title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1774 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Phytogeographic and genetic variation in Sorbus, a traditional antidiabetic medicine—adaptation in action in both a plant and a discipline link: https://peerj.com/articles/2645 last-modified: 2016-11-03 description: Mountain ash (Sorbus decora and S. americana) is used by the Cree Nation of the James Bay region of Quebec (Eeyou Istchee) as traditional medicine. Its potential as an antidiabetic medicine is thought to vary across its geographical range, yet little is known about the factors that affect its antioxidant capacity. Here, we examined metabolite gene expression in relation to antioxidant activity, linking phytochemistry and medicinal potential. Samples of leaf and bark from S. decora and S. americana were collected from 20 populations at four different latitudes. Two genes known to produce antidiabetic substances, flavonol synthase and squalene synthase, were analyzed using quantitative real time PCR. Gene expression was significantly higher for flavonol synthase compared to squalene synthase and increased in the most Northern latitude. Corresponding differences observed in the antioxidant capacity of ethanolic extracts from the bark of Sorbus spp. confirm that plants at higher latitudes increase production of stress-induced secondary metabolites and support Aboriginal perceptions of their higher medicinal potential. Modern genetic techniques such as quantitative real time PCR offer unprecedented resolution to substantiate and scrutinise Aboriginal medicinal plant perception. Furthermore, it offers valuable insights into how environmental stress can trigger an adaptive response resulting in the accumulation of secondary metabolites with human medicinal properties. creator: Anna Bailie creator: Sebastien Renaut creator: Eliane Ubalijoro creator: José A. Guerrero-Analco creator: Ammar Saleem creator: Pierre Haddad creator: John T. Arnason creator: Timothy Johns creator: Alain Cuerrier uri: https://doi.org/10.7717/peerj.2645 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bailie et al. title: Mathematical models are a powerful method to understand and control the spread of Huanglongbing link: https://peerj.com/articles/2642 last-modified: 2016-11-03 description: Huanglongbing (HLB), or citrus greening, is a global citrus disease occurring in almost all citrus growing regions. It causes substantial economic burdens to individual growers, citrus industries and governments. Successful management strategies to reduce disease burden are desperately needed but with so many possible interventions and combinations thereof it is difficult to know which are worthwhile or cost-effective. We review how mathematical models have yielded useful insights into controlling disease spread for other vector-borne plant diseases, and the small number of mathematical models of HLB. We adapt a malaria model to HLB, by including temperature-dependent psyllid traits, “flushing” of trees, and economic costs, to show how models can be used to highlight the parameters that require more data collection or that should be targeted for intervention. We analyze the most common intervention strategy, insecticide spraying, to determine the most cost-effective spraying strategy. We find that fecundity and feeding rate of the vector require more experimental data collection, for wider temperatures ranges. Also, the best strategy for insecticide intervention is to spray for more days rather than pay extra for a more efficient spray. We conclude that mathematical models are able to provide useful recommendations for managing HLB spread. creator: Rachel A. Taylor creator: Erin A. Mordecai creator: Christopher A. Gilligan creator: Jason R. Rohr creator: Leah R. Johnson uri: https://doi.org/10.7717/peerj.2642 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Taylor et al. title: Germination pretreatments to break hard-seed dormancy in Astragalus cicer L. (Fabaceae) link: https://peerj.com/articles/2621 last-modified: 2016-11-03 description: Conservationists often propagate rare species to improve their long-term population viability. However, seed dormancy can make propagation efforts challenging by substantially lowering seed germination. Here I statistically compare several pretreatment options for seeds of Astragalus cicer L.: unscarified controls and scarification via physical damage, hot water, acid, and hydrogen peroxide. Although only 30% of unscarified seeds germinated, just physical scarification significantly improved germination, whereas one treatment, hot water, resulted in no germination at all. I recommend that rare species of Astragalus, as well as other hard-seeded legumes, be pretreated using physical scarification. Other methods may require considerable optimization, wasting precious time and seeds. creator: Joseph M. Statwick uri: https://doi.org/10.7717/peerj.2621 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Statwick title: Phylogeography of Arenaria balearica L. (Caryophyllaceae): evolutionary history of a disjunct endemic from the Western Mediterranean continental islands link: https://peerj.com/articles/2618 last-modified: 2016-11-03 description: Although it has been traditionally accepted that Arenaria balearica (Caryophyllaceae) could be a relict Tertiary plant species, this has never been experimentally tested. Nor have the palaeohistorical reasons underlying the highly fragmented distribution of the species in the Western Mediterranean region been investigated. We have analysed AFLP data (213) and plastid DNA sequences (226) from a total of 250 plants from 29 populations sampled throughout the entire distribution range of the species in Majorca, Corsica, Sardinia, and the Tuscan Archipelago. The AFLP data analyses indicate very low geographic structure and population differentiation. Based on plastid DNA data, six alternative phylogeographic hypotheses were tested using Approximate Bayesian Computation (ABC). These analyses revealed ancient area fragmentation as the most probable scenario, which is in accordance with the star-like topology of the parsimony network that suggests a pattern of long term survival and subsequent in situ differentiation. Overall low levels of genetic diversity and plastid DNA variation were found, reflecting evolutionary stasis of a species preserved in locally long-term stable habitats. creator: Javier Bobo-Pinilla creator: Sara B. Barrios de León creator: Jaume Seguí Colomar creator: Giuseppe Fenu creator: Gianluigi Bacchetta creator: Julio Peñas de Giles creator: María Montserrat Martínez-Ortega uri: https://doi.org/10.7717/peerj.2618 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bobo-Pinilla et al. title: Analyzing pathogen suppressiveness in bioassays with natural soils using integrative maximum likelihood methods in R link: https://peerj.com/articles/2615 last-modified: 2016-11-03 description: The potential of soils to naturally suppress inherent plant pathogens is an important ecosystem function. Usually, pathogen infection assays are used for estimating the suppressive potential of soils. In natural soils, however, co-occurring pathogens might simultaneously infect plants complicating the estimation of a focal pathogen’s infection rate (initial slope of the infection-curve) as a measure of soil suppressiveness. Here, we present a method in R correcting for these unwanted effects by developing a two pathogen mono-molecular infection model. We fit the two pathogen mono-molecular infection model to data by using an integrative approach combining a numerical simulation of the model with an iterative maximum likelihood fit. We show that in presence of co-occurring pathogens using uncorrected data leads to a critical under- or overestimation of soil suppressiveness measures. In contrast, our new approach enables to precisely estimate soil suppressiveness measures such as plant infection rate and plant resistance time. Our method allows a correction of measured infection parameters that is necessary in case different pathogens are present. Moreover, our model can be (1) adapted to use other models such as the logistic or the Gompertz model; and (2) it could be extended by a facilitation parameter if infections in plants increase the susceptibility to new infections. We propose our method to be particularly useful for exploring soil suppressiveness of natural soils from different sites (e.g., in biodiversity experiments). creator: Björn C. Rall creator: Ellen Latz uri: https://doi.org/10.7717/peerj.2615 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Rall and Latz title: Alterations to the middle cerebral artery of the hypertensive-arthritic rat model potentiates intracerebral hemorrhage link: https://peerj.com/articles/2608 last-modified: 2016-11-03 description: AimsWe have recently created an age-dependent hypertensive-mono-arthritic animal model from the stroke-resistant spontaneously hypertensive rat to model populations with autoimmune disease who are hypertensive and are prone to stroke. The model exhibits signs of hemorrhagic stroke (HS) subsequent to chronic inflammation and hypertension. HS is also associated with the inability of middle cerebral arteries to undergo pressure dependent constriction (PDC). We investigated alterations in the cerebrovasculature of our hypertensive mono-arthritic animals that develop stroke.Main MethodsAnimals were fed either a high salt diet (HSD) (4% NaCl) or Purina chow (0.58% NaCl) from weaning. Complete Freund’s Adjuvant (CFA) was injected into the left hind paw at 21–28 weeks; controls received saline and histological and functional studies were performed.ResultsBrain damage was more prominent with the high salt, with inflammation exacerbating the damage. High salt alone significantly decreased middle cerebral artery’s (MCA’s) ability to undergo PDC. Inflammation significantly decreased the ability of cerebrovasculature to respond to pressure step in the regular salt diet. The responses to vasoactive peptides were also significantly attenuated in both inflamed groups regardless of diet.ConclusionInduction of chronic systemic inflammation increases brain damage, and affect the MCA’s vasogenic function, decreasing its ability to respond to intraluminal pressure. HSD further exacerbates organ damage associated with chronic inflammation, further compromising cerebrovascular function, and likely increasing the incidence of intracerebral hemorrhage and injury. creator: Amy Randell creator: Killol Chokshi creator: Brittany Kane creator: Hilary Chang creator: Safaa Naiel creator: Jeffrey G. Dickhout creator: Noriko Daneshtalab uri: https://doi.org/10.7717/peerj.2608 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Randell et al. title: Environmental, land cover and land use constraints on the distributional patterns of anurans: Leptodacylus species (Anura, Leptodactylidae) from Dry Chaco link: https://peerj.com/articles/2605 last-modified: 2016-11-03 description: Subtropical dry forests are among the most vulnerable biomes to land transformation at a global scale. Among them, the Dry Chaco suffers an accelerated change due to agriculture expansion and intensification. The Dry Chaco ecoregion is characterized by high levels of endemisms and species diversity, which are the result of a variety of climates and reliefs, allowing a wide variety of environments. The amphibian group exhibits a high richness in the Dry Chaco, which has been barely studied in relation to land cover changes. We used ecological niche models (ENMs) to assess the potential geographic distribution of 10 Leptodactylus species (Anura, Leptodactylidae), which are mainly distributed within the Dry Chaco. We characterized these distributions environmentally, analyzed their overlap with land cover classes, and assessed their diversity of ecoregions. Also, we evaluated how these species potential distribution is affected by the transformation of land, and quantified the proportional area of the potential distribution in protected areas. We found that temperature seasonality is the main constraint to the occurrence of the species studied, whose main habitats are savannas, grasslands and croplands. The main threats to these species are the effects of climate change over spatial patterns of seasonality, which could affect their breeding and reproduction mode; the loss of their natural habitat; the exposure to contaminants used by intensive agriculture and their underrepresentation in protected areas. creator: Regina Gabriela Medina creator: Maria Laura Ponssa creator: Ezequiel Aráoz uri: https://doi.org/10.7717/peerj.2605 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Medina et al. title: Regional variation in fire weather controls the reported occurrence of Scottish wildfires link: https://peerj.com/articles/2649 last-modified: 2016-11-02 description: Fire is widely used as a traditional habitat management tool in Scotland, but wildfires pose a significant and growing threat. The financial costs of fighting wildfires are significant and severe wildfires can have substantial environmental impacts. Due to the intermittent occurrence of severe fire seasons, Scotland, and the UK as a whole, remain somewhat unprepared. Scotland currently lacks any form of Fire Danger Rating system that could inform managers and the Fire and Rescue Services (FRS) of periods when there is a risk of increased of fire activity. We aimed evaluate the potential to use outputs from the Canadian Fire Weather Index system (FWI system) to forecast periods of increased fire risk and the potential for ignitions to turn into large wildfires. We collated four and a half years of wildfire data from the Scottish FRS and examined patterns in wildfire occurrence within different regions, seasons, between urban and rural locations and according to FWI system outputs. We used a variety of techniques, including Mahalanobis distances, percentile analysis and Thiel-Sen regression, to scope the best performing FWI system codes and indices. Logistic regression showed significant differences in fire activity between regions, seasons and between urban and rural locations. The Fine Fuel Moisture Code and the Initial Spread Index did a tolerable job of modelling the probability of fire occurrence but further research on fuel moisture dynamics may provide substantial improvements. Overall our results suggest it would be prudent to ready resources and avoid managed burning when FFMC > 75 and/or ISI > 2. creator: G. Matt Davies creator: Colin J. Legg uri: https://doi.org/10.7717/peerj.2649 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Davies and Legg title: A public data set of human balance evaluations link: https://peerj.com/articles/2648 last-modified: 2016-11-02 description: The goal of this study was to create a public data set with results of qualitative and quantitative evaluations related to human balance. Subject’s balance was evaluated by posturography using a force platform and by the Mini Balance Evaluation Systems Tests. In the posturography test, we evaluated subjects standing still for 60 s in four different conditions where vision and the standing surface were manipulated: on a rigid surface with eyes open; on a rigid surface with eyes closed; on an unstable surface with eyes open; on an unstable surface with eyes closed. Each condition was performed three times and the order of the conditions was randomized. In addition, the following tests were employed in order to better characterize each subject: Short Falls Efficacy Scale International; International Physical Activity Questionnaire Short Version; and Trail Making Test. The subjects were also interviewed to collect information about their socio-cultural, demographic, and health characteristics. The data set comprises signals from the force platform (raw data for the force, moments of forces, and centers of pressure) of 163 subjects plus one file with information about the subjects and balance conditions and the results of the other evaluations. All the data is available at PhysioNet and at Figshare. creator: Damiana A. Santos creator: Marcos Duarte uri: https://doi.org/10.7717/peerj.2648 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Santos and Duarte title: Seasonal regulation of herbivory and nutrient effects on macroalgal recruitment and succession in a Florida coral reef link: https://peerj.com/articles/2643 last-modified: 2016-11-02 description: Herbivory and nutrient enrichment are drivers of benthic dynamics of coral reef macroalgae; however, their impact may vary seasonally. In this study we evaluated the effects of herbivore pressure, nutrient availability and potential propagule supply on seasonal recruitment and succession of macroalgal communities on a Florida coral reef. Recruitment tiles, replaced every three months, and succession tiles, kept in the field for nine months, were established in an ongoing factorial nutrient enrichment-herbivore exclusion experiment. The ongoing experiment had already created very different algal communities across the different herbivory and nutrient treatments. We tracked algal recruitment, species richness, and species abundance through time. Our results show seasonal variation in the effect of herbivory and nutrient availability on recruitment of coral reef macroalgae. In the spring, when there was higher macroalgal species richness and abundance of recruits, herbivory appeared to have more control on macroalgal community structure than did nutrients. In contrast, there was no effect of either herbivory or nutrient enrichment on macroalgal communities on recruitment tiles in cooler seasons. The abundance of recruits on tiles was positively correlated with the abundance of algal in the ongoing, established experiment, suggesting that propagule abundance is likely a strong influence on algal recruitment and early succession. Results of the present study suggest that abundant herbivorous fishes control recruitment and succession of macroalgae, particularly in the warm season when macroalgal growth is higher. However, herbivory appears less impactful on algal recruitment and community dynamics in cooler seasons. Ultimately, our data suggest that the timing of coral mortality (e.g., summer vs. winter mortality) and freeing of benthic space may strongly influence the dynamics of algae that colonize open space. creator: Alain Duran creator: Ligia Collado-Vides creator: Deron E. Burkepile uri: https://doi.org/10.7717/peerj.2643 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Duran et al.