title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1581 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Planning protected areas network that are relevant today and under future climate change is possible: the case of Atlantic Forest endemic birds link: https://peerj.com/articles/4689 last-modified: 2018-05-24 description: BackgroundA key strategy in biodiversity conservation is the establishment of protected areas. In the future, however, the redistribution of species in response to ongoing climate change is likely to affect species’ representativeness in those areas. Here we quantify the effectiveness of planning protected areas network to represent 151 birds endemic to the Brazilian Atlantic Forest hotspot, under current and future climate change conditions for 2050.MethodsWe combined environmental niche modeling and systematic conservation planning using both a county and a regional level planning strategy. We recognized the conflict between biodiversity conservation and economic development, including socio-economic targets (as opposed to biological only) and using planning units that are meaningful for policy-makers.ResultsWe estimated an average contraction of 29,500 km2 in environmentally suitable areas for birds, representing 52% of currently suitable areas. Still, the most cost-effective solution represented almost all target species, requiring only ca. 10% of the Atlantic Forest counties to achieve that representativeness, independent of strategy. More than 50% of these counties were selected both in the current and future planned networks, representing >83% of the species.DiscussionOur results indicate that: (i) planning protected areas network currently can be useful to represent species under climate change; (ii) the overlapped planning units in the best solution for both current and future conditions can be considered as “no regret” areas; (iii) priority counties are spread throughout the biome, providing specific guidance wherever the possibility of creating protected area arises; and (iv) decisions can occur at different administrative spheres (Federal, State or County) as we found quite similar numerical solutions using either county or regional level strategies. creator: Mariana M. Vale creator: Thiago V. Souza creator: Maria Alice S. Alves creator: Renato Crouzeilles uri: https://doi.org/10.7717/peerj.4689 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Vale et al. title: Altitudinal patterns in breeding bird species richness and density in relation to climate, habitat heterogeneity, and migration influence in a temperate montane forest (South Korea) link: https://peerj.com/articles/4857 last-modified: 2018-05-23 description: Altitudinal patterns in the population ecology of mountain bird species are useful for predicting species occurrence and behavior. Numerous hypotheses about the complex interactions among environmental factors have been proposed; however, these still remain controversial. This study aimed to identify the altitudinal patterns in breeding bird species richness or density and to test the hypotheses that climate, habitat heterogeneity (horizontal and vertical), and heterospecific attraction in a temperate forest, South Korea. We conducted a field survey of 142 plots at altitudes between 200 and 1,400 m a.s.l in the breeding season. A total of 2,771 individuals from 53 breeding bird species were recorded. Altitudinal patterns of species richness and density showed a hump-shaped pattern, indicating that the highest richness and density could be observed at moderate altitudes. Models constructed with 13 combinations of six variables demonstrated that species richness was positively correlated with vertical and horizontal habitat heterogeneity. Density was positively correlated with vertical, but not horizontal habitat heterogeneity, and negatively correlated with migratory bird ratio. No significant relationships were found between spring temperature and species richness or density. Therefore, the observed patterns in species richness support the hypothesis that habitat heterogeneity, rather than climate, is the main driver of species richness. Also, neither habitat heterogeneity nor climate hypotheses fully explains the observed patterns in density. However, vertical habitat heterogeneity does likely help explain observed patterns in density. The heterospecific attraction hypothesis did not apply to the distribution of birds along the altitudinal gradient. Appropriate management of vertical habitat heterogeneity, such as vegetation cover, should be maintained for the conservation of bird diversity in this area. creator: Jin-Yong Kim creator: Sanghun Lee creator: Man-Seok Shin creator: Chang-Hoon Lee creator: Changwan Seo creator: Soo Hyung Eo uri: https://doi.org/10.7717/peerj.4857 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kim et al. title: Primate occurrence across a human-impacted landscape in Guinea-Bissau and neighbouring regions in West Africa: using a systematic literature review to highlight the next conservation steps link: https://peerj.com/articles/4847 last-modified: 2018-05-23 description: BackgroundWest African landscapes are largely characterised by complex agroforest mosaics. Although the West African forests are considered a nonhuman primate hotspot, knowledge on the distribution of many species is often lacking and out-of-date. Considering the fast-changing nature of the landscapes in this region, up-to-date information on primate occurrence is urgently needed, particularly of taxa such as colobines, which may be more sensitive to habitat modification than others. Understanding wildlife occurrence and mechanisms of persistence in these human-dominated landscapes is fundamental for developing effective conservation strategies.MethodsIn this paper, we aim to review current knowledge on the distribution of three threatened primates in Guinea-Bissau and neighbouring regions, highlighting research gaps and identifying priority research and conservation action. We conducted a systematic literature review of primate studies from 1976 to 2016 in Guinea-Bissau, southern Senegal and western Guinea (Boké Region). We mapped historical observation records of chimpanzee (Pan troglodytes verus), Temminck’s red colobus (Pilicolobus badius temminckii) and king colobus (Colobus polykomos), including our preliminary survey data from Dulombi, a newly established National Park (NP) in Guinea-Bissau.ResultsWe found 151 documents, including 87 journal articles, that contained field data on primates in this region. In Guinea-Bissau, nearly all studies focussed south of the Corubal River, including mainly Cantanhez, Cufada, and Boé NP’s. In Senegal, most of the data came from Fongoli and Niokolo-Koba NP. In Boké (Guinea) studies are few, with the most recent data coming from Sangarédi. In Dulombi NP we recorded eight primate species, including chimpanzees, red colobus and king colobus. Across the selected region, chimpanzees, red colobus and king colobus were reported in eleven, twelve and seven protected areas, respectively.DiscussionOur study demonstrates large geographical research gaps particularly for the two colobines. For the first time after more than two decades, we confirm the presence of red colobus and king colobus north of the Corubal River in Guinea-Bissau. The little information available from large parts of the red colobus range raises questions regarding levels of population fragmentation in this species, particularly in Casamance and across northern Guinea-Bissau. There are still no records demonstrating the occurrence of king colobus in Senegal, and the presence of a viable population in north-eastern Guinea-Bissau remains uncertain. While the occurrence of chimpanzees in Guinea-Bissau and Senegal is well documented, data from Boké (Guinea) are sparse and out-of-date. Our approach—the mapping of data gathered from a systematic literature review—allows us to provide recommendations for selecting future geographical survey locations and planning further research and conservation strategies in this region. creator: Elena Bersacola creator: Joana Bessa creator: Amélia Frazão-Moreira creator: Dora Biro creator: Cláudia Sousa creator: Kimberley Jane Hockings uri: https://doi.org/10.7717/peerj.4847 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Bersacola et al. title: Impact of crop residue management on crop production and soil chemistry after seven years of crop rotation in temperate climate, loamy soils link: https://peerj.com/articles/4836 last-modified: 2018-05-23 description: Society is increasingly demanding a more sustainable management of agro-ecosystems in a context of climate change and an ever growing global population. The fate of crop residues is one of the important management aspects under debate, since it represents an unneglectable quantity of organic matter which can be kept in or removed from the agro-ecosystem. The topic of residue management is not new, but the need for global conclusion on the impact of crop residue management on the agro-ecosystem linked to local pedo-climatic conditions has become apparent with an increasing amount of studies showing a diversity of conclusions. This study specifically focusses on temperate climate and loamy soil using a seven-year data set. Between 2008 and 2016, we compared four contrasting residue management strategies differing in the amount of crop residues returned to the soil (incorporation vs. exportation of residues) and in the type of tillage (reduced tillage (10 cm depth) vs. conventional tillage (ploughing at 25 cm depth)) in a field experiment. We assessed the impact of the crop residue management on crop production (three crops—winter wheat, faba bean and maize—cultivated over six cropping seasons), soil organic carbon content, nitrate (${\mathrm{NO}}_{3}^{-}$NO3−), phosphorus (P) and potassium (K) soil content and uptake by the crops. The main differences came primarily from the tillage practice and less from the restitution or removal of residues. All years and crops combined, conventional tillage resulted in a yield advantage of 3.4% as compared to reduced tillage, which can be partly explained by a lower germination rate observed under reduced tillage, especially during drier years. On average, only small differences were observed for total organic carbon (TOC) content of the soil, but reduced tillage resulted in a very clear stratification of TOC and also of P and K content as compared to conventional tillage. We observed no effect of residue management on the ${\mathrm{NO}}_{3}^{-}$NO3− content, since the effect of fertilization dominated the effect of residue management. To confirm the results and enhance early tendencies, we believe that the experiment should be followed up in the future to observe whether more consistent changes in the whole agro-ecosystem functioning are present on the long term when managing residues with contrasted strategies. creator: Marie-Pierre Hiel creator: Sophie Barbieux creator: Jérôme Pierreux creator: Claire Olivier creator: Guillaume Lobet creator: Christian Roisin creator: Sarah Garré creator: Gilles Colinet creator: Bernard Bodson creator: Benjamin Dumont uri: https://doi.org/10.7717/peerj.4836 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Hiel et al. title: Predicting the potential distributions of the invasive cycad scale Aulacaspis yasumatsui (Hemiptera: Diaspididae) under different climate change scenarios and the implications for management link: https://peerj.com/articles/4832 last-modified: 2018-05-23 description: Cycads are an ancient group of gymnosperms that are popular as landscaping plants, though nearly all of them are threatened or endangered in the wild. The cycad aulacaspis scale (CAS), Aulacaspis yasumatsui Takagi (Hemiptera: Diaspididae), has become one of the most serious pests of cycads in recent years; however, the potential distribution range and the management approach for this pest are unclear. A potential risk map of cycad aulacaspis scale was created based on occurrence data under different climatic conditions and topology factors in this study. Furthermore, the future potential distributions of CAS were projected for the periods 2050s and 2070s under three different climate change scenarios (GFDL-CM3, HADGEM2-AO and MIROC5) described in the Special Report on Emissions Scenarios of the IPCC (Intergovernmental Panel on Climate Change). The model suggested high environmental suitability for the continents of Asia and North America, where the species has already been recorded. The potential distribution expansions or reductions were also predicted under different climate change conditions. Temperature of Driest Quarter (Bio9) was the most important factor, explaining 48.1% of the distribution of the species. The results also suggested that highly suitable habitat for CAS would exist in the study area if the mean temperature of 15–20 °C in the driest quarter and a mean temperature of 25–28 °C the wettest quarter. This research provides a theoretical reference framework for developing policy to manage and control this invasive pest. creator: Jiufeng Wei creator: Qing Zhao creator: Wanqing Zhao creator: Hufang Zhang uri: https://doi.org/10.7717/peerj.4832 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wei et al. title: Taxonomic monograph of Oxygyne (Thismiaceae), rare achlorophyllous mycoheterotrophs with strongly disjunct distribution link: https://peerj.com/articles/4828 last-modified: 2018-05-23 description: Oxygyne Schltr. (Thismiaceae) is a rare and little-known genus of achlorophyllous mycoheterotrophic perennial herbs with one of the most remarkable distributions of all angiosperm plant genera globally, being disjunct between Japan and West–Central Africa. Each species is known only from a single location, and in most cases from a single specimen. This monographic study names, describes and maps two new species, Oxygyne duncanii Cheek from cloud forest in SW Region Cameroon and O. frankei Cheek from gallery forest in the Central African Republic, representing the first new Oxygyne species described from Africa in 112 years, and raising the number of described Oxygyne species from four to six. Oxygyne duncanii is remarkable for sharing more morphological characters with two of the three Japanese species (O. hyodoi C.Abe & Akasawa, O. shinzatoi (H. Ohashi) Tsukaya) than with the geographically much closer type species of the genus, O. triandra from Mt Cameroon. Based mainly on herbarium specimens and field observations made in Cameroon and Japan during a series of botanical surveys, we provide descriptions, synonymy, mapping and extinction risk assessments for each species of Oxygyne, together with keys to the genera of Thismiaceae and the species of Oxygyne. The subterranean structures of African Oxygyne are described for the first time, and found to be consistent with those of the Japanese species. We review and reject an earlier proposal that the Japanese species should be segregated from the African species as a separate genus, Saionia Hatus. The only character that separates the two disjunct species groups is now flower colour: blue or partly-blue in the Japanese species compared with orange-brown in the African species. Studies of the pollination biology and mycorrhizal partners of Oxygyne are still lacking. Two of the six species, O. triandra Schltr. and O. hyodoi, appear to be extinct, and the remaining four are assessed as Critically Endangered using the IUCN 2012 criteria. To avoid further extinction, an urgent requirement is for conservation management of the surviving species in the wild. Since few achlorophyllous mycoheterotrophs have been successfully cultivated from seed to maturity, ex situ conservation will not be viable for these species and protection in the wild is the only viable option. While natural habitat survives, further botanical surveys could yet reveal additional new species between Central Africa and Japan. creator: Martin Cheek creator: Hirokazu Tsukaya creator: Paula J. Rudall creator: Kenji Suetsugu uri: https://doi.org/10.7717/peerj.4828 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cheek et al. title: Effects of preservation method on canine (Canis lupus familiaris) fecal microbiota link: https://peerj.com/articles/4827 last-modified: 2018-05-23 description: Studies involving gut microbiome analysis play an increasing role in the evaluation of health and disease in humans and animals alike. Fecal sampling methods for DNA preservation in laboratory, clinical, and field settings can greatly influence inferences of microbial composition and diversity, but are often inconsistent and under-investigated between studies. Many laboratories have utilized either temperature control or preservation buffers for optimization of DNA preservation, but few studies have evaluated the effects of combining both methods to preserve fecal microbiota. To determine the optimal method for fecal DNA preservation, we collected fecal samples from one canine donor and stored aliquots in RNAlater, 70% ethanol, 50:50 glycerol:PBS, or without buffer at 25 °C, 4 °C, and −80 °C. Fecal DNA was extracted, quantified, and 16S rRNA gene analysis performed on Days 0, 7, 14, and 56 to evaluate changes in DNA concentration, purity, and bacterial diversity and composition over time. We detected overall effects on bacterial community of storage buffer (F-value = 6.87, DF = 3, P < 0.001), storage temperature (F-value=1.77, DF = 3, P = 0.037), and duration of sample storage (F-value = 3.68, DF = 3, P < 0.001). Changes in bacterial composition were observed in samples stored in −80 °C without buffer, a commonly used method for fecal DNA storage, suggesting that simply freezing samples may be suboptimal for bacterial analysis. Fecal preservation with 70% ethanol and RNAlater closely resembled that of fresh samples, though RNAlater yielded significantly lower DNA concentrations (DF = 8.57, P < 0.001). Although bacterial composition varied with temperature and buffer storage, 70% ethanol was the best method for preserving bacterial DNA in canine feces, yielding the highest DNA concentration and minimal changes in bacterial diversity and composition. The differences observed between samples highlight the need to consider optimized post-collection methods in microbiome research. creator: Katti R. Horng creator: Holly H. Ganz creator: Jonathan A. Eisen creator: Stanley L. Marks uri: https://doi.org/10.7717/peerj.4827 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Horng et al. title: Evidence-based economic analysis demonstrates that ecosystem service benefits of water hyacinth management greatly exceed research and control costs link: https://peerj.com/articles/4824 last-modified: 2018-05-23 description: Invasive species management can be a victim of its own success when decades of effective control cause memories of past harm to fade and raise questions of whether programs should continue. Economic analysis can be used to assess the efficiency of investing in invasive species control by comparing ecosystem service benefits to program costs, but only if appropriate data exist. We used a case study of water hyacinth (Eichhornia crassipes (Mart.) Solms), a nuisance floating aquatic plant, in Louisiana to demonstrate how comprehensive record-keeping supports economic analysis. Using long-term data sets, we developed empirical and spatio-temporal simulation models of intermediate complexity to project invasive species growth for control and no-control scenarios. For Louisiana, we estimated that peak plant cover would be 76% higher without the substantial growth rate suppression (84% reduction) that appeared due primarily to biological control agents. Our economic analysis revealed that combined biological and herbicide control programs, monitored over an unusually long time period (1975–2013), generated a benefit-cost ratio of about 34:1 derived from the relatively modest costs of $124 million ($2013) compared to the $4.2 billion ($2013) in benefits to anglers, waterfowl hunters, boating-dependent businesses, and water treatment facilities over the 38-year analysis period. This work adds to the literature by: (1) providing evidence of the effectiveness of water hyacinth biological control; (2) demonstrating use of parsimonious spatio-temporal models to estimate benefits of invasive species control; and (3) incorporating activity substitution into economic benefit transfer to avoid overstating benefits. Our study suggests that robust and cost-effective economic analysis is enabled by good record keeping and generalizable models that can demonstrate management effectiveness and promote social efficiency of invasive species control. creator: Lisa A. Wainger creator: Nathan E. Harms creator: Cedric Magen creator: Dong Liang creator: Genevieve M. Nesslage creator: Anna M. McMurray creator: Al F. Cofrancesco uri: https://doi.org/10.7717/peerj.4824 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Immunogenicity evaluation of MS2 phage-mediated chimeric nanoparticle displaying an immunodominant B cell epitope of foot-and-mouth disease virus link: https://peerj.com/articles/4823 last-modified: 2018-05-23 description: Foot-and-mouth disease (FMD) is a highly contagious disease of cloven-hoofed animals that has caused tremendous economic losses worldwide. In this study, we designed a chimeric nanoparticles (CNPs) vaccine that displays the predominant epitope of the serotype O foot-and-mouth disease virus (FMDV) VP1 131-160 on the surface of MS2 phage. The recombinant protein was expressed in Escherichia Coli and can self-assemble into CNPs with diameter at 25–30 nm in vitro. A tandem repeat peptide epitopes (TRE) was prepared as control. Mice were immunized with CNPs, TRE and commercialized synthetic peptide vaccines (PepVac), respectively. The ELISA results showed that CNPs stimulated a little higher specific antibody levels to PepVac, but was significantly higher than the TRE groups. Moreover, the results from specific IFN-γ responses and lymphocyte proliferation test indicated that CNP immunized mice exhibited significantly enhanced cellular immune response compared to TRE. These results suggested that the CNPs constructed in current study could be a potential alternative vaccine in future FMDV control. creator: Guoqiang Wang creator: Yunchao Liu creator: Hua Feng creator: Yumei Chen creator: Suzhen Yang creator: Qiang Wei creator: Juan Wang creator: Dongmin Liu creator: Gaiping Zhang uri: https://doi.org/10.7717/peerj.4823 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: Sample entropy analysis for the estimating depth of anaesthesia through human EEG signal at different levels of unconsciousness during surgeries link: https://peerj.com/articles/4817 last-modified: 2018-05-23 description: Estimating the depth of anaesthesia (DoA) in operations has always been a challenging issue due to the underlying complexity of the brain mechanisms. Electroencephalogram (EEG) signals are undoubtedly the most widely used signals for measuring DoA. In this paper, a novel EEG-based index is proposed to evaluate DoA for 24 patients receiving general anaesthesia with different levels of unconsciousness. Sample Entropy (SampEn) algorithm was utilised in order to acquire the chaotic features of the signals. After calculating the SampEn from the EEG signals, Random Forest was utilised for developing learning regression models with Bispectral index (BIS) as the target. Correlation coefficient, mean absolute error, and area under the curve (AUC) were used to verify the perioperative performance of the proposed method. Validation comparisons with typical nonstationary signal analysis methods (i.e., recurrence analysis and permutation entropy) and regression methods (i.e., neural network and support vector machine) were conducted. To further verify the accuracy and validity of the proposed methodology, the data is divided into four unconsciousness-level groups on the basis of BIS levels. Subsequently, analysis of variance (ANOVA) was applied to the corresponding index (i.e., regression output). Results indicate that the correlation coefficient improved to 0.72 ± 0.09 after filtering and to 0.90 ± 0.05 after regression from the initial values of 0.51 ± 0.17. Similarly, the final mean absolute error dramatically declined to 5.22 ± 2.12. In addition, the ultimate AUC increased to 0.98 ± 0.02, and the ANOVA analysis indicates that each of the four groups of different anaesthetic levels demonstrated significant difference from the nearest levels. Furthermore, the Random Forest output was extensively linear in relation to BIS, thus with better DoA prediction accuracy. In conclusion, the proposed method provides a concrete basis for monitoring patients’ anaesthetic level during surgeries. creator: Quan Liu creator: Li Ma creator: Shou-Zen Fan creator: Maysam F. Abbod creator: Jiann-Shing Shieh uri: https://doi.org/10.7717/peerj.4817 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Liu et al.