Genomic association with pathogen carriage in bighorn sheep (Ovis canadensis)

Genetic composition can influence host susceptibility to, and transmission of, pathogens, with potential population‐level consequences. In bighorn sheep (Ovis canadensis), pneumonia epidemics caused by Mycoplasma ovipneumoniae have been associated with severe population declines and limited recovery across North America. Adult survivors either clear the infection or act as carriers that continually shed M. ovipneumoniae and expose their susceptible offspring, resulting in high rates of lamb mortality for years following the outbreak event. Here, we investigated the influence of genomic composition on persistent carriage of M. ovipneumoniae in a well‐studied bighorn sheep herd in the Wallowa Mountains of Oregon, USA. Using 10,605 SNPs generated using RADseq technology for 25 female bighorn sheep, we assessed genomic diversity metrics and employed family‐based genome‐wide association methodologies to understand variant association and genetic architecture underlying chronic carriage. We observed no differences among genome‐wide diversity metrics (heterozygosity and allelic richness) between groups. However, we identified two variant loci of interest and seven associated candidate genes, which may influence carriage status. Further, we found that the SNP panel explained ~55% of the phenotypic variance (SNP‐based heritability) for M. ovipneumoniae carriage, though there was considerable uncertainty in these estimates. While small sample sizes limit conclusions drawn here, our study represents one of the first to assess the genomic factors influencing chronic carriage of a pathogen in a wild population and lays a foundation for understanding genomic influence on pathogen persistence in bighorn sheep and other wildlife populations. Future research should incorporate additional individuals as well as distinct herds to further explore the genomic basis of chronic carriage.     

Natural history of a bighorn sheep pneumonia epizootic: Source of infection,course of disease,and pathogen clearance

A respiratory disease epizootic at the National Bison Range (NBR) in Montana in 2016–2017 caused an 85% decline in the bighorn sheep population, documented by observations of its unmarked but individually identifiable members, the subjects of an ongoing long‐term study. The index case was likely one of a small group of young bighorn sheep on a short‐term exploratory foray in early summer of 2016. Disease subsequently spread through the population, with peak mortality in September and October and continuing signs of respiratory disease and sporadic mortality of all age classes through early July 2017. Body condition scores and clinical signs suggested that the disease affected ewe groups before rams, although by the end of the epizootic, ram mortality (90% of 71) exceeded ewe mortality (79% of 84). Microbiological sampling 10 years to 3 months prior to the epizootic had documented no evidence of infection or exposure to Mycoplasma ovipneumoniae at NBR, but during the epizootic, a single genetic strain of M. ovipneumoniae was detected in affected animals. Retrospective screening of domestic sheep flocks near the NBR identified the same genetic strain in one flock, presumptively the source of the epizootic infection. Evidence of fatal lamb pneumonia was observed during the first two lambing seasons following the epizootic but was absent during the third season following the death of the last identified M. ovipneumoniae carrier ewe. Monitoring of life‐history traits prior to the epizootic provided no evidence that environmentally and/or demographically induced nutritional or other stress contributed to the epizootic. Furthermore, the epizootic occurred despite proactive management actions undertaken to reduce risk of disease and increase resilience in this population. This closely observed bighorn sheep epizootic uniquely illustrates the natural history of the disease including the (presumptive) source of spillover, course, severity, and eventual pathogen clearance.     

The performance of field sampling for parasite detection in a wild passerine

Parasites can impact the behavior of animals and alter the interplay with ecological factors in their environment. Studying the effects that parasites have on animals thus requires accurate estimates of infections in individuals. However, quantifying parasites can be challenging due to several factors. Laboratory techniques, physiological fluctuations, methodological constraints, and environmental influences can introduce measurement errors, in particular when screening individuals in the wild. These issues are pervasive in ecological studies where it is common to sample study subjects only once. Such factors should be carefully considered when choosing a sampling strategy, yet presently there is little guidance covering the major sources of error. In this study, we estimate the reliability and sensitivity of different sampling practices at detecting two internal parasites—Serratospiculoides amaculata and Isospora sp.—in a model organism, the great tit Parus major. We combine field and captive sampling to assess whether individual parasite infection status and load can be estimated from single field samples, using different laboratory techniques—McMaster and mini‐FLOTAC. We test whether they vary in their performance, and quantify how sample processing affects parasite detection rates. We found that single field samples had elevated rates of false negatives. By contrast, samples collected from captivity over 24 h were highly reliable (few false negatives) and accurate (repeatable in the intensity of infection). In terms of methods, we found that the McMaster technique provided more repeatable estimates than the mini‐FLOTAC for S. amaculata eggs, and both techniques were largely equally suitable for Isospora oocysts. Our study shows that field samples are likely to be unreliable in accurately detecting the presence of parasites and, in particular, for estimating parasite loads in songbirds. We highlight important considerations for those designing host–parasite studies in captive or wild systems giving guidance that can help select suitable methods, minimize biases, and acknowledge possible limitations.     

Epizootic Pneumonia of Bighorn Sheep following Experimental Exposure to Mycoplasma ovipneumoniae

Background

Bronchopneumonia is a population limiting disease of bighorn sheep (Ovis canadensis). The cause of this disease has been a subject of debate. Leukotoxin expressing Mannheimia haemolytica and Bibersteinia trehalosi produce acute pneumonia after experimental challenge but are infrequently isolated from animals in natural outbreaks. Mycoplasma ovipneumoniae, epidemiologically implicated in naturally occurring outbreaks, has received little experimental evaluation as a primary agent of bighorn sheep pneumonia.

Methodology/Principal Findings

In two experiments, bighorn sheep housed in multiple pens 7.6 to 12 m apart were exposed to M. ovipneumoniae by introduction of a single infected or challenged animal to a single pen. Respiratory disease was monitored by observation of clinical signs and confirmed by necropsy. Bacterial involvement in the pneumonic lungs was evaluated by conventional aerobic bacteriology and by culture-independent methods. In both experiments the challenge strain of M. ovipneumoniae was transmitted to all animals both within and between pens and all infected bighorn sheep developed bronchopneumonia. In six bighorn sheep in which the disease was allowed to run its course, three died with bronchopneumonia 34, 65, and 109 days after M. ovipneumoniae introduction. Diverse bacterial populations, predominantly including multiple obligate anaerobic species, were present in pneumonic lung tissues at necropsy.

Conclusions/Significance

Exposure to a single M. ovipneumoniae infected animal resulted in transmission of infection to all bighorn sheep both within the pen and in adjacent pens, and all infected sheep developed bronchopneumonia. The epidemiologic, pathologic and microbiologic findings in these experimental animals resembled those seen in naturally occurring pneumonia outbreaks in free ranging bighorn sheep.     

Predicting distributions of Wolbachia strains through host ecological contact—Who's manipulating whom?

Reproductive isolation in response to divergent selection is often mediated via third‐party interactions. Under these conditions, speciation is inextricably linked to ecological context. We present a novel framework for understanding arthropod speciation as mediated by Wolbachia, a microbial endosymbiont capable of causing host cytoplasmic incompatibility (CI). We predict that sympatric host sister‐species harbor paraphyletic Wolbachia strains that provide CI, while well‐defined congeners in ecological contact and recently diverged noninteracting congeners are uninfected due to Wolbachia redundancy. We argue that Wolbachia provides an adaptive advantage when coupled with reduced hybrid fitness, facilitating assortative mating between co‐occurring divergent phenotypes—the contact contingency hypothesis. To test this, we applied a predictive algorithm to empirical pollinating fig wasp data, achieving up to 91.60% accuracy. We further postulate that observed temporal decay of Wolbachia incidence results from adaptive host purging—adaptive decay hypothesis—but implementation failed to predict systematic patterns. We then account for post‐zygotic offspring mortality during CI mating, modeling fitness clines across developmental resources—the fecundity trade‐off hypothesis. This model regularly favored CI despite fecundity losses. We demonstrate that a rules‐based algorithm accurately predicts Wolbachia infection status. This has implications among other systems where closely related sympatric species encounter adaptive disadvantage through hybridization.     

Attenuation of SARS‐CoV‐2 replication and associated inflammation by concomitant targeting of viral and host cap 2'‐O‐ribose methyltransferases

The SARS‐CoV‐2 infection cycle is a multistage process that relies on functional interactions between the host and the pathogen. Here, we repurposed antiviral drugs against both viral and host enzymes to pharmaceutically block methylation of the viral RNA 2''‐O‐ribose cap needed for viral immune escape. We find that the host cap 2''‐O‐ribose methyltransferase MTr1 can compensate for loss of viral NSP16 methyltransferase in facilitating virus replication. Concomitant inhibition of MTr1 and NSP16 efficiently suppresses SARS‐CoV‐2 replication. Using in silico target‐based drug screening, we identify a bispecific MTr1/NSP16 inhibitor with anti‐SARS‐CoV‐2 activity in vitro and in vivo but with unfavorable side effects. We further show antiviral activity of inhibitors that target independent stages of the host SAM cycle providing the methyltransferase co‐substrate. In particular, the adenosylhomocysteinase (AHCY) inhibitor DZNep is antiviral in in vitro, in ex vivo, and in a mouse infection model and synergizes with existing COVID‐19 treatments. Moreover, DZNep exhibits a strong immunomodulatory effect curbing infection‐induced hyperinflammation and reduces lung fibrosis markers ex vivo. Thus, multispecific and metabolic MTase inhibitors constitute yet unexplored treatment options against COVID‐19.     

Density dependence of daily activity in three ungulate species

Daily activity in herbivores reflects a balance between finding food and safety. The safety‐in‐numbers theory predicts that living in higher population densities increases safety, which should affect this balance. High‐density populations are thus expected to show a more even distribution of activity—that is, spread—and higher activity levels across the day. We tested these predictions for three ungulate species; red deer (Cervus elaphus), roe deer (Capreolus capreolus), and wild boar (Sus scrofa). We used camera traps to measure the level and spread of activity across ten forest sites at the Veluwe, the Netherlands, that widely range in ungulate density. Food availability and hunting levels were included as covariates. Daily activity was more evenly distributed when population density was higher for all three species. Both deer species showed relatively more feeding activity in broad daylight and wild boar during dusk. Activity level increased with population density only for wild boar. Food availability and hunting showed no correlation with activity patterns. These findings indicate that ungulate activity is to some degree density dependent. However, while these patterns might result from larger populations feeling safer as the safety‐in‐numbers theory states, we cannot rule out that they are the outcome of greater intraspecific competition for food, forcing animals to forage during suboptimal times of the day. Overall, this study demonstrates that wild ungulates adjust their activity spread and level based on their population size.     

Gastric stem cells promote inflammation and gland remodeling in response to Helicobacter pylori via Rspo3‐Lgr4 axis

Helicobacter pylori is a pathogen that colonizes the stomach and causes chronic gastritis. Helicobacter pylori can colonize deep inside gastric glands, triggering increased R‐spondin 3 (Rspo3) signaling. This causes an expansion of the “gland base module,” which consists of self‐renewing stem cells and antimicrobial secretory cells and results in gland hyperplasia. The contribution of Rspo3 receptors Lgr4 and Lgr5 is not well explored. Here, we identified that Lgr4 regulates Lgr5 expression and is required for H. pylori‐induced hyperplasia and inflammation, while Lgr5 alone is not. Using conditional knockout mice, we reveal that R‐spondin signaling via Lgr4 drives proliferation of stem cells and also induces NF‐κB activity in the proliferative stem cells. Upon exposure to H. pylori, the Lgr4‐driven NF‐κB activation is responsible for the expansion of the gland base module and simultaneously enables chemokine expression in stem cells, resulting in gland hyperplasia and neutrophil recruitment. This demonstrates a connection between R‐spondin‐Lgr and NF‐κB signaling that links epithelial stem cell behavior and inflammatory responses to gland‐invading H. pylori.     

Structural analyses of the malaria parasite aminoacyl‐tRNA synthetases provide new avenues for antimalarial drug discovery

Malaria is a parasitic illness caused by the genus Plasmodium from the apicomplexan phylum. Five plasmodial species of P. falciparum (Pf), P. knowlesi, P. malariae, P. ovale, and P. vivax (Pv) are responsible for causing malaria in humans. According to the World Malaria Report 2020, there were 229 million cases and ~ 0.04 million deaths of which 67% were in children below 5 years of age. While more than 3 billion people are at risk of malaria infection globally, antimalarial drugs are their only option for treatment. Antimalarial drug resistance keeps arising periodically and thus threatens the main line of malaria treatment, emphasizing the need to find new alternatives. The availability of whole genomes of P. falciparum and P. vivax has allowed targeting their unexplored plasmodial enzymes for inhibitor development with a focus on multistage targets that are crucial for parasite viability in both the blood and liver stages. Over the past decades, aminoacyl‐tRNA synthetases (aaRSs) have been explored as anti‐bacterial and anti‐fungal drug targets, and more recently (since 2009) aaRSs are also the focus of antimalarial drug targeting. Here, we dissect the structure‐based knowledge of the most advanced three aaRSs—lysyl‐ (KRS), prolyl‐ (PRS), and phenylalanyl‐ (FRS) synthetases in terms of development of antimalarial drugs. These examples showcase the promising potential of this family of enzymes to provide druggable targets that stall protein synthesis upon inhibition and thereby kill malaria parasites selectively.     

Plasticity is a locally adapted trait with consequences for ecological dynamics in novel environments

Phenotypic plasticity is predicted to evolve in more variable environments, conferring an advantage on individual lifetime fitness. It is less clear what the potential consequences of that plasticity will have on ecological population dynamics. Here, we use an invertebrate model system to examine the effects of environmental variation (resource availability) on the evolution of phenotypic plasticity in two life history traits—age and size at maturation—in long‐running, experimental density‐dependent environments. Specifically, we then explore the feedback from evolution of life history plasticity to subsequent ecological dynamics in novel conditions. Plasticity in both traits initially declined in all microcosm environments, but then evolved increased plasticity for age‐at‐maturation, significantly so in more environmentally variable environments. We also demonstrate how plasticity affects ecological dynamics by creating founder populations of different plastic phenotypes into new microcosms that had either familiar or novel environments. Populations originating from periodically variable environments that had evolved greatest plasticity had lowest variability in population size when introduced to novel environments than those from constant or random environments. This suggests that while plasticity may be costly it can confer benefits by reducing the likelihood that offspring will experience low survival through competitive bottlenecks in variable environments. In this study, we demonstrate how plasticity evolves in response to environmental variation and can alter population dynamics—demonstrating an eco‐evolutionary feedback loop in a complex animal moderated by plasticity in growth.     

Vitamin D supplementation worsens Alzheimer's progression: Animal model and human cohort studies

Vitamin D deficiency has been epidemiologically linked to Alzheimer''s disease (AD) and other dementias, but no interventional studies have proved causality. Our previous work revealed that the genomic vitamin D receptor (VDR) is already converted into a non‐genomic signaling pathway by forming a complex with p53 in the AD brain. Here, we extend our previous work to assess whether it is beneficial to supplement AD mice and humans with vitamin D. Intriguingly, we first observed that APP/PS1 mice fed a vitamin D‐sufficient diet showed significantly lower levels of serum vitamin D, suggesting its deficiency may be a consequence not a cause of AD. Moreover, supplementation of vitamin D led to increased Aβ deposition and exacerbated AD. Mechanistically, vitamin D supplementation did not rescue the genomic VDR/RXR complex but instead enhanced the non‐genomic VDR/p53 complex in AD brains. Consistently, our population‐based longitudinal study also showed that dementia‐free older adults (n = 14,648) taking vitamin D₃ supplements for over 146 days/year were 1.8 times more likely to develop dementia than those not taking the supplements. Among those with pre‐existing dementia (n = 980), those taking vitamin D₃ supplements for over 146 days/year had 2.17 times the risk of mortality than those not taking the supplements. Collectively, these animal model and human cohort studies caution against prolonged use of vitamin D by AD patients.     

Reproduction in deep‐sea vent shrimps is influenced by diet,with rhythms apparently unlinked to surface production

Variations in offspring production according to feeding strategies or food supply have been recognized in many animals from various ecosystems. Despite an unusual trophic structure based on non‐photosynthetic primary production, these relationships remain largely under‐studied in chemosynthetic ecosystems. Here, we use Rimicaris shrimps as a study case to explore relationships between reproduction, diets, and food supply in these environments. For that, we compared reproductive outputs of three congeneric shrimps differing by their diets. They inhabit vents located under oligotrophic waters of tropical gyres with opposed latitudes, allowing us to also examine the prevalence of phylogenetic vs environmental drivers in their reproductive rhythms. For this, we used both our original data and a compilation of published observations on the presence of ovigerous females covering various seasons over the past 35 years. We report distinct egg production trends between Rimicaris species relying solely on chemosymbiosis—R. exoculata and R. kairei—and one relying on mixotrophy, R. chacei. Besides, our data suggest a reproductive periodicity that does not correspond to seasonal variations in surface production, with substantial proportions of brooding females during the same months of the year, despite those months corresponding to either boreal winter or austral summer depending on the hemisphere. These observations contrast with the long‐standing paradigm in deep‐sea species for which periodic reproductive patterns have always been attributed to seasonal variations of photosynthetic production sinking from the surface. Our results suggest the presence of an intrinsic basis for biological rhythms in the deep sea, and bring to light the importance of having year‐round observations in order to understand the life history of vent animals.     

Pace and shape of senescence in three species of duckweed

Senescence is progressive bodily deterioration associated with declines in survival and fecundity in older age classes. There is great diversity in patterns of senescence across species, but these patterns can be difficult to compare formally due to variation in the absolute time scales in which species live and die: members of some species live for a matter of days, others for millennia. To address this issue, the “pace‐shape” approach was developed to decouple absolute time from analyses and instead standardize life history traits in terms of average life expectancy, facilitating intra‐ and interspecific comparisons. Here, we use this approach to distinguish the generic form of demographic trajectories (shape) from the time scale on which the trajectories occurred (pace) in three species of tiny, free‐floating aquatic plants known as duckweeds (Lemna gibba L., L. minor L., and L. turionifera Landolt), which have mean lifespans of less than a month under typical lab conditions, and exhibit age‐related declines in survivorship and reproduction. Using a randomized block design in which we tracked a final total of 430 individuals, we report differences in pace and shape among the three species. Specifically, the largest, least‐fecund, and typically longest‐lived species, L. gibba, tended to exhibit more rapid decreases in time‐standardized survivorship and fecundity compared with the other two species. This study emphasizes variation in aging patterns that can be found among plant species, including those in the same genus, and provides further validation for the utility of applying the pace and shape approach in interspecific comparisons.     

Using fractal self‐similarity to increase precision of shrub biomass estimates

We show that aerial tips are self‐similar fractals of whole shrubs and present a field method that applies this fact to improves accuracy and precision of biomass estimates of tall‐shrubs, defined here as those with diameter at root collar (DRC) ≥ 2.5 cm. Power function allometry of biomass to stem diameter generates a disproportionate prediction error that increases rapidly with diameter. Thus, biomass should be modeled as a single measure of stem diameter only if stem diameter is less than a threshold D_max. When stem diameter exceeds D_max, then the stem internode should be treated as a conic frustrum requiring two additional measures: a second, node‐adjacent diameter and a length. If the second diameter is less than D_max, then the power function allometry can be applied to the aerial tip; otherwise an additional internode is measured. This “two‐component” allometry—internodes as frustra and aerial tips as shrubs—can reduce estimated biomass error propagated to the plot‐level by as much as 50% or more where very large shrubs are present D_max is any diameter such that the ratio of single‐component to two‐component uncertainty exceeds the ratio of two‐component to single‐component measurement time. Guidelines for estimating D_max based on pilot field data are provided. Tall shrubs are increasing in abundance and distribution across Arctic, alpine, boreal, and dryland ecosystems. Estimating their biomass is important for both ecological studies and carbon accounting. Reducing field‐sample prediction error increases precision in multi‐stage modeling because additional measures efficiently improve plot‐level biomass precision, reducing uncertainty for shrub biomass estimates.     

Behavioral “bycatch” from camera trap surveys yields insights on prey responses to human‐mediated predation risk

Human disturbance directly affects animal populations and communities, but indirect effects of disturbance on species behaviors are less well understood. For instance, disturbance may alter predator activity and cause knock‐on effects to predator‐sensitive foraging in prey. Camera traps provide an emerging opportunity to investigate such disturbance‐mediated impacts to animal behaviors across multiple scales. We used camera trap data to test predictions about predator‐sensitive behavior in three ungulate species (caribou Rangifer tarandus; white‐tailed deer, Odocoileus virginianus; moose, Alces alces) across two western boreal forest landscapes varying in disturbance. We quantified behavior as the number of camera trap photos per detection event and tested its relationship to inferred human‐mediated predation risk between a landscape with greater industrial disturbance and predator activity and a “control” landscape with lower human and predator activity. We also assessed the finer‐scale influence on behavior of variation in predation risk (relative to habitat variation) across camera sites within the more disturbed landscape. We predicted that animals in areas with greater predation risk (e.g., more wolf activity, less cover) would travel faster past cameras and generate fewer photos per detection event, while animals in areas with less predation risk would linger (rest, forage, investigate), generating more photos per event. Our predictions were supported at the landscape‐level, as caribou and moose had more photos per event in the control landscape where disturbance‐mediated predation risk was lower. At a finer‐scale within the disturbed landscape, no prey species showed a significant behavioral response to wolf activity, but the number of photos per event decreased for white‐tailed deer with increasing line of sight (m) along seismic lines (i.e., decreasing visual cover), consistent with a predator‐sensitive response. The presence of juveniles was associated with shorter behavioral events for caribou and moose, suggesting greater predator sensitivity for females with calves. Only moose demonstrated a positive behavioral association (i.e., longer events) with vegetation productivity (16‐day NDVI), suggesting that for other species bottom‐up influences of forage availability were generally weaker than top‐down influences from predation risk. Behavioral insights can be gleaned from camera trap surveys and provide complementary information about animal responses to predation risk, and thus about the indirect impacts of human disturbances on predator–prey interactions.     

Barriers and bridges for sustaining functional habitat networks: A macroecological system analysis of wet grassland landscapes

This study aims at supporting the maintenance of representative functional habitat networks as green infrastructure for biodiversity conservation through transdisciplinary macroecological analyses of wet grassland landscapes and their stewardship systems. We chose ten north European wet grassland case study landscapes from Iceland and the Netherlands in the west to Lithuania and Belarus in the east. We combine expert experiences for 20–30 years, comparative studies made 2011–2017, and longitudinal analyses spanning >70 years. Wader, or shorebird, (Charadrii) assemblages were chosen as a focal species group. We used evidence‐based knowledge and practical experience generated in three steps. (1) Experts from 8 wet grassland landscapes in northern Europe''s west and east mapped factors linked to patterns and processes, and management and governance, in social‐ecological systems that affect states and trends of wet grasslands as green infrastructures for wader birds. (2) To understand wader conservation problems and their dynamic in wet grassland landscapes, and to identify key issues for successful conservation, we applied group modeling using causal loop diagram mapping. (3) Validation was made using the historic development in two additional wet grassland landscapes. Wader conservation was dependent on ten dynamically interacting ecological and social system factors as leverage points for management. Re‐wetting and grazing were common drivers for the ecological and social system, and long‐term economic support for securing farmers’ interest in wader bird conservation. Financial public incentives at higher levels of governance of wetland management are needed to stimulate private income loops. Systems analysis based on contrasting landscape case studies in space and over time can support (1) understanding of complex interactions in social‐ecological systems, (2) collaborative learning in individual wet grassland landscapes, and (3) formulation of priorities for conservation, management, and restoration.