Context‐dependency in carnivore co‐occurrence across a multi‐use conservation landscape

Carnivore intraguild dynamics depend on a complex interplay of environmental affinities and interspecific interactions. Context‐dependency is commonly expected with varying suites of interacting species and environmental conditions but seldom empirically described. In South Africa, decentralized approaches to conservation and the resulting multi‐tenure conservation landscapes have markedly altered the environmental stage that shapes the structure of local carnivore assemblages. We explored assemblage‐wide patterns of carnivore spatial (residual occupancy probability) and temporal (diel activity overlap) co‐occurrence across three adjacent wildlife‐oriented management contexts—a provincial protected area, a private ecotourism reserve, and commercial game ranches. We found that carnivores were generally distributed independently across space, but existing spatial dependencies were context‐specific. Spatial overlap was most common in the protected area, where species occur at higher relative abundances, and in game ranches, where predator persecution presumably narrows the scope for spatial asymmetries. In the private reserve, spatial co‐occurrence patterns were more heterogeneous but did not follow a dominance hierarchy associated with higher apex predator densities. Pair‐specific variability suggests that subordinate carnivores may alternate between pre‐emptive behavioral strategies and fine‐scale co‐occurrence with dominant competitors. Consistency in species‐pairs diel activity asynchrony suggested that temporal overlap patterns in our study areas mostly depend on species'' endogenous clock rather than the local context. Collectively, our research highlights the complexity and context‐dependency of guild‐level implications of current management and conservation paradigms; specifically, the unheeded potential for interventions to influence the local network of carnivore interactions with unknown population‐level and cascading effects.     

Decay of TRPV3 as the genomic trace of epidermal structure changes in the land‐to‐sea transition of mammals

The epidermis plays an indispensable barrier function in animals. Some species have evolved unique epidermal structures to adapt to different environments. Aquatic and semi‐aquatic mammals (cetaceans, manatees, and hippopotamus) are good models to study the evolution of epidermal structures because of their exceptionally thickened stratum spinosum, the lack of stratum granulosum, and the parakeratotic stratum corneum. This study aimed to analyze an upstream regulatory gene transient receptor potential cation channel, subfamily V, member 3 (TRPV3) of epidermal differentiation so as to explore the association between TRPV3 evolution and epidermal changes in mammals. Inactivating mutations were detected in almost all the aquatic cetaceans and several terrestrial mammals. Relaxed selective pressure was examined in the cetacean lineages with inactivated TRPV3, which might contribute to its exceptionally thickened stratum spinosum as the significant thickening of stratum spinosum in TRPV3 knock‐out mouse. However, functional TRPV3 may exist in several terrestrial mammals due to their strong purifying selection, although they have “inactivating mutations.” Further, for intact sequences, relaxed selective constraints on the TRPV3 gene were also detected in aquatic cetaceans, manatees, and semi‐aquatic hippopotamus. However, they had intact TRPV3, suggesting that the accumulation of inactivating mutations might have lagged behind the relaxed selective pressure. The results of this study revealed the decay of TRPV3 being the genomic trace of epidermal development in aquatic and semi‐aquatic mammals. They provided insights into convergently evolutionary changes of epidermal structures during the transition from the terrestrial to the aquatic environment.     

Feeding ecology and diet of the southern geladas (Theropithecus gelada obscurus) in human‐modified landscape,Wollo, Ethiopia

Studying the dietary flexibility of primates that live in human‐modified environments is crucial for understanding their ecological adaptations as well as developing management and conservation plans. Southern gelada (Theropithecus gelada obscurus) is an endemic little‐known subspecies of gelada that inhabits human‐modified landscapes in the northern central highlands of Ethiopia. During an 18‐month period, we conducted this intensive study in an unprotected area of a human‐modified landscape at Kosheme in Wollo to investigate the feeding ecology of southern geladas and their dietary responses to seasonal variations. We quantified the monthly and seasonal diet data from a band of southern geladas using instantaneous scan sampling method at 15‐min intervals, and green grass phenology and availability using visual inspection from the randomly selected permanent plots. The overall average diet of southern geladas at Kosheme constituted grass blades 55.4%, grass undergrounds 13.2%, grass bulbs 5.6%, grass seeds 5.4%, herb leaves 4.0, fruits 7.3%, and cereal crops 5.6%. Grass blade consumption increased with increasing green grass availability, while underground food consumption increased with decreasing green grass availability, and vice versa. Southern geladas spent significantly more time feeding on the grass blades and herb leaves and significantly less time on bulbs during the wet season than the dry season. Underground grass items (rhizomes and corms) were not consumed during the wet season, but made up 22.3% of the dry season diet. Thus, although grass blades are staple diet items for geladas, underground diet items are important “fallback foods” at Kosheme. Our result shows insights into the dietary flexibility southern geladas adopt to cope with human‐modified landscapes of the north‐central Ethiopian Highlands. Thus, the study contributes to a better understanding of how changing environments shape primate ecology and evolution.     

Neutralization of SARS‐CoV‐2 by highly potent,hyperthermostable, and mutation‐tolerant nanobodies

Monoclonal anti‐SARS‐CoV‐2 immunoglobulins represent a treatment option for COVID‐19. However, their production in mammalian cells is not scalable to meet the global demand. Single‐domain (VHH) antibodies (also called nanobodies) provide an alternative suitable for microbial production. Using alpaca immune libraries against the receptor‐binding domain (RBD) of the SARS‐CoV‐2 Spike protein, we isolated 45 infection‐blocking VHH antibodies. These include nanobodies that can withstand 95°C. The most effective VHH antibody neutralizes SARS‐CoV‐2 at 17–50 pM concentration (0.2–0.7 µg per liter), binds the open and closed states of the Spike, and shows a tight RBD interaction in the X‐ray and cryo‐EM structures. The best VHH trimers neutralize even at 40 ng per liter. We constructed nanobody tandems and identified nanobody monomers that tolerate the K417N/T, E484K, N501Y, and L452R immune‐escape mutations found in the Alpha, Beta, Gamma, Epsilon, Iota, and Delta/Kappa lineages. We also demonstrate neutralization of the Beta strain at low‐picomolar VHH concentrations. We further discovered VHH antibodies that enforce native folding of the RBD in the E. coli cytosol, where its folding normally fails. Such “fold‐promoting” nanobodies may allow for simplified production of vaccines and their adaptation to viral escape‐mutations.     

Phospho‐regulation,nucleotide binding and ion access control in potassium‐chloride cotransporters

Potassium‐coupled chloride transporters (KCCs) play crucial roles in regulating cell volume and intracellular chloride concentration. They are characteristically inhibited under isotonic conditions via phospho‐regulatory sites located within the cytoplasmic termini. Decreased inhibitory phosphorylation in response to hypotonic cell swelling stimulates transport activity, and dysfunction of this regulatory process has been associated with various human diseases. Here, we present cryo‐EM structures of human KCC3b and KCC1, revealing structural determinants for phospho‐regulation in both N‐ and C‐termini. We show that phospho‐mimetic KCC3b is arrested in an inward‐facing state in which intracellular ion access is blocked by extensive contacts with the N‐terminus. In another mutant with increased isotonic transport activity, KCC1Δ19, this interdomain interaction is absent, likely due to a unique phospho‐regulatory site in the KCC1 N‐terminus. Furthermore, we map additional phosphorylation sites as well as a previously unknown ATP/ADP‐binding pocket in the large C‐terminal domain and show enhanced thermal stabilization of other CCCs by adenine nucleotides. These findings provide fundamentally new insights into the complex regulation of KCCs and may unlock innovative strategies for drug development.     

Camera trap reveals the co‐occurrence patterns of two sympatric muntjac species in southern Anhui Province,China: No spatial segregation

The competitive relationship and coexistence pattern among close related species have long been one of the hot issues in ecological research. Interspecies interactions can exert important influences on the local distribution of rare species. Black muntjac Muntiacus crinifrons is an endemic species to eastern China, currently restricted to limited regions. In contrast, Chinese muntjac Muntiacus reevesi is the most common and widespread deer in southern China. Both species co‐occur in southern Anhui and western Zhejiang Province. Little is known about the interaction of these two sympatric‐related species. In this study, to investigate the site use determinants and co‐occurrence pattern of the two sympatric muntjac species, we conducted a camera trap survey across about 250 km² in mountainous area of southern Anhui Province, China. We adopted a multistep approach to incorporate habitat preferences while modeling occupancy and detection. We found that the two species did not separate along elevation gradient (range from 400 m to 1,400 m) as described in previous studies. Results of single‐species occupancy models indicated that elevation had positive effects on the site use of both species, while slope had an opposite influence on their site use. Positive effects of elevation on the site use implied that both species try to avoid human interference at low elevations. Significant negative effect of slope on the site use of black muntjac suggested that the species prefer habitat with gentle slope and avoided steep. Co‐occurrence models and species interaction factors provided evidence that the two muntjac species had an independent occupancy (ψ ^{BM CM} = ψ ^{BM cm}, SIF = 1) and exhibited a positive species interaction in detection probability (p ^BM < r ^{BM CM}). Combined with the results of previous studies, we suggested that it was fine differentiation in microhabitats and food resources utilization rather spatial or temporal segregation that allowed the two species co‐occurrence. The site use determinants revealed in our study would be useful for the habitat conservation and restoration for the rare black muntjac, and the co‐occurrence pattern of the two sympatric muntjac species could provide useful information for deep understanding of the coexistence mechanism among forest‐dwelling ungulates.     

Age‐specific habitat preference,carrying capacity,and landscape structure determine the response of population spatial variability to fishing‐driven age truncation

1. Understanding the mechanisms underlying spatial variability of exploited fish is critical for the sustainable management of fish stocks. Empirical studies suggest that size‐selective fishing can elevate fish population spatial variability (i.e., more heterogeneous distribution) through age truncation, making the population less resilient to changing environment. However, species differ in how their spatial variability responds to age truncation and the underlying mechanisms remain unclear.
2. We hypothesize that age‐specific habitat preference, together with environmental carrying capacity and landscape structure, determines the response of population spatial variability to fishing‐induced age truncation. To test these hypotheses, we design an individual‐based model of an age‐structured fish population on a two‐dimensional landscape under size‐selective fishing. Individual fish reproduces and survives, and moves between habitats according to age‐specific habitat preference and density‐dependent habitat selection.
3. Population spatial variability elevates with increasing age truncation, and the response is stronger for populations with stronger age‐specific habitat preference. On a gradient landscape, reducing carrying capacity elevates the relative importance of density dependence in habitat selection, which weakens the response of spatial variability to age truncation for populations with strong age‐specific habitat preference. On a fragmented landscape, both populations with strong and weak age‐specific habitat preferences are restricted at local optimal habitats, and reducing carrying capacity weakens the responses of spatial variability to age truncation for both populations.
4. Synthesis and applications. We demonstrate that to track and predict the changes in population spatial variability under exploitation, it is essential to consider the interactive effects of age‐specific habitat preference, carrying capacity, and landscape structure. To improve spatial management in fisheries, it is crucial to enhance empirical and theoretical developments in the methodology to quantify age‐specific habitat preference of marine fish, and to understand how climatic change influences carrying capacity and landscape continuity.

     

Antelope space‐use and behavior indicate multilevel responses to varying anthropogenic influences in a highly human‐dominated landscape

A primary means of conserving a species or a habitat in a human‐dominated landscape is through promoting coexistence with humans while minimizing conflict. For this, we should understand how wildlife is impacted by direct and indirect human activities. Such information is rare in areas with high human densities. To investigate how animals respond to altered ecological conditions in human‐dominated landscapes, we focused on a wild herbivore of conservation concern in the Krishnasaar Conservation Area (KrCA) in Nepal. Here, blackbuck Antilope cervicapra, a generalist grazer, lives in refugia located with a growing human population. We studied the impacts of humans on habitat use and behavior of blackbuck. We laid 250 × 250 m grid cells in the entire KrCA and carried out indirect sign surveys with three replications for habitat use assessment. We observed herds of blackbuck for 89 h in different habitat types using scan sampling methods. Our habitat‐use survey showed that habitats under intensive human use were hardly used by blackbuck, even when high‐quality forage was available. Habitat openness was the major predictor of habitat use inside the core area, where levels of human activities were low. We also found a positive correlation between habitat use by blackbuck and livestock. Blackbuck were substantially more vigilant when they were in forest than in grassland, again indicating an influence of risk. Overall, blackbuck appear to be sensitive to the risk associated with both natural and anthropogenic factors. Our findings have direct implications for managing human–wildlife interactions in this landscape, specifically regarding strategies for livestock grazing in habitats highly used by blackbuck and concerning predictions of how changing land use will impact the long‐term persistence of blackbuck. Our work suggests that wild herbivores may be able to persist in landscapes with high human densities so long as there are refuges where human activities are relatively low.     

四川海子山自然保护区大中型兽类多样性调查

四川海子山自然保护区地处四川省甘孜藏族自治州理塘县和稻城县境内,东经99°33′00″～100°31′48″, 北纬29°06′36″～30°06′00″,保护区总面积459 161 hm2,区内海拔3 160～6 204 m.主要以山原和丘状高原地形为主.属寒温带,海拔高,属高原气候,年均气温3.0 ℃,年均降水量600～750 mm,雨季为6～8月.全年日照时数为2 637.7 h.随着海拔升高,气温和热量下降,降水量增加.在四川植被区划中属川西山原植被地区、沙鲁里山北部植被小区.保护区植被大致可分为以下7种类型:     

Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial

Advancements in mass spectrometry‐based proteomics have enabled experiments encompassing hundreds of samples. While these large sample sets deliver much‐needed statistical power, handling them introduces technical variability known as batch effects. Here, we present a step‐by‐step protocol for the assessment, normalization, and batch correction of proteomic data. We review established methodologies from related fields and describe solutions specific to proteomic challenges, such as ion intensity drift and missing values in quantitative feature matrices. Finally, we compile a set of techniques that enable control of batch effect adjustment quality. We provide an R package, "proBatch", containing functions required for each step of the protocol. We demonstrate the utility of this methodology on five proteomic datasets each encompassing hundreds of samples and consisting of multiple experimental designs. In conclusion, we provide guidelines and tools to make the extraction of true biological signal from large proteomic studies more robust and transparent, ultimately facilitating reliable and reproducible research in clinical proteomics and systems biology.     

Molecular evidence suggesting the persistence of residual SARS‐CoV‐2 and immune responses in the placentas of pregnant patients recovered from COVID‐19

ObjectivesRecent studies have shown the presence of SARS‐CoV‐2 in the tissues of clinically recovered patients and persistent immune symptoms in discharged patients for up to several months. Pregnant patients were shown to be a high‐risk group for COVID‐19. Based on these findings, we assessed SARS‐CoV‐2 nucleic acid and protein retention in the placentas of pregnant women who had fully recovered from COVID‐19 and cytokine fluctuations in maternal and foetal tissues.Materials and MethodsRemnant SARS‐CoV‐2 in the term placenta was detected using nucleic acid amplification and immunohistochemical staining of the SARS‐CoV‐2 protein. The infiltration of CD14+ macrophages into the placental villi was detected by immunostaining. The cytokines in the placenta, maternal plasma, neonatal umbilical cord, cord blood and amniotic fluid specimens at delivery were profiled using the Luminex assay.ResultsResidual SARS‐CoV‐2 nucleic acid and protein were detected in the term placentas of recovered pregnant women. The infiltration of CD14+ macrophages into the placental villi of the recovered pregnant women was higher than that in the controls. Furthermore, the cytokine levels in the placenta, maternal plasma, neonatal umbilical cord, cord blood and amniotic fluid specimens fluctuated significantly.ConclusionsOur study showed that SARS‐CoV‐2 nucleic acid (in one patient) and protein (in five patients) were present in the placentas of clinically recovered pregnant patients for more than 3 months after diagnosis. The immune responses induced by the virus may lead to prolonged and persistent symptoms in the maternal plasma, placenta, umbilical cord, cord blood and amniotic fluid.     

Variation of the seed endophytic bacteria among plant populations and their plant growth‐promoting activities in a wild mustard plant species,Capsella bursa‐pastoris

Recent studies have revealed that some bacteria can inhabit plant seeds, and they are likely founders of the bacterial community in the rhizosphere of or inside plants at the early developmental stage. Given that the seedling establishment is a critical fitness component of weedy plant species, the effects of seed endophytic bacteria (SEB) on the seedling performance are of particular interest in weed ecology. Here, we characterized the SEB in natural populations of Capsella bursa‐pastoris, a model species of weed ecology. The composition of endophytic bacterial community was evaluated using deep sequencing of a 16S rDNA gene fragment. Additionally, we isolated bacterial strains from seeds and examined their plant growth‐promoting traits. Actinobacteria, Firmicutes, Alpha‐, and Gammaproteobacteria were major bacterial phyla inside seeds. C. bursa‐pastoris natural populations exhibited variable seed microbiome such that the proportion of Actinobacteria and Alphaproteobacteria differed among populations, and 60 out of 82 OTUs occurred only in a single population. Thirteen cultivable bacterial species in six genera (Bacillus, Rhodococcus, Streptomyces, Staphylococcus, Paenibacillus, Pseudomonas) were isolated, and none of them except Staphylococcus haemolyticus were previously reported as seed endophytes. Eight isolates exhibited plant growth‐promoting traits like phosphate solubilization activity, indole‐3‐acetic acid, or siderophore production. Despite the differences in the bacterial communities among plant populations, at least one isolated strain from each population stimulated shoot growth of either C. bursa‐pastoris or its close relative A. thaliana when grown with plants in the same media. These results suggest that a weedy plant species, C. bursa‐pastoris, contains bacterial endophytes inside their seeds, stimulating seedling growth and thereby potentially affecting seedling establishment.     

Elevation‐related climatic factors dominate soil free‐living nematode communities and their co‐occurrence patterns on Mt. Halla,South Korea

Nematodes play vital roles in soil ecosystems. To understand how their communities and coexistence patterns change along the elevation as well as to determine the best explanatory factors underlying these changes, we investigated free‐living soil nematodes on Mt. Halla, South Korea, using an amplicon sequencing approach targeting the 18S rRNA gene. Our results showed that there was significant variation in the community diversity and composition of soil nematodes in relation to elevation. The network interactions between soil nematodes were more intensive at the lower elevations. Climatic variables were responsible explaining the elevational variation in community composition and co‐occurrence pattern of the nematode community. Our study indicated that climatic factors served as the critical environmental filter that influenced not only the community structure but also the potential associations of soil nematodes in the mountain ecosystem of Mt. Halla. These findings enhance the understanding of the community structure and co‐occurrence network patterns and mechanisms of soil nematode along elevation, and the response of soil nematodes to climate change on the vertical scale of mountain ecosystems.     

Density‐dependent demography and movements in a cyclic brown lemming population

Theoretical modeling predicts that both direct and delayed density‐dependence are key factors to generate population cycles. Deciphering density‐dependent processes that lead to variable population growth characterizing different phases of the cycles remains challenging. This is particularly the case for the period of prolonged low densities, which is inherently data deficient. However, demographic analyses based on long‐term capture–mark–recapture datasets can help resolve this question. We relied on a 16‐year (2004–2019) live‐trapping program to analyze the summer demography and movements of a cyclic brown lemming population in the Canadian Arctic. More specifically, we examined if inversely density‐dependent processes could explain why population growth can remain low during the prolonged low phase. We found that the proportion of females in the population was inversely density‐dependent with a strong male‐biased sex ratio at low densities but not at high densities. However, survival of adult females was higher than adult males, but both had lower survival at low densities than at high ones. Distances moved by both adult males and females were density‐dependent, and proportion of females in reproductive condition was weakly density‐dependent as it tended to increase at low density. Individual body condition, measured as monthly change in body mass, was not density‐dependent. Overall, the strong male‐biased sex ratio at very low densities suggests a loss of reproductive potential due to the rarity of females and appears to be the most susceptible demographic factor that could contribute to the prolonged low phase in cyclic brown lemmings. What leads to this sex‐bias in the first place is still unclear, potentially owing to our trapping period limited to the summer, but we suggest that it could be due to high predation rate on breeding females in winter.