title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=181 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Demography and homing behavior in the poorly-known Philippine flat-headed frog Barbourula busuangensis (Anura: Bombinatoridae) link: https://peerj.com/articles/18694 last-modified: 2025-01-14 description: The flat-headed frog, Barbourula busuangensis, is a poorly known, riverine species, endemic to the province of Palawan in the Philippines. We applied capture-mark-recapture (CMR) methods to follow individuals at two sites (Malbato and San Rafael) in the island of Busuanga over 10 months in 2022–2023. We used passive internal transponders (PITs) to mark adult and subadults and single-colored visual internal elastomers (VIEs) for cohorts of juveniles. From a total of 196 frogs PIT-tagged in Malbato and 144 in San Rafael, we obtained overall recapture rates of 49% and 60% respectively. We used the POPAN formulation in MARK software to estimate abundance, survival, movement, and age-class demographics. Our best model estimated an average population size of 268 frogs at Malbato and 232 at San Rafael, and constant survival probabilities (mean ≥ 0.97) at both sites. When adding age classes to the model, abundance of adults was always higher than that of subadults producing an age structure dominated by adults at both sites. Growth rates decreased significantly with body size, being higher in juveniles (1.51 mm/month) and subadults (1.56 mm/month) than in adult frogs (0.60 mm/month). At these growth rates frogs may reach adulthood at 2.5 years, with the oldest individuals likely being over 11 years old. CMR data confirmed site fidelity, and translocation experiments revealed that frogs have the ability to home when displaced 10–50 m upstream and downstream from their original capture site. This is the first long-term study of B. busuangensis using robust field and analysis methods. Our data suggest that B. busuangensis is stable at present in Busuanga, with long-lived adults and dispersing subadults. We expect that these data may serve as baseline of current population abundance, age structure and growth rates which are factors that tend to be affected when species are threatened. In this way it may help researchers and conservation practitioners detect potential changes that may occur as this species confronts the challenges of the Anthropocene. creator: Marta Miñarro creator: Patricia Burrowes creator: Claudia Lansac creator: Gregorio Sánchez-Montes creator: Leticia E. Afuang creator: Ignacio De la Riva uri: https://doi.org/10.7717/peerj.18694 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Miñarro et al. title: Acaricidal and insecticidal activities of entomopathogenic nematodes combined with rosemary essential oil and bacterium-synthesized silver nanoparticles against camel tick, Hyalomma dromedarii and wax moth, Galleria mellonella link: https://peerj.com/articles/18782 last-modified: 2025-01-14 description: An innovative approach to ticks and insect pests management is necessary to mitigate the challenges posed by the indiscriminate use of chemical pesticides, which can lead to resistance development and environmental pollution. Despite their great potential, biological control agents have significant manufacturing, application, and stability limitations. Currently, using phytochemicals, biosynthesized nanoparticles, and bioagents to get rid of arthropods might be a good alternative that would make farmers less worried about residues and resistance. The present investigation was carried out to determine for the first time the in vitro acaricidal and insecticidal efficacies of endogenous two entomopathogenic nematodes (EPNs), Heterorhabditis indica and Steinernema sp. combined with either Proteus mirabilis-synthesized silver nanoparticles or Rosmarinus officinalis essential oil against the camel tick, Hyalomma dromedarii larvae and females, and greater wax moth, Galleria mellonella larvae as well. We also determined the potential effects of these treatments on the biological characteristics of H. dromedarii’s engorged females. We further investigated R. officinalis essential oil (EO) profiling and nanoparticle (AgNPs) characterization. All the evaluated combinations demonstrated synergistic effects on the larvae of G. mellonella and H. dromedarii, as well as on engorged females. When H. indica was mixed with EO or AgNPs, it worked well than when Steinernema sp. was mixed with EO or AgNPs. This was shown by the highest number of tick and insect mortalities and the lowest lethal concentration (LC50) values. One day after G. mellonella was exposed to H. indica (1,000 infective juveniles (IJs)) together with EO at 60 or 40 mg/mL, all tested individuals died. We obtained the same results when H. dromedarii females exposed to the same level of EPN with 60 mg/mL EO, and when H. dromedarii larvae treated with H. indica at 500 IJs + EO at 25 mg/mL. Treatments altered all biological parameters of engorged females, revealing extremely noticeable differences between the treated and untreated groups. Gas chromatography–mass spectrometry (GC-MS) analysis identified a total of 28 compounds in the R. officinalis EO. Visual observation showed a color change from yellow to dark brown for AgNPs biosynthesized from P. mirabilis; the transmission electron microscopy (TEM) image and ultraviolet–visible (UV-Vis) spectrum showed well-dispersed particles with a diameter of 5–45 nm; and the greatest surface plasmon peaked at 320 nm. The results demonstrated the high efficacy of combining EPN, H. indica, with EO to control tick and insect pests. This is due to its acaricidal activity on different stages of H. dromedarii, including larvae and engorged females, and its larvicidal effect on G. mellonella. creator: Bander Albogami creator: Hadeer Darwish creator: Akram Alghamdi creator: Ahmed BahaaEldin Darwish creator: Wafa Mohammed Al-Otaibi creator: Mohamed A. Osman creator: Zamzam M. Al Dhafar creator: Abeer Mousa Alkhaibari creator: Abadi M. Mashlawi creator: Fadi Baakdah creator: Ahmed Noureldeen uri: https://doi.org/10.7717/peerj.18782 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Albogami et al. title: Benchmarking of a time-saving and scalable protocol for the extraction of DNA from diverse viromes link: https://peerj.com/articles/18785 last-modified: 2025-01-14 description: The virome, composed of viruses inhabiting diverse ecosystems, significantly influences microbial community dynamics and host health. The phenol-chloroform DNA extraction protocol for viromes, though effective, is time-intensive and requires the use of multiple toxic chemicals. This study introduces a streamlined, scalable protocol for DNA extraction using a commercially-available kit as an alternative, assessing its performance against the phenol-chloroform method across human fecal, mouse fecal, and soil samples. No significant differences in virome diversity or community composition were seen between methods. Most viral operational taxonomic units (vOTUs) were common to both methods, with only a small percentage unique to either approach. Alpha- and beta-diversity analyses showed no significant impact of the extraction method on virome composition, confirming the kit’s efficacy and versatility on sample types beyond those officially supported by the manufacturer. While the kit approach offers benefits like reduced toxicity and increased throughput, it has limitations such as higher costs and potential issues reliably capturing low-abundance taxa. This protocol provides a viable option for large-scale virome studies, although the phenol-chloroform approach may still be preferable for specific sample types. creator: Michael Shamash creator: Saniya Kapoor creator: Corinne F. Maurice uri: https://doi.org/10.7717/peerj.18785 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Shamash et al. title: Do goats recognise humans cross-modally? link: https://peerj.com/articles/18786 last-modified: 2025-01-14 description: Recognition plays a key role in the social lives of gregarious species, enabling animals to distinguish among social partners and tailor their behaviour accordingly. As domesticated animals regularly interact with humans, as well as members of their own species, we might expect mechanisms used to discriminate between conspecifics to also apply to humans. Given that goats can combine visual and vocal cues to recognise one another, we investigated whether this cross-modal recognition extends to discriminating among familiar humans. We presented 26 goats (17 males and nine females) with facial photographs of familiar people and two repeated playbacks of a voice, either congruent (from the same person) or incongruent with that photograph (from a different person). When cues were incongruent, violating their expectations, we expected goats to show changes in physiological parameters and moreover, respond faster and for longer after playbacks. Accordingly, heart rate decreased as the playback sequence progressed, but only when the face and voice presented were incongruent. Heart rate variability was also affected by congruency, but we were unable to determine precisely where differences lay. However, goats showed no changes in time taken to respond, or how long they responded for (our primary variables of interest). We also found evidence to suggest that shifts in cardiac responses may not have been robust. Although our findings could imply that goats had successfully perceived differences in congruency between the visual and vocal identity information presented, further evidence is needed to determine whether they are capable of cross-modal recognition of humans. creator: Marianne A. Mason creator: Stuart Semple creator: Harry H. Marshall creator: Alan G. McElligott uri: https://doi.org/10.7717/peerj.18786 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Mason et al. title: Sleep-wake patterns of fencing athletes: a long-term wearable device study link: https://peerj.com/articles/18812 last-modified: 2025-01-14 description: ObjectiveSleep is the most efficient means of recovery for athletes, guaranteeing optimal athletic performance. However, many athletes frequently experience sleep problems. Our study aims to describe the sleep-wake patterns of fencing athletes and determine whether factors, such as sex, competitive level and training schedules, could affect the sleep-wake rhythm.MethodsSleep data from 23 fencing athletes were collected using the Huawei Band 6, monitoring key sleep parameters such as bedtime, wake time, duration of deep and light sleep, wake periods, REM sleep duration, and nap duration. During this period, athletes were required to wear the band continuously for 24 hours daily, except bathing, charging, and competition times.ResultsAthletes averaged 7.97 hours of sleep per night, with significant differences observed in wake time (p = 0.015) and midpoint of sleep (p = 0.048) between high-level and low-level athletes, as well as a higher frequency of naps among high-level (χ2 = 11.97, p = 0.001) and female (χ2 = 3.88, p = 0.049) athletes. Nap duration was negatively correlated with night sleep duration (r =  − 0.270, p < 0.001). Athletes were observed for changes in sleep-wake patterns from Monday to Sunday. On Mondays, Wednesdays, and Fridays, when there was no morning training, the athletes’ wake-up time and the midpoint of sleep were shifted significantly backward, and there were significant differences in sleep parameters between training days and rest days.ConclusionThe sleep patterns of athletes differ according to level and gender. The sleep-wake patterns of athletes are influenced by training schedules, indicating the presence of sleep rhythm disruption. creator: Jiansong Dai creator: Xiaofeng Xu creator: Gangrui Chen creator: Jiale Lv creator: Yang Xiao uri: https://doi.org/10.7717/peerj.18812 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Dai et al. title: Identification and mechanistic insights of cell senescence-related genes in psoriasis link: https://peerj.com/articles/18818 last-modified: 2025-01-14 description: BackgroundPsoriasis is a chronic inflammatory skin disease affecting 2–3% of the global population, characterised by red scaly patches that significantly affect patients’ quality of life. Recent studies have suggested that cell senescence, a state in which cells cease to divide and secrete inflammatory mediators, plays a critical role in various chronic diseases, including psoriasis. However, the involvement and mechanisms of action of senescence-related genes in psoriasis remain unclear.MethodsThis study aimed to identify senescence-related genes associated with psoriasis and explore their molecular mechanisms. RNA sequencing data from psoriasis and control samples were obtained from the GEO database. Differential expression analysis was performed using DESeq2 to identify differentially expressed genes (DEGs). The intersection of DEGs with cell senescence-related genes from the CellAge database was used to identify the candidate genes. Protein-protein interaction networks, Gene Ontology, and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted to explore the functions and pathways of these genes. Machine learning algorithms, including Least Absolute Shrinkage and Selection Operator (LASSO) regression and Support vector machine-recursive feature elimination (SVE-RFE), were used to select feature genes that were validated by qRT-PCR. Additionally, an immune cell infiltration analysis was performed to understand the roles of these genes in the immune response to psoriasis.ResultsThis study identified 4,913 DEGs in psoriasis, of which 46 were related to cell senescence. Machine learning highlighted four key genes, CXCL1, ID4, CCND1, and IRF7, as significant. These genes were associated with immune cell infiltration and validated by qRT-PCR, suggesting their potential as therapeutic targets for psoriasis.ConclusionsThis study identified and validated key senescence-related genes involved in psoriasis, providing insights into their molecular mechanisms and potential therapeutic targets and offering a foundation for developing targeted therapies for psoriasis. creator: Guiyan Deng creator: Cheng Xu creator: Dunchang Mo uri: https://doi.org/10.7717/peerj.18818 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Deng et al. title: Exploring freshwater soundscapes of tropical marshland habitats in Southeast Asia: insights into auditory sensory adaptation of wild Siamese fighting fish Betta splendens link: https://peerj.com/articles/18491 last-modified: 2025-01-13 description: While soundscapes shape the structure and function of auditory systems over evolutionary timescales, there is limited information regarding the adaptation of wild fish populations to their natural acoustic environments. This is particularly relevant for freshwater ecosystems, which are extremely diverse and face escalating pressures from human activities and associated noise pollution. The Siamese fighting fish Betta splendens is one of the most important cultured species in the global ornamental fish market and is increasingly recognized as a model organism for genetics and behavioural studies. This air-breathing species (Anabantoidei), characterized by the presence of a suprabranchial labyrinth organ that enhances auditory sensitivity, is native to Southeast Asia and inhabits low flow freshwater ecosystems that are increasingly threatened due to habitat destruction and pollution. We characterized the underwater soundscape, along with various ecological parameters, across five marshland habitats of B. splendens, from lentic waterbodies to small canals near a lake in Chiang Rai province (Thailand). All habitats exhibited common traits of low dissolved oxygen and dense herbaceous vegetation. Soundscapes were relatively quiet with Sound Pressure Level (SPL) around 102–105 dB re 1 µPa and most spectral energy below 1,000 Hz. Sound recordings captured diverse biological sounds, including potential fish vocalizations, but primarily insect sounds. Hearing thresholds were determined using auditory evoked potential (AEP) recordings, revealing best hearing range within 100–400 Hz. Males exhibited lower hearing thresholds than females at 400 and 600 Hz. This low-frequency tuning highlights the potential susceptibility of B. splendens to anthropogenic noise activities. This study provides first characterization of the auditory sensitivity and natural soundscape of B. splendens, establishing an important ground for future hearing research in this species. The information provided on the auditory sensory adaptation of B. splendens emphasizes the importance of preserving quiet soundscapes from lentic freshwater ecosystems. creator: Andreia Ramos creator: David Gonçalves creator: Raquel O. Vasconcelos uri: https://doi.org/10.7717/peerj.18491 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Ramos et al. title: Analysis of the anthropogenic effect on the Silencio River in Salvador Escalante, Michoacán, México link: https://peerj.com/articles/18531 last-modified: 2025-01-13 description: The average annual water availability worldwide is approximately 1,386 trillion cubic hectometers (hm3), of which 97.5% is saltwater and only 2.5% is freshwater. Nearly 70% is not available for human consumption as it is in glaciers, snow, and ice. It is estimated that only 0.77% is accessible freshwater for human use. Mexico has an availability of 451,584.7 million cubic meters (m3) of freshwater, with accessibility and distribution being unequal. The growth in urbanization, population, and industrialization has caused a decrease in water quality, and other parameters. Organic and inorganic contaminants evolved from various sources cause the degradation of water quality. The pollution of aquatic bodies, such as rivers and lakes, is one of the main problems in the world. In Salvador Escalante in México, the domestic wastewaters treatment plant (WWTP) is being exposed to effluents contaminated with metals like copper, cadmium, lead, and mercury. In this work, active sludges from the WWTP were analyzed. First, particle size distribution of flocs was measured by a sedimentation process. Secondly, analysis of the tolerance that microorganisms exhibit to metals (i.e., factors) was performed, based on a 2$\hat {}$ ˆ(4-1) factorial design of experiments at laboratory-scale, measuring pH, chemical oxygen demand (COD) and electrical conductivity (responses). This aims to evaluate the capacity of the WWTP for improve the water quality. Microbiologic cultures were used for a qualitative study of the microorganisms contained in the active sludges; it was found that Enterobacterium does not grow in presence of heavy metals. Cadmium is the most harmful metal for microorganisms according to Pareto diagrams presented in this study. creator: Mario Alberto Pérez-Méndez creator: Guadalupe Selene Fraga-Cruz creator: Gustavo Álvarez-Gómez creator: Fabricio Nápoles-Rivera creator: Gladys Jiménez-García creator: Rafael Maya-Yescas uri: https://doi.org/10.7717/peerj.18531 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Pérez-Méndez et al. title: Insecticides may facilitate the escape of weeds from biological control link: https://peerj.com/articles/18597 last-modified: 2025-01-13 description: BackgroundPreventative pesticide seed treatments (hereafter preventative pest management or PPM) are common corn and soybean treatments, and often include both fungicides and neonicotinoid insecticides. While PPM is intended to protect crops from soil-borne pathogens and early season insect pests, these seed treatments may have detrimental effects on biological control of weed seeds by insects.MethodsHere, in two 3-year corn-soy rotations in Pennsylvania USA, we investigated a PPM approach to insect management compared to an integrated pest management approach (IPM) and a “no (insect) pest management” (NPM) control. This was crossed with a grass cover crop to see if this conservation practice can help recover the ecosystem services affected by chemical pest management practices. We hypothesized that PPM and IPM approaches would release weed seeds from biological control by insects but cover crops would increase biological control. We measured the effect of these treatments on the weed-seed bank, mid-season weed biomass, granivorous insect activity-density, and weed-seed predation.ResultsWe found that, contrary to our hypothesis, planting a cover crop decreased carabid activity-density without consistent differences in weed-seed predation. Pest management and cover crop treatments also had inconsistent effects on the weed-seed bank and mid-season weed biomass, but insecticide use without a cover crop increased the biomass of likely glyphosate-resistant marestail (Erigeron canadensis L.) at the end of the trial. Our results suggest that reducing insecticide use may be important when combating herbicide-resistant weeds. We found planting cover crops and/or avoiding the use of insecticides may combat these problematic weeds. creator: Elizabeth K. Rowen creator: Kirsten Ann Pearsons creator: Richard G. Smith creator: Kyle Wickings creator: John F. Tooker uri: https://doi.org/10.7717/peerj.18597 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2025 Rowen et al. title: Thermal ecology of the Mexican Garter Snake (Thamnophis eques): temporal and spatial variations link: https://peerj.com/articles/18641 last-modified: 2025-01-13 description: Heterogeneous environments provide different daily and seasonal thermal conditions for snakes, resulting in temporal and spatial variations in body temperature (Tb). This study analyzes the Tb of Thamnophis eques in the forest and grassland of a Mexican locality through daily and seasonal profiling. The patterns were obtained from seminatural enclosures in the field with a point sampling strategy to analyze temporal and spatial variations in Tb. The variation of Tb throughout the day was correlated with air and substrate temperatures, both in the grassland and in the forest. The average Tb in the grassland was 0.88 °C greater than in the forest. Our results indicate that T. eques showed differences in Tb between grassland and forest, principally in late spring and early summer during the early rise and late plateau phases, coinciding with the presence of foliage on the willow trees present in the study area, while in late summer and early autumn, the Tb was similar when willow trees canopy cover was absent (May–September). Our results support the hypothesis that the Tb of snakes differ between forests when the willows have leaves and is similar when canopy cover is equivalent, in this case, when tree canopy cover was absent. Our results also shown that T. eques presented daily and seasonal warming patterns similar to other Arizona populations and like those of other northern Gartersnakes. However, this result may not be valid for the entire wide distribution and consequent diversity of habitats of T. eques. The information of Tb in T. eques through daily and seasonal profiles in different habitats could aid in understanding the effects of environmental conditions on the ecological strategies deployed by snakes on habitat selection. creator: Crystian S. Venegas-Barrera creator: Armando Sunny creator: Javier Manjarrez uri: https://doi.org/10.7717/peerj.18641 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2025 Venegas-Barrera et al.