivity) was observed. Nevertheless, there is a clear effect of islands and shallow bathymetry on N2O production as inferred from supersaturations. creator: Imke Grefe creator: Sophie Fielding creator: Karen J. Heywood creator: Jan Kaiser uri: https://doi.org/10.7717/peerj.5100 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Grefe et al. title: Genetic analysis of water loss of excised leaves associated with drought tolerance in wheat link: https://peerj.com/articles/5063 last-modified: 2018-07-06 description: BackgroundWheat is widely affected by drought. Low excised-leaf water loss (ELWL) has frequently been associated with improved grain yield under drought. This study dissected the genetic control of ELWL in wheat, associated physiological, morphological and anatomical leaf traits, and compared these with yield QTLs.MethodsNinety-four hexaploid wheat (Triticum aestivum L.) doubled haploids, mapped with over 700 markers, were tested for three years for ELWL from detached leaf 4 of glasshouse-grown plants. In one experiment, stomata per unit area and leaf thickness parameters from leaf cross-sections were measured. QTLs were identified using QTLCartographer.ResultsELWL was significantly negatively correlated with leaf length, width, area and thickness. Major QTLs for ELWL during 0–3 h and 3–6 h were coincident across trials on 3A, 3B, 4B, 5B, 5D, 6B, 7A, 7B, 7D and frequently coincident (inversely) with leaf size QTLs. Yield in other trials was sometimes associated with ELWL and leaf size phenotypically and genotypically, but more frequently under non-droughted than droughted conditions. QTL coincidence showed only ELWL to be associated with drought/control yield ratio.DiscussionOur results demonstrated that measures of ELWL and leaf size were equally effective predictors of yield, and both were more useful for selecting under favourable than stressed conditions. creator: Ilona Mieczysława Czyczyło-Mysza creator: Izabela Marcińska creator: Edyta Skrzypek creator: Jan Bocianowski creator: Kinga Dziurka creator: Dragana Rančić creator: Radenko Radošević creator: Sofija Pekić-Quarrie creator: Dejan Dodig creator: Stephen Alexander Quarrie uri: https://doi.org/10.7717/peerj.5063 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Czyczyło-Mysza et al. title: Automatic analysis of treadmill running to estimate times to fatigue and exhaustion in rodents link: https://peerj.com/articles/5017 last-modified: 2018-07-06 description: IntroductionThe determination of fatigue and exhaustion in experimental animals is complicated by the subjective nature of the measurement. Typically, it requires an observer to watch exercising animals, e.g. rats running on the treadmill, and to identify the time of the event. In this study, we hypothesized that automatic analysis of the time-averaged position of a rat on a treadmill could be an objective way for estimating times to fatigue and exhaustion. To test this hypothesis, we compared these times measured by a human observer to the results of an automated video tracking system.MethodsRats, previously familiarized to running on the treadmill, ran at a fixed speed with zero incline, until exhaustion. The experiments were performed at either room temperature (24 °C) or in a hot environment (32 °C). Each experiment was video recorded. A trained observer estimated the times to fatigue and exhaustion. Then, video tracking software was used to determine the position of the animals on the treadmill belt. The times to fatigue and exhaustion were determined, based on the position on the treadmill using predefined criteria.ResultsManual scores and the average position on the treadmill had significant correlation. Both the observer and the automated video tracking determined that exercise in a hot environment, compared with the exercise at room temperature, results in shorter times to exhaustion and fatigue. Also, estimates of times made by the observer and the automated video tracking were not statistically different from each other.DiscussionA similarity between the estimates of times to fatigue and exhaustion made by the observer and the automated technique suggests that video tracking of rodents running on a treadmill can be used to determine both parameters in experimental studies. Video tracking technique allows for a more objective measure and would allow for an increased performance in experimentation. The Supplemental information to this manuscript contains an Excel file, which includes the code in Virtual Basic with freeware license, to process and visualize running data and automatically estimate the times to fatigue and exhaustion. Instructions for the software are also included. creator: Dmitry V. Zaretsky creator: Hannah Kline creator: Maria V. Zaretskaia creator: Daniel E. Rusyniak uri: https://doi.org/10.7717/peerj.5017 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zaretsky et al. title: Variable retention harvesting influences belowground plant-fungal interactions of Nothofagus pumilio seedlings in forests of southern Patagonia link: https://peerj.com/articles/5008 last-modified: 2018-07-06 description: BackgroundThe post-harvest recovery and sustained productivity of Nothofagus pumilio forests in Tierra del Fuego may be affected by the abundance and composition of ectomycorrhizal fungi (EMF). Timber harvesting alters EMF community structure in many managed forests, but the impacts of harvesting can vary with the management strategy. The implementation of variable retention (VR) management can maintain, increase, or decrease the diversity of many species, but the effects of VR on EMF in the forests of southern Patagonia have not been studied, nor has the role of EMF in the regeneration process of these forests.MethodsWe evaluated the effects of VR management on the EMF community associated with N. pumilio seedlings. We quantified the abundance, composition, and diversity of EMF across aggregate (AR) and dispersed (DR) retention sites within VR managed areas, and compared them to primary forest (PF) unmanaged stands. EMF assemblage and taxonomic identities were determined by ITS-rDNA sequencing of individual root tips sampled from 280 seedlings across three landscape replicates. To better understand seedling performance, we tested the relationships between EMF colonization, EMF taxonomic composition, seedling biomass, and VR treatment.ResultsThe majority of EMF taxa were Basidiomycota belonging to the families Cortinariaceae (n = 29), Inocybaceae (n = 16), and Thelephoraceae (n = 8), which was in agreement with other studies of EMF diversity in Nothofagus forests. EMF richness and colonization was reduced in DR compared to AR and PF. Furthermore, EMF community composition was similar between AR and PF, but differed from the composition in DR. EMF community composition was correlated with seedling biomass and soil moisture. The presence of Peziza depressa was associated with higher seedling biomass and greater soil moisture, while Inocybe fibrillosibrunnea and Cortinarius amoenus were associated with reduced seedling biomass and lower soil moisture. Seedling biomass was more strongly related to retention type than EMF colonization, richness, or composition.DiscussionOur results demonstrate reduced EMF attributes and altered composition in VR treatments relative to PF stands, with stronger impacts in DR compared to AR. This suggests that VR has the potential to improve the conservation status of managed stands by supporting native EMF in AR. Our results also demonstrate the complex linkages between retention treatments, fungal community composition, and tree growth at individual and stand scales. creator: Rebecca E. Hewitt creator: Donald Lee Taylor creator: Teresa N. Hollingsworth creator: Christopher B. Anderson creator: Guillermo Martínez Pastur uri: https://doi.org/10.7717/peerj.5008 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hewitt et al. title: Who bears the cost of forest conservation? link: https://peerj.com/articles/5106 last-modified: 2018-07-05 description: BackgroundWhile the importance of conserving ecosystems for sustainable development is widely recognized, it is increasingly evident that despite delivering global benefits, conservation often comes at local cost. Protected areas funded by multilateral lenders have explicit commitments to ensure that those negatively affected are adequately compensated. We make the first comparison of the magnitude and distribution of the local costs of a protected area with the magnitude and distribution of the compensation provided under the World Bank social safeguard policies (Performance Standard 5).MethodsIn the Ankeniheny-Zahamena Corridor (a new protected area and REDD+ pilot project in eastern Madagascar), we used choice experiments to estimate local opportunity costs (n = 453) which we annualized using a range of conservative assumptions concerning discount rates. Detailed surveys covering farm inputs and outputs as well as off-farm income (n = 102) allowed us to explore these opportunity costs as a proportion of local incomes. Intensive review of publically available documents provided estimates of the number of households that received safeguard compensation and the amount spent per household. We carried out a contingent valuation exercise with beneficiaries of this compensation two years after the micro-development projects were implemented (n = 62) to estimate their value as perceived by beneficiaries.ResultsConservation restrictions result in very significant costs to forest communities. The median net present value of the opportunity cost across households in all sites was US$2,375. When annualized, these costs represent 27–84% of total annual income for median-income households; significantly higher proportionally for poorer households. Although some households have received compensation, we conservatively estimate that more than 50% of eligible households (3,020 households) have not. Given the magnitude of compensation (based both on amount spent and valuation by recipients two years after the compensation was distributed) relative to costs, we argue that no one was fully compensated. Achieving full compensation will require an order of magnitude more than was spent but we suggest that this should be affordable given the global value of forest conservation.DiscussionBy analyzing in unprecedented depth both the local costs of conservation, and the compensation distributed under donor policies, we demonstrate that despite well-intentioned policies, some of the poorest people on the planet are still bearing the cost of forest conservation. Unless significant extra funding is provided by the global beneficiaries of conservation, donors’ social safeguarding requirements will not be met, and forest conservation in developing countries will jeopardize, rather than contribute to, sustainable development goals. creator: Mahesh Poudyal creator: Julia P.G. Jones creator: O. Sarobidy Rakotonarivo creator: Neal Hockley creator: James M. Gibbons creator: Rina Mandimbiniaina creator: Alexandra Rasoamanana creator: Nilsen S. Andrianantenaina creator: Bruno S. Ramamonjisoa uri: https://doi.org/10.7717/peerj.5106 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Poudyal et al. title: Trabecular bone patterning in the hominoid distal femur link: https://peerj.com/articles/5156 last-modified: 2018-07-05 description: BackgroundIn addition to external bone shape and cortical bone thickness and distribution, the distribution and orientation of internal trabecular bone across individuals and species has yielded important functional information on how bone adapts in response to load. In particular, trabecular bone analysis has played a key role in studies of human and nonhuman primate locomotion and has shown that species with different locomotor repertoires display distinct trabecular architecture in various regions of the skeleton. In this study, we analyse trabecular structure throughout the distal femur of extant hominoids and test for differences due to locomotor loading regime.MethodsMicro-computed tomography scans of Homo sapiens (n = 11), Pan troglodytes (n = 18), Gorilla gorilla (n = 14) and Pongo sp. (n = 7) were used to investigate trabecular structure throughout the distal epiphysis of the femur. We predicted that bone volume fraction (BV/TV) in the medial and lateral condyles in Homo would be distally concentrated and more anisotropic due to a habitual extended knee posture at the point of peak ground reaction force during bipedal locomotion, whereas great apes would show more posteriorly concentrated BV/TV and greater isotropy due to a flexed knee posture and more variable hindlimb use during locomotion.ResultsResults indicate some significant differences between taxa, with the most prominent being higher BV/TV in the posterosuperior region of the condyles in Pan and higher BV/TV and anisotropy in the posteroinferior region in Homo. Furthermore, trabecular number, spacing and thickness differ significantly, mainly separating Gorilla from the other apes.DiscussionThe trabecular architecture of the distal femur holds a functional signal linked to habitual behaviour; however, there was more similarity across taxa and greater intraspecific variability than expected. Specifically, there was a large degree of overlap in trabecular structure across the sample, and Homo was not as distinct as predicted. Nonetheless, this study offers a comparative sample of trabecular structure in the hominoid distal femur and can contribute to future studies of locomotion in extinct taxa. creator: Leoni Georgiou creator: Tracy L. Kivell creator: Dieter H. Pahr creator: Matthew M. Skinner uri: https://doi.org/10.7717/peerj.5156 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Georgiou et al. title: Motor self-regulation in goats (Capra aegagrus hircus) in a detour-reaching task link: https://peerj.com/articles/5139 last-modified: 2018-07-05 description: Motor self-regulation is the ability to inhibit a prepotent response to a salient cue in favour of a more appropriate response. Motor self-regulation is an important component of the processes that interact to generate effective inhibitory control of behaviour, and is theorized to be a prerequisite of complex cognitive abilities in humans and other animals. In a large comparative study using the cylinder task, motor self-regulation was studied in 36 different species, mostly birds and primates. To broaden the range of species to comprehensively evaluate this phenomenon, motor self-regulation was studied in the domestic goat, which is a social ungulate species and moderate food specialist. Using the cylinder task, goats were first trained to perform a detour-reaching response to retrieve a reward from an opaque cylinder. Subsequently, an otherwise identical transparent cylinder was substituted for the opaque cylinder over 10 test trials. The goats’ ability to resist approaching the visible reward directly by touching the cylinder and to retain the trained detour-reaching response was measured. The results indicated that goats showed motor self-regulation at a level comparable to or better than that of many of the bird and mammal species tested to date. However, the individual reaction patterns revealed large intra- and inter-individual variability regarding motor self-regulation. An improvement across trials was observed only in latency to make contact with the reward; no improvement in the proportion of accurate trials was observed. A short, distinct pointing gesture by the experimenter during baiting did not have any impact on the side of the cylinder to which the goats detoured. In half of goats, individual side biases were observed when detouring to the side of the cylinder, but there was no bias at the population level for either the left or right side. The results underline the need for a detailed examination of individual performance and additional measures to achieve a complete understanding of animal performance in motor self-regulation tasks. creator: Jan Langbein uri: https://doi.org/10.7717/peerj.5139 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Langbein title: Influence of elevated CO2 on development and food utilization of armyworm Mythimna separata fed on transgenic Bt maize infected by nitrogen-fixing bacteria link: https://peerj.com/articles/5138 last-modified: 2018-07-05 description: BackgroundBt crops will face a new ecological risk of reduced effectiveness against target-insect pests owing to the general decrease in exogenous-toxin content in Bt crops grown under elevated carbon dioxide (CO2). The method chosen to deal with this issue may affect the sustainability of transgenic crops as an effective pest management tool, especially under future atmospheric CO2 level raising.MethodsIn this study, rhizobacterias, as being one potential biological regulator to enhance nitrogen utilization efficiency of crops, was selected and the effects of Bt maize (Line IE09S034 with Cry1Ie vs. its parental line of non-Bt maize Xianyu 335) infected by Azospirillum brasilense (AB) and Azotobacter chroococcum (AC) on the development and food utilization of the target Mythimna separate under ambient and double-ambient CO2 in open-top chambers from 2016 to 2017.ResultsThe results indicated that rhizobacteria infection significantly increased the larval life-span, pupal duration, relative consumption rate and approximate digestibility of M. separata, and significantly decreased the pupation rate, pupal weight, adult longevity, fecundity, relative growth rate, efficiency of conversion of digested food and efficiency of conversion of ingested food of M. separata fed on Bt maize, while here were opposite trends in development and food utilization of M. separata fed on non-Bt maize infected with AB and AC compared with the control buffer in 2016 and 2017 regardless of CO2 level.DiscussionSimultaneously, elevated CO2 and Bt maize both had negative influence on the development and food utilization of M. separata. Presumably, CO2 concentration arising in future significantly can increase their intake of food and harm to maize crop; however, Bt maize infected with rhizobacterias can reduce the field hazards from M. separata and the application of rhizobacteria infection can enhance the resistance of Bt maize against target lepidoptera pests especially under elevated CO2. creator: Zhuo Li creator: Megha N. Parajulee creator: Fajun Chen uri: https://doi.org/10.7717/peerj.5138 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Li et al. title: Enriched environment prevents oxidative stress in zebrafish submitted to unpredictable chronic stress link: https://peerj.com/articles/5136 last-modified: 2018-07-05 description: BackgroundThe enriched environment (EE) is a laboratory housing model that emerged from efforts to minimize the impact of environmental conditions on laboratory animals. Recently, we showed that EE promoted positive effects on behavior and cortisol levels in zebrafish submitted to the unpredictable chronic stress (UCS) protocol. Here, we expanded the characterization of the effects of UCS protocol by assessing parameters of oxidative status in the zebrafish brain and reveal that EE protects against the oxidative stress induced by chronic stress.MethodsZebrafish were exposed to EE (21 or 28 days) or standard housing conditions and subjected to the UCS protocol for seven days. Oxidative stress parameters (lipid peroxidation (TBARS), reactive oxygen species (ROS) levels, non-protein thiol (NPSH) and total thiol (SH) levels, superoxide dismutase (SOD) and catalase (CAT) activities were measured in brain homogenate.ResultsOur results revealed that UCS increased lipid peroxidation and ROS levels, while decreased NPSH levels and SOD activity, suggesting oxidative damage. EE for 28 days prevented all changes induced by the UCS protocol, and EE for 21 days prevented the alterations on NPSH levels, lipid peroxidation and ROS levels. Both EE for 21 or 28 days increased CAT activity.DiscussionOur findings reinforce the idea that EE exerts neuromodulatory effects in the zebrafish brain. EE promoted positive effects as it helped maintain the redox homeostasis, which may reduce the susceptibility to stress and its oxidative impact. creator: Matheus Marcon creator: Ricieri Mocelin creator: Adrieli Sachett creator: Anna M. Siebel creator: Ana P. Herrmann creator: Angelo Piato uri: https://doi.org/10.7717/peerj.5136 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Marcon et al. title: Testing accuracy in 2D and 3D geometric morphometric methods for cut mark identification and classification link: https://peerj.com/articles/5133 last-modified: 2018-07-05 description: The analysis of bone surface modifications (BSMs) is a prominent part of paleoanthropological studies, namely taphonomic research. Behavioral interpretations of the fossil record hinge strongly upon correct assessment of BSMs. With the significant impact of microscopic analysis to the study of BSMs, multiple authors have discussed the reliability of these technological improvements for gaining resolution in BSM discrimination. While a certain optimism is present, some important questions are ignored and others overemphasized without appropriate empirical support. This specifically affects the study of cut marks. A diversity of geometric morphometric approaches applied to the study of cut marks have resulted in the coexistence (and competition) of different 2D and 3D methods. The present work builds upon the foundation of experiments presented by Maté-González et al. (2015), Courtenay et al. (2017) and Otárola-Castillo et al. (2018) to contrast for the first time 2D and 3D methods in their resolution of cut mark interpretation and classification. The results presented here show that both approaches are equally valid and that the use of sophisticated 3D methods do not contribute to an improvement in accuracy. creator: Lloyd A. Courtenay creator: Miguel Ángel Maté-González creator: Julia Aramendi creator: José Yravedra creator: Diego González-Aguilera creator: Manuel Domínguez-Rodrigo uri: https://doi.org/10.7717/peerj.5133 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Courtenay et al.