title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1484 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Different environmental gradients affect different measures of snake β-diversity in the Amazon rainforests link: https://peerj.com/articles/5628 last-modified: 2018-09-24 description: Mechanisms generating and maintaining biodiversity at regional scales may be evaluated by quantifying β-diversity along environmental gradients. Differences in assemblages result in biotic complementarities and redundancies among sites, which may be quantified through multi-dimensional approaches incorporating taxonomic β-diversity (TBD), functional β-diversity (FBD) and phylogenetic β-diversity (PBD). Here we test the hypothesis that snake TBD, FBD and PBD are influenced by environmental gradients, independently of geographic distance. The gradients tested are expected to affect snake assemblages indirectly, such as clay content in the soil determining primary production and height above the nearest drainage determining prey availability, or directly, such as percentage of tree cover determining availability of resting and nesting sites, and climate (temperature and precipitation) causing physiological filtering. We sampled snakes in 21 sampling plots, each covering five km2, distributed over 880 km in the central-southern Amazon Basin. We used dissimilarities between sampling sites to quantify TBD, FBD and PBD, which were response variables in multiple-linear-regression and redundancy analysis models. We show that patterns of snake community composition based on TBD, FBD and PBD are associated with environmental heterogeneity in the Amazon. Despite positive correlations between all β-diversity measures, TBD responded to different environmental gradients compared to FBD and PBD. Our findings suggest that multi-dimensional approaches are more informative for ecological studies and conservation actions compared to a single diversity measure. creator: Rafael de Fraga creator: Miquéias Ferrão creator: Adam J. Stow creator: William E. Magnusson creator: Albertina P. Lima uri: https://doi.org/10.7717/peerj.5628 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 de Fraga et al. title: Identification of an aquaculture poriferan “Pest with Potential” and its phylogenetic implications link: https://peerj.com/articles/5586 last-modified: 2018-09-24 description: Correct identification and classification of sponges is challenging due to ambiguous or misleading morphological features. A particular case is a blue keratose sponge occasionally referred to as the “Blue Photo Sponge” among aquarists, which appears frequently (and in several cases unintended) in private aquaria. This spicule-less species, occasionally specified as Collospongia auris Bergquist, Cambie & Kernan 1990, not only displays a high phenotypic plasticity in growth form and colour, it also proliferates in aquacultures under standard conditions unlike most other sponges. Therefore, this species is regarded as a pest for most aquarists. In turn, the ease of cultivation and propagation in aquacultures qualifies this species as a model organism for a wide array of scientific applications. For these purposes, correct identification and classification are indispensable. We reconstructed ribosomal gene trees and determined this species as Lendenfeldia chondrodes (De Laubenfels, 1954) (Phyllospongiinae), distant to Collospongia auris, and corroborated by skeletal features. Additionally, the resulting phylogeny corroborated major shortcomings of the current Phyllospongiinae classification—its consequences are discussed. creator: Adrian Galitz creator: Steve de C. Cook creator: Merrick Ekins creator: John N. A. Hooper creator: Peter T. Naumann creator: Nicole J. de Voogd creator: Muhammad Abdul Wahab creator: Gert Wörheide creator: Dirk Erpenbeck uri: https://doi.org/10.7717/peerj.5586 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Galitz et al. title: Morphometric traits in the fine-leaved fescues depend on ploidy level: the case of Festuca amethystina L. link: https://peerj.com/articles/5576 last-modified: 2018-09-24 description: BackgroundPolyploid specimens are usually characterized by greater exuberance: they reach larger sizes and/or have a larger number of some organs. Festuca amethystina L. belongs to the section Aulaxyper. Based on morphological features, four subspecies of F. amethystina have been already identified. On the other hand, it has two cytotypes: diploid and tetraploid. The main aim of our study was to distinguish morphological differences between the cytotypes of F. amethystina, assuming that its phenotype differs significantly.MethodsThe nuclear DNA content was measured by flow cytometry in dry leaves from specimens originating from 13 populations of F. amethystina. Several macrometric and micrometric traits of stems, spikelets and leaf blades were taken into account in the comparative analysis of two cytotypes.ResultsIn the case of cytotypes, specimens of tetraploids were larger than diploids. The conducted morphometric analysis of leaf cross-sections showed significant differences between the cytotypes.DiscussionThe research has confirmed for the first time that in the case of F. amethystina the principle of greater exuberance of polyploids is true. Differences between the cytotypes are statistically significant, however, they are not enough to make easy the distinction of cytotypes on the basis of the measurements themselves. Our findings favor the rule known in Festuca taxonomy as a whole, i.e. that the ploidy level can be one of the main classification criteria. creator: Agnieszka Rewicz creator: Przemysław Piotr Tomczyk creator: Marcin Kiedrzyński creator: Katarzyna Maria Zielińska creator: Iwona Jędrzejczyk creator: Monika Rewers creator: Edyta Kiedrzyńska creator: Tomasz Rewicz uri: https://doi.org/10.7717/peerj.5576 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rewicz et al. title: Population genetics of the main population of brown bears in southwest Asia link: https://peerj.com/articles/5660 last-modified: 2018-09-21 description: Genetic studies of the Eurasian brown bear (Ursus arctos) have so far focused on populations from Europe and North America, although the largest distribution area of brown bears is in Asia. In this study, we reveal population genetic parameters for the brown bear population inhabiting the Grand Kaçkar Mountains (GKM) in the north east of Turkey, western Lesser Caucasus. Using both hair (N = 147) and tissue samples (N = 7) collected between 2008 and 2014, we found substantial levels of genetic variation (10 microsatellite loci). Bear samples (hair) taken from rubbing trees worked better for genotyping than those from power poles, regardless of the year collected. Genotyping also revealed that bears moved between habitat patches, despite ongoing massive habitat alterations and the creation of large water reservoirs. This population has the potential to serve as a genetic reserve for future reintroductions in the Middle East. Due to the importance of the GKM population for on-going and future conservation actions, the impacts of habitat alterations in the region ought to be minimized; e.g., by establishing green bridges or corridors over reservoirs and major roads to maintain habitat connectivity and gene flow among populations in the Lesser Caucasus. creator: Hüseyin Ambarlı creator: Deniz Mengüllüoğlu creator: Jörns Fickel creator: Daniel W. Förster uri: https://doi.org/10.7717/peerj.5660 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Ambarlı et al. title: A secretory hexokinase plays an active role in the proliferation of Nosema bombycis link: https://peerj.com/articles/5658 last-modified: 2018-09-21 description: The microsporidian Nosema bombycis is an obligate intracellular parasite of Bombyx mori, that lost its intact tricarboxylic acid cycle and mitochondria during evolution but retained its intact glycolysis pathway. N. bombycis hexokinase (NbHK) is not only a rate-limiting enzyme of glycolysis but also a secretory protein. Indirect immunofluorescence assays and recombinant HK overexpressed in BmN cells showed that NbHK localized in the nucleus and cytoplasm of host cell during the meront stage. When N. bombycis matured, NbHK tended to concentrate at the nuclei of host cells. Furthermore, the transcriptional profile of NbHK implied it functioned during N. bombycis’ proliferation stages. A knock-down of NbHK effectively suppressed the proliferation of N. bombycis indicating that NbHK is an important protein for parasite to control its host. creator: Yukang Huang creator: Shiyi Zheng creator: Xionge Mei creator: Bin Yu creator: Bin Sun creator: Boning Li creator: Junhong Wei creator: Jie Chen creator: Tian Li creator: Guoqing Pan creator: Zeyang Zhou creator: Chunfeng Li uri: https://doi.org/10.7717/peerj.5658 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Huang et al. title: Does Twitter language reliably predict heart disease? A commentary on Eichstaedt et al. (2015a) link: https://peerj.com/articles/5656 last-modified: 2018-09-21 description: We comment on Eichstaedt et al.’s (2015a) claim to have shown that language patterns among Twitter users, aggregated at the level of US counties, predicted county-level mortality rates from atherosclerotic heart disease (AHD), with “negative” language being associated with higher rates of death from AHD and “positive” language associated with lower rates. First, we examine some of Eichstaedt et al.’s apparent assumptions about the nature of AHD, as well as some issues related to the secondary analysis of online data and to considering counties as communities. Next, using the data files supplied by Eichstaedt et al., we reproduce their regression- and correlation-based models, substituting mortality from an alternative cause of death—namely, suicide—as the outcome variable, and observe that the purported associations between “negative” and “positive” language and mortality are reversed when suicide is used as the outcome variable. We identify numerous other conceptual and methodological limitations that call into question the robustness and generalizability of Eichstaedt et al.’s claims, even when these are based on the results of their ridge regression/machine learning model. We conclude that there is no good evidence that analyzing Twitter data in bulk in this way can add anything useful to our ability to understand geographical variation in AHD mortality rates. creator: Nicholas J.L. Brown creator: James C. Coyne uri: https://doi.org/10.7717/peerj.5656 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Brown and Coyne title: How much genetic variation is stored in the endangered and fragmented shrub Tetraena mongolica Maxim? link: https://peerj.com/articles/5645 last-modified: 2018-09-21 description: Tetraena mongolica Maxim (Zygophyllaceae) is an endangered species endemic to western Inner Mongolia and China, and is currently threatened by habitat loss and human over-exploitation. We explored the genetic background, its genetic diversity, population structure, and demographic history, based on 12 polymorphic nuclear microsatellite loci. Our results indicated high genetic diversity in extant populations, but no distinguishable gene cluster corresponding with a specific biogeography. Population demography analysis using a MSVAR indicated a strong, recent population decline approximately 5,455 years ago. These results suggest that the Yellow River and Zhuozi Mountain range may not prevent pollination between populations. Finally, we surmised that the population demography of T. mongolica was likely to have been affected by early mankind activities. creator: Yingbiao Zhi creator: Zhonglou Sun creator: Ping Sun creator: Kai Zhao creator: Yangnan Guo creator: Dejian Zhang creator: Baowei Zhang uri: https://doi.org/10.7717/peerj.5645 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhi et al. title: Short-tailed mice with a long fossil record: the genus Leggadina (Rodentia: Muridae) from the Quaternary of Queensland, Australia link: https://peerj.com/articles/5639 last-modified: 2018-09-21 description: The genus Leggadina (colloquially known as ‘short-tailed mice’) is a common component of Quaternary faunas of northeastern Australia. They represent a member of the Australian old endemic murid radiation that arrived on the continent sometime during the late Cenozoic. Here we describe two new species of extinct Leggadina from Quaternary cave deposits as well as additional material of the extinct Leggadina macrodonta. Leggadina irvini sp. nov. recovered from Middle-Upper (late) Pleistocene cave deposits near Chillagoe, northeastern Queensland, is the biggest member of the genus, being substantially larger than any other species so far described. Leggadina webbi sp. nov. from Middle Pleistocene cave deposits at Mount Etna, central eastern Queensland, shares features with the oldest species of the genus, the Early Pleistocene L. gregoriensis. Based on the current palaeoecological interpretation of the type locality, L. webbi, represents the only member of the genus that inhabited rainforest. The succession of Leggadina species through the late Quaternary suggests an ecological replacement of the extinct large-bodied L. irvini with the extant, small-bodied L. lakedownesis at Chillagoe. At Mt. Etna, the extinct rainforest species L. webbi is replaced with the extant xeric-adapted L. forresti during the latest Middle Pleistocene. This replacement is associated with a mid-Pleistocene shift towards progressive intensifying seasonal and arid climates. Our study adds to the growing list of small-bodied faunal extinctions during the late Quaternary of northern Australia. creator: Jonathan Cramb creator: Gilbert J. Price creator: Scott A. Hocknull uri: https://doi.org/10.7717/peerj.5639 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Cramb et al. title: Interleukin 35 induced Th2 and Tregs bias under normal conditions in mice link: https://peerj.com/articles/5638 last-modified: 2018-09-21 description: ObjectiveThe benefits of IL-35 treatment have been verified in multiple animal models of diseases, while its influence on T cells immunity under normal condition still needs to be elucidated. The present study was designed to investigate the effects modulating IL-35 levels in vivo and in vitro on T cells, response and also the effects on T cells subsets in normal mice.MethodsA plasmid pMSCV-IL-35-GFP carrying mouse linear IL-35 fragment with two subunits joint together was constructed and the heterodimer expression was confirmed. Normal mice were randomly divided into three groups and received an intravenous injection of PBS, pMSCV-GFP and pMSCV-IL-35-GFP respectively. After 72 h, spleen tissues and peripheral blood were harvested for following analysis. Meanwhile, splenic T cells were isolated and incubated with 10, 30, or 50 ng/mL recombinant IL-35 factor for 24 h with the addition of anti-CD3/CD28 in vitro. T-cell subsets were assessed by Fluorescence activated cell sorting (FACS) and related cytokines together with effector molecules were determined by real time PCR.ResultsWestern blotting confirmed a 52 kDa band in the cell lysate of HEK 293T transducted with pMSCV-IL-35-GFP plasmid, indicating a successful expression of IL-35. Ebi3 and IL-12A, two subunits of IL-35, could be identified 72 h post DNA injection. IL-35 upregulation in vivo effectively inhibit CD4+ and CD8+ T cell proliferation and Th1 cytokine secretion. Effector molecules of CD8+ T cells were also remarkably suppressed. On the contrary, high level of IL-35 significantly induced CD4+ CD25+ Tregs and Th2 enhancement. The in vitro study provided similar results.ConclusionThe results indicated Th1 and CD8+ T cell inhibition and Th2 and Tregs bias in the presence of IL-35 under a normal state which partly contributed to its therapeutic potential. creator: Xiaoning Zhang creator: Zhiqiang Zhang creator: Zhiqiang He creator: Mingyan Ju creator: Jiaci Li creator: Jinghua Yuan creator: Yaqing Jing creator: Keqiu Li creator: Yi Liu creator: Guang Li uri: https://doi.org/10.7717/peerj.5638 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Zhang et al. title: Plant dominance in a subalpine montane meadow: biotic vs. abiotic controls of subordinate diversity within and across sites link: https://peerj.com/articles/5619 last-modified: 2018-09-21 description: BackgroundUnderstanding the underlying factors that determine the relative abundance of plant species is critical to predict both biodiversity and ecosystem function. Biotic and abiotic factors can shape the distribution and the relative abundance of species across natural communities, greatly influencing local biodiversity.MethodsUsing a combination of an observational study and a five-year plant removal experiment we: (1) documented how plant diversity and composition of montane meadow assemblages vary along a plant dominance gradient using an observational study; (2) tracked above- and belowground functional traits of co-dominant plant species Potentilla and Festuca along a plant dominance gradient in an observational study; (3) determined whether plant species diversity and composition was directly influenced by commonly occurring species Potentilla and Festuca with the use of a randomized plot design, 5-year plant removal experiment (no removal control, Potentilla removed, Festuca removed, n = 10).ResultsWe found that subordinate species diversity and compositional dissimilarity were greatest in Potentilla and Festuca co-dominated sites, where neither Potentilla nor Festuca dominated, rather than at sites where either species became dominant. Further, while above- and belowground plant functional traits varied along a dominance gradient, they did so in a way that inconsistently predicted plant species relative abundance. Also, neither variation in plant functional traits of Festuca and Potentilla nor variation in resources and conditions (such as soil nitrogen and temperature) explained our subordinate diversity patterns. Finally, neither Potentilla nor Festuca influenced subordinate diversity or composition when we directly tested for their impacts in a plant removal experiment.DiscussionTaken together, patterns of subordinate diversity and composition were likely driven by abiotic factors rather than biotic interactions. As a result, the role of abiotic factors influencing local-level species interactions can be just as important as biotic interactions themselves in structuring plant communities. creator: Erika LaPlante creator: Lara Souza uri: https://doi.org/10.7717/peerj.5619 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 LaPlante and Souza