title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1624 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis link: https://peerj.com/articles/4386 last-modified: 2018-02-20 description: Chelonid alphaherpesvirus 5 (ChHV5) is a herpesvirus associated with fibropapillomatosis (FP) in sea turtles worldwide. Single-locus typing has previously shown differentiation between Atlantic and Pacific strains of this virus, with low variation within each geographic clade. However, a lack of multi-locus genomic sequence data hinders understanding of the rate and mechanisms of ChHV5 evolutionary divergence, as well as how these genomic changes may contribute to differences in disease manifestation. To assess genomic variation in ChHV5 among five Hawaii and three Florida green sea turtles, we used high-throughput short-read sequencing of long-range PCR products amplified from tumor tissue using primers designed from the single available ChHV5 reference genome from a Hawaii green sea turtle. This strategy recovered sequence data from both geographic regions for approximately 75% of the predicted ChHV5 coding sequences. The average nucleotide divergence between geographic populations was 1.5%; most of the substitutions were fixed differences between regions. Protein divergence was generally low (average 0.08%), and ranged between 0 and 5.3%. Several atypical genes originally identified and annotated in the reference genome were confirmed in ChHV5 genomes from both geographic locations. Unambiguous recombination events between geographic regions were identified, and clustering of private alleles suggests the prevalence of recombination in the evolutionary history of ChHV5. This study significantly increased the amount of sequence data available from ChHV5 strains, enabling informed selection of loci for future population genetic and natural history studies, and suggesting the (possibly latent) co-infection of individuals by well-differentiated geographic variants. creator: Cheryl L. Morrison creator: Luke Iwanowicz creator: Thierry M. Work creator: Elizabeth Fahsbender creator: Mya Breitbart creator: Cynthia Adams creator: Deb Iwanowicz creator: Lakyn Sanders creator: Mathias Ackermann creator: Robert S. Cornman uri: https://doi.org/10.7717/peerj.4386 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: title: Ground beetles in city forests: does urbanization predict a personality trait? link: https://peerj.com/articles/4360 last-modified: 2018-02-20 description: BackgroundUrbanization leads to substantial changes in natural habitats with profound effects on wildlife. Understanding behavioural responses to such environmental change is essential for identifying which organisms may adapt, as behaviour is often the first response to altered conditions. Individuals in more urbanized habitats may be expected to be more exploratory and bolder than their conspecifics in less urbanized habitats as they may be better able to cope with novel challenges.MethodsIn a two-year field study we tested ground beetles from differently urbanized forests for their exploratory behaviour (in a novel environment) and their risk-taking (death-feigning). In total, we tested ca. 3,000 individuals of four forest-dwelling ground beetle species from eight within-city forest patches. In the second year, we also transferred ca. 800 tested individuals of two species to the laboratory to test for consistent behavioural differences (i.e. personality differences) under standardised conditions.ResultsIndividuals were generally more exploratory in more urbanized than in less urbanized areas but only in one year of the study. Exploratory behaviour was not predicted by population density but increased with temperature or showed a temperature optimum. Exploration was consistent over time and individuals that were more exploratory also took higher risks.DiscussionWe demonstrated that species which are generally less directly exposed to human activities (e.g., most invertebrates) show behavioural responses to urbanization. Effects of urbanization were year-dependent, suggesting that other environmental conditions interacted with effects of urbanization on beetle behaviour. Furthermore, our results indicate that different personality compositions might cause behavioural differences among populations living in differently urbanized habitats. creator: Wiebke Schuett creator: Berit Delfs creator: Richard Haller creator: Sarah Kruber creator: Simone Roolfs creator: Desiree Timm creator: Magdalena Willmann creator: Claudia Drees uri: https://doi.org/10.7717/peerj.4360 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Schuett et al. title: The Far East taiga forest: unrecognized inhospitable terrain for migrating Arctic-nesting waterbirds? link: https://peerj.com/articles/4353 last-modified: 2018-02-20 description: The degree of inhospitable terrain encountered by migrating birds can dramatically affect migration strategies and their evolution as well as influence the way we develop our contemporary flyway conservation responses to protect them. We used telemetry data from 44 tagged individuals of four large-bodied, Arctic breeding waterbird species (two geese, a swan and one crane species) to show for the first time that these birds fly non-stop over the Far East taiga forest, despite their differing ecologies and migration routes. This implies a lack of suitable taiga refuelling habitats for these long-distance migrants. These results underline the extreme importance of northeast China spring staging habitats and of Arctic areas prior to departure in autumn to enable birds to clear this inhospitable biome, confirming the need for adequate site safeguard to protect these populations throughout their annual cycle. creator: Xin Wang creator: Lei Cao creator: Inga Bysykatova creator: Zhenggang Xu creator: Sonia Rozenfeld creator: Wooseog Jeong creator: Didier Vangeluwe creator: Yunlin Zhao creator: Tianhe Xie creator: Kunpeng Yi creator: Anthony David Fox uri: https://doi.org/10.7717/peerj.4353 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Wang et al. title: Acute sleep fragmentation does not alter pro-inflammatory cytokine gene expression in brain or peripheral tissues of leptin-deficient mice link: https://peerj.com/articles/4423 last-modified: 2018-02-19 description: Obesity and sleep fragmentation (SF) are often co-occurring pro-inflammatory conditions in patients with obstructive sleep apnea. Leptin is a peptide hormone produced by adipocytes that has anorexigenic effects upon appetite while regulating immunity. The role of leptin in mediating inflammatory responses to SF is incompletely understood. Male C57BL/6j (lean) and ob/ob mice (leptin-deficient mice exhibiting obese phenotype) were subjected to SF or control conditions for 24 h using an automated SF chamber. Trunk blood and tissue samples from the periphery (liver, spleen, fat, and heart) and brain (hypothalamus, prefrontal cortex, and hippocampus) were collected. Quantitative PCR was used to determine relative cytokine gene expression of pro-inflammatory (IL-1β, TNF-α) and anti-inflammatory (TGF-β1) cytokines. Enzyme-linked immunosorbent assay (ELISA) was used to determine serum corticosterone concentration. Ob/ob mice exhibited elevated cytokine gene expression in liver (TNF-α, TGF-β1), heart (TGF-β1), fat (TNF-α), and brain (hippocampus, hypothalamus, prefrontal cortex: IL-1β, TNF-α) compared with wild-type mice. Conversely, leptin deficiency decreased pro-inflammatory cytokine gene expression in heart (IL-1β, TNF-α). SF significantly increased IL-1β and TNF-α gene expression in fat and TGF-β1 expression in spleen relative to controls, but only in wild-type mice. SF increased basal serum corticosterone regardless of genotype. Taken together, these findings suggest that leptin deficiency affects cytokine gene expression differently in the brain compared to peripheral tissues with minimal interaction from acute SF. creator: Jennifer E. Dumaine creator: Noah T. Ashley uri: https://doi.org/10.7717/peerj.4423 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Dumaine and Ashley title: How has our knowledge of dinosaur diversity through geologic time changed through research history? link: https://peerj.com/articles/4417 last-modified: 2018-02-19 description: Assessments of dinosaur macroevolution at any given time can be biased by the historical publication record. Recent studies have analysed patterns in dinosaur diversity that are based on secular variations in the numbers of published taxa. Many of these have employed a range of approaches that account for changes in the shape of the taxonomic abundance curve, which are largely dependent on databases compiled from the primary published literature. However, how these ‘corrected’ diversity patterns are influenced by the history of publication remains largely unknown. Here, we investigate the influence of publication history between 1991 and 2015 on our understanding of dinosaur evolution using raw diversity estimates and shareholder quorum subsampling for the three major subgroups: Ornithischia, Sauropodomorpha, and Theropoda. We find that, while sampling generally improves through time, there remain periods and regions in dinosaur evolutionary history where diversity estimates are highly volatile (e.g. the latest Jurassic of Europe, the mid-Cretaceous of North America, and the Late Cretaceous of South America). Our results show that historical changes in database compilation can often substantially influence our interpretations of dinosaur diversity. ‘Global’ estimates of diversity based on the fossil record are often also based on incomplete, and distinct regional signals, each subject to their own sampling history. Changes in the record of taxon abundance distribution, either through discovery of new taxa or addition of existing taxa to improve sampling evenness, are important in improving the reliability of our interpretations of dinosaur diversity. Furthermore, the number of occurrences and newly identified dinosaurs is still rapidly increasing through time, suggesting that it is entirely possible for much of what we know about dinosaurs at the present to change within the next 20 years. creator: Jonathan P. Tennant creator: Alfio Alessandro Chiarenza creator: Matthew Baron uri: https://doi.org/10.7717/peerj.4417 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Tennant et al. title: Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula link: https://peerj.com/articles/4402 last-modified: 2018-02-19 description: The Psychrobacter genus is a cosmopolitan and diverse group of aerobic, cold-adapted, Gram-negative bacteria exhibiting biotechnological potential for low-temperature applications including bioremediation. Here, we present the draft genome sequence of a bacterium from the Psychrobacter genus isolated from a sediment sample from King George Island, Antarctica (3,490,622 bp; 18 scaffolds; G + C = 42.76%). Using phylogenetic analysis, biochemical properties and scanning electron microscopy the bacterium was identified as Psychrobacter glacincola BNF20, making it the first genome sequence reported for this species. P. glacincola BNF20 showed high tellurite (MIC 2.3 mM) and chromate (MIC 6.0 mM) resistance, respectively. Genome-wide nucleotide identity comparisons revealed that P. glacincola BNF20 is highly similar (>90%) to other uncharacterized Psychrobacter spp. such as JCM18903, JCM18902, and P11F6. Bayesian multi-locus phylogenetic analysis showed that P. glacincola BNF20 belongs to a polyphyletic clade with other bacteria isolated from polar regions. A high number of genes related to metal(loid) resistance were found, including tellurite resistance genetic determinants located in two contigs: Contig LIQB01000002.1 exhibited five ter genes, each showing putative promoter sequences (terACDEZ), whereas contig LIQB1000003.2 showed a variant of the terZ gene. Finally, investigating the presence and taxonomic distribution of ter genes in the NCBI’s RefSeq bacterial database (5,398 genomes, as January 2017), revealed that 2,623 (48.59%) genomes showed at least one ter gene. At the family level, most (68.7%) genomes harbored one ter gene and 15.6% exhibited five (including P. glacincola BNF20). Overall, our results highlight the diverse nature (genetic and geographic diversity) of the Psychrobacter genus, provide insights into potential mechanisms of metal resistance, and exemplify the benefits of sampling remote locations for prospecting new molecular determinants. creator: Claudia Melissa Muñoz-Villagrán creator: Katterinne N. Mendez creator: Fabian Cornejo creator: Maximiliano Figueroa creator: Agustina Undabarrena creator: Eduardo Hugo Morales creator: Mauricio Arenas-Salinas creator: Felipe Alejandro Arenas creator: Eduardo Castro-Nallar creator: Claudio Christian Vásquez uri: https://doi.org/10.7717/peerj.4402 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Muñoz-Villagrán et al. title: A comparative bioinformatic analysis of C9orf72 link: https://peerj.com/articles/4391 last-modified: 2018-02-19 description: C9orf72 is associated with frontotemporal dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS), both of which are devastating neurodegenerative diseases. Findings suggest that an expanded hexanucleotide repeat in the non-coding region of the C9orf72 gene is the most common cause of familial FTD and ALS. Despite considerable efforts being made towards discerning the possible disease-causing mechanism/s of this repeat expansion mutation, the biological function of C9orf72 remains unclear. Here, we present the first comprehensive genomic study on C9orf72 gene. Analysis of the genomic level organization of C9orf72 across select species revealed architectural similarity of syntenic regions between human and mouse but a lack of conservation of the repeat-harboring intron 1 sequence. Information generated in this study provides a broad genomic perspective of C9orf72 which would form a basis for subsequent experimental approaches and facilitate future mechanistic and functional studies on this gene. creator: Shalini Iyer creator: K. Ravi Acharya creator: Vasanta Subramanian uri: https://doi.org/10.7717/peerj.4391 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Iyer et al. title: Ants contribute to pollination but not to reproduction in a rare calcareous grassland forb link: https://peerj.com/articles/4369 last-modified: 2018-02-19 description: The number of plants pollinated by ants is surprisingly low given the abundance of ants and the fact that they are common visitors of angiosperms. Generally ants are considered as nectar robbers that do not provide pollination service. We studied the pollination system of the endangered dry grassland forb Euphorbia seguieriana and found two ant species to be the most frequent visitors of its flowers. Workers of Formica cunicularia carried five times more pollen than smaller Tapinoma erraticum individuals, but significantly more viable pollen was recovered from the latter. Overall, the viability of pollen on ant cuticles was significantly lower (p < 0.001)—presumably an antibiotic effect of the metapleural gland secretion. A marking experiment suggested that ants were unlikely to facilitate outcrossing as workers repeatedly returned to the same individual plant. In open pollinated plants and when access was given exclusively to flying insects, fruit set was nearly 100%. In plants visited by ants only, roughly one third of flowers set fruit, and almost none set fruit when all insects were excluded. The germination rate of seeds from flowers pollinated by flying insects was 31 ± 7% in contrast to 1 ± 1% resulting from ant pollination. We conclude that inbreeding depression may be responsible for the very low germination rate in ant pollinated flowers and that ants, although the most frequent visitors, play a negligible or even deleterious role in the reproduction of E. seguieriana. Our study reiterates the need to investigate plant fitness effects beyond seed set in order to confirm ant-plant mutualisms. creator: Michael Rostás creator: Felix Bollmann creator: David Saville creator: Michael Riedel uri: https://doi.org/10.7717/peerj.4369 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rostás et al. title: Chimpanzees (Pan troglodytes) display limited behavioural flexibility when faced with a changing foraging task requiring tool use link: https://peerj.com/articles/4366 last-modified: 2018-02-19 description: Behavioural flexibility, the ability to alter behaviour in response to environmental feedback, and to relinquish previously successful solutions to problems, is a crucial ability in allowing organisms to adapt to novel environments and environmental change; it is essential to cumulative cultural change. To explore this ability in chimpanzees, 18 individuals (Pan troglodytes) were presented with an artificial foraging task consisting of a tube partially filled with juice that could be reached by hand or retrieved using tool materials to hand. Effective solutions were then restricted in the second phase of the study by narrowing the diameter of the tube, necessitating the abandonment of previously successful solutions. Chimpanzees showed limited behavioural flexibility in comparison to some previous studies, increasing their use of effective techniques, but also continuing to attempt solutions that had been rendered ineffective. This adds to a literature reporting divergent evidence for flexibility (the ability to alter behaviour in response to environmental feedback, and to relinquish previously successful solutions to problems) versus conservatism (a reluctance or inability to explore or adopt novel solutions to problems when a solution is already known) in apes. creator: Rachel A. Harrison creator: Andrew Whiten uri: https://doi.org/10.7717/peerj.4366 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Harrison and Whiten title: Authorial and institutional stratification in open access publishing: the case of global health research link: https://peerj.com/articles/4269 last-modified: 2018-02-19 description: Using a database of recent articles published in the field of Global Health research, we examine institutional sources of stratification in publishing access outcomes. Traditionally, the focus on inequality in scientific publishing has focused on prestige hierarchies in established print journals. This project examines stratification in contemporary publishing with a particular focus on subscription vs. various Open Access (OA) publishing options. Findings show that authors working at lower-ranked universities are more likely to publish in closed/paywalled outlets, and less likely to choose outlets that involve some sort of Article Processing Charge (APCs; gold or hybrid OA). We also analyze institutional differences and stratification in the APC costs paid in various journals. Authors affiliated with higher-ranked institutions, as well as hospitals and non-profit organizations pay relatively higher APCs for gold and hybrid OA publications. Results suggest that authors affiliated with high-ranked universities and well-funded institutions tend to have more resources to choose pay options with publishing. Our research suggests new professional hierarchies developing in contemporary publishing, where various OA publishing options are becoming increasingly prominent. Just as there is stratification in institutional representation between different types of publishing access, there is also inequality within access types. creator: Kyle Siler creator: Stefanie Haustein creator: Elise Smith creator: Vincent Larivière creator: Juan Pablo Alperin uri: https://doi.org/10.7717/peerj.4269 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Siler et al.