title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=810 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Adding pieces to the puzzle: insights into diversity and distribution patterns of Cumacea (Crustacea: Peracarida) from the deep North Atlantic to the Arctic Ocean link: https://peerj.com/articles/12379 last-modified: 2021-11-11 description: The Nordic Seas have one of the highest water-mass diversities in the world, yet large knowledge gaps exist in biodiversity structure and biogeographical distribution patterns of the deep macrobenthic fauna. This study focuses on the marine bottom-dwelling peracarid crustacean taxon Cumacea from northern waters, using a combined approach of morphological and molecular techniques to present one of the first insights into genetic variability of this taxon. In total, 947 specimens were assigned to 77 morphologically differing species, representing all seven known families from the North Atlantic. A total of 131 specimens were studied genetically (16S rRNA) and divided into 53 putative species by species delimitation methods (GMYC and ABGD). In most cases, morphological and molecular-genetic delimitation was fully congruent, highlighting the overall success and high quality of both approaches. Differences were due to eight instances resulting in either ecologically driven morphological diversification of species or morphologically cryptic species, uncovering hidden diversity. An interspecific genetic distance of at least 8% was observed with a clear barcoding gap for molecular delimitation of cumacean species. Combining these findings with data from public databases and specimens collected during different international expeditions revealed a change in the composition of taxa from a Northern Atlantic-boreal to an Arctic community. The Greenland-Iceland-Scotland-Ridge (GIS-Ridge) acts as a geographical barrier and/or predominate water masses correspond well with cumacean taxa dominance. A closer investigation on species level revealed occurrences across multiple ecoregions or patchy distributions within defined ecoregions. creator: Carolin Uhlir creator: Martin Schwentner creator: Kenneth Meland creator: Jon Anders Kongsrud creator: Henrik Glenner creator: Angelika Brandt creator: Ralf Thiel creator: Jörundur Svavarsson creator: Anne-Nina Lörz creator: Saskia Brix uri: https://doi.org/10.7717/peerj.12379 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Uhlir et al. title: Temperature-induced changes in egg white antimicrobial concentrations during pre-incubation do not influence bacterial trans-shell penetration but do affect hatchling phenotype in Mallards link: https://peerj.com/articles/12401 last-modified: 2021-11-11 description: Microbiome formation and assemblage are essential processes influencing proper embryonal and early-life development in neonates. In birds, transmission of microbes from the outer environment into the egg’s interior has been found to shape embryo viability and hatchling phenotype. However, microbial transmission may be affected by egg-white antimicrobial proteins (AMPs), whose concentration and antimicrobial action are temperature-modulated. As both partial incubation and clutch covering with nest-lining feathers during the pre-incubation period can significantly alter temperature conditions acting on eggs, we experimentally investigated the effects of these behavioural mechanisms on concentrations of both the primary and most abundant egg-white AMPs (lysozyme and avidin) using mallard (Anas platyrhychos) eggs. In addition, we assessed whether concentrations of egg-white AMPs altered the probability and intensity of bacterial trans-shell penetration, thereby affecting hatchling morphological traits in vivo. We observed higher concentrations of lysozyme in partially incubated eggs. Clutch covering with nest-lining feathers had no effect on egg-white AMP concentration and we observed no association between concentration of egg-white lysozyme and avidin with either the probability or intensity of bacterial trans-shell penetration. The higher egg-white lysozyme concentration was associated with decreased scaled body mass index of hatchlings. These outcomes demonstrate that incubation prior to clutch completion in precocial birds can alter concentrations of particular egg-white AMPs, though with no effect on bacterial transmission into the egg in vivo. Furthermore, a higher egg white lysozyme concentration compromised hatchling body condition, suggesting a potential growth-regulating role of lysozyme during embryogenesis in precocial birds. creator: Jana Svobodová creator: Jakub Kreisinger creator: Veronika Gvoždíková Javůrková uri: https://doi.org/10.7717/peerj.12401 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Svobodová et al. title: Habitat connectivity and resource selection in an expanding bobcat (Lynx rufus) population link: https://peerj.com/articles/12460 last-modified: 2021-11-11 description: Terrestrial carnivores are among the most imperiled species worldwide, yet some species are resilient and are recovering in human-dominated landscapes after decades or centuries of absence. Bobcat (Lynx rufus) populations were extirpated from much of Midwestern US in the mid-1800’s, and are currently expanding and recolonizing their former range. In this study, we investigated multi-scale habitat selection for Ohio’s expanding bobcat population, and examined habitat connectivity in order to evaluate the conduits for dispersal statewide. We used citizen observations collected between 1978 and 2019 and logistic regression to evaluate population-level habitat selection, and GPS telemetry data for 20 individuals collected between 2012 and 2014 and a distribution-weighted exponential Resource Selection Function to evaluate individual-level habitat selection within home ranges. At the population level, bobcats selected for higher amounts of forest and pasture (at a 50 km2 scale) and herbaceous vegetation (at 15–50 50 km2 scales), thus overall heterogeneous forested habitat. At individual (home range) level, bobcats selected for forested habitats with low road density and farther away from high traffic roads; they also showed weak selection for open habitat at the home range level. Male home ranges were significantly greater than female home ranges. Lastly, we used the population-level spatial outputs (i.e. habitat suitability map) to parameterize habitat connectivity models using circuit theory in the program Circuitscape. We tested three relationships between habitat suitability and resistance to movement and used a subset of data on potential dispersing individuals to evaluate which relationship performed best. All three relationships performed almost equally well, and we calculated a weighted averaged connectivity map as our final map. Habitat was highly permeable to movements between core areas of two genetically distinct subpopulations located in southeastern Ohio. We also identified potential dispersal corridors from the core areas to other regions of Ohio dominated by agriculture and suburban development via forested riparian corridors. Overall, our analysis offers new information on habitat selection and connectivity in a rebounding felid population and offers important ecological information for wildlife management strategies. We recommend that the suitability and connectivity models should be periodically updated until the population reaches an equilibrium, and be integrated with data from neighboring states for a comprehensive assessment of a conservation success story. creator: Viorel D. Popescu creator: Madeline Kenyon creator: Ryan K. Brown creator: Marissa A. Dyck creator: Suzanne Prange creator: William E. Peterman creator: Catherine Dennison uri: https://doi.org/10.7717/peerj.12460 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Popescu et al. title: Environmental changes in Yellow River Delta with terrace construction and agricultural cropping link: https://peerj.com/articles/12469 last-modified: 2021-11-11 description: BackgroundCrude flats in delta areas are often saline–alkaline and unsuitable for agricultural cropping. In the 1990s, people residing in the Yellow River delta constructed terraces on the flats for agricultural development. Herein, we investigated environmental changes resulting from this agricultural development and evaluated whether the current land use is effective and sustainable.MethodsWe sampled soil and weeds from croplands, terrace slopes, and crude flats within the delta terrace landscape. The measured soil properties included soil salinity, pH, total N, total P, and organic matter in different lands and soil layers: 0–10, 10–20, and 20–30 cm. The surveyed weed characteristics were the biomass of roots and rhizomes, species composition, life form, cover and height. These indices were statistically verified by different land types and soil layers.ResultsSoil salinity in the terrace crop lands was found to have reduced to <4 g·kg−1, whereas in the crude flats, remained >6 g·kg−1. Soil pH in the terrace croplands was surprisingly increased to >9 ; meanwhile, organic matter content decreased drastically, which is significantly different from that observed in the case of terrace slopes and crude flats. Total N and P content in the terrace crop lands were seemingly unchanged on averages but at the depths >20 cm, they reduced unavoidably. Plant underground organs were relatively scarcer in the croplands than in the other lands. Weeds grew well on the terrace slopes but were insufficient in the croplands. Overall, terrace construction is effective for developing coastal saline flats for agricultural use, but the traditional land use in the Yellow River delta has caused chronic soil degradation that is against a sustainable productive industry. creator: Dongxiao He creator: Jianmin Chu creator: Hongxiao Yang uri: https://doi.org/10.7717/peerj.12469 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 He et al. title: Lower limb kinetic comparisons between the chasse step and one step footwork during stroke play in table tennis link: https://peerj.com/articles/12481 last-modified: 2021-11-11 description: BackgroundBiomechanical footwork research during table tennis performance has been the subject of much interest players and exercise scientists. The purpose of this study was to investigate the lower limb kinetic characteristics of the chasse step and one step footwork during stroke play using traditional discrete analysis and one-dimensional statistical parameter mapping.MethodsTwelve national level 1 table tennis players (Height: 172 ± 3.80 cm, Weight: 69 ± 6.22 kg, Age: 22 ± 1.66 years, Experience: 11 ± 1.71 year) from Ningbo University volunteered to participate in the study. The kinetic data of the dominant leg during the chasse step and one step backward phase (BP) and forward phase (FP) was recorded by instrumented insole systems and a force platform. Paired sample T tests were used to analyze maximum plantar force, peak pressure of each plantar region, the force time integral and the pressure time integral. For SPM analysis, the plantar force time series curves were marked as a 100% process. A paired-samples T-test in MATLAB was used to analyze differences in plantar force.ResultsOne step produced a greater plantar force than the chasse step during 6.92–11.22% BP (P = 0.039). The chasse step produced a greater plantar force than one step during 53.47–99.01% BP (P < 0.001). During the FP, the chasse step showed a greater plantar force than the one step in 21.06–84.06% (P < 0.001). The one step produced a higher maximum plantar force in the BP (P = 0.032) and a lower maximum plantar force in the FP (P = 0) compared with the chasse step. The one step produced greater peak pressure in the medial rearfoot (P = 0) , lateral rearfoot (P = 0) and lateral forefoot (P = 0.042) regions than the chasse step during BP. In FP, the chasse step showed a greater peak pressure in the Toe (P = 0) than the one step. The one step had a lower force time integral (P = 0) and greater pressure time integral (P = 0) than the chasse step in BP, and the chasse step produced a greater force time integral (P = 0) and pressure time integral (P = 0.001) than the one step in the FP.ConclusionThe findings indicate that athletes can enhance plantarflexion function resulting in greater weight transfer, facilitating a greater momentum during the 21.06–84.06% of FP. This is in addition to reducing the load on the dominant leg during landing by utilizing a buffering strategy. Further to this, consideration is needed to enhance the cushioning capacity of the sole heel and the stiffness of the toe area. creator: Yuqi He creator: Dong Sun creator: Xiaoyi Yang creator: Gusztáv Fekete creator: Julien S. Baker creator: Yaodong Gu uri: https://doi.org/10.7717/peerj.12481 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 He et al. title: Current state of infection and prevalence of giardiasis in Malaysia: a review of 20 years of research link: https://peerj.com/articles/12483 last-modified: 2021-11-11 description: BackgroundGiardiasis is a neglected parasitic zoonotic disease caused by Giardia duodenalis that is often overlooked despite the damage inflicted upon humans and domestic/wild animals. Lack of surveillance studies, low sensitivity of diagnostic tools, and resistance to giardiasis treatment add to the challenge in managing giardiasis, leaving a gap that continues to render giardiasis a silent threat to public health worldwide. This situation is not much different in Malaysia, where giardiasis remains a public health problem, especially in the indigenous communities. Realizing the existence of gaps in the literature and information on giardiasis in Malaysia, this review aims to revisit and update the situation of giardiasis in Malaysia based on articles published in 20 years from 2000 to 2020, providing estimates on the incidence of giardiasis in humans, animals, and the environment, which may inform efforts to prevent and control the impact of giardiasis in the country.MethodologyWe searched PubMed, Science Direct, and Scopus using MeSH terms and text keywords “Giardia duodenalis OR Giardia intestinalis OR Giardia lamblia OR intestinal protozoa AND Malaysia”. Information was collected from all giardiasis reports published between 2000 and 2020.ResultsGiardiasis in Malaysia is more prevalent among the poorest segments of the population, namely the indigenous communities and people living in densely populated areas such as slums and prisons, due to low standard of personal hygiene, unsafe water resources, and improper sanitation. While the prevalence data is hugely dependent on microscopic fecal examination in epidemiological studies of giardiasis, current studies mostly focused on species identification and genotype distribution by multilocus genotyping. Thus far, the outbreak of giardiasis has not been reported in the country, but the disease was found to be significantly associated with stunting, wasting, and malnutrition among children of the indigenous communities. Surveillance studies also discovered the simultaneous presence of Giardia in the animal-environments, including wild animals, ruminants, and treated and untreated water. The data collected here will be a useful addition to the literature body on giardiasis in Malaysia, which can be exploited in efforts to prevent and control the impact of giardiasis in the country.ConclusionsThe last 10 years have shown that the overall mean rate of giardiasis in Malaysia is quite encouraging at 13.7%. While this figure appears to be declining, there has been a slight increase in the prevalence of underweight, stunting, and wasting among rural children in 2019. The fact that giardiasis is linked to long-term childhood developmental problems, indicates that addressing and providing better disease control against giardiasis should be a priority in supporting the national agenda to achieve Malaysia Global Nutrition Targets by 2025. creator: Norhamizah Roshidi creator: Nur Hassanah Mohd Hassan creator: Asma Abdul Hadi creator: Norsyahida Arifin uri: https://doi.org/10.7717/peerj.12483 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Roshidi et al. title: Transcriptome analysis and functional identification of GmMYB46 in soybean seedlings under salt stress link: https://peerj.com/articles/12492 last-modified: 2021-11-11 description: Salinity is one of the major abiotic stress that limits crop growth and productivity. We investigated the transcriptomes of salt-treated soybean seedlings versus a control using RNA-seq to better understand the molecular mechanisms of the soybean (Glycine max L.) response to salt stress. Transcriptome analysis revealed 1,235 differentially expressed genes (DEGs) under salt stress. Several important pathways and key candidate genes were identified by KEGG enrichment. A total of 116 differentially expressed transcription factors (TFs) were identified, and 17 TFs were found to belong to MYB families. Phylogenetic analysis revealed that these TFs may be involved in salt stress adaptation. Further analysis revealed that GmMYB46 was up-regulated by salt and mannitol and was localized in the nucleus. The salt tolerance of transgenic Arabidopsis overexpressing GmMYB46 was significantly enhanced compared to wild-type (WT). GmMYB46 activates the expression of salt stress response genes (P5CS1, SOD, POD, NCED3) in Arabidopsis under salt stress, indicating that the GmMYB46 protein mediates the salt stress response through complex regulatory mechanisms. This study provides information with which to better understand the molecular mechanism of salt tolerance in soybeans and to genetically improve the crop. creator: Xun Liu creator: Xinxia Yang creator: Bin Zhang uri: https://doi.org/10.7717/peerj.12492 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Liu et al. title: Genetic diversity of ‘Very Important Pharmacogenes’ in two South-Asian populations link: https://peerj.com/articles/12294 last-modified: 2021-11-10 description: ObjectivesReliable identification of population-specific variants is important for building the single nucleotide polymorphism (SNP) profile. In this study, genomic variation using allele frequency differences of pharmacologically important genes for Gujarati Indians in Houston (GIH) and Indian Telugu in the U.K. (ITU) from the 1000 Genomes Project vis-à-vis global population data was studied to understand its role in drug response.MethodsJoint genotyping approach was used to derive variants of GIH and ITU independently. SNPs of both these populations with significant allele frequency variation (minor allele frequency ≥ 0.05) with super-populations from the 1000 Genomes Project and gnomAD based on Chi-square distribution with p-value of ≤ 0.05 and Bonferroni’s multiple adjustment tests were identified. Population stratification and fixation index analysis was carried out to understand genetic differentiation. Functional annotation of variants was carried out using SnpEff, VEP and CADD score.ResultsPopulation stratification of VIP genes revealed four clusters viz., single cluster of GIH and ITU, one cluster each of East Asian, European, African populations and Admixed American was found to be admixed. A total of 13 SNPs belonging to ten pharmacogenes were identified to have significant allele frequency variation in both GIH and ITU populations as compared to one or more super-populations. These SNPs belong to VKORC1 (rs17708472, rs2359612, rs8050894) involved in Vitamin K cycle, cytochrome P450 isoforms CYP2C9 (rs1057910), CYP2B6 (rs3211371), CYP2A2 (rs4646425) and CYP2A4 (rs4646440); ATP-binding cassette (ABC) transporter ABCB1 (rs12720067), DPYD1 (rs12119882, rs56160474) involved in pyrimidine metabolism, methyltransferase COMT (rs9332377) and transcriptional factor NR1I2 (rs6785049). SNPs rs1544410 (VDR), rs2725264 (ABCG2), rs5215 and rs5219 (KCNJ11) share high fixation index (≥ 0.5) with either EAS/AFR populations. Missense variants rs1057910 (CYP2C9), rs1801028 (DRD2) and rs1138272 (GSTP1), rs116855232 (NUDT15); intronic variants rs1131341 (NQO1) and rs115349832 (DPYD) are identified to be ‘deleterious’.ConclusionsAnalysis of SNPs pertaining to pharmacogenes in GIH and ITU populations using population structure, fixation index and allele frequency variation provides a premise for understanding the role of genetic diversity in drug response in Asian Indians. creator: Neeraj Bharti creator: Ruma Banerjee creator: Archana Achalere creator: Sunitha Manjari Kasibhatla creator: Rajendra Joshi uri: https://doi.org/10.7717/peerj.12294 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Bharti et al. title: Polygamous breeding system identified in the distylous genus Psychotria: P. manillensis in the Ryukyu archipelago, Japan link: https://peerj.com/articles/12318 last-modified: 2021-11-10 description: Distyly is a genetic polymorphism composed of long-and short-styled flowers in a population. The evolutionary breakdown of distyly has been reported in many taxa, and mainly involves a shift toward monomorphism or dioecism. However, a shift toward monoecism has not been reported in distylous species. Psychotria (Rubiaceae), one of the world largest genera, consists of distylous species and their derivatives. In our preliminary study, however, we identified some monoecious individuals in a population of Psychotria manillensis. To understand the breeding system and reproductive biology of P. manillensis, we investigated floral traits, open fruit set, and flower visitors, and performed hand pollination and bagging experiments in five populations of Okinawa and Iriomote islands, Ryukyu Islands, Japan. The populations of P. manillensis were composed mainly of monoecious individuals (54%), followed by female (30%), male (14%), and hermaphroditic (2%) individuals at the time of flower collection. Of the collected flowers, 93% were functionally unisexual (male or female), whereas only 6.5% were perfect (hermaphroditic). However, some individuals changed sex mainly towards increasing femaleness during the flowering period. Moreover, 35% of the studied plants changed their sexual expression over the years. P. manillensis showed self-compatibility and no agamospermy. The fruit set under open pollination varied among populations and years (1.8–21.9%), but it was significantly higher than that of auto-selfing (0.68–1.56%). Wasps and flies were the main flower visitors and probably the main pollinators of the species. In conclusion, P. manillensis was revealed to be polygamous, involving monoecious, female, male, and hermaphroditic individuals. This is the first report of the polygamous breeding system not only in the genus Psychotria, but also in all heterostylous taxa. creator: Kenta Watanabe creator: Akira Shimizu creator: Takashi Sugawara uri: https://doi.org/10.7717/peerj.12318 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Watanabe et al. title: Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata link: https://peerj.com/articles/12335 last-modified: 2021-11-10 description: BackgroundCorals, which form the foundation of biodiverse reef ecosystems, are under threat from warming oceans. Reefs provide essential ecological services, including food, income from tourism, nutrient cycling, waste removal, and the absorption of wave energy to mitigate erosion. Here, we studied the coral thermal stress response using network methods to analyze transcriptomic and polar metabolomic data generated from the Hawaiian rice coral Montipora capitata. Coral nubbins were exposed to ambient or thermal stress conditions over a 5-week period, coinciding with a mass spawning event of this species. The major goal of our study was to expand the inventory of thermal stress-related genes and metabolites present in M. capitata and to study gene-metabolite interactions. These interactions provide the foundation for functional or genetic analysis of key coral genes as well as provide potentially diagnostic markers of pre-bleaching stress. A secondary goal of our study was to analyze the accumulation of sex hormones prior to and during mass spawning to understand how thermal stress may impact reproductive success in M. capitata.MethodsM. capitata was exposed to thermal stress during its spawning cycle over the course of 5 weeks, during which time transcriptomic and polar metabolomic data were collected. We analyzed these data streams individually, and then integrated both data sets using MAGI (Metabolite Annotation and Gene Integration) to investigate molecular transitions and biochemical reactions.ResultsOur results reveal the complexity of the thermal stress phenome in M. capitata, which includes many genes involved in redox regulation, biomineralization, and reproduction. The size and number of modules in the gene co-expression networks expanded from the initial stress response to the onset of bleaching. The later stages involved the suppression of metabolite transport by the coral host, including a variety of sodium-coupled transporters and a putative ammonium transporter, possibly as a response to reduction in algal productivity. The gene-metabolite integration data suggest that thermal treatment results in the activation of animal redox stress pathways involved in quenching molecular oxygen to prevent an overabundance of reactive oxygen species. Lastly, evidence that thermal stress affects reproductive activity was provided by the downregulation of CYP-like genes and the irregular production of sex hormones during the mass spawning cycle. Overall, redox regulation and metabolite transport are key components of the coral animal thermal stress phenome. Mass spawning was highly attenuated under thermal stress, suggesting that global climate change may negatively impact reproductive behavior in this species. creator: Amanda Williams creator: Jananan S. Pathmanathan creator: Timothy G. Stephens creator: Xiaoyang Su creator: Eric N. Chiles creator: Dennis Conetta creator: Hollie M. Putnam creator: Debashish Bhattacharya uri: https://doi.org/10.7717/peerj.12335 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Williams et al.