Annual changes in biomass amount and feeding potential of shrubby rangelands in maquis formation
Background This study evaluated the extent to which the endemic herbaceous and woody species of shrubby rangelands met the roughage needs of grazing animals throughout the year. Methods The biomass, botanical composition, and quality of hay were investigated in the shrubby rangelands in Paşaköy of the Ayvacık districts in Çanakkale over the course of a year. Plant samples were taken from the herbaceous species monthly and from the grazing parts of the shrubs in May and November. Results The total amount of biomass (hay + shrub) in the rangeland was found to be 30.448 kg/ha. Shrubs made up 18.78% of the rangeland, while the annual species comprised 54.96%, and perennial herbs covered 26.26% of the total biomass. Crude protein (CP) ratios of herbaceous species decreased continuously from March (13.58%) to September (6.73%), and then increased. A similar change was also seen in pure ash (PA) ratios. The CP ratios in the shrub species were high in spring and decreased in autumn and there was an irregular variation in PA rates. Oak had the highest PA ratio during the spring, while thuja had the highest ratio in autumn, and Juniperus oxycedrus during the winter months. In herbaceous species, cell wall components (NDF, ADF, and ADL) reached their highest levels in summer and decreased in spring and winter. However, in shrubs, these components varied according to the species and were generally lowest in spring and then increased in autumn and winter. Here, it was determined that year-round grazing is a suitable grazing system in the shrubby rangelands of the Mediterranean zone, and animals are able to find fresh forage in the rangelands due to the presence of shrubs. However, since the contribution of shrubs to the total forage production is low, additional roughage should be provided, except in the spring when the production and quality of hay increase. These practices may contribute to better livestock management.
Alatürk et al. (2023) Annual changes in biomass amount and feeding potential of shrubby rangelands in maquis formation. PeerJ 11:e15204 https://doi.org/10.7717/peerj.15204
CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability
Genomic instability is an important hallmark of cancer and more recently has been identified in others like neurodegenrative diseases. Chromosomal instability, as a measure of genomic instability, has been used to characterize clinical and biological phenotypes associated with these diseases by measuring structural and numerical chromosomal alterations. There have been multiple chromosomal instability scores developed across many studies in the literature; however, these scores have not been compared because of the lack of a single tool available to calculate and facilitate these various metrics. Here, we provide an R package CINmetrics, that calculates six different chromosomal instability scores and allows direct comparison between them. We also demonstrate how these scores differ by applying CINmetrics to breast cancer data from The Cancer Genome Atlas (TCGA). The package is available on CRAN at https://cran.rproject.org/package=CINmetrics and on GitHub at https://github.com/lasseignelab/CINmetrics.
Oza et al. (2023) CINmetrics: an R package for analyzing copy number aberrations as a measure of chromosomal instability. PeerJ 11:e15244 https://doi.org/10.7717/peerj.15244
Characterization of the populations of upside-down jellyfish in Jardines de la Reina National Park, Cuba
Upside-down jellyfish are a group of benthic scyphozoans belonging to the genus Cassiopea, whose members are in symbiosis with dinoflagellates and inhabit tropical and subtropical waters. Although there are some studies of the genus in the Caribbean, these are limited. In Cuba, the group’s studies are restricted to reports on taxonomic lists and, as far as we know, no one has performed any analyzes of the densities of these jellyfish in seagrass or mangrove ecosystems in Cuba. In this work, the populations of Cassiopea spp. in Jardines de la Reina National Park (JRNP) were characterized, for the first time for this Marine Protected Area and Cuba. One hundred 1m2 square frames were placed at 14 JRNP sites. For each site, the species, density, size of the individuals and abiotic factors were determined. Density and diameter comparisons were made between sites, zones and regions within the JRNP. The percentage of the benthic cover was determined and a correlation was made between density and diameter. A total of 10,803 individuals were recorded, of which 7,618 belong to Cassiopea xamachana and 3,185 belong to Cassiopea frondosa. Both species share a niche and no evident segregation was detected according to abiotic variables. Significant differences were detected in comparisons of density and size across sites and zones. Density and size in the JRNP were negatively correlated, and higher aggregations of the species were observed at lower sizes. Density mean values ranged from 2.18 to 14.52 ind. /m2 with maximum values of 79 ind. /m2. Cayo Alcatraz was the site found to have the highest density while Cachiboca was the site with the lowest density. The average bell diameter size of the individuals ranged from 9.34 to 15.31 cm for the sampled sites, with minimum and maximum values of 2.5 cm and 32.6 cm. The smallest size was recorded at Cayo Alcatraz while the largest size was reported for Boca de las Anclitas. The environmental factors evaluated showed no significant relationship with the density or diameter of Cassiopea, while the Thalassia testudinum cover was negatively correlated with Cassiopea density at all fourteen sites in the JRNP. The percentage of Cassiopea coverage was higher than those reported in the literature, with four sites exceeding 20% coverage. In general, the populations of Cassiopea spp. in the JRNP did not differ greatly, although a higher density was observed towards the eastern region of the park. It was shown for the first time for the species that density and size have a negative correlation. Future studies are required to quantify the impact of Cassiopea on coastal marine ecosystem processes, and to further determine how anthropogenic changes may be altering the function of these tropical ecosystems.
Morejón-Arrojo et al. (2023) Characterization of the populations of upside-down jellyfish in Jardines de la Reina National Park, Cuba. PeerJ 11:e15254 https://doi.org/10.7717/peerj.15254
Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera
Ribosomal intragenomic variability in prokaryotes and eukaryotes is a genomic feature commonly studied for its inflationary impact on molecular diversity assessments. However, the evolutionary mechanisms and distribution of this phenomenon within a microbial group are rarely explored. Here, we investigate the intragenomic variability in 33 species of planktonic foraminifera, calcifying marine protists, by inspecting 2,403 partial SSU sequences obtained from single-cell clone libraries. Our analyses show that polymorphisms are common among planktonic foraminifera species, but the number of polymorphic sites significantly differs among clades. With our molecular simulations, we could assess that most of these mutations are located in paired regions that do not affect the secondary structure of the SSU fragment. Finally, by mapping the number of polymorphic sites on the phylogeny of the clades, we were able to discuss the evolution and potential sources of intragenomic variability in planktonic foraminifera, linking this trait to the distinctive nuclear and genomic dynamics of this microbial group.
Greco et al. (2023) Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera. PeerJ 11:e15255 https://doi.org/10.7717/peerj.15255
East Timor as an important source of cashew (Anacardium occidentale L.) genetic diversity
Background Cashew (Anacardium occidentale L.) is a crop currently grown in several tropical countries because of the economic importance of cashew nuts. Despite its enormous economic worth, limited research has been conducted on the molecular diversity of cashew genetic resources. In this study, a wide comprehensive assessment of the genetic diversity of cashew trees in East Timor was performed using microsatellites (SSRs) to evaluate intraspecific diversity and population structuring. Methods A total of 207 individual cashew trees, including trees from East Timor (11), and outgroup populations from Indonesia (one) and Mozambique (two), were analyzed with 16 cashew-specific SSRs. A comprehensive sampling of cashew trees within East Timor was performed, covering the distribution of cashew orchards in the country. Genetic diversity indices were calculated, and population structuring was determined using three different approaches: genetic distances (UPGMA and NJ), AMOVA, and individual-based clustering methods through Bayesian (STRUCTURE) and multivariate (DAPC) analyses. Results The population structuring analysis revealed that the genetic diversity of cashew populations in East Timor was higher in this study than previously reported for cashew trees. A higher allelic richness was found within cashew populations in East Timor compared with the outgroup populations (Mozambique and Indonesia), reinforced by the presence of private alleles. Moreover, our study showed that cashew populations in East Timor are grouped into two dissimilar genetic groups, which may suggest multiple cashew introductions over time. These new cashew genetic resources could be explored for future crop improvement. Conclusions Crop diversity underpins the productivity, resilience, and adaptive capacity of agriculture. Therefore, this study provides useful information regarding genetic diversity and population structure that can be harnessed to improve cashew production in East Timor. This data is also important to creating a country-specific genetic cashew signature to increase cashew market value.
Guterres et al. (2023) East Timor as an important source of cashew (Anacardium occidentale L.) genetic diversity. PeerJ 11:e14894 https://doi.org/10.7717/peerj.14894
Personality traits, rank attainment, and siring success throughout the lives of male chimpanzees of Gombe National Park
Personality traits in many taxa correlate with fitness. Several models have been developed to try to explain how variation in these traits is maintained. One model proposes that variation persists because it is linked to trade-offs between current and future adaptive benefits. Tests of this model’s predictions, however, are scant in long-lived species. To test this model, we studied male chimpanzees living in Gombe National Park, Tanzania. We operationalized six personality traits using ratings on 19 items. We used 37 years of behavioral and genetic data to assemble (1) daily rank scores generated from submissive vocalizations and (2) records of male siring success. We tested whether the association between two personality traits, Dominance and Conscientiousness, and either rank or reproductive success, varied over the life course. Higher Dominance and lower Conscientiousness were associated with higher rank, but the size and direction of these relationships did not vary over the life course. In addition, independent of rank at the time of siring, higher Dominance and lower Conscientiousness were related to higher siring success. Again, the size and direction of these relationships did not vary over the life course. The trade-off model, therefore, may not hold in long-lived and/or slowly reproducing species. These findings also demonstrate that ratings are a valid way to measure animal personality; they are related to rank and reproductive success. These traits could therefore be used to test alternative models, including one that posits that personality variation is maintained by environmental heterogeneity, in studies of multiple chimpanzee communities.
Weiss et al. (2023) Personality traits, rank attainment, and siring success throughout the lives of male chimpanzees of Gombe National Park. PeerJ 11:e15083 https://doi.org/10.7717/peerj.15083
In silico screening of chalcones and flavonoids as potential inhibitors against yellow head virus 3C-like protease
Yellow head virus (YHV) is one of the most important pathogens in prawn cultivation. The outbreak of YHV could potentially result in collapses in aquaculture industries. Although a flurry of development has been made in searching for preventive and therapeutic approaches against YHV, there is still no effective therapy available in the market. Previously, computational screening has suggested a few cancer drugs to be used as YHV protease (3CLpro) inhibitors. However, their toxic nature is still of concern. Here, we exploited various computational approaches, such as deep learning-based structural modeling, molecular docking, pharmacological prediction, and molecular dynamics simulation, to search for potential YHV 3CLpro inhibitors. A total of 272 chalcones and flavonoids were in silico screened using molecular docking. The bioavailability, toxicity, and specifically drug-likeness of hits were predicted. Among the hits, molecular dynamics simulation and trajectory analysis were performed to scrutinize the compounds with high binding affinity. Herein, the four selected compounds including chalcones cpd26, cpd31 and cpd50, and a flavonoid DN071_f could be novel potent compounds to prevent YHV and GAV propagation in shrimp. The molecular mechanism at the atomistic level is also enclosed that can be used to further antiviral development.
Boonthaworn et al. (2023) In silico screening of chalcones and flavonoids as potential inhibitors against yellow head virus 3C-like protease. PeerJ 11:e15086 https://doi.org/10.7717/peerj.15086
Hidden diversity: comparative functional morphology of humans and other species
Gastrointestinal (GI) morphology plays an important role in nutrition, health, and epidemiology; yet limited data on GI variation have been collected since 1885. Here we demonstrate that students can collect reliable data sets on gut morphology; when they do, they reveal greater morphological variation for some structures in the GI tract than has been documented in the published literature. We discuss trait variability both within and among species, and the implications of that variability for evolution and epidemiology. Our results show that morphological variation in the GI tract is associated with each organ’s role in food processing. For example, the length of many structures was found to vary significantly with feeding strategy. Within species, the variability illustrated by the coefficients of variation suggests that selective constraints may vary with function. Within humans, we detected significant Pearson correlations between the volume of the liver and the length of the appendix (t-value = 2.5278, df = 28, p = 0.0174, corr = 0.4311) and colon (t-value = 2.0991, df = 19, p = 0.0494, corr = 0.4339), as well as between the lengths of the small intestine and colon (t-value = 2.1699, df = 17, p = 0.0445, corr = 0.4657), which are arguably the most vital organs in the gut for nutrient absorption. Notably, intraspecific variation in the small intestine can be associated with life history traits. In humans, females demonstrated consistently and significantly longer small intestines than males (t-value15 = 2.245, p = 0.0403). This finding supports the female canalization hypothesis, specifically, increased female investment in the digestion and absorption of lipids.
McKenney et al. (2023) Hidden diversity: comparative functional morphology of humans and other species. PeerJ 11:e15148 https://doi.org/10.7717/peerj.15148
Effects of ambient temperature on atopic dermatitis and attributable health burden: a 6-year time-series study in Chengdu, China
Background Despite increasing public concerns about the widespread health effects of climate change, the impacts of ambient temperature on atopic dermatitis (AD) remain poorly understood. Objectives We aimed to explore the effect of ambient temperature on AD and to estimate the burdens of AD attributed to extreme temperature. Methods Data on outpatients with AD and climate conditions in Chengdu, China were collected. A distributed lag nonlinear model (DLNM) was adopted to explore the association between daily mean temperature and AD outpatient visits. Subgroup analysis was used to identify vulnerable populations. Attributable burden was estimated by the epidemiological attributable method. Results We analyzed 10,747 outpatient visits from AD patients at West China Hospital in Chengdu between January 1, 2015, and December 31, 2020. Both low (<19.6 °C) and high temperatures (>25.3 °C) were associated with increased AD outpatient visits, with the increase being more pronounced at low temperature, as evidenced by a 160% increase in visits when the temperature dropped below zero from the minimum mortality temperature (22.8 °C). Children and males were the most susceptible populations. Approximately 25.4% of AD outpatient visits were associated with temperatures, causing an excessive 137161.5 US dollars of health care expenditures during this 6-year period. Conclusions Both high and low temperatures, particularly low temperatures, were significantly associated with an increased risk of AD, with children and males showing the strongest associations. Extreme environmental temperature has been identified as one of the major factors promoting the development of AD. However, individual patient-level exposures still needed to be investigated in future studies to confirm the causality between temperature and AD.
Chen et al. (2023) Effects of ambient temperature on atopic dermatitis and attributable health burden: a 6-year time-series study in Chengdu, China. PeerJ 11:e15209 https://doi.org/10.7717/peerj.15209
Mapping the global distribution of invasive pest Drosophila suzukii and parasitoid Leptopilina japonica: implications for biological control
Insect pest invasions cause significant damage to crop yields, and the resultant economic losses are truly alarming. Climate change and trade liberalization have opened new ways of pest invasions. Given the consumer preference towards organic agricultural products and environment-friendly nature of natural pest control strategies, biological control is considered to be one of the potential options for managing invasive insect pests. Drosophila suzukii (Drosophilidae) is an extremely damaging fruit pest, demanding development of effective and sustainable biological control strategies. In this study, we assessed the potential of the parasitoid Leptopilina japonica (Figitidae) as a biocontrol agent for D. suzukii using ecological niche modeling approaches. We developed global-scale models for both pest and parasitoid to identify four components necessary to derive a niche based, target oriented prioritization approach to plan biological control programs for D. suzukii: (i) potential distribution of pest D. suzukii, (ii) potential distribution of parasitoid L. japonica, (iii) the degree of overlap in potential distributions of pest and parasitoid, and (iv) biocontrol potential of this system for each country. Overlapping suitable areas of pest and parasitoid were identified at two different thresholds and at the most desirable threshold (E = 5%), potential for L. japonica mediated biocontrol management existed in 125 countries covering 1.87 × 107 km2, and at the maximum permitted threshold (E = 10%), land coverage was reduced to 1.44 × 107 km2 in 121 countries. Fly pest distributional information as a predictor variable was not found to be improving parasitoid model performance, and globally, only in half of the countries, >50% biocontrol coverage was estimated. We therefore suggest that niche specificities of both pest and parasitoid must be included in site-specific release planning of L. japonica for effective biocontrol management aimed at D. suzukii. This study can be extended to design cost-effective pre-assessment strategies for implementing any biological control management program.
Spatial and Geographic Information Science
Nair et al. (2023) Mapping the global distribution of invasive pest Drosophila suzukii and parasitoid Leptopilina japonica: implications for biological control. PeerJ 11:e15222 https://doi.org/10.7717/peerj.15222