title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1462 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Don’t worry, be active: how to facilitate the detection of errors in immersive virtual environments link: https://peerj.com/articles/5844 last-modified: 2018-10-29 description: The current research aims to study the link between the type of vision experienced in a collaborative immersive virtual environment (active vs. multiple passive), the type of error one looks for during a cooperative multi-user exploration of a design project (affordance vs. perceptual violations), and the type of setting in which multi-user perform (field in Experiment 1 vs. laboratory in Experiment 2). The relevance of this link is backed by the lack of conclusive evidence on an active vs. passive vision advantage in cooperative search tasks within software based on immersive virtual reality (IVR). Using a yoking paradigm based on the mixed usage of simultaneous active and multiple passive viewings, we found that the likelihood of error detection in a complex 3D environment was characterized by an active vs. multi-passive viewing advantage depending on: (1) the degree of knowledge dependence of the type of error the passive/active observers were looking for (low for perceptual violations, vs. high for affordance violations), as the advantage tended to manifest itself irrespectively from the setting for affordance, but not for perceptual violations; and (2) the degree of social desirability possibly induced by the setting in which the task was performed, as the advantage occurred irrespectively from the type of error in the laboratory (Experiment 2) but not in the field (Experiment 1) setting. Results are relevant to future development of cooperative software based on IVR used for supporting the design review. A multi-user design review experience in which designers, engineers and end-users all cooperate actively within the IVR wearing their own head mounted display, seems more suitable for the detection of relevant errors than standard systems characterized by a mixed usage of active and passive viewing. creator: Sara Rigutti creator: Marta Stragà creator: Marco Jez creator: Giulio Baldassi creator: Andrea Carnaghi creator: Piero Miceu creator: Carlo Fantoni uri: https://doi.org/10.7717/peerj.5844 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Rigutti et al. title: Association of urban forest landscape characteristics with biomass and soil carbon stocks in Harbin City, Northeastern China link: https://peerj.com/articles/5825 last-modified: 2018-10-29 description: BackgroundUrban forests help in mitigating carbon emissions; however, their associations with landscape patterns are unclear. Understanding the associations would help us to evaluate urban forest ecological services and favor urban forest management via landscape regulations. We used Harbin, capital city of the northernmost province in China, as an example and hypothesized that the urban forests had different landscape metrics among different forest types, administrative districts, and urban–rural gradients, and these differences were closely associated with forest carbon sequestration in the biomass and soils.MethodsWe extracted the urban forest tree coverage area on the basis of 2 GF-1 remote sensing images and object-oriented based classification method. The analysis of forest landscape patterns and estimation of carbon storage were based on tree coverage data and 199 plots. We also examined the relationships between forest landscape metrics and carbon storage on the basis of forest types, administrative districts, ring roads, and history of urban settlements by using statistical methods.ResultsThe small patches covering an area of less than 0.5 ha accounted for 72.6% of all patches (average patch size, 0.31 ha). The mean patch size (AREA_MN) and largest patch index (LPI) were the highest in the landscape and relaxation forest and Songbei District. The landscape shape index (LSI) and number of patches linearly decreased along rural-urban gradients (p < 0.05). The tree biomass carbon storage varied from less than 10 thousand tons in the urban center (first ring road region and 100-year regions) to more than 100 thousand tons in the rural regions (fourth ring road and newly urbanized regions). In the same urban–rural gradients, soil carbon storage varied from less than five thousand tons in the urban centers to 73–103 thousand tons in the rural regions. The association analysis indicated that the total forest area was the key factor that regulates total carbon storage in trees and soils. However, in the case of carbon density (ton ha−1), AREA_MN was strongly associated with tree biomass carbon, and soil carbon density was negatively related to LSI (p < 0.01) and AREA_MN (p < 0.05), but positively related to LPI (p < 0.05).DiscussionThe urban forests were more fragmented in Harbin than in other provincial cities in Northeastern China, as shown by the smaller patch size, more complex patch shape, and larger patch density. The decrease in LSI along the rural-urban gradients may contribute to the forest carbon sequestrations in downtown regions, particularly underground soil carbon accumulation, and the increasing patch size may benefit tree carbon sequestration. Our findings help us to understand how forest landscape metrics are associated with carbon storage function. These findings related to urban forest design may maximize forest carbon sequestration services and facilitate in precisely estimating the forest carbon sink. creator: Hailiang Lv creator: Wenjie Wang creator: Xingyuan He creator: Chenhui Wei creator: Lu Xiao creator: Bo Zhang creator: Wei Zhou uri: https://doi.org/10.7717/peerj.5825 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Lv et al. title: Effects of agricultural management on phyllosphere fungal diversity in vineyards and the association with adjacent native forests link: https://peerj.com/articles/5715 last-modified: 2018-10-29 description: Agriculture is one of the main drivers of land conversion, and agriculture practices can impact on microbial diversity. Here we characterized the phyllosphere fungal diversity associated with Carménère grapevines under conventional and organic agricultural management. We also explored the fungal diversity present in the adjacent sclerophyllous forests to explore the potential role of native forest on vineyard phyllosphere. After conducting D2 and ITS2 amplicon sequencing, we found that fungal diversity indices did not change between conventional and organic vineyards, but community structure was sensitive to the agricultural management. On the other hand, we found a high proportion of shared fungal OTUs between vineyards and native forests. In addition, both habitats had similar levels of fungal diversity despite forest samples were derived from multiple plant species. In contrast, the community structure was different in both habitats. Interestingly, the native forest had more unidentified species and unique OTUs than vineyards. Forest dominant species were Aureobasidium pullulans and Endoconidioma populi, whereas Davidiella tassiana, Didymella sp., and Alternaria eichhorniae were more abundant in vineyards. Overall, this study argues that a better understanding of the relationship native forests and agroecosystems is needed for maintaining and enhancing ecosystem services provided by natural ecosystems. Finally, knowledge of microbial communities living in the Chilean Mediterranean biome is needed for appropriate conservation management of these biomes and their classification as biodiversity hotspots. creator: Luis E. Castañeda creator: Toshiko Miura creator: Roland Sánchez creator: Olga Barbosa uri: https://doi.org/10.7717/peerj.5715 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Castañeda et al. title: Body size and temperature effects on standard metabolic rate for determining metabolic scope for activity of the polychaete Hediste (Nereis) diversicolor link: https://peerj.com/articles/5675 last-modified: 2018-10-29 description: Considering the ecological importance and potential value of Hediste diversicolor, a better understanding of its metabolic rate and potential growth rates is required. The aims of this study are: (i) to describe key biometric relationships; (ii) to test the effects of temperature and body size on standard metabolic rate (as measure by oxygen consumption) to determine critical parameters, namely Arrhenius temperature (TA), allometric coefficient (b) and reaction rate; and (iii) to determine the metabolic scope for activity (MSA) of H. diversicolor for further comparison with published specific growth rates. Individuals were collected in a Mediterranean lagoon (France). After 10 days of acclimatization, 7 days at a fixed temperature and 24 h of fasting, resting oxygen consumption rates (VO2) were individually measured in the dark at four different temperatures (11, 17, 22 and 27 °C) in worms weighing from 4 to 94 mgDW (n = 27 per temperature). Results showed that DW and L3 were the most accurate measurements of weight and length, respectively, among all the metrics tested. Conversion of WW (mg), DW (mg) and L3 (mm) were quantified with the following equations: DW = 0.15 × WW, L3 = 0.025 × TL(mm) + 1.44 and DW = 0.8 × L33.68. Using an equation based on temperature and allometric effects, the allometric coefficient (b) was estimated at 0.8 for DW and at 2.83 for L3. The reaction rate (VO2) equaled to 12.33 µmol gDW−1 h−1 and 0.05 µmol mm L3−1 h−1 at the reference temperature (20 °C, 293.15 K). Arrhenius temperature (TA) was 5,707 and 5,664 K (for DW and L3, respectively). Metabolic scope for activity ranged from 120.1 to 627.6 J gDW−1 d−1. Predicted maximum growth rate increased with temperature, with expected values of 7–10% in the range of 15–20 °C. MSA was then used to evaluate specific growth rates (SGR) in several experiments. This paper may be used as a reference and could have interesting applications in the fields of aquaculture, ecology and biogeochemical processes. creator: Helena Lopes Galasso creator: Marion Richard creator: Sébastien Lefebvre creator: Catherine Aliaume creator: Myriam D. Callier uri: https://doi.org/10.7717/peerj.5675 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Galasso et al. title: Egg perivitelline fluid of the invasive snail Pomacea canaliculata affects mice gastrointestinal function and morphology link: https://peerj.com/articles/5314 last-modified: 2018-10-29 description: BackgroundSpecies beloging to the genus Pomacea (Ampullariidae), often referred as apple snails, are freshwater, amphibious snails native to South, Central and North America. Some species such as P. canaliculata have become a driver of ecosystem changes in wetlands and an important rice and taro pest after its introduction to Asia and other parts of the world. Females deposit colored egg clutches above the waterline, a reproductive strategy that exposes the eggs to harsh conditions and terrestrial predation. However, eggs have no reported predators in their native range, probably because of the acquisition of unparalleled biochemical defenses provided by a set of proteins (perivitellins) that nourish embryos and protect them from predators and abiotic factors. Notably, ingestion of egg perivitelline fluid (PVF) decreases rat growth rate and alters their gastrointestinal morphology. The aim of the study is to determine the effect of apple snail egg PVF on mice gut digestive activity, morphology and nutrient absorption.MethodsCarbohydrate digestion by intestinal disaccharidases (sucrase-isomaltase and maltase-glucoamylase) was evaluated ex vivo in mice gavaged with 1 or 4 doses of PVF. Changes in gut morphological and absorptive surface were measured. In addition, alteration on nutrient absorption rates, transport pathways and intestinal permeability was evaluated by luminal perfusions of small intestine with radiolabeled L-proline (absorbed by paracellular and transcellular pathways) and L-arabinose (absorbed exclusively by paracellular pathway).ResultsPerivitelline fluid affected mice displayed significant morphological changes in the small intestine epithelium inducing the appearance of shorter and wider villi as well as fused villi. This resulted in a diminished absorptive surface, notably in the proximal portion. Likewise, the activity of disaccharidases diminished in the proximal portion of the intestine. Total absorption of L-proline increased in treated mice in a dose-dependent manner. There were no differences neither in the ratio of paracellular-to-transcellular absorption of L-proline nor in gut permeability as revealed by the clearance of L-arabinose.DiscussionOral administration of apple snail PVF to mice adversely alters gut morphophysiology by reducing the intestinal absorptive surface, affecting enzymes of sugar metabolism and increasing the absorption rate of nutrients without affecting the relative contribution of the absorption pathways or gut permeability. These results further support the role of PVF in passive anti-predator defenses in Pomacea snail eggs that target the digestive system. creator: Matías Giglio creator: Cintia Garro creator: Enrique Caviedes-Vidal creator: Horacio Heras uri: https://doi.org/10.7717/peerj.5314 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Giglio et al. title: Using accelerometers to develop time-energy budgets of wild fur seals from captive surrogates link: https://peerj.com/articles/5814 last-modified: 2018-10-26 description: BackgroundAccurate time-energy budgets summarise an animal’s energy expenditure in a given environment, and are potentially a sensitive indicator of how an animal responds to changing resources. Deriving accurate time-energy budgets requires an estimate of time spent in different activities and of the energetic cost of that activity. Bio-loggers (e.g., accelerometers) may provide a solution for monitoring animals such as fur seals that make long-duration foraging trips. Using low resolution to record behaviour may aid in the transmission of data, negating the need to recover the device.MethodsThis study used controlled captive experiments and previous energetic research to derive time-energy budgets of juvenile Australian fur seals (Arctocephalus pusillus) equipped with tri-axial accelerometers. First, captive fur seals and sea lions were equipped with accelerometers recording at high (20 Hz) and low (1 Hz) resolutions, and their behaviour recorded. Using this data, machine learning models were trained to recognise four states—foraging, grooming, travelling and resting. Next, the energetic cost of each behaviour, as a function of location (land or water), season and digestive state (pre- or post-prandial) was estimated. Then, diving and movement data were collected from nine wild juvenile fur seals wearing accelerometers recording at high- and low- resolutions. Models developed from captive seals were applied to accelerometry data from wild juvenile Australian fur seals and, finally, their time-energy budgets were reconstructed.ResultsBehaviour classification models built with low resolution (1 Hz) data correctly classified captive seal behaviours with very high accuracy (up to 90%) and recorded without interruption. Therefore, time-energy budgets of wild fur seals were constructed with these data. The reconstructed time-energy budgets revealed that juvenile fur seals expended the same amount of energy as adults of similar species. No significant differences in daily energy expenditure (DEE) were found across sex or season (winter or summer), but fur seals rested more when their energy expenditure was expected to be higher. Juvenile fur seals used behavioural compensatory techniques to conserve energy during activities that were expected to have high energetic outputs (such as diving).DiscussionAs low resolution accelerometry (1 Hz) was able to classify behaviour with very high accuracy, future studies may be able to transmit more data at a lower rate, reducing the need for tag recovery. Reconstructed time-energy budgets demonstrated that juvenile fur seals appear to expend the same amount of energy as their adult counterparts. Through pairing estimates of energy expenditure with behaviour this study demonstrates the potential to understand how fur seals expend energy, and where and how behavioural compensations are made to retain constant energy expenditure over a short (dive) and long (season) period. creator: Monique A. Ladds creator: Marcus Salton creator: David P. Hocking creator: Rebecca R. McIntosh creator: Adam P. Thompson creator: David J. Slip creator: Robert G. Harcourt uri: https://doi.org/10.7717/peerj.5814 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ladds et al. title: Size-dependent functional response of Xenopus laevis feeding on mosquito larvae link: https://peerj.com/articles/5813 last-modified: 2018-10-26 description: Predators can play an important role in regulating prey abundance and diversity, determining food web structure and function, and contributing to important ecosystem services, including the regulation of agricultural pests and disease vectors. Thus, the ability to predict predator impact on prey is an important goal in ecology. Often, predators of the same species are assumed to be functionally equivalent, despite considerable individual variation in predator traits known to be important for shaping predator–prey interactions, like body size. This assumption may greatly oversimplify our understanding of within-species functional diversity and undermine our ability to predict predator effects on prey. Here, we examine the degree to which predator–prey interactions are functionally homogenous across a natural range of predator body sizes. Specifically, we quantify the size-dependence of the functional response of African clawed frogs (Xenopus laevis) preying on mosquito larvae (Culex pipiens). Three size classes of predators, small (15–30 mm snout-vent length), medium (50–60 mm) and large (105–120 mm), were presented with five densities of prey to determine functional response type and to estimate search efficiency and handling time parameters generated from the models. The results of mesocosm experiments showed that type of functional response of X. laevis changed with size: small predators exhibited a Type II response, while medium and large predators exhibited Type III responses. Functional response data showed an inversely proportional relationship between predator attack rate and predator size. Small and medium predators had highest and lowest handling time, respectively. The change in functional response with the size of predator suggests that predators with overlapping cohorts may have a dynamic impact on prey populations. Therefore, predicting the functional response of a single size-matched predator in an experiment may misrepresent the predator’s potential impact on a prey population. creator: Corey J. Thorp creator: Mhairi E. Alexander creator: James R. Vonesh creator: John Measey uri: https://doi.org/10.7717/peerj.5813 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Thorp et al. title: Three, two, one! Revision of the long-bodied sphaerodorids (Sphaerodoridae, Annelida) and synonymization of Ephesiella, Ephesiopsis and Sphaerodorum link: https://peerj.com/articles/5783 last-modified: 2018-10-26 description: BackgroundLong-bodied sphaerodorids (Annelida, Sphaerodoridae) is the common name for members of the three closely and morphologically homogenous currently accepted genera of benthic marine bristle worms: Ephesiella, Ephesiopsis and Sphaerodorum. Members of this group share the presence of two dorsal and longitudinal rows of macrotubercles with terminal papillae, and two longitudinal rows of microtubercles, features that are unique among sphaerodorids. Genera are distinguished by the chaetae morphology. Members of Ephesiella are characterised by having compound chaetae (except, sometimes, simple chaetae in the first chaetigers), Sphaerodorum bear only simple chaetae, and Ephesiopsis have both compound and simple chaetae in all parapodia.MethodsMitochondrial (partial COI and 16S rDNA) and nuclear (partial 18S rDNA and 28S rDNA) sequence data of long-bodied sphaerodorids with compound and simple chaetae, and an outgroup of additional seven sphaerodorid species were analysed separately and in combination using Bayesian inference (BA), and Maximum Likelihood (ML) methods. Long-bodied sphaerodorids from around the world (including type specimens) were examined under a range of optical equipment in order to evaluate putative generic and specific diagnostic features, in addition to intraspecific variability.ResultsPhylogenetic analyses of mitochondrial and nuclear DNA sequences of specimens identified as Ephesiella and Sphaerodorum, based on chaeta morphology, were performed. Sphaerodorum and Ephesiella were recovered as paraphyletic and nested within each other. Revision of current nominal species diagnostic features are performed and discussed.DiscussionResults contradict current generic definitions. Recovery of paraphyletic compound and simple chaetae clades urge the synonymization of these two genera of long-bodied sphaerodorids. Morphological data also suggest the synonymization of Ephesiopsis. creator: María Capa creator: Torkild Bakken creator: Karin Meißner creator: Arne Nygren uri: https://doi.org/10.7717/peerj.5783 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Capa et al. title: Evolution of African barbs from the Lake Victoria drainage system, Kenya link: https://peerj.com/articles/5762 last-modified: 2018-10-26 description: The Lake Victoria drainage basin (LVD) in Kenya is home to ten nominal species of small barbs (Enteromius) and one of large barbs (Labeobarbus altianalis). A recent molecular study genetically characterized small barbs in this region and found evidence of introgression between certain species, complicating the taxonomy and species identification of these fishes. This study aimed to extend our understanding on the evolution of these fishes by: (1) determining whether putatively pure individuals of Enteromius cercops are found in the Kenyan LVD, as the previous study only found hybrid individuals of this species in this region; (2) testing the sister relationship between Enteromius profundus, endemic to Lake Victoria, and Enteromius radiatus, also found in Lake Victoria, which had been previously synonymized; (3) examining the phylogenetic relationships of small barbs of the Kenyan LVD with those reported from other ichthyological provinces of Africa; and (4) examining the phylogenetic relationships of Labeobarbus altianalis with other Labeobarbus species. To this end, we obtained mitochondrial Cytochrome b and nuclear Growth Hormone (GH) intron 2 gene sequences of nine Enteromius species from the LVD in Kenya, as well as cytochrome b sequences for L. altianalis. We conducted Maximum likelihood and Bayesian phylogenetic analyses to establish their evolutionary relationships in relation to many other barbs specimens from Africa. Phylogenetic analyses did not reveal instances of hybridization/introgression among the individuals sequenced by us. A sister relationship between E. profundus and E. radiatus was not found. This latter species shows instead a sister relationship with a lineage comprised of two species from West Africa. Other sister relationships between taxa from the East coast and other ecoregions from Africa are observed, suggesting that past drainage connections and vicariant events contributed to the diversification of Enteromius. Finally, only a single haplotype was recovered among the L. altianalis individuals examined, which is most similar to a specimen from Lake Edward in Uganda. creator: Violet M. Ndeda creator: Mariana Mateos creator: Luis A. Hurtado uri: https://doi.org/10.7717/peerj.5762 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ndeda et al. title: Spatial analyses of threats to ecosystem service hotspots in Greater Durban, South Africa link: https://peerj.com/articles/5723 last-modified: 2018-10-26 description: BackgroundPopulation growth at all scales and rapid rates of urbanization, particularly in the global South, are placing increasing pressure on ecosystems and their ability to provide services essential for human well-being. The spatial consideration of threats to ecosystem services related to changes in land use is necessary in order to avoid undue impacts on society due to the loss or reduced supply of ecosystem services. This study assesses the potential threats of land use change from strategic and local development proposals to ecosystem services in the city of Durban.MethodsWe analysed the spatial relationship between five categories of ecosystem service hotspots (carbon storage, water yield, sediment retention, nutrient retention and flood attenuation) and urban land use change related to selected strategic planning proposals, development proposals and sand-mining applications in Durban, South Africa (eThekwini Municipality) with a view to determining the consequences for progress towards a more sustainable development path in the city. We identified the potential levels of threat related to habitat destruction or transformation for the five categories of ecosystem services and a subset of 13 ecosystem service hotspots, using GIS spatial analysis tools.ResultsThe results show that on average, should Durban’s strategic development plans be realised, approximately 42% loss of ecosystem service hotspots is expected in the two municipal town-planning regions assessed. With respect to development applications between 2009 and 2012, approximately 36% of all environmental impact assessments and 84% of sand mining applications occurred within ecosystem service hotspots within Durban.DiscussionThe findings highlight the tension between short-term development pressures and longer-term sustainability goals and confirm that current planning and development proposals pose a threat to ecosystems and their ability to deliver services that support human well-being in Durban. We suggest practical solutions to include ecosystem services into local government decision-making. creator: Rashieda Davids creator: Mathieu Rouget creator: Richard Boon creator: Debra Roberts uri: https://doi.org/10.7717/peerj.5723 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Davids et al.