title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=728 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Association of toll-like receptors single nucleotide polymorphisms with HBV and HCV infection: research status link: https://peerj.com/articles/13335 last-modified: 2022-04-19 description: BackgroundHepatitis B virus (HBV) and hepatitis C virus (HCV) infections have become increasingly severe worldwide and are a threat to public health. There have been a number of studies conducted recently on the relationship of single nucleotide polymorphisms (SNPs) to innate immune receptor genes such as toll-like receptors (TLRs). Some literature suggests that SNPs of TLRs are associated with HBV and HCV infection. We summarized the role of TLRs gene polymorphisms associated with HBV and HCV infections and explored their possible mechanisms of action.MethodologyPubMed and Web of Science were used to perform the literature review. Related articles and references were identified and used to analyze the role of TLRs gene polymorphism in HBV and HCV infection.ResultsTLRs gene polymorphisms may have beneficial or detrimental effects in HBV and HCV infection, and some SNPs can affect disease progression or prognosis. They affect the disease state by altering gene expression or protein synthesis; however, the mechanism of action is not clearly understood.ConclusionsSingle nucleotide polymorphisms of TLRs play a role in HBV and HCV infection, but the mechanism of action still needs to be explored in future studies. creator: Yaxin Xu creator: Wentao Xue creator: Hongwei Gao creator: Jiabo Cui creator: Lingzhi Zhao creator: Chongge You uri: https://doi.org/10.7717/peerj.13335 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xu et al. title: Water stress and nitrogen supply affect floral traits and pollination of the white mustard, Sinapis alba (Brassicaceae) link: https://peerj.com/articles/13009 last-modified: 2022-04-18 description: Changes in environmental conditions are likely to have a complex effect on the growth of plants, their phenology, plant-pollinator interactions, and reproductive success. The current world is facing an ongoing climate change along with other human-induced environmental changes. Most research has focused on the impact of increasing temperature as a major driving force for climate change, but other factors may have important impacts on plant traits and pollination too and these effects may vary from season to season. In addition, it is likely that the effects of multiple environmental factors, such as increasing temperature, water availability, and nitrogen enrichment are not independent. Therefore, we tested the impact of two key factors—water, and nitrogen supply—on plant traits, pollination, and seed production in Sinapis alba (Brassicaceae) in three seasons defined as three temperature conditions with two levels of water and nitrogen supply in a factorial design. We collected data on multiple vegetative and floral traits and assessed the response of pollinators in the field. Additionally, we evaluated the effect of growing conditions on seed set in plants exposed to pollinators and in hand-pollinated plants. Our results show that water stress impaired vegetative growth, decreased flower production, and reduced visitation by pollinators and seed set, while high amount of nitrogen increased nectar production under low water availability in plants grown in the spring. Temperature modulated the effect of water and nitrogen availability on vegetative and floral traits and strongly affected flowering phenology and flower production. We demonstrated that changes in water and nitrogen availability alter plant vegetative and floral traits, which impacts flower visitation and consequently plant reproduction. We conclude that ongoing environmental changes such as increasing temperature, altered precipitation regimes and nitrogen enrichment may thus affect plant-pollinator interactions with negative consequences for the reproduction of wild plants and insect-pollinated crops. creator: Asma Akter creator: Jan Klečka uri: https://doi.org/10.7717/peerj.13009 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Akter and Klečka title: Concentration and quantification of Tilapia tilapinevirus from water using a simple iron flocculation coupled with probe-based RT-qPCR link: https://peerj.com/articles/13157 last-modified: 2022-04-18 description: BackgroundTilapia tilapinevirus, also known as tilapia lake virus (TiLV), is a significant virus that is responsible for the die-off of farmed tilapia across the globe. The detection and quantification of the virus using environmental RNA (eRNA) from pond water samples represents a potentially non-invasive and routine strategy for monitoring pathogens and early disease forecasting in aquaculture systems.MethodsHere, we report a simple iron flocculation method for concentrating viruses in water, together with a newly-developed hydrolysis probe quantitative RT-qPCR method for the detection and quantification of TiLV.ResultsThe RT-qPCR method designed to target a conserved region of the TiLV genome segment 9 has a detection limit of 10 viral copies per µL of template. The method had a 100% analytical specificity and sensitivity for TiLV. The optimized iron flocculation method was able to recover 16.11 ± 3.3% of the virus from water samples spiked with viral cultures. Tilapia and water samples were collected for use in the detection and quantification of TiLV disease during outbreaks in an open-caged river farming system and two earthen fish farms. TiLV was detected from both clinically sick and asymptomatic fish. Most importantly, the virus was successfully detected from water samples collected from different locations in the affected farms (i.e., river water samples from affected cages (8.50 × 103 to 2.79 × 105 copies/L) and fish-rearing water samples, sewage, and reservoir (4.29 × 103 to 3.53 × 104 copies/L)). By contrast, TiLV was not detected in fish or water samples collected from two farms that had previously experienced TiLV outbreaks and from one farm that had never experienced a TiLV outbreak. In summary, this study suggests that the eRNA detection system using iron flocculation, coupled with probe based-RT-qPCR, is feasible for use in the concentration and quantification of TiLV from water. This approach may be useful for the non-invasive monitoring of TiLV in tilapia aquaculture systems and may support evidence-based decisions on biosecurity interventions needed. creator: Suwimon Taengphu creator: Pattanapon Kayansamruaj creator: Yasuhiko Kawato creator: Jerome Delamare-Deboutteville creator: Chadag Vishnumurthy Mohan creator: Ha Thanh Dong creator: Saengchan Senapin uri: https://doi.org/10.7717/peerj.13157 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Taengphu et al. title: Differentiation patterns of emperor moths (Lepidoptera: Saturniidae: Saturniinae) of a continental island: divergent evolutionary history driven by Pleistocene glaciations link: https://peerj.com/articles/13240 last-modified: 2022-04-18 description: BackgroundOn the basis of molecular dating, Pleistocene glaciations have been proposed as the major driving force of biota speciation in the Palearctic and the pre-Quaternary origin of Amazonian taxa. However, the major driving factors in East Asia remain unclear. All 16 saturniine species inhabiting Taiwan with congeners of populations, subspecies, or species in East Asia constitute research objects for addressing the mode of speciation because of the repeated formation and disappearance of a landbridge from the Asian mainland to Taiwan during glacial cycles.MethodsThe genetic divergences of mitochondrial cytochrome c oxidase subunit I (COI) and 16S rDNA and the nuclear 28S rDNA of the saturniine species from Taiwan and the Asian mainland were assessed to determine the monophyly of each genus and species of Saturniinae. Moreover, 519 saturniine COI sequences of 114 taxa from adjacent East and Southeast Asian populations and closely related species were retrieved from GenBank and analyzed. The differentiation timing and possible origination of the insular saturniines were elucidated based on phylogenetic relationships, haplotype networks, and lineage calibrations.ResultsApproximately 90% of intraspecific COI divergence was <2%; all divergences exceeding 2% originated from comparisons between allopatric populations or subspecies. Relationship analyses revealed that multiple introductions likely occurred in insular saturniines and that some East Asian saturniines were paraphyletic as deduced by analyzing endemic insular species. Calibration dating revealed that Taiwanese endemic saturniines split from sibling Asian species 0.2–2.7 million years ago (Mya), whereas subspecific-level and population-level splitting events occurred 0.1–1.7 Mya and 0.2–1.2 Mya, respectively. Moreover, phylogenetic patterns combined with geographical distributions revealed that hill-distributed Taiwanese saturniines are closely related to those from southern China and Southeast Asia, whereas saturniines inhabiting altitudes higher than 1,500 m in Taiwan have siblings distributed in temperate Northeast Asia.DiscussionThe Global DNA Barcoding Initiative was successfully applied to study the population genetic structure in species. Most Formosan saturniines are distinct and monophyletic, reflecting the vicariant barrier of the Taiwan Strait; Pleistocene glacial cycles provided opportunities for insular saturniines to experience repeated isolation from and secondary contact with the continental mainland. Each insular saturniine may have evolved with a unique differentiation timing pattern that possibly emerged in the Early, Middle, or Late Pleistocene with these patterns differing from the consistent pattern that occurred in the temperate Palearctic and tropical Amazonian regions. Moreover, multiple migrations or artificial genetic admixtures may have also occurred, as suggested by the coexistence of two divergent lineages in a few Taiwanese saturniines. creator: Wen-Bin Yeh creator: Cheng-Lung Tsai creator: Thai-Hong Pham creator: Shipher Wu creator: Chia-Wei Chang creator: Hong-Minh Bui uri: https://doi.org/10.7717/peerj.13240 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yeh et al. title: Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris link: https://peerj.com/articles/13268 last-modified: 2022-04-18 description: BackgroundThe genus Calidris (Charadriiformes, Scolopacidae) includes shorebirds known as dunlin, knots, and sanderlings. The relationships between species nested within Calidris, including Eurynorynchus, Limicola and Aphriza, are not well-resolved.MethodsSamples were collected from Xiaoyangkou, Rudong County, Jiangsu Province, China. Mitogenomes were sequenced using the Illumina Novaseq 6000 platform for PE 2 × 150 bp sequencing, and then checked for PCR products. Protein-coding genes were determined using an Open Reading Frame Finder. tRNAscan-SE, MITOS, and ARWEN were used to confirm tRNA and rRNA annotations. Bioinformatic analyses were conducted using DnaSP 5.1 and MEGA X. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses.ResultsWe sequenced and annotated the mitogenome of five species and obtained four complete mitogenomes and one nearly complete mitogenome. Circular mitogenomes displayed moderate size variation, with a mean length of 16,747 bp, ranging from 16,642 to 16,791 bp. The mitogenome encoded a control region and a typical set of 37 genes containing two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. There were four start codons, four stop codons, and one incomplete stop codon (T–). The nucleotide composition was consistently AT-biased. The average uncorrected pairwise distances revealed heterogeneity in the evolutionary rate for each gene; the COIII had a slow evolutionary rate, whereas the ATP8 gene had a fast rate. dN/dS analysis indicated that the protein-coding genes were under purifying selection. The genetic distances between species showed that the greatest genetic distance was between Eurynorhynchus pygmeus and Limicola falcinellus (22.5%), and the shortest was between E. pygmeus and Calidris ruficollis (12.8%). Phylogenetic trees revealed that Calidris is not a monophyletic genus, as species from the genera Eurynorynchus and Limicola were nested within Calidris. The molecular data obtained in this study are valuable for research on the taxonomy, population genetics, and evolution of birds in the genus Calidris. creator: Wan Chen creator: Keer Miao creator: Junqi Wang creator: Hao Wang creator: Wan Sun creator: Sijia Yuan creator: Site Luo creator: Chaochao Hu creator: Qing Chang uri: https://doi.org/10.7717/peerj.13268 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen et al. title: Mitogenomics and phylogenetics of twelve species of African Saturniidae (Lepidoptera) link: https://peerj.com/articles/13275 last-modified: 2022-04-18 description: African Saturniidae (Lepidoptera) include numerous species consumed at the caterpillar stage throughout the continent, and their importance to local communities as a source of nutrition and seasonal income cannot be overestimated. However, baseline genetic data with utility for the characterization of their diversity, phylogeography and phylogenetic relationships have remained scarce compared to their Asian counterparts. To bridge this gap, we sequenced the mitochondrial genomes of 12 species found in southern Africa for comparative mitogenomics and phylogenetic reconstruction of the family, including the first representatives of the tribes Eochroini and Micragonini. Mitochondrial gene content and organization were conserved across all Saturniidae included in the analyses. The phylogenetic positions of the 12 species were assessed in the context of publicly available mitogenomes using Bayesian inference and maximum likelihood (ML) methods. The monophyly of the tribes Saturniini, Attacini, Bunaeini and Micragonini, the sister relationship between Saturniini and Attacini, and the placement of Eochroa trimenii and Rhodinia fugax in the tribes Eochroini and Attacini, respectively, were strongly supported. These results contribute to significantly expanding genetic data available for African Saturniidae and allow for the development of new mitochondrial markers in future studies. creator: Zwannda Nethavhani creator: Rieze Straeuli creator: Kayleigh Hiscock creator: Ruan Veldtman creator: Andrew Morton creator: Rolf G. Oberprieler creator: Barbara van Asch uri: https://doi.org/10.7717/peerj.13275 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nethavhani et al. title: How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships? link: https://peerj.com/articles/13285 last-modified: 2022-04-18 description: The Gastropoda contains 80% of existing mollusks and is the most diverse animal class second only to the Insecta. However, the deep phylogeny of gastropods has been controversial for a long time. Especially the position of Patellogastropoda is a major uncertainty. Morphology and some mitochondria studies concluded that Patellogastropoda is likely to be sister to all other gastropods (Orthogastropoda hypothesis), while transcriptomic and other mitogenomic studies indicated that Patellogastropoda and Vetigastropoda are sister taxa (Psilogastropoda). With the release of high-quality genomes, orthologous genes can be better identified and serve as powerful candidates for phylogenetic analysis. The question is, given the current limitations on the taxon sampling side, how many markers are needed to provide robust results. Here, we identified single-copy orthologous genes (SOGs) from 14 gastropods species with whole genomes available which cover five main gastropod subclasses. We generated different datasets from 395 to 1610 SOGs by allowing species missing in different levels. We constructed gene trees of each SOG, and inferred species trees from different collections of gene trees. We found as the number of SOGs increased, the inferred topology changed from Patellogastropoda being sister to all other gastropods to Patellogastropoda being sister to Vetigastropoda + Neomphalina (Psilogastropoda s.l.), with considerable support. Our study thus rejects the Orthogastropoda concept showing that the selection of the representative species and use of sufficient informative sites greatly influence the analysis of deep gastropod phylogeny. creator: Zeyuan Chen creator: Michael Schrödl uri: https://doi.org/10.7717/peerj.13285 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Chen and Schrödl title: Phenotypic variation of Chitala chitala (Hamilton, 1822) from Indian rivers using truss network and geometric morphometrics link: https://peerj.com/articles/13290 last-modified: 2022-04-18 description: Chitala chitala (Hamilton, 1822) is an economically important food fish species occurring throughout Indian rivers, which also has ornamental value. This study focuses on morphological variations in C. chitala from seven river basins across India namely; Son, Tons, Ken, Brahmaputra, Ganga, Gomti and Gandak. A truss network was constructed by interconnecting nine landmarks to generate 36 morphometric variables extracted from digital images of specimens sampled from the study locations. Transformed truss measurements were subjected to principal component analysis (PCA), canonical discriminant function analysis (CDFA) and discriminant analyses of principal components (DAPC). DAPC function coefficients performed much better in capturing the variation pattern and discrimination between the rivers which was not achieved using CDFA. Eight truss variables were identified with significant and highest loading for truss variables on principal components and coefficients on discriminant function from DAPC contributing to maximum variation between the rivers. Performance graph and functional distribution of identified truss variables clearly indicated distinction between the rivers. Thin plate spline analysis and procrustes shape analysis further showed the variation in morphology between specimens across the rivers. The significant parameters differentiating specimens from different rivers were linked to dorsal fin origin, the base of the pectoral fin and the perpendicular point on the anal fin from the dorsal fin origin. Variation in the hydrodynamics of the rivers studied might be possibly affecting the fin kinematics and consequently leading to adaption seen as phenotypic variation in C. chitala. The results showcased in the present study shall help in better understanding of intra-specific diversity which is significant for management and conservation of a species. creator: Rejani Chandran creator: Achal Singh creator: Rajeev K. Singh creator: Sangeeta Mandal creator: Kantharajan Ganesan creator: Priyanka Sah creator: Pradipta Paul creator: Abhinav Pathak creator: Nimisha Dutta creator: Ramashankar Sah creator: Kuldeep K. Lal creator: Vindhya Mohindra uri: https://doi.org/10.7717/peerj.13290 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Chandran et al. title: The sterile insect technique is protected from evolution of mate discrimination link: https://peerj.com/articles/13301 last-modified: 2022-04-18 description: BackgroundThe sterile insect technique (SIT) has been used to suppress and even extinguish pest insect populations. The method involves releasing artificially reared insects (usually males) that, when mating with wild individuals, sterilize the broods. If administered on a large enough scale, the sterility can collapse the population. Precedents from other forms of population suppression, especially chemicals, raise the possibility of resistance evolving against the SIT. Here, we consider resistance in the form of evolution of female discrimination to avoid mating with sterile males. Is resistance evolution expected?MethodsWe offer mathematical models to consider the dynamics of this process. Most of our models assume a constant-release protocol, in which the same density of males is released every generation, regardless of wild male density. A few models instead assume proportional release, in which sterile releases are adjusted to be a constant proportion of wild males.ResultsWe generally find that the evolution of female discrimination, although favored by selection, will often be too slow to halt population collapse when a constant-release implementation of the SIT is applied appropriately and continually. The accelerating efficacy of sterile males in dominating matings as the population collapses works equally against discriminating females as against non-discriminating females, and rare genes for discrimination are too slow to ascend to prevent the loss of females that discriminate. Even when migration from source populations sustains the treated population, continued application of the SIT can prevent evolution of discrimination. However, periodic premature cessation of the SIT does allow discrimination to evolve. Likewise, use of a ‘proportional-release’ protocol is also prone to escape from extinction if discriminating genotypes exist in the population, even if those genotypes are initially rare. Overall, the SIT is robust against the evolution of mate discrimination provided care is taken to avoid some basic pitfalls. The models here provide insight for designing programs to avoid those pitfalls. creator: James J. Bull creator: Richard Gomulkiewicz uri: https://doi.org/10.7717/peerj.13301 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Bull and Gomulkiewicz title: Differences in lower limb muscle activation between global and selective instability devices in single-leg stance in healthy active subjects link: https://peerj.com/articles/13317 last-modified: 2022-04-18 description: BackgroundBalance and strength training are frequent strategies to address lower limb injuries, including ankle injuries, which are usually performed in single-leg stance on global instability devices, producing generalized muscular activation of the lower limb. In this context, new specific instability devices arise from the need to selectively work the ankle, specifically the peroneus longus. This study aimed to compare the EMG muscle activation of the peroneus longus, as well as other lower limbs muscles, in a single-leg stance on different balance training devices (BOSU, wobble board, power board, and Blackboard) in standing or squatting positions.MethodsTwenty healthy recreationally trained subjects participated in the study. Subjects performed three repetitions of 15 s (one for familiarization and two for measurement) in standing and squatting positions on the floor, BOSU, wobble board, power board, and Blackboard. Surface electromyography (EMG) was used to record activity of the peroneus longus, soleus, gastrocnemius medialis, tibialis anterior, rectus femoris, and gluteus maximus.ResultsThe main outcome was that no differences were found for the peroneus longus normalized EMG, neither between devices (p = 0.09) nor between conditions (p = 0.11), nor in the interaction between them (p = 0.16). For the normalized EMG of the other muscles, there were multiple differences between devices and conditions. Of the devices studied, the Blackboard was the one that implied a lower activation of the lower limb muscles and a lower degree of instability, activating the peroneus longus similarly to global instability devices. The BOSU and wobble board achieved high levels of EMG muscle activation for most muscles of the lower limbs. Therefore, they should be considered as potential devices for work in highly unstable conditions or when high activation levels are sought. creator: Mariana Sánchez-Barbadora creator: Alba Cuerda-Del Pino creator: Javier González-Rosalén creator: Noemi Moreno-Segura creator: Adrian Escriche-Escuder creator: Rodrigo Martín-San Agustín uri: https://doi.org/10.7717/peerj.13317 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sánchez-Barbadora et al.