title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1078 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The oldest record of the Steller sea lion Eumetopias jubatus (Schreber, 1776) from the early Pleistocene of the North Pacific link: https://peerj.com/articles/9709 last-modified: 2020-08-27 description: The extant genera of fur seals and sea lions of the family Otariidae (Carnivora: Pinnipedia) are thought to have emerged in the Pliocene or the early Pleistocene in the North Pacific. Among them, the Steller sea lion (Eumetopias jubatus) is the largest and distributed both in the western and eastern North Pacific. In contrast to the limited distribution of the current population around the Japanese Islands that is now only along the coast of Hokkaido, their fossil records have been known from the middle and late Pleistocene of Honshu Island. One such important fossil specimen has been recorded from the upper lower Pleistocene Omma Formation (ca. 1.36–0.83 Ma) in Kanazawa, Ishikawa Prefecture, Japan, which now bears the institutional number GKZ-N 00001. Because GKZ-N 00001 is the earliest fossil having been identified as a species of the sea lion genus Eumetopias, it is of importance to elucidate the evolutionary history of that genus. The morphometric comparisons were made among 51 mandibles of fur seals and sea lions with GKZ-N 00001. As results of bivariate analyses and PCA based on 39 measurements for external morphologies with internal structures by CT scan data, there is almost no difference between GKZ-N 00001 and extant male individuals of E. jubatus. In this regard, GKZ-N 00001 is identified specifically as the Steller sea lion E. jubatus. Consequently, it is recognized as the oldest Steller sea lion in the North Pacific. About 0.8 Ma, the distribution of the Steller sea lion had been already established at least in the Japan Sea side of the western North Pacific. creator: Nahoko Tsuzuku creator: Naoki Kohno uri: https://doi.org/10.7717/peerj.9709 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Tsuzuku and Kohno title: The influence of bait on remote underwater video observations in shallow-water coastal environments associated with the North-Eastern Atlantic link: https://peerj.com/articles/9744 last-modified: 2020-08-27 description: The use of baited remote underwater video (BRUV) for examining and monitoring marine biodiversity in temperate marine environments is rapidly growing, however many aspects of their effectiveness relies on assumptions based on studies from the Southern Hemisphere. The addition of bait to underwater camera systems acts as a stimulus for attracting individuals towards the camera field of view, however knowledge of the effectiveness of different bait types in northern temperate climbs is limited, particularly in dynamic coastal environments. Studies in the Southern Hemisphere indicate that oily baits are most effective whilst bait volume and weight do not impact BRUV effectiveness to any great degree. The present study assesses the influence of four bait types (mackerel, squid, crab and no bait (control)) on the relative abundance, taxonomic diversity and faunal assemblage composition at two independent locations within the North-Eastern Atlantic region; Swansea Bay, UK and Ria Formosa Lagoon, Portugal. Two different bait quantities (50 g and 350 g) were further trialled in Swansea Bay. Overall, patterns showed that baited deployments recorded statistically higher values of relative abundance and taxonomic diversity when compared to un-baited deployments in Swansea Bay but not in Ria Formosa Lagoon. No statistical evidence singled out one bait type as best performing for attracting higher abundances and taxonomic diversity in both locations. Faunal assemblage composition was however found to differ with bait type in Swansea Bay, with mackerel and squid attracting higher abundances of scavenging species compared to the crab and control treatments. With the exception of squid, bait quantity had minimal influence on bait attractiveness. It is recommended for consistency that a minimum of 50 g of cheap, oily fish such as mackerel is used as bait for BRUV deployments in shallow dynamic coastal environments in the North-Eastern Atlantic Region. creator: Robyn E. Jones creator: Ross A. Griffin creator: Stephanie R. Januchowski-Hartley creator: Richard K.F. Unsworth uri: https://doi.org/10.7717/peerj.9744 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jones et al. title: High moon brightness and low ambient temperatures affect sloth predation by harpy eagles link: https://peerj.com/articles/9756 last-modified: 2020-08-27 description: BackgroundClimate plays a key role in the life histories of tropical vertebrates. However, tropical forests are only weakly seasonal compared with temperate and boreal regions. For species with limited ability to control core body temperature, even mild climatic variation can determine major behavioural outcomes, such as foraging and predator avoidance. In tropical forests, sloths are the arboreal vertebrate attaining the greatest biomass density, but their capacity to regulate body temperature is limited, relying on behavioural adaptations to thermoregulate. Sloths are largely or strictly nocturnal, and depend on crypsis to avoid predation. The harpy eagle (Harpia harpyja) is a sloth-specialist and exerts strong top-down control over its prey species. Yet the role of environmental variables on the regulation of predator–prey interactions between sloths and harpy eagles are unknown. The harpy eagle is considered Near Threatened. This motivated a comprehensive effort to reintroduce this species into parts of Mesoamerica. This effort incidentally enabled us to understand the prey profile of harpy eagles over multiple seasons.MethodsOur study was conducted between 2003 and 2009 at Soberanía National Park, Panamá. Telemetered harpy eagles were seen hunting and feeding on individual prey species. For each predation event, field assistants systematically recorded the species killed. We analysed the effects of climatic conditions and vegetation phenology on the prey species profile of harpy eagles using generalised linear mixed models.ResultsHere we show that sloth predation by harpy eagles was negatively affected by nocturnal ambient light (i.e. bright moonshine) and positively affected by seasonally cool temperatures. We suggest that the first ensured low detectability conditions for sloths foraging at night and the second posed a thermally unsuitable climate that forced sloths to forage under riskier daylight. We showed that even moderate seasonal variation in temperature can influence the relationship between a keystone tropical forest predator and a dominant prey item. Therefore, predator–prey ecology in the tropics can be modulated by subtle changes in environmental conditions. The seasonal effects shown here suggest important demographic consequences for sloths, which are under top-down regulation from harpy eagle predation, perhaps limiting their geographic distribution at higher latitudes. creator: Everton B.P. de Miranda creator: Caio F. Kenup creator: Edwin Campbell-Thompson creator: Felix H. Vargas creator: Angel Muela creator: Richard Watson creator: Carlos A. Peres creator: Colleen T. Downs uri: https://doi.org/10.7717/peerj.9756 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Miranda et al. title: Plastid transit peptides—where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution link: https://peerj.com/articles/9772 last-modified: 2020-08-27 description: Subcellular relocalization of proteins determines an organism’s metabolic repertoire and thereby its survival in unique evolutionary niches. In plants, the plastid and its various morphotypes import a large and varied number of nuclear-encoded proteins to orchestrate vital biochemical reactions in a spatiotemporal context. Recent comparative genomics analysis and high-throughput shotgun proteomics data indicate that there are a large number of plastid-targeted proteins that are either semi-conserved or non-conserved across different lineages. This implies that homologs are differentially targeted across different species, which is feasible only if proteins have gained or lost plastid targeting peptides during evolution. In this study, a broad, multi-genome analysis of 15 phylogenetically diverse genera and in-depth analyses of pangenomes from Arabidopsis and Brachypodium were performed to address the question of how proteins acquire or lose plastid targeting peptides. The analysis revealed that random insertions or deletions were the dominant mechanism by which novel transit peptides are gained by proteins. While gene duplication was not a strict requirement for the acquisition of novel subcellular targeting, 40% of novel plastid-targeted genes were found to be most closely related to a sequence within the same genome, and of these, 30.5% resulted from alternative transcription or translation initiation sites. Interestingly, analysis of the distribution of amino acids in the transit peptides of known and predicted chloroplast-targeted proteins revealed monocot and eudicot-specific preferences in residue distribution. creator: Ryan W. Christian creator: Seanna L. Hewitt creator: Grant Nelson creator: Eric H. Roalson creator: Amit Dhingra uri: https://doi.org/10.7717/peerj.9772 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2020 Christian et al. title: Association of impaired fasting glucose and Type 2 Diabetes Mellitus with brain volume changes in Alzheimer’s Disease patients analyzed by MRI: a retrospective study link: https://peerj.com/articles/9801 last-modified: 2020-08-27 description: ObjectivesAlzheimer’s disease (AD), impaired fasting glucose (IFG), and Type 2 diabetes mellitus (T2DM) were reported associated with smaller brain volumes. Nevertheless, the association of hyperglycemia with brain volume changes in AD patients remains unclear. To investigate this issue, structural magnetic resonance imaging was used to compare brain volumes among AD patients with different fasting glucose levels.MethodsEighty-five AD patients were divided into three groups based on their fasting glucose level as suggested by the American Diabetes Association: normal fasting glucose group (AD_NFG, n = 45), AD_IFG group (n = 15), and AD_T2DM group (n = 25). Sagittal 3D T1-weighted images were obtained to calculate the brain volume. Brain parenchyma and 33 brain structures were automatically segmented. Each regional volume was analyzed among groups. For regions with statistical significance, partial correlation analysis was used to evaluate their relationships with fasting glucose level, corrected for Mini-Mental State Examination score, age, education level, cholesterol, triglyceride, and blood pressure.ResultsCompared with the AD_IFG and AD_NFG groups, the volume of pons in AD_T2DM group was significantly smaller. Fasting glucose was negatively correlated with pontine volume.ConclusionsT2DM may exacerbate pontine atrophy in AD patients, and fasting glucose level is associated with pontine volume. creator: Weiwei Wang creator: Leongtim Wong creator: Lin Shi creator: Yishan Luo creator: Zhanhua Liang creator: Chunbo Dong creator: Qingwei Song creator: Tieli Liu creator: Qing Zhang creator: Ailian Liu creator: Yanwei Miao creator: Jianlin Wu uri: https://doi.org/10.7717/peerj.9801 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Association analysis between chronic obstructive pulmonary disease and polymorphisms in circadian genes link: https://peerj.com/articles/9806 last-modified: 2020-08-27 description: BackgroundCircadian genes have been suggested to play an important role in lung pathology. However, it remains unknown whether polymorphisms of these genes are associated with chronic obstructive pulmonary disease (COPD). Here, we aimed to investigate the association of circadian genes polymorphisms with COPD in a case-control study of 477 COPD patient and 323 control Han Chinese persons.MethodsGenotyping assays were carried out for nine single nucleotide polymorphisms (SNPs) from five circadian genes (PER3, CLOCK, RORB, BMAL1 and CRY2) that were previously identified in lung pathology. Age, sex, BMI and smoking status and comorbidities were recorded for all subjects.ResultsNo significant association was found in all SNP sites in overall subjects and no significant difference was found in age, sex, smoking status stratification analysis.DiscussionThe findings of this investigation indicated the effect of circadian genes polymorphisms on COPD susceptibility may only be small and possibly dependent on the subject factors, such as age and sex. creator: Guo Chen creator: Jingwei Zhang creator: Lijuan Zhang creator: Xuan Xiong creator: Dongke Yu creator: Yuan Zhang uri: https://doi.org/10.7717/peerj.9806 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Chen et al. title: Quantitative proteomics suggests changes in the carbohydrate metabolism of maize in response to larvae of the belowground herbivore Holotrichia parallela link: https://peerj.com/articles/9819 last-modified: 2020-08-27 description: The larvae of Holotrichia parallela, a destructive belowground herbivore, may cause yield losses of up to 20% in maize in a typical year. To understand the protein-level mechanisms governing the response of maize to this herbivore, tandem mass tag (TMT) quantitative proteomics was used for the comparative analysis of protein abundance in the maize roots after H. parallela larval attack. A total of 351 upregulated proteins and 303 downregulated proteins were identified. Pathway enrichment analysis revealed that the differentially abundant proteins (DAPs) were most strongly associated with carbohydrate and energy metabolism pathways, such as glycolysis, pentose phosphate pathway and fructose and mannose metabolism. Most glycolysis-related proteins were significantly induced. In addition, H. parallela larval attack decreased the glucose concentrations in the roots. This study demonstrates that maize can manipulate carbohydrate metabolism by modifying glycolysis and pentose phosphate pathway response to root-feeding herbivorous attackers. The results of this study may help to establish a foundation for further functional studies of key protein-mediated responses to H. parallela larvae in maize. creator: Yu Pan creator: Shiwen Zhao creator: Zhun Wang creator: Xiao Wang creator: Xinxin Zhang creator: Yunshuo Lee creator: Jinghui Xi uri: https://doi.org/10.7717/peerj.9819 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Pan et al. title: Growth parameter k and location affect body size responses to spatial protection by exploited rockfishes link: https://peerj.com/articles/9825 last-modified: 2020-08-27 description: For many fish taxa, trophic position and relative fecundity increase with body size, yet fisheries remove the largest individuals, altering food webs and reducing population productivity. Marine reserves and other forms of spatial protection can help mitigate this problem, but the effectiveness of these management tools may vary interspecifically and spatially. Using visual survey data collected on the Central Coast of British Columbia, for 12 species of exploited rockfish we found that body size responses to spatial fishery closures depended on interspecific variation in growth parameter k (the rate at which the asymptotic body size is approached) and on location. For two closures, relative body sizes were larger at protected than at adjacent fished sites, and these differences were greater for species with lower k values. Reduced fishery mortality likely drove these results, as an unfished species did not respond to spatial protection. For three closures, however, body sizes did not differ between protected and adjacent fished sites, and for another closure species with higher k values were larger at fished than at protected sites while species with lower k values had similar sizes in both treatments. Variation in the age of closures is unlikely to have influenced results, as most data were collected when closures were 13 to 15-years-old. Rather, the lack of larger fish inside four of six spatial fishery closures potentially reflects a combination of smaller size of the area protected, poor fisher compliance, and lower oceanographic productivity. Interspecific differences in movement behavior did not affect body size responses to spatial protection. To improve understanding, additional research should be conducted at deeper depths encompassing the distribution of older, larger fish. Our study—which was conceptualized and executed by an alliance of Indigenous peoples seeking to restore rockfishes—illustrates how life history and behavioral theory provide a useful lens for framing and interpreting species differences in responses to spatial protection. creator: Madeleine McGreer creator: Alejandro Frid creator: Tristan Blaine creator: Sandie Hankewich creator: Ernest Mason creator: Mike Reid creator: Hannah Kobluk uri: https://doi.org/10.7717/peerj.9825 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 McGreer et al. title: Why people select the outpatient clinic of medical centers: a nationwide analysis in Taiwan link: https://peerj.com/articles/9829 last-modified: 2020-08-27 description: IntroductionIn contrast to other countries, Taiwan’s National Health Insurance (NHI) program allows patients to freely select the specialists and tiers of medical care facility without a referral. Some medical centers in Taiwan receive over 10,000 outpatients per day. In the NHI program, the co-payment was increased for high-tier facilities for outpatient visits in 2002, 2005, and 2017. However, the policies only mildly reduced the use of high-tier medical care facilities. The main purpose of this study was to evaluate the factors contributing to the patients’ selection of the outpatient clinic of medical centers without a referral.MethodsAn online anonymous survey was conducted by using the Google Forms platform utilizing a self-constructed questionnaire from September to October 2018. A nationwide sample in Taiwan was recruited using convenience sampling through social media. Based on a literature review and a focus group, 20 factors that may affect the choice of the outpatient institution were constructed. The associations between items that affect the patients selection of outpatient clinics were assessed using exploratory factor analysis. Principal axis factoring was performed to identify the major factors affecting the decision. Multiple logistic regression was performed to determine which factors satisfactorily explained “visiting the outpatient clinic of the medical center for an illness without a referral.”ResultsDuring the survey period, 5,060 people browsed the online survey, and 1,003 responded and completed the online questionnaire. Therefore, the response rate was 19.8%. A total of 987 valid responses was collected. Exploratory factor analysis revealed that three main factors, namely the “physician factor”, “image and reputation factor”, and “facility and medication factor”, affected the selection of outpatient clinics. A series of logistic regressions indicated that patients who reported that hospital facilities, high-quality drugs, and diverse specialties were very important were more likely to select the outpatient clinic of a medical center (OR = 2.218, 95% CI [1.514–3.249]). Patients who reported that physician factors were very important were less likely to select a medical center (OR = 0.717, 95% CI [0.523–0.984]). Patients who were previously satisfied with their experience of the primary clinics or had a regular family doctor were less likely to choose a medical center (OR = 0.509, 95% CI -0.435–0.595] and OR = 0.676, 95% CI [0.471–0.969]).ConclusionIn Taiwan, patients with good primary medical experience and regular family physicians had significantly lower rates by selecting the outpatient clinic of a medical center. The results of this study support that the key to establishing graded medical care is to prioritize the strengthening of the primary medical system. creator: Ming-Hwai Lin creator: Hsiao-Ting Chang creator: Tzeng-Ji Chen creator: Shinn-Jang Hwang uri: https://doi.org/10.7717/peerj.9829 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lin et al. title: In situ SEM/EDS compositional characterization of osteocytes and blood vessels in fossil and extant turtles on untreated bone surfaces; different preservational pathways microns away link: https://peerj.com/articles/9833 last-modified: 2020-08-27 description: Osteocytes and blood vessels are the main cellular and tissue components of the bone tissue of vertebrates. Evidence of these soft-tissue microstructures has been widely documented in the fossil record of Mesozoic and Cenozoic turtles. However, all these studies have characterized morphologically and elementally these microstructures via isolation from the fossilized bone matrix where they were preserved or in ground sections, which could raise skepticism about the results due to potential cross-contamination or reagents effects. Fossil turtle bones from three different localities with distinct preservation environments and geological settings, including Mongolemys elegans from the Late Cretaceous of Mongolia, Allaeochelys crassesculpta from the Eocene of Germany, and a podocnemidid indet. from the Miocene of Colombia are studied here. Bone from two extant turtle species, Lepidochelys olivacea, and Podocnemis lewyana, as well as a commercial chicken Gallus gallus were used for comparisons. Scanning Electron Microscopy-Energy Dispersive Spectroscopy analyses performed directly on untreated fresh surfaces show that osteocytes-like in the fossil turtle bone are mostly composed of iron and manganese. In contrast, the in situ blood vessels-like of the fossil turtles, as well as those from the extant taxa are rich in elements typically organic in origin (carbon and nitrogen), which are absent to minimally present in the surrounding bone or rock matrix; this suggests a possible endogenous composition for these fossil structures. Also, the results presented here show that although originally both (osteocytes and blood vessels) are organic soft components of bone as evidenced in the extant turtles and chicken, they can experience completely different preservational pathways only microns away from each other in the same fossil bone. creator: Edwin-Alberto Cadena uri: https://doi.org/10.7717/peerj.9833 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Cadena