Spatio-temporal dynamics of pneumonia in bighorn sheep

Movement decisions driving metapopulation connectivity respond to social resources in a long-lived ungulate, bighorn sheep (Ovis canadensis)

The spatial availability of social resources is speculated to structure animal movement decisions, but the effects of social resources on animal movements are difficult to identify because social resources are rarely measured. Here, we assessed whether varying availability of a key social resource-access to receptive mates-produces predictable changes in movement decisions among bighorn sheep in Nevada, the United States. We compared the probability that males made long-distance 'foray' movements, a critical driver of connectivity, across three ecoregions with varying temporal duration of a socially mediated factor, breeding season. We used a hidden Markov model to identify foray events and then quantified the effects of social covariates on the probability of foray using a discrete choice model. We found that males engaged in forays at higher rates when the breeding season was short, suggesting that males were most responsive to the social resource when its existence was short lived. During the breeding season, males altered their response to social covariates, relative to the non-breeding season, though patterns varied, and age was associated with increased foray probability. Our results suggest that animals respond to the temporal availability of social resources when making the long-distance movements that drive connectivity. This article is part of the theme issue 'The spatial-social interface: a theoretical and empirical integration'.

Infection-nutrition feedbacks: fat supports pathogen clearance but pathogens reduce fat in a wild mammal

Though far less obvious than direct effects (clinical disease or mortality), the indirect influences of pathogens are difficult to estimate but may hold fitness consequences. Here, we disentangle the directional relationships between infection and energetic reserves, evaluating the hypotheses that energetic reserves influence infection status of the host and that infection elicits costs to energetic reserves. Using repeated measures of fat reserves and infection status in individual bighorn sheep (Ovis canadensis) in the Greater Yellowstone Ecosystem, we documented that fat influenced ability to clear pathogens (Mycoplasma ovipneumoniae) and infection with respiratory pathogens was costly to fat reserves. Costs of infection approached, and in some instances exceeded, costs of rearing offspring to independence in terms of reductions to fat reserves. Fat influenced probability of clearing pathogens, pregnancy and over-winter survival; from an energetic perspective, an animal could survive for up to 23 days on the amount of fat that was lost to high levels of infection. Cost of pathogens may amplify trade-offs between reproduction and survival. In the absence of an active outbreak, the influence of resident pathogens often is overlooked. Nevertheless, the energetic burden of pathogens likely has consequences for fitness and population dynamics, especially when food resources are insufficient.

Spatial and temporal analysis of haemorrhagic septicaemia outbreaks in India over three decades (1987-2016)

Haemorrhagic septicaemia (HS) is an economically important disease affecting cattle and buffaloes and the livelihoods of small-holder farmers that depend upon them. The disease is caused by Gram-negative bacterium, Pasteurella multocida, and is considered to be endemic in many states of India with more than 25,000 outbreaks in the past three decades. Currently, there is no national policy for control of HS in India. In this study, we analysed thirty year (1987-2016) monthly data on HS outbreaks using different statistical and mathematical methods to identify spatial variability and temporal patterns (seasonality, periodicity). There was zonal variation in the trend and seasonality of HS outbreaks. Overall, South zone reported maximum proportion of the outbreaks (70.2%), followed by East zone (7.2%), Central zone (6.4%), North zone (5.6%), West zone (5.5%) and North-East zone (4.9%). Annual state level analysis indicated that the reporting of HS outbreaks started at different years independently and there was no apparent transmission between the states. The results of the current study are useful for the policy makers to design national control programme on HS in India and implement state specific strategies. Further, our study and strategies could aid in implementation of similar approaches in HS endemic tropical countries around the world.

Restoration of bighorn sheep: History, successes, and remaining conservation issues

Mammals are imperiled worldwide, primarily from habitat loss or modification, and exhibit downward trends in their populations and distributions. Likewise, large-bodied herbivores have undergone a collapse in numbers and are at the highest extinction risk of all mammals. Bighorn sheep (Ovis canadensis) are among those large-bodied herbivores that possess a slow-paced life history, suffer from debilitating diseases, and have experienced range contractions across their historical distribution since the late 1800s. Translocations and reintroductions of these mountain ungulates are key aspects of restoration and often are used to re-establish populations in historical habitat or to supplement declining herds. Millions of US dollars and much effort by state and federal natural resource agencies, as well as public and private organizations, have been expended to restore bighorn sheep. Despite those efforts, translocated populations of bighorn sheep have not always been successful. We assessed restoration of bighorn sheep to provide insights in the context of conservation of populations of bighorn sheep, because this management tool is a frequently used to re-establish populations. We focused briefly on past efforts to restore bighorn sheep populations and followed with updates on the value of habitat enhancements, genetic issues, the importance of ecotypic or phenotypic adaptations when restoring populations, predation, and disease transmission. We also raised issues and posed questions that have potential to affect future decisions regarding the restoration of bighorn sheep. This information will help conservationists improve the success of conserving these iconic large mammals.

Animal movement and associated infectious disease risk in a metapopulation

Animal movements among habitat patches or populations are important for maintaining long-term genetic and demographic viability, but connectivity may also facilitate disease spread and persistence. Understanding factors that influence animal movements is critical to understanding potential transmission risk and persistence of communicable disease in spatially structured systems. We evaluated effects of sex, age and Mycoplasma ovipneumoniae infection status at capture on intermountain movements and seasonal movement rates observed in desert bighorn sheep (Ovis canadensis nelsoni) using global positioning system collar data from 135 individuals (27 males, 108 females) in 14 populations between 2013 and 2018, following a pneumonia outbreak linked to the pathogen M. ovipneumoniae in the Mojave Desert, California, USA. Based on logistic regression analysis, intermountain movements were influenced by sex, age and most notably, infection status at capture: males, older animals and uninfected individuals were most likely to make such movements. Based on multiple linear regression analysis, females that tested positive for M. ovipneumoniae at capture also had lower mean daily movement rates that were further influenced by season. Our study provides empirical evidence of a pathogenic infection decreasing an individual's future mobility, presumably limiting that pathogen's ability to spread, and ultimately influencing transmission risk within a spatially structured system.

Host vs. pathogen evolutionary arms race: Effects of exposure history on individual response to a genetically diverse pathogen

Introduction

Throughout their range, bighorn sheep (Ovis canadensis) populations have seen significant disease-associated declines. Unfortunately, understanding of the underlying epidemiological processes driving the disease dynamics in this species has hindered conservation efforts aimed at improving the health and long-term viability of these populations. Individual response to pathogen exposure emerges from dynamic interactions between competing evolutionary processes within the host and pathogen. The host’s adaptive immune system recognizes pathogens and mounts a defensive response. Pathogens have evolved strategies to overcome adaptive immune defenses including maintaining high genetic diversity through rapid evolution. The outcomes of this evolutionary warfare determine the success of pathogen invasion of the host and ultimately the success of conservation efforts.

Methods

During an epizootic dominated by a single strain, we explore these host-pathogen dynamics by examining the variation in effects of pathogen invasion on captive bighorn sheep with differing histories of exposure to genetically diverse strains of Mycoplasma ovipneumoniae (Movi). We monitored clinical signs of disease and sampled animals and their environment to detect spread of Movi among 37 bighorn sheep separated into nine pens based on known exposure histories.

Results

We documented Movi transmission within and across pens and we detected Movi DNA in air, water, and invertebrate samples. Higher levels of antibody to Movi prior to the epizootic were associated with a lower likelihood of presenting clinical signs of pneumonia. Nonetheless, higher antibody levels in symptomatic individuals were associated with more severe progressive disease, increased probability and speed of pneumonia-induced mortality, and reduced likelihood of returning to a healthy state. Bighorn sheep with previous exposure to a strain other than the predominant epizootic strain were more likely to recover.

Discussion

Our results indicate that Movi-strain variability was sufficient to overwhelm the adaptive host immunological defenses. This outcome indicates, in free-ranging herds, past exposure is likely insufficient to protect bighorn sheep from infection by new Movi strains, although it influences the progression of disease and recovery within the herd. Therefore, given Movi-strain variability and the lack of immunological protection from past exposure, focusing management efforts on minimizing the introduction of Movi into bighorn herds, through separation of domestic and bighorn sheep and avoidance of management activities that create commingling of bighorn sheep carrying differing Movi strains, will likely be the most effective approach for reducing the effects of disease and achieving bighorn sheep conservation goals.

Pathogen surveillance and epidemiology in endangered Peninsular bighorn sheep (Ovis canadensis nelsoni)

Peninsular bighorn sheep (Ovis canadensis nelsoni) are found exclusively in Southern California and Baja Mexico. They are federally endangered due to multiple threats, including introduced infectious disease. From 1981 - 2017, we conducted surveillance for 16 pathogens and estimated population sizes, adult survival, and lamb survival. We used mixed effects regression models to assess disease patterns at the individual and population levels. Pathogen infection/exposure prevalence varied both spatially and temporally. Our findings indicate that the primary predictor of individual pathogen infection/exposure was the region in which an animal was captured, implying that transmission is driven by local ecological or behavioral factors. Higher Mycoplasma ovipneumoniae seropositivity was associated with lower lamb survival, consistent with lambs having high rates of pneumonia-associated mortality, which may be slowing population recovery. There was no association between M. ovipneumoniae and adult survival. Adult survival was positively associated with population size and parainfluenza-3 virus seroprevalence in the same year, and orf virus seroprevalence in the previous year. Peninsular bighorn sheep are recovering from small population sizes in a habitat of environmental extremes, compounded by infectious disease. Our research can help inform future pathogen surveillance and population monitoring for the long-term conservation of this population.

Using transcriptomics to predict and visualize disease status in bighorn sheep (Ovis canadensis)

Increasing risk of pathogen spillover coupled with overall declines in wildlife population abundance in the Anthropocene make infectious disease a relevant concern for species conservation worldwide. While emerging molecular tools could improve our diagnostic capabilities and give insight into mechanisms underlying wildlife disease risk, they have rarely been applied in practice. Here, employing a previously reported gene transcription panel of common immune markers to track physiological changes, we present a detailed analysis over the course of both acute and chronic infection in one wildlife species where disease plays a critical role in conservation, bighorn sheep (Ovis canadensis). Differential gene transcription patterns distinguished between infection statuses over the course of acute infection and differential correlation (DC) analyses identified clear changes in gene co-transcription patterns over the early stages of infection, with transcription of four genes-TGFb, AHR, IL1b and MX1-continuing to increase even as transcription of other immune-associated genes waned. In a separate analysis, we considered the capacity of the same gene transcription panel to aid in differentiating between chronically infected animals and animals in other disease states outside of acute disease events (an immediate priority for wildlife management in this system). We found that this transcription panel was capable of accurately identifying chronically infected animals in the test dataset, though additional data will be required to determine how far this ability extends. Taken together, our results showcase the successful proof of concept and breadth of potential utilities that gene transcription might provide to wildlife disease management, from direct insight into mechanisms associated with differential disease response to improved diagnostic capacity in the field.

Bighorn sheep show similar in-host responses to the same pathogen strain in two contrasting environments

Ecological context-the biotic and abiotic environment, along with its influence on population mixing dynamics and individual susceptibility-is thought to have major bearing on epidemic outcomes. However, direct comparisons of wildlife disease events in contrasting ecological contexts are often confounded by concurrent differences in host genetics, exposure histories, or pathogen strains. Here, we compare disease dynamics of a Mycoplasma ovipneumoniae spillover event that affected bighorn sheep populations in two contrasting ecological contexts. One event occurred on the herd's home range near the Rio Grande Gorge in New Mexico, while the other occurred in a captive facility at Hardware Ranch in Utah. While data collection regimens varied, general patterns of antibody signal strength and symptom emergence were conserved between the two sites. Symptoms appeared in the captive setting an average of 12.9 days postexposure, average time to seroconversion was 24.9 days, and clinical signs peaked at approximately 36 days postinfection. These patterns were consistent with serological testing and subsequent declines in symptom intensity in the free-ranging herd. At the captive site, older animals exhibited more severe declines in body condition and loin thickness, higher symptom burdens, and slower antibody response to the pathogen than younger animals. Younger animals were more likely than older animals to clear infection by the time of sampling at both sites. The patterns presented here suggest that environment may not be a major determinant of epidemiological outcomes in the bighorn sheep-M. ovipneumoniae system, elevating the possibility that host- or pathogen-factors may be responsible for observed variation.

Disease Ecology of a Low-Virulence Mycoplasma ovipneumoniae Strain in a Free-Ranging Desert Bighorn Sheep Population

Simple Summary

Like many wildlife diseases, bighorn sheep pneumonia can vary in burden. Here, we report on a bighorn sheep pneumonia event that showed much lower symptom and mortality burdens than have been documented previously. We provide detailed descriptions of symptoms, diagnostic testing results, and mixing patterns throughout the population, and end by discussing mechanisms that could have generated the distinct disease ecology associated with this event.

Abstract

Infectious pneumonia associated with the bacterial pathogen Mycoplasma ovipneumoniae is an impediment to bighorn sheep (Ovis canadensis) population recovery throughout western North America, yet the full range of M. ovipneumoniae virulence in bighorn sheep is not well-understood. Here, we present data from an M. ovipneumoniae introduction event in the Zion desert bighorn sheep (Ovis canadensis nelsoni) population in southern Utah. The ensuing disease event exhibited epidemiology distinct from what has been reported elsewhere, with virtually no mortality (0 adult mortalities among 70 animals tracked over 118 animal-years; 1 lamb mortality among 40 lambs tracked through weaning in the two summers following introduction; and lamb:ewe ratios of 34.9:100 in the year immediately after introduction and 49.4:100 in the second year after introduction). Individual-level immune responses were lower than expected, and M. ovipneumoniae appeared to fade out approximately 1.5 to 2 years after introduction. Several mechanisms could explain the limited burden of this M. ovipneumoniae event. First, most work on M. ovipneumoniae has centered on Rocky Mountain bighorn sheep (O. c. candensis), but the Zion bighorns are members of the desert subspecies (O. c. nelsoni). Second, the particular M. ovipneumoniae strain involved comes from a clade of strains associated with weaker demographic responses in other settings. Third, the substructuring of the Zion population may have made this population more resilient to disease invasion and persistence. The limited burden of the disease event on the Zion bighorn population underscores a broader point in wildlife disease ecology: that one size may not fit all events.

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.

A metapopulation model of social group dynamics and disease applied to Yellowstone wolves

The population structure of social species has important consequences for both their demography and transmission of their pathogens. We develop a metapopulation model that tracks two key components of a species' social system: average group size and number of groups within a population. While the model is general, we parameterize it to mimic the dynamics of the Yellowstone wolf population and two associated pathogens: sarcoptic mange and canine distemper. In the initial absence of disease, we show that group size is mainly determined by the birth and death rates and the rates at which groups fission to form new groups. The total number of groups is determined by rates of fission and fusion, as well as environmental resources and rates of intergroup aggression. Incorporating pathogens into the models reduces the size of the host population, predominantly by reducing the number of social groups. Average group size responds in more subtle ways: infected groups decrease in size, but uninfected groups may increase when disease reduces the number of groups and thereby reduces intraspecific aggression. Our modeling approach allows for easy calculation of prevalence at multiple scales (within group, across groups, and population level), illustrating that aggregate population-level prevalence can be misleading for group-living species. The model structure is general, can be applied to other social species, and allows for a dynamic assessment of how pathogens can affect social structure and vice versa.

Previously Unrecognized Exposure of Desert Bighorn Sheep (Ovis canadensis nelsoni) to Mycoplasma ovipneumoniae in the California Mojave Desert

A 2013 outbreak of respiratory disease in bighorn sheep from California's Mojave Desert metapopulation caused high mortality in at least one population. Subsequent PCR and strain-typing indicate widespread infection of a single strain of Mycoplasma ovipneumoniae throughout this region. Serosurvey of archived samples showed that some populations have had antibodies to M. ovipneumoniae since at least 1986, although pre-2013 strain-type data are unavailable.

Impact of Mycoplasma ovipneumoniae on juvenile bighorn sheep (Ovis canadensis) survival in the northern Basin and Range ecosystem

Determining the demographic impacts of wildlife disease is complex because extrinsic and intrinsic drivers of survival, reproduction, body condition, and other factors that may interact with disease vary widely. Mycoplasma ovipneumoniae infection has been linked to persistent mortality in juvenile bighorn sheep (Ovis canadensis), although mortality appears to vary widely across subspecies, populations, and outbreaks. Hypotheses for that variation range from interactions with nutrition, population density, genetic variation in the pathogen, genetic variation in the host, and other factors. We investigated factors related to survival of juvenile bighorn sheep in reestablished populations in the northern Basin and Range ecosystem, managed as the formerly-recognized California subspecies (hereafter, "California lineage"). We investigated whether survival probability of 4-month juveniles would vary by (1) presence of M. ovipneumoniae-infected or exposed individuals in populations, (2) population genetic diversity, and (3) an index of forage suitability. We monitored 121 juveniles across a 3-year period in 13 populations in southeastern Oregon and northern Nevada. We observed each juvenile and GPS-collared mother semi-monthly and established 4-month capture histories for the juvenile to estimate survival. All collared adult females were PCR-tested at least once for M. ovipneumoniae infection. The presence of M. ovipneumoniae-infected juveniles was determined by observing juvenile behavior and PCR-testing dead juveniles. We used a known-fate model with different time effects to determine if the probability of survival to 4 months varied temporally or was influenced by disease or other factors. We detected dead juveniles infected with M. ovipneumoniae in only two populations. Derived juvenile survival probability at four months in populations where infected juveniles were not detected was more than 20 times higher. Detection of infected adults or adults with antibody levels suggesting prior exposure was less predictive of juvenile survival. Survival varied temporally but was not strongly influenced by population genetic diversity or nutrition, although genetic diversity within most study area populations was very low. We conclude that the presence of M. ovipneumoniae can cause extremely low juvenile survival probability in translocated bighorn populations of the California lineage, but found little influence that genetic diversity or nutrition affect juvenile survival. Yet, after the PCR+ adult female in one population died, subsequent observations found 11 of 14 ( 79%) collared adult females had surviving juveniles at 4-months, suggesting that targeted removals of infected adults should be evaluated as a management strategy.

Co-infection best predicts respiratory viral infection in a wild host

The dynamics of directly transmitted pathogens in natural populations are likely to result from the combined effects of host traits, pathogen biology, and interactions among pathogens within a host. Discovering how these factors work in concert to shape variation in pathogen dynamics in natural host-multi-pathogen systems is fundamental to understanding population health. Here, we describe temporal variation in incidence and then elucidate the effect of hosts trait, season and pathogen co-occurrence on host infection risk using one of the most comprehensive studies of co-infection in a wild population: a suite of seven directly transmitted viral and bacterial respiratory infections from a 4-year study of 200 free-ranging African buffalo Syncerus caffer. Incidence of upper respiratory infections was common throughout the study-five out of the seven pathogens appeared to be consistently circulating throughout our study population. One pathogen exhibited clear outbreak dynamics in our final study year and another was rarely detected. Co-infection was also common in this system: The strongest indicator of pathogen occurrence for respiratory viruses was in fact the presence of other viral respiratory infections. Host traits had minimal effects on odds of pathogen occurrence but did modify pathogen-pathogen associations. In contrast, only season predicted bacterial pathogen occurrence. Though a combination of environmental, behavioural, and physiological factors work together to shape disease dynamics, we found pathogen associations best determined infection risk. Our study demonstrates that, in the absence of very fine-scale data, the intricate changes among these factors are best represented by co-infection.

Evaluating wildlife translocations using genomics: A bighorn sheep case study

Wildlife restoration often involves translocation efforts to reintroduce species and supplement small, fragmented populations. We examined the genomic consequences of bighorn sheep (Ovis canadensis) translocations and population isolation to enhance understanding of evolutionary processes that affect population genetics and inform future restoration strategies. We conducted a population genomic analysis of 511 bighorn sheep from 17 areas, including native and reintroduced populations that received 0-10 translocations. Using the Illumina High Density Ovine array, we generated datasets of 6,155 to 33,289 single nucleotide polymorphisms and completed clustering, population tree, and kinship analyses. Our analyses determined that natural gene flow did not occur between most populations, including two pairs of native herds that had past connectivity. We synthesized genomic evidence across analyses to evaluate 24 different translocation events and detected eight successful reintroductions (i.e., lack of signal for recolonization from nearby populations) and five successful augmentations (i.e., reproductive success of translocated individuals) based on genetic similarity with the source populations. A single native population founded six of the reintroduced herds, suggesting that environmental conditions did not need to match for populations to persist following reintroduction. Augmentations consisting of 18-57 animals including males and females succeeded, whereas augmentations of two males did not result in a detectable genetic signature. Our results provide insight on genomic distinctiveness of native and reintroduced herds, information on the relative success of reintroduction and augmentation efforts and their associated attributes, and guidance to enhance genetic contribution of augmentations and reintroductions to aid in bighorn sheep restoration.

Removal of chronic Mycoplasma ovipneumoniae carrier ewes eliminates pneumonia in a bighorn sheep population

Chronic pathogen carriage is one mechanism that allows diseases to persist in populations. We hypothesized that persistent or recurrent pneumonia in bighorn sheep (Ovis canadensis) populations may be caused by chronic carriers of Mycoplasma ovipneumoniae (Mo). Our experimental approach allowed us to address a conservation need while investigating the role of chronic carriage in disease persistence.We tested our hypothesis in two bighorn sheep populations in South Dakota, USA. We identified and removed Mo chronic carriers from the Custer State Park (treatment) population. Simultaneously, we identified carriers but did not remove them from the Rapid City population (control). We predicted removal would result in decreased pneumonia, mortality, and Mo prevalence. Both population ranges had similar habitat and predator communities but were sufficiently isolated to preclude intermixing.We classified chronic carriers as adults that consistently tested positive for Mo carriage over a 20-month sampling period (n = 2 in the treatment population; n = 2 in control population).We failed to detect Mo or pneumonia in the treatment population after chronic carrier removal, while both remained in the control. Mortality hazard for lambs was reduced by 72% in the treatment population relative to the control (CI = 36%, 91%). There was also a 41% reduction in adult mortality hazard attributable to the treatment, although this was not statistically significant (CI = 82% reduction, 34% increase). Synthesis and Applications: These results support the hypothesis that Mo is a primary causative agent of persistent or recurrent respiratory disease in bighorn sheep populations and can be maintained by a few chronic carriers. Our findings provide direction for future research and management actions aimed at controlling pneumonia in wild sheep and may apply to other diseases.

Genetic structure of Mycoplasma ovipneumoniae informs pathogen spillover dynamics between domestic and wild Caprinae in the western United States

Spillover diseases have significant consequences for human and animal health, as well as wildlife conservation. We examined spillover and transmission of the pneumonia-associated bacterium Mycoplasma ovipneumoniae in domestic sheep, domestic goats, bighorn sheep, and mountain goats across the western United States using 594 isolates, collected from 1984 to 2017. Our results indicate high genetic diversity of M. ovipneumoniae strains within domestic sheep, whereas only one or a few strains tend to circulate in most populations of bighorn sheep or mountain goats. These data suggest domestic sheep are a reservoir, while the few spillovers to bighorn sheep and mountain goats can persist for extended periods. Domestic goat strains form a distinct clade from those in domestic sheep, and strains from both clades are found in bighorn sheep. The genetic structure of domestic sheep strains could not be explained by geography, whereas some strains are spatially clustered and shared among proximate bighorn sheep populations, supporting pathogen establishment and spread following spillover. These data suggest that the ability to predict M. ovipneumoniae spillover into wildlife populations may remain a challenge given the high strain diversity in domestic sheep and need for more comprehensive pathogen surveillance.

Seasonal host life-history processes fuel disease dynamics at different spatial scales

Understanding the drivers underlying disease dynamics is still a major challenge in disease ecology, especially in the case of long-term disease persistence. Even though there is a strong consensus that density-dependent factors play an important role for the spread of diseases, the main drivers are still discussed and, more importantly, might differ between invasion and persistence periods. Here, we analysed long-term outbreak data of classical swine fever, an important disease in both wild boar and livestock, prevalent in the wild boar population from 1993 to 2000 in Mecklenburg-Vorpommern, Germany. We report outbreak characteristics and results from generalized linear mixed models to reveal what factors affected infection risk on both the landscape and the individual level. Spatiotemporal outbreak dynamics showed an initial wave-like spread with high incidence during the invasion period followed by a drop of incidence and an increase in seroprevalence during the persistence period. Velocity of spread increased with time during the first year of outbreak and decreased linearly afterwards, being on average 7.6 km per quarter. Landscape- and individual-level analyses of infection risk indicate contrasting seasonal patterns. During the persistence period, infection risk on the landscape level was highest during autumn and winter seasons, probably related to spatial behaviour such as increased long-distance movements and contacts induced by rutting and escaping movements. In contrast, individual-level infection risk peaked in spring, probably related to the concurrent birth season leading to higher densities, and was significantly higher in piglets than in reproductive animals. Our findings highlight that it is important to investigate both individual- and landscape-level patterns of infection risk to understand long-term persistence of wildlife diseases and to guide respective management actions. Furthermore, we highlight that exploring different temporal aggregation of the data helps to reveal important seasonal patterns, which might be masked otherwise.

Respiratory pathogens and their association with population performance in Montana and Wyoming bighorn sheep populations

Respiratory disease caused by Mycoplasma ovipneumoniae and Pasteurellaceae poses a formidable challenge for bighorn sheep (Ovis canadensis) conservation. All-age epizootics can cause 10–90% mortality and are typically followed by multiple years of enzootic disease in lambs that hinders post-epizootic recovery of populations. The relative frequencies at which these epizootics are caused by the introduction of novel pathogens or expression of historic pathogens that have become resident in the populations is unknown. Our primary objectives were to determine how commonly the pathogens associated with respiratory disease are hosted by bighorn sheep populations and assess demographic characteristics of populations with respect to the presence of different pathogens. We sampled 22 bighorn sheep populations across Montana and Wyoming, USA for Mycoplasma ovipneumoniae and Pasteurellaceae and used data from management agencies to characterize the disease history and demographics of these populations. We tested for associations between lamb:ewe ratios and the presence of different respiratory pathogen species. All study populations hosted Pasteurellaceae and 17 (77%) hosted Mycoplasma ovipneumoniae. Average lamb:ewe ratios for individual populations where both Mycoplasma ovipneumoniae and Pasteurellaceae were detected ranged from 0.14 to 0.40. However, average lamb:ewe ratios were higher in populations where Mycoplasma ovipneumoniae was not detected (0.37, 95% CI: 0.27–0.51) than in populations where it was detected (0.25, 95% CI: 0.21–0.30). These findings suggest that respiratory pathogens are commonly hosted by bighorn sheep populations and often reduce recruitment rates; however ecological factors may interact with the pathogens to determine population-level effects. Elucidation of such factors could provide insights for management approaches that alleviate the effects of respiratory pathogens in bighorn sheep. Nevertheless, minimizing the introduction of novel pathogens from domestic sheep and goats remains imperative to bighorn sheep conservation.

A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data

The development of high-throughput sequencing technologies is dramatically increasing the use of single nucleotide polymorphisms (SNPs) across the field of genetics, but most parentage studies of wild populations still rely on microsatellites. We developed a bioinformatic pipeline for identifying SNP panels that are informative for parentage analysis from restriction site-associated DNA sequencing (RADseq) data. This pipeline includes options for analysis with or without a reference genome, and provides methods to maximize genotyping accuracy and select sets of unlinked loci that have high statistical power. We test this pipeline on small populations of Mexican gray wolf and bighorn sheep, for which parentage analyses are expected to be challenging due to low genetic diversity and the presence of many closely related individuals. We compare the results of parentage analysis across SNP panels generated with or without the use of a reference genome, and between SNPs and microsatellites. For Mexican gray wolf, we conducted parentage analyses for 30 pups from a single cohort where samples were available from 64% of possible mothers and 53% of possible fathers, and the accuracy of parentage assignments could be estimated because true identities of parents were known a priori based on field data. For bighorn sheep, we conducted maternity analyses for 39 lambs from five cohorts where 77% of possible mothers were sampled, but true identities of parents were unknown. Analyses with and without a reference genome produced SNP panels with ≥95% parentage assignment accuracy for Mexican gray wolf, outperforming microsatellites at 78% accuracy. Maternity assignments were completely consistent across all SNP panels for the bighorn sheep, and were 74.4% consistent with assignments from microsatellites. Accuracy and consistency of parentage analysis were not reduced when using as few as 284 SNPs for Mexican gray wolf and 142 SNPs for bighorn sheep, indicating our pipeline can be used to develop SNP genotyping assays for parentage analysis with relatively small numbers of loci.

Detection of Mycoplasma ovipneumoniae in Pneumonic Mountain Goat ( Oreamnos americanus) Kids

We documented bronchopneumonia in seven mountain goat ( Oreamnos americanus) kid mortalities between 2011 and 2015 following a pneumonia epizootic in bighorn sheep ( Ovis canadensis) and sympatric mountain goats in the adjacent East Humboldt Range and Ruby Mountains in Elko County, Nevada, US. Gross and histologic lesions resembled those described in bighorn lambs following all-age epizootics, and Mycoplasma ovipneumoniae was detected with real-time PCR in the lower and upper respiratory tracts of all kids. Mannheimia haemolytica, with one isolate being leukotoxigenic, was cultured from the upper respiratory tract of five kids, and in one kid, a leukotoxigenic strain of Mannheimia glucosida was isolated from both upper and lower respiratory tracts. During this same period, 75 mountain goats within the two populations were marked and sampled for respiratory pathogens, and M. ovipneumoniae, leukotoxigenic Bibersteinia trehalosi, and Mannheimia haemolytica were identified. The M. ovipneumoniae recovered from the kid mortalities shared the same DNA sequence-based strain type detected in the adult goats and sympatric bighorn sheep during and after the 2009-10 pneumonia outbreak. Clinical signs in affected kids, as well as decreased annual kid recruitment, also resembled reports in bighorn lambs from some herds following all-age pneumonia-associated die-offs. Mycoplasma ovipneumoniae, Pasteurellaceae spp., and other respiratory bacterial pathogens should be considered as a cause of pneumonia with potential population-limiting effects in mountain goats.

Evaluating sample size to estimate genetic management metrics in the genomics era

Inbreeding and relationship metrics among and within populations are useful measures for genetic management of wild populations, but accuracy and precision of estimates can be influenced by the number of individual genotypes analysed. Biologists are confronted with varied advice regarding the sample size necessary for reliable estimates when using genomic tools. We developed a simulation framework to identify the optimal sample size for three widely used metrics to enable quantification of expected variance and relative bias of estimates and a comparison of results among populations. We applied this approach to analyse empirical genomic data for 30 individuals from each of four different free-ranging Rocky Mountain bighorn sheep (Ovis canadensis canadensis) populations in Montana and Wyoming, USA, through cross-species application of an Ovine array and analysis of approximately 14,000 single nucleotide polymorphisms (SNPs) after filtering. We examined intra- and interpopulation relationships using kinship and identity by state metrics, as well as FST between populations. By evaluating our simulation results, we concluded that a sample size of 25 was adequate for assessing these metrics using the Ovine array to genotype Rocky Mountain bighorn sheep herds. However, we conclude that a universal sample size rule may not be able to sufficiently address the complexities that impact genomic kinship and inbreeding estimates. Thus, we recommend that a pilot study and sample size simulation using R code we developed that includes empirical genotypes from a subset of populations of interest would be an effective approach to ensure rigour in estimating genomic kinship and population differentiation.

Age-specific infectious period shapes dynamics of pneumonia in bighorn sheep

Superspreading, the phenomenon where a small proportion of individuals contribute disproportionately to new infections, has profound effects on disease dynamics. Superspreading can arise through variation in contacts, infectiousness or infectious periods. The latter has received little attention, yet it drives the dynamics of many diseases of critical public health, livestock health and conservation concern. Here, we present rare evidence of variation in infectious periods underlying a superspreading phenomenon in a free-ranging wildlife system. We detected persistent infections of Mycoplasma ovipneumoniae, the primary causative agent of pneumonia in bighorn sheep (Ovis canadensis), in a small number of older individuals that were homozygous at an immunologically relevant genetic locus. Interactions among age-structure, genetic composition and infectious periods may drive feedbacks in disease dynamics that determine the magnitude of population response to infection. Accordingly, variation in initial conditions may explain divergent population responses to infection that range from recovery to catastrophic decline and extirpation.

Exposure of bighorn sheep to domestic goats colonized with Mycoplasma ovipneumoniae induces sub-lethal pneumonia

BACKGROUND

Bronchopneumonia is a population limiting disease of bighorn sheep (Ovis canadensis) that has been associated with contact with domestic Caprinae. The disease is polymicrobial but is initiated by Mycoplasma ovipneumoniae, which is commonly carried by both domestic sheep (O. aries) and goats (Capra aegagrus hircus). However, while previous bighorn sheep comingling studies with domestic sheep have resulted in nearly 100% pneumonia mortality, only sporadic occurrence of fatal pneumonia was reported from previous comingling studies with domestic goats. Here, we evaluated the ability of domestic goats of defined M. ovipneumoniae carriage status to induce pneumonia in comingled bighorn sheep.

METHODOLOGY/PRINCIPAL FINDINGS

In experiment 1, three bighorn sheep naïve to M. ovipneumoniae developed non-fatal respiratory disease (coughing, nasal discharge) following comingling with three naturally M. ovipneumoniae-colonized domestic goats. Gross and histological lesions of pneumonia, limited to small areas on the ventral and lateral edges of the anterior and middle lung lobes, were observed at necropsies conducted at the end of the experiment. A control group of three bighorn sheep from the same source housed in isolation during experiment 1 remained free of observed respiratory disease. In experiment 2, three bighorn sheep remained free of observed respiratory disease while comingled with three M. ovipneumoniae-free domestic goats. In experiment 3, introduction of a domestic goat-origin strain of M. ovipneumoniae to the same comingled goats and bighorn sheep used in experiment 2 resulted in clinical signs of respiratory disease (coughing, nasal discharge) in both host species. At the end of experiment 3, gross and histological evidence of pneumonia similar to that observed in experiment 1 bighorn sheep was observed in both affected bighorn sheep and domestic goats.

CONCLUSIONS/SIGNIFICANCE

M. ovipneumoniae strains carried by domestic goats were transmitted to comingled bighorn sheep, triggering development of pneumonia. However, the severity of the disease was markedly milder than that seen in similar experiments with domestic sheep strains of the bacterium.

Contact and contagion: Probability of transmission given contact varies with demographic state in bighorn sheep

Understanding both contact and probability of transmission given contact are key to managing wildlife disease. However, wildlife disease research tends to focus on contact heterogeneity, in part because the probability of transmission given contact is notoriously difficult to measure. Here, we present a first step towards empirically investigating the probability of transmission given contact in free-ranging wildlife. We used measured contact networks to test whether bighorn sheep demographic states vary systematically in infectiousness or susceptibility to Mycoplasma ovipneumoniae, an agent responsible for bighorn sheep pneumonia. We built covariates using contact network metrics, demographic information and infection status, and used logistic regression to relate those covariates to lamb survival. The covariate set contained degree, a classic network metric describing node centrality, but also included covariates breaking the network metrics into subsets that differentiated between contacts with yearlings, ewes with lambs, and ewes without lambs, and animals with and without active infections. Yearlings, ewes with lambs, and ewes without lambs showed similar group membership patterns, but direct interactions involving touch occurred at a rate two orders of magnitude higher between lambs and reproductive ewes than between any classes of adults or yearlings, and one order of magnitude higher than direct interactions between multiple lambs. Although yearlings and non-reproductive bighorn ewes regularly carried M. ovipneumoniae, our models suggest that a contact with an infected reproductive ewe had approximately five times the odds of producing a lamb mortality event of an identical contact with an infected dry ewe or yearling. Consequently, management actions targeting infected animals might lead to unnecessary removal of young animals that carry pathogens but rarely transmit. This analysis demonstrates a simple logistic regression approach for testing a priori hypotheses about variation in the odds of transmission given contact for free-ranging hosts, and may be broadly applicable for investigations in wildlife disease ecology.

Disease introduction is associated with a phase transition in bighorn sheep demographics

Ecological theory suggests that pathogens are capable of regulating or limiting host population dynamics, and this relationship has been empirically established in several settings. However, although studies of childhood diseases were integral to the development of disease ecology, few studies show population limitation by a disease affecting juveniles. Here, we present empirical evidence that disease in lambs constrains population growth in bighorn sheep (Ovis canadensis) based on 45 years of population-level and 18 years of individual-level monitoring across 12 populations. While populations generally increased (λ = 1.11) prior to disease introduction, most of these same populations experienced an abrupt change in trajectory at the time of disease invasion, usually followed by stagnant-to-declining growth rates (λ = 0.98) over the next 20 years. Disease-induced juvenile mortality imposed strong constraints on population growth that were not observed prior to disease introduction, even as adult survival returned to pre-invasion levels. Simulations suggested that models including persistent disease-induced mortality in juveniles qualitatively matched observed population trajectories, whereas models that only incorporated all-age disease events did not. We use these results to argue that pathogen persistence may pose a lasting, but under-recognized, threat to host populations, particularly in cases where clinical disease manifests primarily in juveniles.

How Respiratory Pathogens Contribute to Lamb Mortality in a Poorly Performing Bighorn Sheep ( Ovis canadensis ) Herd

We evaluated bighorn sheep ( Ovis canadensis ) ewes and their lambs in captivity to examine the sources and roles of respiratory pathogens causing lamb mortality in a poorly performing herd. After seven consecutive years of observed December recruitments of <10%, 13 adult female bighorn sheep from the remnant Gribbles Park herd in Colorado, US were captured and transported to the Thorne-Williams Wildlife Research Center in Wyoming in March 2013. Ewes were sampled repeatedly over 16 mo. In April 2014, ewes were separated into individual pens prior to lambing. Upon death, lambs were necropsied and tested for respiratory pathogens. Six lambs developed clinical respiratory disease and one lamb was abandoned. Pathology from an additional six lambs born in 2013 was also evaluated. Mycoplasma ovipneumoniae , leukotoxigenic Mannheimia spp., leukotoxigenic Bibersteinia trehalosi , and Pasteurella multocida all contributed to lamb pneumonia. Histopathology suggested a continuum of disease, with lesions typical of pasteurellosis predominating in younger lambs and lesions typical of mycoplasmosis predominating in older lambs. Mixed pathology was observed in lambs dying between these timeframes. We suspected that all the ewes in our study were persistently infected and chronically shedding the bacteria that contributed to summer lamb mortality.

Role of carriers in the transmission of pneumonia in bighorn sheep (Ovis canadensis)

In the absence of livestock contact, recurring lamb mortality in bighorn sheep (Ovis canadensis) populations previously exposed to pneumonia indicates the likely presence of carriers of pneumonia-causing pathogens, and possibly inadequate maternally derived immunity. To investigate this problem we commingled naïve, pregnant ewes (n=3) with previously exposed rams (n=2). Post-commingling, all ewes and lambs born to them acquired pneumonia-causing pathogens (leukotoxin-producing Pasteurellaceae and Mycoplasma ovipneumoniae), with subsequent lamb mortality between 4-9 weeks of age. Infected ewes became carriers for two subsequent years and lambs born to them succumbed to pneumonia. In another experiment, we attempted to suppress the carriage of leukotoxin-producing Pasteurellaceae by administering an antibiotic to carrier ewes, and evaluated lamb survival. Lambs born to both treatment and control ewes (n=4 each) acquired pneumonia and died. Antibody titers against leukotoxin-producing Pasteurellaceae in all eight ewes were ‘protective’ (>1:800 and no apparent respiratory disease); however their lambs were either born with comparatively low titers, or with high (but non-protective) titers that declined rapidly within 2-8 weeks of age, rendering them susceptible to fatal disease. Thus, exposure to pneumonia-causing pathogens from carrier ewes, and inadequate titers of maternally derived protective antibodies, are likely to render bighorn lambs susceptible to fatal pneumonia.

Summary: Previously exposed bighorn sheep can become carriers and transmit respiratory pathogens to naïve animals. Successive crops of lambs acquire pathogens and inadequate passive immunity and subsequently succumb to pneumonia.

Evidence of Bovine viral diarrhea virus Infection in Three Species of Sympatric Wild Ungulates in Nevada: Life History Strategies May Maintain Endemic Infections in Wild Populations

Evidence for bovine viral diarrhea virus (BVDV) infection was detected in 2009–2010 while investigating a pneumonia die-off in Rocky Mountain bighorn sheep (Ovis canadensis, canadensis), and sympatric mountain goats (Oreamnos americanum) in adjacent mountain ranges in Elko County, Nevada. Seroprevalence to BVDV-1 was 81% (N = 32) in the bighorns and 100% (N = 3) in the mountain goats. Serosurveillance from 2011 to 2015 of surviving bighorns and mountain goats as well as sympatric mule deer (Odocoileus hemionus), indicated a prevalence of 72% (N = 45), 45% (N = 51), and 51% (N = 342) respectively. All species had antibody titers to BVDV1 and BVDV2. BVDV1 was isolated in cell culture from three bighorn sheep and a mountain goat kid. BVDV2 was isolated from two mule deer. Six deer (N = 96) sampled in 2013 were positive for BVDV by antigen-capture ELISA on a single ear notch. Wild ungulates and cattle concurrently graze public and private lands in these two mountain ranges, thus providing potential for interspecies viral transmission. Like cattle, mule deer, mountain goats, and bighorn sheep can be infected with BVDV and can develop clinical disease including immunosuppression. Winter migration patterns that increase densities and species interaction during the first and second trimester of gestation may contribute to the long term maintenance of the virus in these wild ungulates. More studies are needed to determine the population level impacts of BVDV infection on these three species.

Costs and benefits of group living with disease: a case study of pneumonia in bighorn lambs (Ovis canadensis)

Group living facilitates pathogen transmission among social hosts, yet temporally stable host social organizations can actually limit transmission of some pathogens. When there are few between-subpopulation contacts for the duration of a disease event, transmission becomes localized to subpopulations. The number of per capita infectious contacts approaches the subpopulation size as pathogen infectiousness increases. Here, we illustrate that this is the case during epidemics of highly infectious pneumonia in bighorn lambs (Ovis canadensis). We classified individually marked bighorn ewes into disjoint seasonal subpopulations, and decomposed the variance in lamb survival to weaning into components associated with individual ewes, subpopulations, populations and years. During epidemics, lamb survival varied substantially more between ewe-subpopulations than across populations or years, suggesting localized pathogen transmission. This pattern of lamb survival was not observed during years when disease was absent. Additionally, group sizes in ewe-subpopulations were independent of population size, but the number of ewe-subpopulations increased with population size. Consequently, although one might reasonably assume that force of infection for this highly communicable disease scales with population size, in fact, host social behaviour modulates transmission such that disease is frequency-dependent within populations, and some groups remain protected during epidemic events.