title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=661 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics model Pimephales promelas link: https://peerj.com/articles/13954 last-modified: 2022-08-25 description: BackgroundThe fathead minnow (Pimephales promelas) is a model species for toxicological research. A high-quality genome reference sequence is available, and genomic methods are increasingly used in toxicological studies of the species. However, phylogenetic relationships within the genus remain incompletely known and little population-genomic data are available for fathead minnow despite the potential effects of genetic background on toxicological responses. On the other hand, a wealth of extant samples is stored in museum collections that in principle allow fine-scale analysis of contemporary and historical genetic variation.MethodsHere we use short-read shotgun resequencing to investigate sequence variation among and within Pimephales species. At the genus level, our objectives were to resolve phylogenetic relationships and identify genes with signatures of positive diversifying selection. At the species level, our objective was to evaluate the utility of archived-sample resequencing for detecting selective sweeps within fathead minnow, applied to a population introduced to the San Juan River of the southwestern United States sometime prior to 1950.ResultsWe recovered well-supported but discordant phylogenetic topologies for nuclear and mitochondrial sequences that we hypothesize arose from mitochondrial transfer among species. The nuclear tree supported bluntnose minnow (P. notatus) as sister to fathead minnow, with the slim minnow (P. tenellus) and bullhead minnow (P. vigilax) more closely related to each other. Using multiple methods, we identified 11 genes that have diversified under positive selection within the genus. Within the San Juan River population, we identified selective-sweep regions overlapping several sets of related genes, including both genes that encode the giant sarcomere protein titin and the two genes encoding the MTORC1 complex, a key metabolic regulator. We also observed elevated polymorphism and reduced differentation among populations (FST) in genomic regions containing certain immune-gene clusters, similar to what has been reported in other taxa. Collectively, our data clarify evolutionary relationships and selective pressures within the genus and establish museum archives as a fruitful resource for characterizing genomic variation. We anticipate that large-scale resequencing will enable the detection of genetic variants associated with environmental toxicants such as heavy metals, high salinity, estrogens, and agrichemicals, which could be exploited as efficient biomarkers of exposure in natural populations. creator: Katy E. Klymus creator: Robert A. Hrabik creator: Nathan L. Thompson creator: Robert S. Cornman uri: https://doi.org/10.7717/peerj.13954 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: ©2022 Klymus et al. title: Heterochronies and allometries in the evolution of the hominid cranium: a morphometric approach using classical anthropometric variables link: https://peerj.com/articles/13991 last-modified: 2022-08-25 description: This article studies the evolutionary change of allometries in the relative size of the two main cranial modules (neurocranium and splanchnocranium) in the five living hominid species and a diverse sample of extinct hominins. We use six standard craniometric variables as proxies for the length, width and height of each cranial module. Factor analysis and two-block partial least squares (2B-PLS) show that the great apes and modern humans share a pervasive negative ontogenetic allometry in the neurocranium and a positive one in the splanchnocranium. This developmental constraint makes it possible to interpret the cranial heterochronies in terms of ontogenetic scaling processes (i.e., extensions or truncations of the ancestral ontogenetic trajectory) and lateral transpositions (i.e., parallel translations of the entire trajectory starting from a different shape for a given cranial size). We hypothesize that ontogenetic scaling is the main evolutionary modality in the australopithecines while in the species of Homo it is also necessary to apply transpositions. Both types of processes are coordinated in Homo, which result in an evolutionary trend toward an increase in brain size and in the degree of paedomorphosis from the earliest habilines. creator: Juan Antonio Pérez-Claros creator: Paul Palmqvist uri: https://doi.org/10.7717/peerj.13991 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Pérez-Claros and Palmqvist title: Energy demands in high-intensity intermittent taekwondo specific exercises link: https://peerj.com/articles/13654 last-modified: 2022-08-24 description: BackgroundTaekwondo is an intermittent Olympic combat sport, which shows an aerobic predominance in matches and high participation of alactic metabolism for actions that determine competitive success. However, there is no information on energetic contribution systems in different high-intensity intermittent exercises for metabolic conditioning with specific movements. The study aimed to measure the physiological demands, mainly the energy expenditure, in taekwondo-specific high-intensity intermittent exercises (HIIE).MethodsThis study recruited ten male black belt athletes with a mean age of 20.2 ± 4 years, body mass of 62.8 ± 10.5 kg and height of 170.6 ± 7.8 cm, and total practice time of 11.8 ± 5.4 years. Subjects performed an incremental specific test and three different HIIE protocols on nonconsecutive days, and all comprised three 2-min rounds and 1 min of recovery between rounds. Heart rate, oxygen consumption, and blood lactate were measured. Energetic expenditure of aerobic, alactic, and lactic metabolisms was estimated through oxygen consumption, excess post-exercise oxygen consumption, and peak blood lactate after each round.ResultsFor the mean of the three rounds, the TKDtest100 resulted in higher absolute and relative contribution from the aerobic metabolism (52.4 ± 4%; p = 0.01) and lower than the 35:5 relative alactic contribution (48.7 ± 5.4%; p = 0.03).ConclusionThe mean of the three rounds for 35:5 and 15:10:5 presented similar absolute and relative contributions of aerobic and alactic metabolisms, whereas the TKDtest100 was a predominantly aerobic activity. We emphasize that aerobic metabolism was predominant from the second round in the 15:10:5 and 100%TKDtest protocols and in the last round of the 35:5 protocol. creator: Charles Bartel creator: Victor S. Coswig creator: Gabriel V. Protzen creator: Fabricio B. Del Vecchio uri: https://doi.org/10.7717/peerj.13654 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Bartel et al. title: Changes and response mechanism of sugar and organic acids in fruits under water deficit stress link: https://peerj.com/articles/13691 last-modified: 2022-08-24 description: The content and the ratio of soluble sugars and organic acids in fruits are significant indicators for fruit quality. They are affected by multiple environmental factors, in which water-deficient is the most concern. Previous studies found that the content of soluble sugars and organic acids in fruit displayed great differences under varied water stress. It is important to clarify the mechanism of such difference and to provide researchers with systematic knowledge about the response to drought stress and the mechanism of sugar and acid changes in fruits, so that they can better carry out the study of fruit quality under drought stress. Therefore, the researchers studied dozens of research articles about the content of soluble sugar and organic acid, the activity of related metabolic enzymes, and the expression of related metabolic genes in fruits under water stress, and the stress response of plants to water stress. We found that after plants perceived and transmitted the signal of water deficit, the expression of genes related to the metabolism of soluble sugars and organic acids changed. It was then affected the synthesis of metabolic enzymes and changed their metabolic rate, ultimately leading to changes in soluble sugar and organic acid content. Based on the literature review, we described the pathway diagrams of sugar metabolism, organic acid metabolism, mainly malic acid, tartaric acid, and citric acid metabolism, and of the response to drought stress. From many aspects including plants’ perception of water stress signal, signal conversion and transmission, induced gene expression, the changes in soluble sugar and the enzyme activities of organic acids, as well as the final sugar and acid content in fruits, this thesis summarized previous studies on the influence of water stress on soluble sugars and the metabolism of organic acids in fruits. creator: Wei-Feng Ma creator: Yan-Biao Li creator: Guo-Jie Nai creator: Guo-Ping Liang creator: Zong-Huan Ma creator: Bai-Hong Chen creator: Juan Mao uri: https://doi.org/10.7717/peerj.13691 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Ma et al. title: Identifying sources of variation in parasite aggregation link: https://peerj.com/articles/13763 last-modified: 2022-08-24 description: Aggregation of macroparasites among hosts is a near-universal pattern, and has important consequences for the stability of host-parasite associations and the impacts of disease. Identifying which potential drivers are contributing to levels of aggregation observed in parasite-host associations is challenging, particularly for observational studies. We apply beta regressions in a Bayesian framework to determine predictors of aggregation, quantified using Poulin’s index of discrepancy (D), for 13 species of parasites infecting Icelandic Rock Ptarmigan (Lagopus muta) collected over 12 years. 1,140 ptarmigan were collected using sampling protocols maximizing consistency of sample sizes and of composition of host ages and sexes represented across years from 2006–2017. Parasite species, taxonomic group (insect, mite, coccidian, or nematode), and whether the parasite was an ecto- or endoparasite were tested as predictors of aggregation, either alone or by modulating an effect of parasite mean abundance on D. Parasite species was an important predictor of aggregation in models. Despite variation in D across samples and years, relatively consistent aggregation was demonstrated for each specific host-parasite association, but not for broader taxonomic groups, after taking sample mean abundance into account. Furthermore, sample mean abundance was consistently and inversely related to aggregation among the nine ectoparasites, however no relationship between mean abundance and aggregation was observed among the four endoparasites. We discuss sources of variation in observed aggregation, sources both statistical and biological in nature, and show that aggregation is predictable, and distinguishable, among infecting species. We propose explanations for observed patterns and call for the review and re-analysis of parasite and other symbiont distributions using beta regression to identify important drivers of aggregation—both broad and association-specific. creator: André Morrill creator: Ólafur K. Nielsen creator: Karl Skírnisson creator: Mark R. Forbes uri: https://doi.org/10.7717/peerj.13763 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Morrill et al. title: Deteriorated sleep quality and influencing factors among undergraduates in northern Guizhou, China link: https://peerj.com/articles/13833 last-modified: 2022-08-24 description: BackgroundThe sleep quality of undergraduates is considerably worse than that in general population, a cross sectional study was conducted to evaluate sleep quality and identify related factors.MethodsAll participants from the freshmen to senior were recruited by the stratified cluster sampling from December 1, 2018 to January 12, 2019. The questionnaire used in this research was primarily composed of three sections: demographic characteristics, Pittsburgh Sleep Quality Index (PSQI) questionnaire and influencing factors of sleep quality. The data were analyzed using SPSS 18.0.ResultsA total of 1,063 valid questionnaires were collected. Among them, 53.7% subjects suffered poor sleep quality. PSQI general score was 5.94 ± 2.73. There were significantly differences in sleep quality in sex, majors and grades. The survey reported that women suffered worse sleep quality than that of men, and medical students suffered worse sleep quality than non-medical students. Meanwhile, it also found that freshmen had better sleep quality than that of sophomores and juniors, sophomores suffered worst sleep quality. The logistic regression analysis showed that bad physical condition (OR (Odds ratio): 2.971 (2.034∼4.339)) and smoking (OR: 1.754 (1.258∼2.446)) were associated with poor sleep quality in males. However, more factors associated with poor sleep quality among females were found, including noisy dormitory environment (OR: 2.025 (1.354-3.030)), skipping breakfast more times per week (OR: 1.332 (1.031∼1.721)), drinking coffee before sleep (OR: 2.111 (1.155∼3.861)), playing with mobile phones for more than 45 minutes before sleep (OR: 1.745 (1.210∼2.515)), more time spent playing games per day (OR: 1.347 (1.048∼1.730)), bad physical condition (OR: 2.507 (1.797-3.497)), and severe academic stress (OR: 1.561 (1.126-2.166)).ConclusionAbout half of college students experienced poor sleep, and poor sleep quality was prevalent in women, medical students, and sophomores. Moreover, there were more risk factors associated with the poor sleep quality of women than with men. Health policymakers should fully consider these factors in improving the sleep quality of college students. creator: Yanna Zhou creator: Shixing Bo creator: Sujian Ruan creator: Qingxue Dai creator: Yingkuan Tian creator: Xiuquan Shi uri: https://doi.org/10.7717/peerj.13833 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhou et al. title: Co-expression network analysis of genes and networks associated with wheat pistillody link: https://peerj.com/articles/13902 last-modified: 2022-08-24 description: Crop male sterility has great value in theoretical research and breeding application. HTS-1, whose stamens transformed into pistils or pistil-like structures, is an important male sterility material selecting from Chinese Spring three-pistil (CSTP) wheat. However the molecular mechanism of pistillody development in HTS-1 remains a mystery. RNA-seq data of 11 wheat tissues were obtained from the National Center for Biotechnology Information (NCBI), including the stamens of CSTP and the pistils and pistillodic stamen of HTS-1. The Salmon program was utilized to quantify the gene expression levels of the 11 wheat tissues; and gene quantification results were normalized by transcripts per million (TPM). In total, 58,576 genes were used to construct block-wise network by co-expression networks analysis (WGCNA) R package. We obtained all of modules significantly associated with the 11 wheat tissues. AgriGO V2.0 was used to do Gene Ontology (GO) enrichment analysis; and genes and transcription factors (TFs) in these significant modules about wheat pistillody development were identified from GO enrichment results. Basic local alignment search tool (BLAST) was used to align HTS-1 proteins with the published pistillody-related proteins and TFs. Genes about wheat pistillody development were analyzed and validated by qRT-PCR. The MEturquoise, MEsaddlebrown, MEplum, MEcoral1, MElightsteelblue1, and MEdarkslateblue modules were significantly corelated to pistillodic stamen (correlation p < 0.05). Moreover, 206 genes related to carpel development (GO:0048440) or gynoecium development (GO:0048467) were identified only in the MEturquoise module by Gene Ontology (GO) analysis, and 42 of 206 genes were hub genes in MEturquoise module. qRT-PCR results showed that 38 of the 42 hub genes had highly expressed in pistils and pistillodic stamens than in stamens. A total of 15 pistillody development-related proteins were validated by BLAST. Transcription factors (TFs) were also analyzed in the MEturquoise module, and 618 TFs were identified. In total, 56 TFs from 11 families were considered to regulate the development of pistillodic stamen. The co-expression network showed that six of HB and three of BES1 genes were identified in 42 hub genes. This indicated that TFs played important roles in wheat pistillody development. In addition, there were 11 of ethylene-related genes connected with TFs or hub genes, suggesting the important roles of ethylene-related genes in pistillody development. These results provide important insights into the molecular interactions underlying pistillody development. creator: Zhenyong Chen creator: Mingli Liao creator: Zaijun Yang creator: Weiying Chen creator: Shuhong Wei creator: Jian Zou creator: Zhengsong Peng uri: https://doi.org/10.7717/peerj.13902 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chen et al. title: Embedding the value of coastal ecosystem services into climate change adaptation planning link: https://peerj.com/articles/13463 last-modified: 2022-08-23 description: Coastal habitats, such as salt marshes and dune systems, can protect communities from hazards by reducing coastline exposure. However, these critical habitats and their diverse ecosystem services are threatened by coastal development and the impacts from a changing climate. Ever increasing pressure on coastal habitats calls for coastal climate adaptation efforts that mitigate or adapt to these pressures in ways that maintain the integrity of coastal landscapes. An important challenge for decisionmakers is determining the best mitigation and adaptation strategies that not only protect human lives and property, but also safeguard the ability of coastal habitats to provide a broad suite of benefits. Here, we present a potential pathway for local-scale climate change adaptation planning through the identification and mapping of natural habitats that provide the greatest benefits to coastal communities. The methodology coupled a coastal vulnerability model with a climate adaptation policy assessment in an effort to identify priority locations for nature-based solutions that reduce vulnerability of critical assets using feasible land-use policy methods. Our results demonstrate the critical role of natural habitats in providing the ecosystem service of coastal protection in California. We found that specific dune habitats play a key role in reducing erosion and inundation of the coastline and that several wetland areas help to absorb energy from storms and provide a protective service for the coast of Marin county, California, USA. Climate change and adaptation planning are globally relevant issues in which the scalability and transferability of solutions must be considered. This work outlines an iterative approach for climate adaptation planning at a local-scale, with opportunity to consider the scalability of an iterative science-policy engagement approach to regional, national, and international levels. creator: Lisa M. Wedding creator: Sarah Reiter creator: Monica Moritsch creator: Eric Hartge creator: Jesse Reiblich creator: Don Gourlie creator: Anne Guerry uri: https://doi.org/10.7717/peerj.13463 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wedding et al. title: Sperm quality of artificially matured shortfinned eel is not affected by human chorionic gonadotropin dose and route of administration link: https://peerj.com/articles/13742 last-modified: 2022-08-23 description: BackgroundAcquisition of high quality sperm is key to the artificial propagation of eels in captivity, but fertility drugs are expensive and repeated handling is stressful to the fish. An interrupted treatment regime (an initial hormone injection to stimulate spermatogenesis, followed several weeks later by weekly booster injections to induce sperm maturation) for acquisition of sperm in captive male eels has promise for high sperm quality on the one hand, and animal welfare benefits on the other. To further develop this approach for shortfinned eel, Anguilla australis, we evaluated the efficacy of (i) different initial doses of human chorionic gonadotropin (hCG) and (ii) route of administration.MethodsMale eels were artificially induced to mature with a single injection of 0, 250, 500 or 1,000 IU/fish of hCG, administered either intramuscularly (IM) or intraperitoneally (IP). Sperm maturation was induced with 150 IU hCG/fish from week 5 onwards and sperm collected for evaluation of quality by computer-assisted sperm analysis.ResultsControl males did not mature and hence, sperm could not be retrieved and analysed, but all other treatments were effective in inducing testicular maturation. Milt volume tended to be higher for fish injected IM compared to those injected IP, whereas hCG dose had no effect. Conversely, the concentration of spermatozoa tended to be higher for several sperm collection time points in IP-injected than in IM-injected fish. Sperm quality, represented by percent motility, percent progressive motility and curvilinear velocity, was equal in fish given an initial dose of 250 IU hCG to those given higher initial doses of hCG.ConclusionsWe recommend that an initial dose of 250 IU hCG/fish be administered to induce spermatogenesis in male A. australis, and, after a period of 4–5 weeks, weekly booster injections of ∼150 IU hCG/fish be administered in the day prior to sperm collection; both routes of administration (IM or IP) are equally effective. We contend that an interrupted treatment regime has notable benefits for induced maturation in male anguillids, as it reduces fish handling and manipulation and reduces the resources required to produce high quality sperm. creator: Sean L. Divers creator: Sheri L. Johnson creator: P. Mark Lokman uri: https://doi.org/10.7717/peerj.13742 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Divers et al. title: Accurate image-based identification of macroinvertebrate specimens using deep learning—How much training data is needed? link: https://peerj.com/articles/13837 last-modified: 2022-08-23 description: Image-based methods for species identification offer cost-efficient solutions for biomonitoring. This is particularly relevant for invertebrate studies, where bulk samples often represent insurmountable workloads for sorting, identifying, and counting individual specimens. On the other hand, image-based classification using deep learning tools have strict requirements for the amount of training data, which is often a limiting factor. Here, we examine how classification accuracy increases with the amount of training data using the BIODISCOVER imaging system constructed for image-based classification and biomass estimation of invertebrate specimens. We use a balanced dataset of 60 specimens of each of 16 taxa of freshwater macroinvertebrates to systematically quantify how classification performance of a convolutional neural network (CNN) increases for individual taxa and the overall community as the number of specimens used for training is increased. We show a striking 99.2% classification accuracy when the CNN (EfficientNet-B6) is trained on 50 specimens of each taxon, and also how the lower classification accuracy of models trained on less data is particularly evident for morphologically similar species placed within the same taxonomic order. Even with as little as 15 specimens used for training, classification accuracy reached 97%. Our results add to a recent body of literature showing the huge potential of image-based methods and deep learning for specimen-based research, and furthermore offers a perspective to future automatized approaches for deriving ecological data from bulk arthropod samples. creator: Toke T. Høye creator: Mads Dyrmann creator: Christian Kjær creator: Johnny Nielsen creator: Marianne Bruus creator: Cecilie L. Mielec creator: Maria S. Vesterdal creator: Kim Bjerge creator: Sigurd A. Madsen creator: Mads R. Jeppesen creator: Claus Melvad uri: https://doi.org/10.7717/peerj.13837 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Høye et al.