title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=532 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Mismatch between IUCN range maps and species interactions data illustrated using the Serengeti food web link: https://peerj.com/articles/14620 last-modified: 2023-02-10 description: BackgroundRange maps are a useful tool to describe the spatial distribution of species. However, they need to be used with caution, as they essentially represent a rough approximation of a species’ suitable habitats. When stacked together, the resulting communities in each grid cell may not always be realistic, especially when species interactions are taken into account. Here we show the extent of the mismatch between range maps, provided by the International Union for Conservation of Nature (IUCN), and species interactions data. More precisely, we show that local networks built from those stacked range maps often yield unrealistic communities, where species of higher trophic levels are completely disconnected from primary producers.MethodologyWe used the well-described Serengeti food web of mammals and plants as our case study, and identify areas of data mismatch within predators’ range maps by taking into account food web structure. We then used occurrence data from the Global Biodiversity Information Facility (GBIF) to investigate where data is most lacking.ResultsWe found that most predator ranges comprised large areas without any overlapping distribution of their prey. However, many of these areas contained GBIF occurrences of the predator.ConclusionsOur results suggest that the mismatch between both data sources could be due either to the lack of information about ecological interactions or the geographical occurrence of prey. We finally discuss general guidelines to help identify defective data among distributions and interactions data, and we recommend this method as a valuable way to assess whether the occurrence data that are being used, even if incomplete, are ecologically accurate. creator: Gracielle T. Higino creator: Francis Banville creator: Gabriel Dansereau creator: Norma Rocio Forero Muñoz creator: Fredric Windsor creator: Timothée Poisot uri: https://doi.org/10.7717/peerj.14620 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Higino et al. title: Comparative chloroplast genomics of three species of Bulbophyllum section Cirrhopetalum (Orchidaceae), with an emphasis on the description of a new species from Eastern Himalaya link: https://peerj.com/articles/14721 last-modified: 2023-02-10 description: BackgroundChloroplast (cp) genomes are useful and informative molecular markers used for species determination and phylogenetic analysis. Bulbophyllum is one of the most taxonomically complex taxa in Orchidaceae. However, the genome characteristics of Bulbophyllum are poorly understood.MethodsBased on comparative morphological and genomic analysis, a new species Bulbophyllum pilopetalum from eastern Himalaya belonging to section Cirrhopetalum is described and illustrated. This study used chloroplast genomic sequences and ribosomal DNA (nrDNA) analysis to distinguish the new Bulbophyllum species and determine its phylogenetic position. An additional phylogenetic analysis was conducted using 74 coding sequences from 15 complete chloroplast genomes from the genus Bulbophyllum, as well as nrDNA sequences and two chloroplast DNA sequences from 33 Bulbophyllun species.ResultsThe new species is morphologically similar to B. pingnanense, B. albociliatum, and B. brevipedunculatum in vegetative and floral morphology, but it can be distinguished by its ovate-triangle dorsal sepal without a marginal ciliate. The chloroplast genome of the new Bulbophyllum species is 151,148 bp in length, and includes a pair of inverted repeats (IRs) of 25,833 bp, a large single-copy region (LSC) of 86,138 bp, and a small single-copy region (SSC) of 13,300 bp. The chloroplast genome includes 108 unique genes encoding 75 proteins, 30 tRNAs, and four rRNAs. Compared with the cp genomes of its two most closely-related species, B. pingnanense and B. albociliatum, this chloroplast genome exhibited great interspecific divergence and contained several Indels that were specific to the new species. The plastid tree showed that B. pilopetalum is most closely-related to B. pingnanense. The phylogenetic tree based on combined nrDNA and chloroplast DNA sequences indicated that section Cirrhopetalum was monophyletic and B. pilopetalum was a member of this section.DiscussionThe taxonomic status of the new species is strongly supported by cp genome data. Our study highlights the importance of using the complete cp genome to identify species, elucidate the taxonomy, and reconstruct the phylogeny of plant groups with complicated taxonomic problems. creator: Mengkai Li creator: Lu Tang creator: Jianping Deng creator: Hanqing Tang creator: Shicheng Shao creator: Zhen Xing creator: Yan Luo uri: https://doi.org/10.7717/peerj.14721 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Li et al. title: Low-stress livestock handling protects cattle in a five-predator habitat link: https://peerj.com/articles/14788 last-modified: 2023-02-10 description: Given the ecological importance of top predators, societies are turning to non-lethal methods for coexistence. Coexistence is challenging when livestock graze within wild predator habitats. We report a randomized, controlled experiment to evaluate low-stress livestock handling (L-SLH), a form of range riding, to deter grizzly (brown) bears, gray wolves, cougars, black bears, and coyotes in Southwestern Alberta. The treatment condition was supervision by two newly hired and trained range riders and an experienced L-SLH-practicing range rider. This treatment was compared against a baseline pseudo-control condition of the experienced range rider working alone. Cattle experienced zero injuries or deaths in either condition. We infer that inexperienced range riders trained and supervised by an experienced rider did not raise or lower the risk to cattle. Also, predators did not shift to the cattle herds protected by fewer range riders. We found a correlation suggesting grizzly bears avoided herds visited more frequently by range riders practicing L-SLH. More research is required to compare different forms of range riding. However, pending experimental evaluation of other designs, we recommend use of L-SLH. We discuss the cobenefits of this husbandry method. creator: Naomi X. Louchouarn creator: Adrian Treves uri: https://doi.org/10.7717/peerj.14788 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Louchouarn and Treves title: Abnormal expression of SLIT3 induces intravillous vascularization dysplasia in ectopic pregnancy link: https://peerj.com/articles/14850 last-modified: 2023-02-10 description: ObjectiveTo investigate whether the morphology, capillary number, and transcriptome expression profiles of ectopic pregnancy (EP) villi differ from those of normal pregnancy (NP) villi.MethodsHematoxylin-eosin (HE) and immunohistochemistry (IHC) staining for CD31 were conducted to compare differences in morphology and capillary number between EP and NP villi. Differentially expressed (DE) miRNAs and mRNAs were determined from transcriptome sequencing of both types of villi and used to construct a miRNA–mRNA network, from which hub genes were identified. Candidate DE-miRNAs and DE-mRNAs were validated by quantitative reverse transcription (qRT)-PCR. Correlations were identified between the number of capillaries and serum beta human chorionic gonadotropin (β-HCG) levels and between the expression levels of hub genes associated with angiogenesis and β-HCG levels.ResultsThe mean and total cross-sectional areas of placental villi were significantly increased in EP compared with NP villi. Capillary density was greatly reduced in EP villi and was positively correlated with β-HCG levels. A total of 49 DE-miRNAs and 625 DE-mRNAs were identified from the sequencing data. An integrated analysis established a miRNA–mRNA network containing 32 DE-miRNAs and 103 DE-mRNAs. Based on the validation of hub mRNAs and miRNAs in the network, a regulatory pathway involving miR-491-5p–SLIT3 was discovered, which may have a role in the development of villous capillaries.ConclusionVillus morphology, capillary number, and miRNA/mRNA expression profiles in villous tissues were aberrant in EP placentas. Specifically, SLIT3, which is regulated by miR-491-5p, may contribute to the regulation of villous angiogenesis and was established as a putative predictor of chorionic villus development, providing a basis for future research. creator: Qian Zhu creator: Xiaoya Zhao creator: Duo Zhang creator: Wei Xia creator: Jian Zhang uri: https://doi.org/10.7717/peerj.14850 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhu et al. title: Rapid growth in Late Cretaceous sea turtles reveals life history strategies similar to extant leatherbacks link: https://peerj.com/articles/14864 last-modified: 2023-02-10 description: Modern sea turtle long bone osteohistology has been surprisingly well-studied, as it is used to understand sea turtle growth and the timing of life history events, thus informing conservation decisions. Previous histologic studies reveal two distinct bone growth patterns in extant sea turtle taxa, with Dermochelys (leatherbacks) growing faster than the cheloniids (all other living sea turtles). Dermochelys also has a unique life history compared to other sea turtles (large size, elevated metabolism, broad biogeographic distribution, etc.) that is likely linked to bone growth strategies. Despite the abundance of data on modern sea turtle bone growth, extinct sea turtle osteohistology is virtually unstudied. Here, long bone microstructure of the large, Cretaceous sea turtle Protostega gigas is examined to better understand its life history. Humeral and femoral analysis reveals bone microstructure patterns similar to Dermochelys with variable but sustained rapid growth through early ontogeny. Similarities between Progostegea and Dermochelys osteohistology suggest similar life history strategies like elevated metabolic rates with rapid growth to large body size and sexual maturity. Comparison to the more basal protostegid Desmatochelys indicates elevated growth rates are not present throughout the entire Protostegidae, but evolved in larger and more derived taxa, possibly in response to Late Cretaceous ecological changes. Given the uncertainties in the phylogenetic placement of the Protostegidae, these results either support convergent evolution towards rapid growth and elevated metabolism in both derived protostegids and dermochelyids, or a close evolutionary relationship between the two taxa. Better understanding the evolution and diversity of sea turtle life history strategies during the Late Cretaceous greenhouse climate can also impact current sea turtle conservation decisions. creator: Laura E. Wilson uri: https://doi.org/10.7717/peerj.14864 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wilson title: Parenting styles, maladaptive coping styles, and disturbed eating attitudes and behaviors: a multiple mediation analysis in patients with feeding and eating disorders link: https://peerj.com/articles/14880 last-modified: 2023-02-10 description: BackgroundAlthough preliminary studies support the roles of unhealthy parenting styles and maladaptive coping styles in increasing rates of disturbed eating attitudes and behaviors (EAB) and clinically significant feeding and eating disorders (FED), underlying mechanisms have not been well-recognized. This study aims to investigate the factors associated with disturbed EAB and the mediating roles of overcompensation and avoidance coping styles in the relationship between different types of parenting styles and disturbed EAB among patients with FED.MethodsA total of 102 patients with FED in Zahedan, Iran, participating in this cross-sectional study (from April to March 2022) completed a sociodemographic information form and self-report measures of parenting styles, maladaptive coping styles, and EAB. Model 4 of Hayes’ PROCESS macro in SPSS was employed to identify and explain the mechanism or process that underlies an observed relationship between study variables.ResultsThe results showed that authoritarian parenting style, overcompensation and avoidance coping styles, and female gender might be related to disturbed EAB. The overall hypothesis that overcompensation and avoidance coping styles mediated the effect of fathers’ and mothers’ authoritarian parenting styles on disturbed EAB was also supported.ConclusionsOur findings highlighted the necessity of evaluating particular unhealthy parenting styles and maladaptive coping styles as the important possible risk factors in the development and maintenance of higher level of disturbance in EAB among patients with FED. However, more research is needed to explore individual, family, and peer risk factors for disturbed EAB among these patients. creator: Mohsen Khosravi creator: Seyed Teymur Seyedi Asl creator: Alireza Nazari Anamag creator: Milad SabzehAra Langaroudi creator: Jafar Moharami creator: Sadegh Ahmadi creator: Alireza Ganjali creator: Zahra Ghiasi creator: Mohammad Nafeli creator: Rashya Kasaeiyan uri: https://doi.org/10.7717/peerj.14880 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Khosravi et al. title: Disparities in COVID-19 incidence and fatality rates at high-altitude link: https://peerj.com/articles/14473 last-modified: 2023-02-06 description: BackgroundSARS-CoV-2 has affected every demography disproportionately, including even the native highland populations. Hypobaric-hypoxic settings at high-altitude (HA, >2,500 masl) present an extreme environment that impacts the survival of permanent residents, possibly including SARS-CoV-2. Conflicting hypotheses have been presented for COVID-19 incidence and fatality at HA.ObjectivesTo evaluate protection or risk against COVID-19 incidence and fatality in humans under hypobaric-hypoxic environment of high-altitude (>2,501 masl).MethodsGlobal COVID-19 data of March 2020-21, employed from official websites of the Indian Government, John Hopkins University, and Worldometer were clustered into 6 altitude categories. Clinical cofactors and comorbidities data were evaluated with COVID-19 incidence and fatality. Extensive comparisons and correlations using several statistical tools estimated the risk and protection.ResultsOf relevance, data analyses revealed four distinct responses, namely, partial risk, total risk, partial protection, and total protection from COVID-19 at high-altitude indicating a mixed baggage and complexity of the infection. Surprisingly, it included the countries within the same geographic region. Moreover, body mass index, hypertension, and diabetes correlated significantly with COVID-19 incidence and fatality rate (P ≤ 0.05).ConclusionsVaried patterns of protection and risk against COVID-19 incidence and fatality were observed among the high-altitude populations. It is though premature to generalize COVID-19 effects on any particular demography without further extensive studies. creator: Bilal Ahmed Abbasi creator: Neha Chanana creator: Tsering Palmo creator: Qadar Pasha uri: https://doi.org/10.7717/peerj.14473 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Abbasi et al. title: Epidemiological correlates of overweight and obesity in the Northern Cape Province, South Africa link: https://peerj.com/articles/14723 last-modified: 2023-02-09 description: BackgroundIn the past several decades, obesity has become a major public health issue worldwide, associated with increased rates of chronic disease and death. Like many developing nations, South Africa is experiencing rapid increases in BMI, and as a result, evidence-based preventive strategies are needed to reduce the increasing burden of overweight and obesity. This study aimed to determine the prevalence and predictors of overweight and obesity among a multi-ethnic cohort from the rural Northern Cape of South Africa.MethodsThese data were collected as part of a tuberculosis (TB) case-control study, with 395 healthy control participants included in the final analysis. Overweight and obesity were defined according to WHO classification. Multivariate linear models of BMI were generated using sex, age, education level, smoking, alcohol consumption, and diabetes as predictor variables. We also used multivariable logistic regression analysis to assess the relationship of these factors with overweight and obesity.ResultsThe average BMI in our study cohort was 25.2. The prevalence of overweight was 18.0% and the prevalence of obesity was 25.0%. We find that female sex, being older, having more years of formal education, having diabetes, and being in a rural area are all positively associated with BMI in our dataset. Women (OR = 5.6, 95% CI [3.3–9.8]), rural individuals (OR = 3.3, 95% CI [1.9–6.0]), older individuals (OR = 1.02, 95% CI [1–1.04]), and those with more years of education (OR = 1.2, 95% CI [1.09–1.32]) were all more likely to be overweight or obese. Alternatively, being a smoker is negatively associated with BMI and decreases one’s odds of being overweight or obese (OR = 0.28, 95% CI [0.16–0.46]).ConclusionsWe observed a high prevalence of overweight and obesity in this study. The odds of being overweight and obese were higher in women, those living in rural areas, and those with more education, and increases with age. Community-based interventions to control obesity in this region should pay special attention to these groups. creator: Mackenzie H. Smith creator: Justin W. Myrick creator: Oshiomah Oyageshio creator: Caitlin Uren creator: Jamie Saayman creator: Sihaam Boolay creator: Lena van der Westhuizen creator: Cedric Werely creator: Marlo Möller creator: Brenna M. Henn creator: Austin W. Reynolds uri: https://doi.org/10.7717/peerj.14723 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Smith et al. title: Comparison of carbon content between plantation and natural regeneration seedlings in Durango, Mexico link: https://peerj.com/articles/14774 last-modified: 2023-02-09 description: Forest plantations and natural forests perform a relevant role in capturing CO2 and reducing greenhouse gas concentrations. The objective of this study was to compare the diameter increment, biomass and carbon accumulation in a plantation of Pinus durangensis and a naturally regenerated stand. The data were collected from 32 circular plots of 100 m2 (16 plots in the planted site and 16 in naturally regenerated area). At each plot, the diameter at the base (cm) and height (m) of all seedlings were measured using a Vernier and tape measure, and a seedling was destructively sampled collecting one cross-section at the base of the stump. The annual ring-width increment of each sampled seedling was recorded to obtain its diameter at the base and estimate annual aboveground biomass and carbon accumulation through allometric equations. The response variables were evaluated using mixed-effects ANOVA models. Results indicated that there were significant differences (P ≤ 0.05) on annual tree-ring width growth, biomass and carbon accumulation. The plantation seedlings showed significantly higher growth rates, biomass and carbon accumulation at most evaluated years. After 7 years of growth the lines of current annual increment (CAI) and mean annual increment (MAI) in basal diameter for both the plantation and the natural regeneration have not yet intersected. Both forest plantations and naturally regenerated stands of the studied tree species may be suitable alternatives to promote CO2 capture and increase timber production. creator: Jesús Alejandro Soto-Cervantes creator: José Javier Corral-Rivas creator: Pedro Antonio Domínguez-Calleros creator: Pablito Marcelo López-Serrano creator: Eusebio Montiel-Antuna creator: Emily García-Montiel creator: Alberto Pérez-Luna uri: https://doi.org/10.7717/peerj.14774 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Soto-Cervantes et al. title: RANK signaling in osteoclast precursors results in a more permissive epigenetic landscape and sexually divergent patterns of gene expression link: https://peerj.com/articles/14814 last-modified: 2023-02-09 description: BackgroundSex is an important risk factor in the development of osteoporosis and other bone loss disorders, with women often demonstrating greater susceptibility than men. While variation in sex steroids, such as estradiol, accounts for much of the risk, there are likely additional non-endocrine factors at transcriptional and epigenetic levels that result in a higher rate of bone loss in women. Identification of these factors could improve risk assessment and therapies to preserve and improve bone health.MethodsOsteoclast precursors were isolated male and female C57Bl/6 mice and cultured with either MCSF alone or MCSF and RANKL. Following the culture period RNA was isolated for RNA sequencing and DNA was isolated for tagmentation and ATAC sequencing. RNA-Seq and ATAC-seq were evaluated via pathway analysis to identify sex- and RANKL-differential transcription and chromatin accessibility.ResultsOsteoclasts demonstrated significant alterations in gene expression compared to macrophages with both shared and differential pathways between the sexes. Transcriptional pathways differentially regulated between male and female cells were associated with immunological functions with evidence of greater sensitivity in male macrophages and female osteoclasts. ATAC-Seq revealed a large increase in chromatin accessibility following RANKL treatment with few alterations attributable to sex. Comparison of RNA-Seq and ATAC-seq data revealed few common pathways suggesting that many of the transcriptional changes of osteoclastogenesis occur independently of chromatin remodeling. creator: Abigail L. Keever creator: Kathryn M. Collins creator: Rachel A. Clark creator: Amber L. Framstad creator: Jason W. Ashley uri: https://doi.org/10.7717/peerj.14814 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Keever et al.