title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1032 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis) link: https://peerj.com/articles/10186 last-modified: 2020-10-21 description: Conservation genetic approaches for elasmobranchs have focused on regions of the mitochondrial genome or a handful of nuclear microsatellites. High-throughput sequencing offers a powerful alternative for examining population structure using many loci distributed across the nuclear and mitochondrial genomes. These single nucleotide polymorphisms are expected to provide finer scale and more accurate population level data; however, there have been few genomic studies applied to elasmobranch species. The desire to apply next-generation sequencing approaches is often tempered by the costs, which can be offset by pooling specimens prior to sequencing (pool-seq). In this study, we assess the utility of pool-seq by applying this method to the same individual silky sharks, Carcharhinus falciformis, previously surveyed with the mtDNA control region in the Atlantic and Indian Oceans. Pool-seq methods were able to recover the entire mitochondrial genome as well as thousands of nuclear markers. This volume of sequence data enabled the detection of population structure between regions of the Atlantic Ocean populations, undetected in the previous study (inter-Atlantic mitochondrial SNPs FST values comparison ranging from 0.029 to 0.135 and nuclear SNPs from 0.015 to 0.025). Our results reinforce the conclusion that sampling the mitochondrial control region alone may fail to detect fine-scale population structure, and additional sampling across the genome may increase resolution for some species. Additionally, this study shows that the costs of analyzing 4,988 loci using pool-seq methods are equivalent to the standard Sanger-sequenced markers and become less expensive when large numbers of individuals (>300) are analyzed. creator: Derek W. Kraft creator: Emily E. Conklin creator: Evan W. Barba creator: Melanie Hutchinson creator: Robert J. Toonen creator: Zac H. Forsman creator: Brian W. Bowen uri: https://doi.org/10.7717/peerj.10186 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kraft et al. title: DNA barcoding for identification of anuran species in the central region of South America link: https://peerj.com/articles/10189 last-modified: 2020-10-21 description: The use of COI barcodes for specimen identification and species discovery has been a useful molecular approach for the study of Anura. Here, we establish a comprehensive amphibian barcode reference database in a central area of South America, in particular for specimens collected in Mato Grosso do Sul state (Brazil), and to evaluate the applicability of the COI gene for species-level identification. Both distance- and tree-based methods were applied for assessing species boundaries and the accuracy of specimen identification was evaluated. A total of 204 mitochondrial COI barcode sequences were evaluated from 22 genera and 59 species (19 newly barcoded species). Our results indicate that morphological and molecular identifications converge for most species, however, some species may present cryptic species due to high intraspecific variation, and there is a high efficiency of specimen identification. Thus, we show that COI sequencing can be used to identify anuran species present in this region. creator: Ricardo Koroiva creator: Luís Reginaldo Ribeiro Rodrigues creator: Diego José Santana uri: https://doi.org/10.7717/peerj.10189 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Koroiva et al. title: Structure and functions of Yellow-breasted Boubou (Laniarius atroflavus) solos and duets link: https://peerj.com/articles/10214 last-modified: 2020-10-21 description: BackgroundBirds have extremely well-developed acoustic communication and have become popular in bioacoustics research. The majority of studies on bird song have been conducted in the temperate zones where usually males of birds sing to attract females and defend territories. In over 360 bird species mostly inhabiting the tropics both males and females sing together in duets. Avian duets are usually formed when a male and female coordinate their songs. We focused on a species with relatively weakly coordinated duets, with male solo as the prevailing vocalisation type.MethodsInstead of analysing a set of recordings spread over a long time, we analysed whole day microphone-array recordings of the Yellow-breasted Boubou (Laniarius atroflavus), a species endemic to West African montane rainforests. We described the structure of the solo and duet vocalisations and temporal characteristics of daily activity based on 5,934 vocal bouts of 18 focal pairs and their neighbours.ResultsBirds had small, sex specific repertoires. All males shared three types of loud whistles functioning as song type repertoires in both solos and duets. Females vocalised with five types of harsh, atonal notes with a more variable and usually lower amplitude. Three of them were produced both as solos and in duets, while two seem to function as alarm and excitement calls given almost exclusively as a solo. Solos were the most common vocalisation mode (75.4%), with males being more vocally active than females. Duets accounted for 24.6% of all vocalisations and in most cases were initiated by males (81%). The majority of duets were simple (85.1%) consisting of a single male and female song type, but altogether 38 unique duet combinations were described. Males usually initiated singing at dawn and for this used one particular song type more often than expected by chance. Male solo and duet activities peaked around dawn, while female solos were produced evenly throughout the day.DiscussionYellow-breasted Boubou is a duetting species in which males are much more vocal than females and duetting is not a dominating type of vocal activity. Duet structure, context and timing of daily production support the joint resource defence hypothesis and mate guarding/prevention hypotheses, however maintaining pair contact also seems to be important. This study provides for the first time the basic quantitative data describing calls, solos and duet songs in the Yellow-breasted Boubou. creator: Amie Wheeldon creator: Paweł Szymański creator: Michał Budka creator: Tomasz S. Osiejuk uri: https://doi.org/10.7717/peerj.10214 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wheeldon et al. title: DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data link: https://peerj.com/articles/10216 last-modified: 2020-10-21 description: For the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and, as such, drives proteomics. MS/MS spectra need to be assigned a peptide sequence for which two strategies exist. Either database search or de novo sequencing can be employed to establish peptide spectrum matches. For database search, mzIdentML is the current community standard for data representation. There is no community standard for representing de novo sequencing results, but we previously proposed the de novo markup language (DNML). At the moment, each de novo sequencing solution uses different data representation, complicating downstream data integration, which is crucial since ensemble predictions may be more useful than predictions of a single tool. We here propose the de novo MS Ontology (DNMSO), which can, for example, provide many-to-many mappings between spectra and peptide predictions. Additionally, an application programming interface (API) that supports any file operation necessary for de novo sequencing from spectra input to reading, writing, creating, of the DNMSO format, as well as conversion from many other file formats, has been implemented. This API removes all overhead from the production of de novo sequencing tools and allows developers to concentrate on algorithm development completely. We make the API and formal descriptions of the format freely available at https://github.com/savastakan/dnmso. creator: Savaş Takan creator: Jens Allmer uri: https://doi.org/10.7717/peerj.10216 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Takan and Allmer title: High microphone signal-to-noise ratio enhances acoustic sampling of wildlife link: https://peerj.com/articles/9955 last-modified: 2020-10-20 description: BackgroundAutomated sound recorders are a popular sampling tool in ecology. However, the microphones themselves received little attention so far, and specifications that determine the recordings’ sound quality are seldom mentioned. Here, we demonstrate the importance of microphone signal-to-noise ratio for sampling sonant animals.MethodsWe tested 12 different microphone models in the field and measured their signal-to-noise ratios and detection ranges. We also measured the vocalisation activity of birds and bats that they recorded, the bird species richness, the bat call types richness, as well as the performance of automated detection of bird and bat calls. We tested the relationship of each one of these measures with signal-to-noise ratio in statistical models.ResultsMicrophone signal-to-noise ratio positively affects the sound detection space areas, which increased by a factor of 1.7 for audible sound, and 10 for ultrasound, from the lowest to the highest signal-to-noise ratio microphone. Consequently, the sampled vocalisation activity increased by a factor of 1.6 for birds, and 9.7 for bats. Correspondingly, the species pool of birds and bats could not be completely detected by the microphones with lower signal-to-noise ratio. The performance of automated detection of bird and bat calls, as measured by its precision and recall, increased significantly with microphone signal-to-noise ratio.DiscussionMicrophone signal-to-noise ratio is a crucial characteristic of a sound recording system, positively affecting the acoustic sampling performance of birds and bats. It should be maximised by choosing appropriate microphones, and be quantified independently, especially in the ultrasound range. creator: Kevin F.A. Darras creator: Franziska Deppe creator: Yvonne Fabian creator: Agus P. Kartono creator: Andres Angulo creator: Bjørn Kolbrek creator: Yeni A. Mulyani creator: Dewi M. Prawiradilaga uri: https://doi.org/10.7717/peerj.9955 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Darras et al. title: Insect pollination is important in a smallholder bean farming system link: https://peerj.com/articles/10102 last-modified: 2020-10-20 description: BackgroundMany crops are dependent on pollination by insects. Habitat management in agricultural landscapes can support pollinator services and even augment crop production. Common bean (Phaseolus vulgaris L.) is an important legume for the livelihoods of smallholder farmers in many low-income countries, particularly so in East Africa. While this crop is autogamous, it is frequently visited by pollinating insects that could improve yields. However, the value of pollination services to common beans (Kariasii) yield is not known.MethodsWe carried out pollinator-exclusion experiments to determine the contribution of insect pollinators to bean yields. We also carried out a fluorescent-dye experiment to evaluate the role of field margins as refuge for flower-visitors.ResultsSignificantly higher yields, based on pods per plant and seeds per pod, were recorded from open-pollinated and hand-pollinated flowers compared to plants from which pollinators had been excluded indicating that flower visitors contribute significantly to bean yields. Similarly, open and hand-pollinated plants recorded the highest mean seed weight. Extrapolation of yield data to field scale indicated a potential increase per hectare from 681 kg in self-pollinated beans to 1,478 kg in open-pollinated beans indicating that flower visitors contributed significantly to crop yield of beans. Our marking study indicated that flower-visiting insects including bees, flies and lepidopterans moved from the field margin flowers into the bean crop. Overall, these results show that insect pollinators are important for optimising bean yields and an important food security consideration on smallholder farms. Field margin vegetation also provides habitat for flower-visiting insects that pollinate beans. Hence, non-crop habitats merit further research focusing on establishing which field margin species are most important and their capacity to support other ecosystem services such as natural pest regulation or even pests. creator: Filemon Elisante creator: Patrick Ndakidemi creator: Sarah E.J. Arnold creator: Steven R. Belmain creator: Geoff M. Gurr creator: Iain Darbyshire creator: Gang Xie creator: Philip C. Stevenson uri: https://doi.org/10.7717/peerj.10102 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Elisante et al. title: Isolation and evolutionary analyses of porcine epidemic diarrhea virus in Asia link: https://peerj.com/articles/10114 last-modified: 2020-10-20 description: Porcine epidemic diarrhea virus (PEDV) is a leading cause of diarrhea in pigs worldwide. Virus isolation and genetic evolutionary analysis allow investigations into the prevalence of epidemic strains and provide data for the clinical diagnosis and vaccine development. In this study, we investigated the genetic characteristics of PEDV circulation in Asia through virus isolation and comparative genomics analysis. APEDV strain designated HB2018 was isolated from a pig in a farm experiencing a diarrhea outbreak. The complete genome sequence of HB2018 was 28,138 bp in length. Phylogenetic analysis of HB2018 and 207 PEDVs in Asia showed that most PEDV strains circulating in Asia after 2010 belong to genotype GII, particularly GII-a. The PEDV vaccine strain CV777 belonged to GI, and thus, unmatched genotypes between CV777 and GII-a variants might partially explain incomplete protection by the CV777-derived vaccine against PEDV variants in China. In addition, we found the S protein of variant strains contained numerous mutations compared to the S protein of CV777, and these mutations occurred in the N-terminal domain of the S protein. These mutations may influence the antigenicity, pathogenicity, and neutralization properties of the variant strains. creator: Wan Liang creator: Danna Zhou creator: Chao Geng creator: Keli Yang creator: Zhengying Duan creator: Rui Guo creator: Wei Liu creator: Fangyan Yuan creator: Zewen Liu creator: Ting Gao creator: Ling Zhao creator: Dongwan Yoo creator: Yongxiang Tian uri: https://doi.org/10.7717/peerj.10114 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liang et al. title: Visual duration bisection in profoundly deaf individuals link: https://peerj.com/articles/10133 last-modified: 2020-10-20 description: BackgroundPrevious research has been designed to study the effect of hearing loss on supra-second duration estimation in the visual channel and position effect of visual abilities among deaf populations. The current study aimed to investigate the sub-second duration perception of different visual fields in profoundly deaf individuals.MethodsA total of 16 profoundly deaf undergraduates and 16 hearing undergraduates completed a visual duration bisection task in which participants made judgments about whether a series of probe durations that were linearly spaced from 200 ms to 800 ms at 100 ms intervals were more similar to a standard short duration (200 ms) or a standard long duration (800 ms). The probe stimuli were presented in the center, left, or right of the screen. A repeated measure analysis of variance (ANOVA) with a between-participants factor of group and a within-participants factor of position, and a one-sample t-test were conducted.ResultsThe Weber ratio (WR) values of deaf participants were significantly higher than those of hearing participants, regardless of the presented positions of the visual stimulus. The bisection point (BP) value of deaf participants was significantly lower than 500 ms (average mean of 200/800 ms) and the BP value of hearing participants did not significantly differ from 500 ms, although the overall difference of BP values between the deaf group and hearing group did not reach significance. For deaf participants, the BP value in the center condition was significantly lower than 500 ms; however, the difference between the BP value in the left condition and 500 ms did not reach significance, indicating that their duration discrimination accuracy in the left visual field was better than that in the center visual field.ConclusionsHearing loss impaired visual sub-second duration perception, and deaf individuals showed a left visual field advantage of duration discrimination accuracy during the visual duration bisection task. creator: Feng Zhang creator: Kaige Jin creator: Sainan Zhang uri: https://doi.org/10.7717/peerj.10133 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: Polarity and epithelial-mesenchymal transition of retinal pigment epithelial cells in proliferative vitreoretinopathy link: https://peerj.com/articles/10136 last-modified: 2020-10-20 description: Under physiological conditions, retinal pigment epithelium (RPE) is a cellular monolayer composed of mitotically quiescent cells. Tight junctions and adherens junctions maintain the polarity of RPE cells, and are required for cellular functions. In proliferative vitreoretinopathy (PVR), upon retinal tear, RPE cells lose cell-cell contact, undergo epithelial-mesenchymal transition (EMT), and ultimately transform into myofibroblasts, leading to the formation of fibrocellular membranes on both surfaces of the detached retina and on the posterior hyaloids, which causes tractional retinal detachment. In PVR, RPE cells are crucial contributors, and multiple signaling pathways, including the SMAD-dependent pathway, Rho pathway, MAPK pathways, Jagged/Notch pathway, and the Wnt/β-catenin pathway are activated. These pathways mediate the EMT of RPE cells, which play a key role in the pathogenesis of PVR. This review summarizes the current body of knowledge on the polarized phenotype of RPE, the role of cell-cell contact, and the molecular mechanisms underlying the RPE EMT in PVR, emphasizing key insights into potential approaches to prevent PVR. creator: Hui Zou creator: Chenli Shan creator: Linlin Ma creator: Jia Liu creator: Ning Yang creator: Jinsong Zhao uri: https://doi.org/10.7717/peerj.10136 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zou et al. title: Mining the potential prognostic value of synaptosomal-associated protein 25 (SNAP25) in colon cancer based on stromal-immune score link: https://peerj.com/articles/10142 last-modified: 2020-10-20 description: BackgroundColon cancer is one of the deadliest tumors worldwide. Stromal cells and immune cells play important roles in cancer biology and microenvironment across different types of cancer. This study aimed to identify the prognostic value of stromal/immune cell-associated genes for colon cancer in The Cancer Genome Atlas (TCGA) database using bioinformatic technology.MethodsThe gene expression data and corresponding clinical information of colon cancer were downloaded from TCGA database. Stromal and immune scores were estimated based on the ESTIMATE algorithm. Sanger software was used to identify the differentially expressed genes (DEGs) and prognostic DEGs based on stromal and immune scores. External validation of prognostic biomarkers was conducted in Gene Expression Omnibus (GEO) database. Gene ontology (GO) analysis, pathway enrichment analysis, and gene set enrichment analysis (GSEA) were used for functional analysis. STRING and Cytoscape were used to assess the protein-protein interaction (PPI) network and screen hub genes. Quantitative real-time PCR (qRT-PCR) was used to validate the expression of hub genes in clinical tissues. Synaptosomal-associated protein 25 (SNAP25) was selected for analyzing its correlations with tumor-immune system in the TISIDB database.ResultsWorse overall survivals of colon cancer patients were found in high stromal score group (2963 vs. 1930 days, log-rank test P = 0.038) and high immune score group (2894 vs. 2230 days, log-rank test P = 0.076). 563 up-regulated and 9 down-regulated genes were identified as stromal-immune score-related DEGs. 70 up-regulated DEGs associated with poor outcomes were identified by COX proportional hazard regression model, and 15 hub genes were selected later. Then, we verified aquaporin 4 (AQP4) and SNAP25 as prognostic biomarkers in GEO database. qRT-PCR results revealed that AQP4 and SNAP25 were significantly elevated in colon cancer tissues compared with adjacent normal tissues (P = 0.003, 0.001). GSEA and TISIDB suggested that SNAP25 involved in cancer-related signaling pathway, immunity and metabolism progresses.ConclusionSNAP25 is a microenvironment-related and immune-related gene that can predict poor outcomes in colon cancer. creator: Jinyan Zou creator: Darong Duan creator: Changfa Yu creator: Jie Pan creator: Jinwei Xia creator: Zaixing Yang creator: Shasha Cai uri: https://doi.org/10.7717/peerj.10142 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zou et al.