Trends and biases in African large carnivore population assessments: identifying priorities and opportunities from a systematic review of two decades of research
African large carnivores have undergone significant range and population declines over recent decades. Although conservation planning and the management of threatened species requires accurate assessments of population status and monitoring of trends, there is evidence that biodiversity monitoring may not be evenly distributed or occurring where most needed. Here, we provide the first systematic review of African large carnivore population assessments published over the last two decades (2000–2020), to investigate trends in research effort and identify knowledge gaps. We used generalised linear models (GLMs) and generalised linear mixed models (GLMMs) to identify taxonomic and geographical biases, and investigated biases associated with land use type and author nationality. Research effort was significantly biased towards lion (Panthera leo) and against striped hyaena (Hyaena hyaena), despite the latter being the species with the widest continental range. African wild dog (Lycaon pictus) also exhibited a negative bias in research attention, although this was partly explained by its relatively restricted distribution. The number of country assessments for a species was significantly positively associated with its geographic range in that country. Population assessments were biased towards southern and eastern Africa, particularly South Africa and Kenya. Northern, western, and central Africa were generally under-represented. Most studies were carried out in photographic tourism protected areas under government management, while non-protected and trophy hunting areas received less attention. Outside South Africa, almost half of studies (41%) did not include authors from the study country, suggesting that significant opportunities exist for capacity building in range states. Overall, large parts of Africa remain under-represented in the literature, and opportunities exist for further research on most species and in most countries. We develop recommendations for actions aimed at overcoming the identified biases and provide researchers, practitioners, and policymakers with priorities to help inform future research and monitoring agendas.
Strampelli et al. (2022) Trends and biases in African large carnivore population assessments: identifying priorities and opportunities from a systematic review of two decades of research. PeerJ 10:e14354 https://doi.org/10.7717/peerj.14354
Combined transcriptome and proteome analysis of yak PASMCs under hypoxic and normoxic conditions
Background Yaks are animals that have lived in plateau environments for generations. Yaks can adapt to the hypoxic plateau environment and also pass this adaptability on to the next generation. The lungs are the most important respiratory organs for mammals to adapt to their environment. Pulmonary artery smooth muscle cells play an important role in vascular remodeling under hypoxia, but the genetic mechanism underpinning the yak’s ability to adapt to challenging plateau conditions is still unknown. Methods A tandem mass tag (TMT) proteomics study together with an RNA-seq transcriptome analysis were carried out on pulmonary artery smooth muscle cells (PASMCs) that had been grown for 72 hours in both normoxic (20% O2) and hypoxic (1% O2) environments. RNA and TP (total protein) were collected from the hypoxic and normoxic groups for RNA-seq transcriptome sequencing and TMT marker protein quantification, and RT-qPCR validation was performed. Results A total of 17,711 genes and 6,859 proteins were identified. Further, 5,969 differentially expressed genes (DEGs) and 531 differentially expressed proteins (DEPs) were identified in the comparison group, including 2,924 and 186 upregulated genes and proteins and 3,045 and 345 down-regulated genes and proteins, respectively. The transcriptomic and proteomic analyses revealed that 109 DEGs and DEPs were highly positively correlated, with 77 genes showing the same expression trend. Nine overlapping genes were identified in the HIF-1 signaling pathway, glycolysis / gluconeogenesis, central carbon metabolism in cancer, PPAR signaling pathway, AMPK signaling pathway, and cholesterol metabolism (PGAM1, PGK1, TPI1, HMOX1, IGF1R, OLR1, SCD, FABP4 and LDLR), suggesting that these differentially expressed genes and protein functional classifications are related to the hypoxia-adaptive pathways. Overall, our study offers abundant data for further analysis of the molecular mechanisms in yak PASMCs and their adaptability to different oxygen concentrations.
Zhang et al. (2022) Combined transcriptome and proteome analysis of yak PASMCs under hypoxic and normoxic conditions. PeerJ 10:e14369 https://doi.org/10.7717/peerj.14369
Confirmation of the southern African distribution of the marine sponge Hymeniacidon perlevis (Montagu, 1814) in the context of its global dispersal
Background Intertidal rocky shore surveys along the South African coastline (∼3,000 km) have demonstrated the presence and abundance of the encrusting orange sponge Hymeniacidon perlevis (Montagu, 1814), a well-known globally distributed species. After analysing the southern African populations, we gained a better understanding of the genetic structure of this now-accepted global species. Apart from confirming the presence of a single population of H. perlevis, we also determined its distribution in the southern African intertidal rocky shore ecosystem, compared its genetic diversity to congeners, predict its global distribution via environmental niche modelling, and discussed possible underlying mechanisms controlling the species’ global distribution. Methods We surveyed the South African coastline and sampled sponges at 53 rocky shore sites spanning over 3,000 km, from Grosse Bucht south of Lüderitz (Namibia) to Kosi Bay on the east coast of South Africa. DNA sequences of the nuclear rDNA internal transcribed spacer (ITS1) and the COI mitochondrial gene were obtained from 61 samples and compared them to a world-wide sample of other H. perlevis sequences. Using environmental predictor variables from the global dataset BIO-ORACLE, we predicted the probability of global occurrence of the species using an ensemble of eight distribution models. Results South African specimens were found to be 99–100% identical to other populations of H. perlevis (=H. sinapium) from other world-wide regions. The presence of a single population of H. perlevis in southern Africa is supported by genetic data, extending its distribution to a relatively wide geographical range spanning more than 4,000 km along the temperate southern African coast. The predicted global occurrence by ensemble model matched well with the observed distribution. Surface temperature mean and range were the most important predictor variables. Conclusion While H. perlevis appears to have been introduced in many parts of the world, its origins in Europe and southern Africa are unclear.
Samaai et al. (2022) Confirmation of the southern African distribution of the marine sponge Hymeniacidon perlevis (Montagu, 1814) in the context of its global dispersal. PeerJ 10:e14388 https://doi.org/10.7717/peerj.14388
Influence of tannic acid concentration on the physicochemical characteristics of saliva of spider monkeys (Ateles geoffroyi)
Tannins are a chemical defense mechanism of plants consumed by herbivores. Variations in salivary physicochemical characteristics such as pH, total protein concentration (TP), and presence of proline-rich proteins (PRPs) in animals have been reported as a mechanism to protect the oral cavity when consuming food with variations in pH and tannins. Variations in salivary physiochemistry as adaptations for consuming tannin-rich foods have been found in omnivorous and folivorous primates, but have not yet been reported in frugivorous species such as spider monkeys. We therefore assessed changes in pH using test strips, TP concentration by measuring absorbance at 595 nm in a spectrophotometer and salivary PRPs using the SDS-PAGE electrophoresis technique in the saliva of nine captive spider monkeys in response to the consumption of solutions with different concentrations of tannic acid. The results showed variations in pH, TP concentration and the presence and variation of possible salivary PRPs associated with tannic acid concentration. These findings suggest that spider monkeys may tailor their salivary physicochemical characteristics in response to the ingestion of potentially toxic compounds.
Ramírez-Torres et al. (2022) Influence of tannic acid concentration on the physicochemical characteristics of saliva of spider monkeys (Ateles geoffroyi). PeerJ 10:e14402 https://doi.org/10.7717/peerj.14402
Canopy spectral reflectance indices correlate with yield traits variability in bread wheat genotypes under drought stress
Drought stress is a major issue impacting wheat growth and yield worldwide, and it is getting worse as the world’s climate changes. Thus, selection for drought-adaptive traits and drought-tolerant genotypes are essential components in wheat breeding programs. The goal of this study was to explore how spectral reflectance indices (SRIs) and yield traits in wheat genotypes changed in irrigated and water-limited environments. In two wheat-growing seasons, we evaluated 56 preselected wheat genotypes for SRIs, stay green (SG), canopy temperature depression (CTD), biological yield (BY), grain yield (GY), and yield contributing traits under control and drought stress, and the SRIs and yield traits exhibited higher heritability (H2) across the growing years. Diverse SRIs associated with SG, pigment content, hydration status, and aboveground biomass demonstrated a consistent response to drought and a strong association with GY. Under drought stress, GY had stronger phenotypic correlations with SG, CTD, and yield components than in control conditions. Three primary clusters emerged from the hierarchical cluster analysis, with cluster I (15 genotypes) showing minimal changes in SRIs and yield traits, indicating a relatively higher level of drought tolerance than clusters II (26 genotypes) and III (15 genotypes). The genotypes were appropriately assigned to distinct clusters, and linear discriminant analysis (LDA) demonstrated that the clusters differed significantly. It was found that the top five components explained 73% of the variation in traits in the principal component analysis, and that vegetation and water-based indices, as well as yield traits, were the most important factors in explaining genotypic drought tolerance variation. Based on the current study’s findings, it can be concluded that proximal canopy reflectance sensing could be used to screen wheat genotypes for drought tolerance in water-starved environments.
Mohi-Ud-Din et al. (2022) Canopy spectral reflectance indices correlate with yield traits variability in bread wheat genotypes under drought stress. PeerJ 10:e14421 https://doi.org/10.7717/peerj.14421
Comparison of frozen-thawed embryo transfer strategies for the treatment of infertility in young women: a retrospective study
Objective To investigate transfer strategies in the frozen-thawed embryo transfer (FET) cycle. Methods The clinical data of 1,652 FET patients were divided into five groups according to the number and quality of the transferred blastocyst: high-quality single blastocyst group (group A, n = 558), high-quality plus poor-quality double blastocyst group (group B, n = 435), poor-quality double blastocyst group (group C, n = 241), high-quality double blastocyst group (group D, n = 298), and poor-quality single blastocyst group (group E, n = 120). Inter-group comparison analyses of primary conditions, pregnancy outcomes and neonatal outcomes were then performed. Results Group A had the highest embryo implantation rate (67.38%), significantly different from the implantation rates of the other four groups. The gemellary pregnancy rate (1.60%), preterm birth rate (5.58%), neonatal birth weight (3,350g [3,000g, 3,650g]), neonatal birth age (39.57 weeks [38.71, 40.34]), and incidence of low birth weight (7.02%) in group A were different from those in groups B, C, and D, but did not significantly differ from those in group E. Moreover, the proportions of male infants born in groups A (56.86%) and D (59.41%) were significantly higher than those in the other three groups. Double blastocyst transfer (0.528, 95% CI [0.410–0.680], P < 0.001) and high-quality blastocyst transfer (0.609, 95% CI [0.453–0.820], P = 0.001) were found to be protective factors for live birth. In addition, double blastocyst transfer was also the largest risk factor for pregnancy complications (3.120, 95% CI [2.323–4.190], P < 0.001) and neonatal complications (2.230, 95% CI [1.515–3.280], P < 0.001), especially for gemellary pregnancy (59.933, 95% CI [27.298–131.58], P < 0.001) and preterm birth (3.840, 95% CI [2.272–6.489], P < 0.001). Based on the ROC curves, a double blastocyst transfer could predict gemellary pregnancy reliably with a high area under the curve (AUC = 78.53%). Additionally, a double blastocyst transfer could effectively predict a high risk of pregnancy complications (AUC = 65.90%), neonatal complications (AUC = 64.80%) and preterm birth (AUC = 66.20%). Conclusion The live birth rate of frozen-thawed high-quality single blastocyst transfer is lower than that of double high-quality blastocyst transfer, which can significantly increase the embryo implantation rate. High-quality single blastocyst transfer also significantly lowers the risk of gemellary pregnancy, preterm birth, and low birth weight, and can significantly improve maternal and infant outcomes. After weighing the pros and cons of live birth with pregnancy and neonatal complications, the authors believe that high-quality single blastocyst transfer is the optimal FET strategy for young women and is worthy of further clinical application. Despite this recommendation, high-quality single blastocyst transfer can increase the risk of monozygotic twins, as well as significantly increase the proportion of male infants born.
Wu et al. (2022) Comparison of frozen-thawed embryo transfer strategies for the treatment of infertility in young women: a retrospective study. PeerJ 10:e14424 https://doi.org/10.7717/peerj.14424
Scaredy-cats don’t succeed: behavioral traits predict problem-solving success in captive felidae
Behavioral traits can be determined from the consistency in an animal’s behaviors across time and situations. These behavioral traits may have been differentially selected in closely related species. Studying the structure of these traits across species within an order can inform a better understanding of the selection pressures under which behavior evolves. These adaptive traits are still expected to vary within individuals and might predict general cognitive capacities that facilitate survival, such as behavioral flexibility. We derived five facets (Flexible/Friendly, Fearful/Aggressive, Uninterested, Social/Playful, and Cautious) from behavioral trait assessments based on zookeeper surveys in 52 Felidae individuals representing thirteen species. We analyzed whether age, sex, species, and these facets predicted success in a multi access puzzle box–a measure of innovation. We found that Fearful/Aggressive and Cautious facets were negatively associated with success. This research provides the first test of the association between behavioral trait facets and innovation in a diverse group of captive felidae. Understanding the connection between behavioral traits and problem-solving can assist in ensuring the protection of diverse species in their natural habitats and ethical treatment in captivity.
O’Connor et al. (2022) Scaredy-cats don’t succeed: behavioral traits predict problem-solving success in captive felidae. PeerJ 10:e14453 https://doi.org/10.7717/peerj.14453
Recovery of sweet taste preference in adult rats following bilateral chorda tympani nerve transection
Background Numerous studies have noted the effect of chorda tympani (CT) nerve transection on taste sensitivity yet very few have directly observed its effects on taste receptor and taste signaling protein expressions in the tongue tissue. Methods In this study, bilateral CT nerve transection was performed in adult Sprague Dawley rats after establishing behavioral taste preference for sweet, bitter, and salty taste via short term two-bottle preference testing using a lickometer setup. Taste preference for all animals were subsequently monitored. The behavioral testing was paired with tissue sampling and protein expression analysis. Paired groups of CT nerve transected animals (CTX) and sham operated animals (SHAM) were sacrificed 7, 14, and 28 days post operation. Results Immunofluorescence staining of extracted tongue tissues shows that CT nerve transection resulted in micro-anatomical changes akin to previous investigations. Among the three taste qualities tested, only the preference for sweet taste was drastically affected. Subsequent results of the short-term two-bottle preference test indicated recovery of sweet taste preference over the course of 28 days. This recovery could possibly be due to maintenance of T1R3, GNAT3, and TRPM5 proteins allowing adaptable recovery of sweet taste preference despite down-regulation of both T1R2 and Sonic hedgehog proteins in CTX animals. This study is the first known attempt to correlate the disruption in taste preference with the altered expression of taste receptors and taste signaling proteins in the tongue brought about by CT nerve transection.
Padalhin et al. (2022) Recovery of sweet taste preference in adult rats following bilateral chorda tympani nerve transection. PeerJ 10:e14455 https://doi.org/10.7717/peerj.14455
A transitional species of Daspletosaurus Russell, 1970 from the Judith River Formation of eastern Montana
Here we describe a new derived tyrannosaurine, Daspletosaurus wilsoni sp. nov., from Judithian strata (~76.5 Ma) intermediate in age between either of the previously described species of this genus. D. wilsoni displays a unique combination of ancestral and derived characteristics, including a cornual process of the lacrimal reduced in height relative to D. torosus and more basal tyrannosaurines, and a prefrontal with a long axis oriented more rostrally than in D. horneri and more derived tyrannosaurines. The description of this taxon provides insight into evolutionary mode in Tyrannosaurinae, lending strength to previous hypotheses of anagenesis within Daspletosaurus and increasing the resolution with which the evolution of this lineage can be reconstructed. Cladistic phylogenetic methods, stratigraphy, and qualitative analysis of the morphology of relevant taxa supports an anagenetic model for the origin of morphological novelty in this genus, highlighting the predominance of anagenetic evolution among contemporary dinosaur lineages.
Warshaw et al. (2022) A transitional species of Daspletosaurus Russell, 1970 from the Judith River Formation of eastern Montana. PeerJ 10:e14461 https://doi.org/10.7717/peerj.14461
Stroke-related length of hospitalization trends and in-hospital mortality in Peru
Background Peru faces challenges to provide adequate care to stroke patients. Length of hospitalization and in-hospital mortality are two well-known indicators of stroke care. We aimed to describe the length of stay (LOS) of stroke in Peru, and to assess in-hospital mortality risk due to stroke, and subtypes. Methods This retrospective cohort study used hospitalization registries coding with ICD-10 from 2002 to 2017 (N = 98,605) provided by the Ministry of Health; in-hospital mortality was available for 2016–2017 (N = 6,566). Stroke cases aged ≥35 years were divided into subarachnoid hemorrhage (I60), intracerebral hemorrhage (I61), cerebral infarction (I63), and stroke not specified as hemorrhage or infarction (I64). Data included stroke LOS and in-hospital mortality; socio-demographic and clinical variables. We fitted a region- and hospital level-stratified Weibull proportional hazard model to assess the in-hospital mortality. Results The median LOS was 7 days (IQR: 4–13). Hemorrhagic strokes had median LOS longer than ischemic strokes and stroke not specified as hemorrhage or infarction (P = <0.001). The case fatality rate (CFR) of patients with stroke was 11.5% (95% CI [10–12%]). Subarachnoid hemorrhage (HR = 2.45; 95% CI [1.91–3.14]), intracerebral hemorrhage (HR = 1.95; 95% CI [1.55–2.46]), and stroke not specified as hemorrhage or infarction (HR = 1.45; 95% CI [1.16–1.81]) were associated with higher in-hospital mortality risk in comparison to ischemic strokes. Discussion Between 2002 and 2017, LOS due to stroke has not changed in Peru in stroke patients discharged alive. Hemorrhagic cases had the longest LOS and highest in-hospital mortality risk during 2016 and 2017. The findings of our study seem to be consistent with a previous study carried out in Peru and similar to that of HIC and LMIC, also there is an increased median LOS in stroke cases managed in specialized centers. Likewise, LOS seems to depend on the type of stroke, where ischemic stroke cases have the lowest LOS. Peru needs to improve access to stroke care.
Labán-Seminario et al. (2022) Stroke-related length of hospitalization trends and in-hospital mortality in Peru. PeerJ 10:e14467 https://doi.org/10.7717/peerj.14467