title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=720 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Predicting surface abundance of federally threatened Jollyville Plateau Salamanders (Eurycea tonkawae) to inform management activities at a highly modified urban spring link: https://peerj.com/articles/13359 last-modified: 2022-05-02 description: Urban expansion has contributed to the loss of habitat for range restricted species across the globe. Managing wildlife populations within these urban settings presents the challenge of balancing human and wildlife needs. Jollyville Plateau Salamanders (Eurycea tonkawae) are a range restricted, federally threatened, species of neotenic brook salamander endemic to central Texas. Almost the entire geographic range of E. tonkawae is embedded in the Austin, Cedar Park, and Round Rock metropolitan areas of Travis and Williamson counties, Texas. Among E. tonkawae occupied sites, Brushy Creek Spring has experienced some of the most extensive anthropogenic disturbance. Today the site consists of small groundwater outlets that emerge in the seams within a concrete culvert underlying a highway. Salamanders persist within this system though they are rarely detected. Here, we model the occurrence of salamanders within the surface habitat of Brushy Creek Spring using generalized linear models. In the absence of available data regarding the amount of water that is discharged from the spring, we use accumulated rainfall as a proxy for discharge to estimate salamander abundance. Additionally, we present evidence of reproduction, recruitment, and subterranean movement by E. tonkawae throughout this site. Infrastructure maintenance is inevitable at Brushy Creek Spring. We intend for our results to inform when maintenance should occur, i.e., during environmental conditions when salamanders are less likely to be observed in the surface habitat, to avoid unnecessary impacts to this federally threatened species. creator: Zachary C. Adcock creator: Andrew R. MacLaren creator: Ryan M. Jones creator: Andrea Villamizar-Gomez creator: Ashley E. Wall creator: Kemble White IV creator: Michael R. J. Forstner uri: https://doi.org/10.7717/peerj.13359 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Adcock et al. title: Scavenging vs hunting affects behavioral traits of an opportunistic carnivore link: https://peerj.com/articles/13366 last-modified: 2022-05-02 description: BackgroundHuman-induced changes to ecosystems transform the availability of resources to predators, including altering prey populations and increasing access to anthropogenic foods. Opportunistic predators are likely to respond to altered food resources by changing the proportion of food they hunt versus scavenge. These shifts in foraging behavior will affect species interactions through multiple pathways, including by changing other aspects of predator behavior such as boldness, innovation, and social structure.MethodsTo understand how foraging behavior impacts predator behavior, we conducted a controlled experiment to simulate hunting by introducing a prey model to captive coyotes (Canis latrans) and compared their behavior to coyotes that continued to scavenge over one year. We used focal observations to construct behavioral budgets, and conducted novel object, puzzle box, and conspecific tests to evaluate boldness, innovation, and response to conspecifics.ResultsWe documented increased time spent resting by hunting coyotes paired with decreased time spent active. Hunting coyotes increased boldness and persistence but there were no changes in innovation. Our results illustrate how foraging behavior can impact other aspects of behavior, with potential ecological consequences to predator ecology, predator-prey dynamics, and human-wildlife conflict; however, the captive nature of our study limits specific conclusions related to wild predators. We conclude that human-induced behavioral changes could have cascading ecological implications that are not fully understood. creator: Mitchell A. Parsons creator: Andrew Garcia creator: Julie K. Young uri: https://doi.org/10.7717/peerj.13366 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Parsons et al. title: How beavers affect riverine aquatic macroinvertebrates: a review link: https://peerj.com/articles/13180 last-modified: 2022-04-29 description: BackgroundAs ecosystem engineers, the construction of dams by beavers alters stream habitat physically and biologically, making them a species of interest for habitat restoration. Beaver-created habitat changes affect a wide range of aquatic invertebrate species. However, despite numerous individual studies of how beavers affect aquatic macroinvertebrate assemblages, there has been no evaluation of the consensus of these effects across studies.MethodologyWe collated and examined studies comparing beaver-created ponds to nearby lotic reaches to determine general trends in aquatic macroinvertebrate richness, density, biomass, and functional composition between habitats. From this evidence, we highight knowledge gaps in how beaver activity affects aquatic macroinvertebrates.ResultsOverall, in the majority of studies, aquatic macroinvertebrate richness was higher in nearby lotic reaches compared to beaver-created ponds, but richness at coarser scales (gamma diversity) increased with the addition of beaver ponds due to increased habitat heterogeneity. Functional feeding group (FFG) patterns were highly context-dependent, though predator taxa were generally more abundant in beaver ponds than adjacent lotic reaches. Site-specific geomorphological changes, coupled with dam or riparian zone characteristics and resulting differences in basal food resources likely shape other FFG responses.ConclusionsWe identify a lack of long-term studies at single or multiple sites and conclude that fine-scale approaches may improve our understanding of the dynamics of macroinvertebrates within the freshwater realm and beyond. Due to the context-dependent nature of each study, further systematic studies of beaver engineering effects across a wider variety of environmental conditions and wetland types will also help inform land and species management decisions, such as where to prioritize protection of beaver habitats in the face of a global freshwater biodiversity crisis, or where to restore beaver populations to deliver maximum benefit. creator: Susan Washko creator: Nigel Willby creator: Alan Law uri: https://doi.org/10.7717/peerj.13180 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Washko et al. title: The influencing factors for distribution patterns of resident and migrant bird species richness along elevational gradients link: https://peerj.com/articles/13258 last-modified: 2022-04-29 description: The latitudinal and elevational patterns of species richness of resident and migrant birds have been of interest to researchers over the past few decades, and various hypotheses have been proposed to explain the factors that may affect these patterns. This study aimed to shed light on the elevational distribution patterns of resident and migrant bird species richness by examining biotic and abiotic factors such as climate, and habitat heterogeneity using a piecewise structural equation model (pSEM). The overall pattern of resident species richness showed a decreasing trend with increasing elevation, whereas that of migrant species richness showed an increasing trend. The mid-peak pattern of species richness was affected by a combination of resident and migrant species and not by either resident or migrant species. Our results showed that resident species were distributed in lower elevation regions with higher mean spring temperatures, whereas migrant species were found in higher elevation regions with lower mean spring temperatures and higher overstory vegetation coverage. Although high elevation conditions might adversely affect the reproduction of migrant birds, higher overstory vegetation coverage at high elevations seemed to compensate for this by providing a better nesting and roosting environment. Despite the significance of habitat diversity and understory vegetation coverage in univariate linear regression models, multiple regression models of the interconnection of ecological processes demonstrated that mean spring temperature and overstory vegetation coverage were more explanatory than other variables. creator: Jin-Yong Kim creator: Jongmin Yoon creator: Yu-Seong Choi creator: Soo Hyung Eo uri: https://doi.org/10.7717/peerj.13258 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Kim et al. title: Chronic psychological stress alters gene expression in rat colon epithelial cells promoting chromatin remodeling, barrier dysfunction and inflammation link: https://peerj.com/articles/13287 last-modified: 2022-04-29 description: Chronic stress is commonly associated with enhanced abdominal pain (visceral hypersensitivity), but the cellular mechanisms underlying how chronic stress induces visceral hypersensitivity are poorly understood. In this study, we examined changes in gene expression in colon epithelial cells from a rat model using RNA-sequencing to examine stress-induced changes to the transcriptome. Following chronic stress, the most significantly up-regulated genes included Atg16l1, Coq10b, Dcaf13, Nat2, Ptbp2, Rras2, Spink4 and down-regulated genes including Abat, Cited2, Cnnm2, Dab2ip, Plekhm1, Scd2, and Tab2. The primary altered biological processes revealed by network enrichment analysis were inflammation/immune response, tissue morphogenesis and development, and nucleosome/chromatin assembly. The most significantly down-regulated process was the digestive system development/function, whereas the most significantly up-regulated processes were inflammatory response, organismal injury, and chromatin remodeling mediated by H3K9 methylation. Furthermore, a subpopulation of stressed rats demonstrated very significantly altered gene expression and transcript isoforms, enriched for the differential expression of genes involved in the inflammatory response, including upregulation of cytokine and chemokine receptor gene expression coupled with downregulation of epithelial adherens and tight junction mRNAs. In summary, these findings support that chronic stress is associated with increased levels of cytokines and chemokines, their downstream signaling pathways coupled to dysregulation of intestinal cell development and function. Epigenetic regulation of chromatin remodeling likely plays a prominent role in this process. Results also suggest that super enhancers play a primary role in chronic stress-associated intestinal barrier dysfunction. creator: John W. Wiley creator: Gerald A. Higgins creator: Shuangsong Hong uri: https://doi.org/10.7717/peerj.13287 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wiley et al. title: Phylogeography of Amygdalus mongolica in relation to Quaternary climatic aridification and oscillations in northwestern China link: https://peerj.com/articles/13345 last-modified: 2022-04-29 description: Quaternary period geological events and climatic oscillations significantly affect the geographic structure and genetic diversity of species distribution in arid northwestern China. Amygdalus mongolica is a relict and endangered shrub that occurs primarily in arid areas of northwestern China. Based on variation patterns present at three cpDNA regions (psbK-psbI, trnL-trnF and trnV) and in one nDNA sequence (ITS1-ITS4) in 174 individuals representing 15 populations, the spatial genetic structure and demographic history of A. mongolica was examined across its entire geographic range. The 17 different haplotypes and 10 ribotypes showed two lineages, distributed across the Western (Mazong Mountains, Hexi Corridor, and Alxa Left Banner) and Eastern regions (Urad Houqi, Yinshan Mountains, Urad Zhongqi, and Daqing Mountains) according to the median-joining network and the BI (Bayesian inference) and ML (Maximum likelihood) trees. AMOVA analysis demonstrated that over 65% of the observed genetic variation was related to this lineage split. The expansions of the Ulanbuhe and Tengger deserts and the eastward extension of the Yinshan Mountains since the Quaternary period likely interrupted gene flow and triggered the observed divergence in the two allopatric regions; arid landscape fragmentation accompanied by local environmental heterogeneity further increased local adaptive differentiation between the Western and Eastern groups. Based on the evidence from phylogeographical patterns and the distribution of genetic variation, A. mongolica distributed in the eastern and western regions are speculated to have experienced eastward migration along the southern slopes of the Lang Mountains and westward migration along the margins of the Ulanbuhe and Tengger deserts to the Hexi Corridor, respectively. For setting a conservation management plan, it is recommended that the south slopes of the Lang Mountains and northern Helan Mountains be identified as the two primary conservation areas, as they have high genetic variation and habitats that are more suitable. creator: Lin Zhang creator: Fangfang Sun creator: Songmei Ma creator: Chuncheng Wang creator: Bo Wei creator: Yunling Zhang uri: https://doi.org/10.7717/peerj.13345 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Acidity and availability of aluminum, iron and manganese as factors affecting germination in European acidic dry and alkaline xerothermic grasslands link: https://peerj.com/articles/13255 last-modified: 2022-04-28 description: Germination ecology of 10 species from acidic dry grasslands and 10 species from alkaline xerothermic grasslands was studied. The seeds were subjected to different pH, iron (Fe), manganese (Mn) and aluminum (Al) treatments under controlled conditions. Effects of ionic (chlorides) and chelated forms (HBED chelates) of Fe and Mn were also compared. Final germination percentage (FGP) and index of germination velocity (IGV) were calculated. The results indicate that pH and extremely high availability of Al are the major edaphic filters regulating germination-based revegetation, while availability of Fe and Mn is of the secondary importance. Both chelates and ionic forms of Fe and Mn exerted similar effects on the ability of seeds to complete germination. It suggests that both chelates are not hazardous for early ontogenetic stages of plants. Neither group has group-specific adaptations pertaining to germination characteristics in the context of the studied chemical stimuli, which indicates a diversity of germination strategies and individual species-specific reactions to the tested factors. creator: Mateusz Wala creator: Jeremi Kołodziejek creator: Tomasz Wilk uri: https://doi.org/10.7717/peerj.13255 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wala et al. title: Soil characteristic changes and quality evaluation of degraded desert steppe in arid windy sandy areas link: https://peerj.com/articles/13100 last-modified: 2022-04-28 description: Grassland degradation has become a serious problem in some areas, making it necessary to quantitatively evaluate this process and its related factors. The study area was the arid windy sandy area in eastern Ningxia. The purpose of this study was to explore how soil properties and quality change during the process of grassland degradation in arid windy sandy areas. We looked at undegraded, lightly degraded, moderately degraded, and severely degraded desert steppe to study the physical, chemical, and biological changes at 0–5 cm, 5–15 cm, and 15–30 cm soil depths at different degradation degrees. We also analyzed the correlations across soil factors, established the minimum data set, and used the soil quality index (SQI) to evaluate the soil quality of grassland at different degradation degrees. The results showed that with grassland degradation, the soil bulk density increased; the soil clay, moisture, organic matter, total nitrogen, and available potassium content decreased; and the number of soil bacteria, actinomycetes, and fungi, as well as the activity of urease, polyphenol oxidase, protease, phosphatase, and sucrase, decreased. As soil depth increased, soil bulk density increased; the soil moisture, organic matter, available potassium, and available phosphorus content decreased; and soil microorganisms accumulated in the upper soil of undegraded, lightly, and moderately degraded grassland. There was also a positive correlation among the soil clay content, moisture content, organic matter content, total nitrogen content, available potassium content, microorganism quantity, and enzyme activity, while soil bulk density was negatively correlated with the above factors. The minimum data set for the soil quality evaluation of the degraded desert steppe was comprised of soil organic matter content, soil total nitrogen content, soil available phosphorus content, and phosphatase activity. Based on the minimum data set, we calculated the SQI of the grassland at different degradation degrees and found that the ranking based on overall soil quality was undegraded >lightly degraded >moderately degraded >severely degraded grassland. The results showed that the degradation of desert steppe in arid windy sandy areas had relatively consistent effects on the physical, chemical, and biological traits of the soil. The minimum data set can be used to replace the total data set when evaluating the soil quality of the desert steppe at different degrees of degradation. creator: Jing Ma creator: Jianrong Qin creator: Hongbin Ma creator: Yao Zhou creator: Yan Shen creator: Yingzhong Xie creator: Dongmei Xu uri: https://doi.org/10.7717/peerj.13100 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ma et al. title: Differentiated historical demography and ecological niche forming present distribution and genetic structure in coexisting two salamanders (Amphibia, Urodela, Hynobiidae) in a small island, Japan link: https://peerj.com/articles/13202 last-modified: 2022-04-28 description: BackgroundThe climatic oscillations in the Quaternary period considerably shaped the distribution and population genetic structure of organisms. Studies on the historical dynamics of distribution and demography not only reflect the current geographic distribution but also allow us to understand the adaption and genetic differentiation of species. However, the process and factors affecting the present distribution and genetic structure of many taxa are still poorly understood, especially for endemic organisms to small islands.MethodsHere, we integrated population genetic and ecological niche modelling approaches to investigate the historical distribution and demographic dynamics of two co-existing salamanders on Tsushima Island, Japan: the true H. tsuensis (Group A), and Hynobius sp. (Group B). We also examined the hypothesis on the equivalency and similarity of niches of these groups by identity and background tests for ecological niche space.ResultsOur result showed that Group A is considered to have undergone a recent population expansion after the Last Glacial Maximum while it is unlikely to have occurred in Group B. The highest suitability was predicted for Group A in southern Tsushima Island, whereas the northern part of Tsushima Island was the potential distribution of Group B. The results also suggested a restricted range of both salamanders during the Last Interglacial and Last Glacial Maximum, and recent expansion in Mid-Holocene. The genetic landscape-shape interpolation analysis and historical suitable area of ecological niche modelling were consistent, and suggested refugia used during glacial ages in southern part for Group A, and in northern part of Tsushima Island for Group B. Additionally, we found evidence of nonequivalence for the ecological niche of the two groups of the salamanders, although our test could not show either niche divergence or conservatism based on the background tests. The environmental predictors affecting the potential distribution of each group also showed distinctiveness, leading to differences in selecting suitable areas. Finally, the combination of population genetics and ecological modeling has revealed the differential demographic/historical response between coexisting two salamanders on a small island. creator: Keita Niwa creator: Dung Van Tran creator: Kanto Nishikawa uri: https://doi.org/10.7717/peerj.13202 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Niwa et al. title: Point prevalence of non-melanoma and melanoma skin cancers in Australian surfers and swimmers in Southeast Queensland and Northern New South Wales link: https://peerj.com/articles/13243 last-modified: 2022-04-28 description: BackgroundSurfing and swimming are two popular outdoor aquatic activities in Australia with an estimated 2.7 million surfers and three million swimmers; however, these activities are associated with intermittent exposure to ultraviolet radiation. Our aim was to determine the point prevalence of pre-skin cancer (actinic keratosis (PSC)), non-melanoma (NMSC) and melanoma skin cancers (MSC) in Australian surfers and swimmers.MethodsThis cross-sectional study involved Australian surfers who completed a survey that included physiological demographics, aquatic activity-specific demographics, history of skin cancer followed by screening.ResultsA total of 171 surfers (n = 116) and swimmers (n = 55) participated in the study. Both groups were identified as having a history of skin cancer (surfers 41.4%, swimmers 36.4%) and a family history of skin cancer (surfers 52.6%, swimmers 43.6%). The majority of both groups reported using a high percentage of a chemical or physical skin cancer prevention strategy (surfers 100%, Swimmers 92.7%, P = 0.003). Significantly more surfers were identified with a skin cancer of any type vs. swimmers (50% vs. 27.3%; OR 2.67; P = 0.005) with most the common skin cancer being PSC (44.7% vs. 11.3%, P = 0.076) followed by basal cell carcinoma (BCC) (24.2% vs. 7.6%, P = 0.068). There was a total of seven MSC identified in surfers and swimmers (4.6% vs. 0.8%, respectively, P = 0.137). Most skin cancers in surfers were located on the face (28.0%) followed by the arm and back (12.1% each), whereas in swimmers, the majority of skin cancers were identified on the face (17.3%), followed by the arm and lower leg (15.4% each). The highest number of melanomas were identified in surfers (n = 6) and mainly located on the face (n = 2) and back (n = 2). There was a single melanoma identified on the back in a swimmer. With the groups combined, the majority (42.9%) of melanomas were identified on the back in participants, followed by the face (28.6%). Rates per 100,000 of NMSC and MSC in surfers and swimmers (respectively) were BCC (11,206 vs. 14,545), squamous cell carcinoma (SCC) in situ (13,793 vs. 12,727), SCC (1,724 vs. 3,636) and MSC (5,172 vs. 1,818). When compared to the general Australian population, surfers and swimmers had higher odds ratios (OR), which included BCCs (OR 7.3 and 9.4, respectively), SCCs (OR 1.7 and 3.5, respectively) and MSC (OR 96.7 and 18.8, respectively).ConclusionSurfers and swimmers had consistently higher rates of PSC, NMSC and MSC than the general Australian population. Point prevalence of MSC (groups combined) was 76-fold higher than the general Australian population. These findings highlight the clinical importance of regular skin cancer screenings in individuals who surf or swim for early detection and treatment of skin cancer. Additionally, these aquatic enthusiasts should be advised of the benefits of sun protection strategies such as chemical and physical barriers to reduce the likelihood of developing skin cancer. creator: Mike Climstein creator: Brendan Doyle creator: Michael Stapelberg creator: Nedeljka Rosic creator: Isolde Hertess creator: James Furness creator: Vini Simas creator: Joe Walsh uri: https://doi.org/10.7717/peerj.13243 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Climstein et al.