Assessing changes in functional connectivity in a desert bighorn sheep metapopulation after two generations

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.

Spatio-temporal genetic structure of the striped field mouse (Apodemus agrarius) populations inhabiting national parks in South Korea: Implications for conservation and management of protected areas

Population or habitat connectivity is a key component in maintaining species and community-level regional biodiversity as well as intraspecific genetic diversity. Ongoing human activities cause habitat destruction and fragmentation, which exacerbate the connectivity due to restricted animal movements across local habitats, eventually resulting in the loss of biodiversity. The Baekdudaegan Mountain Range (BMR) on the Korean Peninsula represents “biodiversity hotspots” and eight of the 22 Korean national parks are located within the BMR. Given the striped field mouse (Apodemus agrarius) is the most common and ecologically important small mammals in these protected areas, the population genetic assessment of this species will allow for identifying “genetic diversity hotspots” and also “genetic barriers” that may hinder gene flow, and will therefore inform on effective conservation and management efforts for the national park habitats. We collected samples from hair, tail, or buccal swabs for 252 A. agrarius individuals in 2015 and 2019. By using mitochondrial DNA cytochrome b (cyt b) sequences and nine microsatellite loci, we determined levels of genetic diversity, genetic differentiation, and gene flow among eight national park populations of A. agrarius along the BMR. We found high levels of genetic diversity but the occurrences of inbreeding for all the nine samples analyzed. Our results also indicated that there was detectable temporal genetic variation between the 2015 and 2019 populations in the Jirisan National Park, which is probably due to a short-term decline in genetic diversity caused by reduced population sizes. We also found a well-admixed shared gene pool among the national park populations. However, a significant positive correlation between geographic and genetic distances was detected only in mtDNA but not microsatellites, which might be attributed to different dispersal patterns between sexes. There was a genetic barrier to animal movements around the Woraksan National Park areas. The poor habitat connectivity surrounding these areas can be improved by establishing an ecological corridor. Our findings of the presence of genetic barriers in some protected areas provide insights into the conservation and management efforts to improve the population or habitat connectivity among the national parks.

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.

Population connectivity patterns of genetic diversity, immune responses and exposure to infectious pneumonia in a metapopulation of desert bighorn sheep

Habitat fragmentation is an important driver of biodiversity loss and can be remediated through management actions aimed at maintenance of natural connectivity in metapopulations. Connectivity may protect populations from infectious diseases by preserving immunogenetic diversity and disease resistance. However, connectivity could exacerbate the risk of infectious disease spread across vulnerable populations. We tracked the spread of a novel strain of Mycoplasma ovipneumoniae in a metapopulation of desert bighorn sheep Ovis canadensis nelsoni in the Mojave Desert to investigate how variation in connectivity among populations influenced disease outcomes. M. ovipneumoniae was detected throughout the metapopulation, indicating that the relative isolation of many of these populations did not protect them from pathogen invasion. However, we show that connectivity among bighorn sheep populations was correlated with higher immunogenetic diversity, a protective immune response and lower disease prevalence. Variation in protective immunity predicted infection risk in individual bighorn sheep and was associated with heterozygosity at genetic loci linked to adaptive and innate immune signalling. Together, these findings may indicate that population connectivity maintains immunogenetic diversity in bighorn sheep populations in this system and has direct effects on immune responses in individual bighorn sheep and their susceptibility to infection by a deadly pathogen. Our study suggests that the genetic benefits of population connectivity could outweigh the risk of infectious disease spread and supports conservation management that maintains natural connectivity in metapopulations.

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.

Spatial genetic structure of Rocky Mountain bighorn sheep (Ovis canadensis canadensis) at the northern limit of their native range

The Canadian Rocky Mountains are one of the few places on Earth where the spatial genetic structure of wide-ranging species has been relatively unaffected by anthropogenic disturbance. We characterized the spatial genetic structure of Rocky Mountain bighorn sheep (Ovis canadensis canadensis Shaw, 1804) in the northern portion of their range. Using microsatellites from 1495 individuals and mitochondrial DNA sequences from 188 individuals, we examined both broad- and fine-scale spatial genetic structure, assessed sex-biased gene flow within the northern portion of the species range, and identified geographic patterns of genetic diversity. We found that broad-scale spatial genetic structure was consistent with barriers to movement created by major river valleys. The fine-scale spatial genetic structure was characterized by a strong isolation-by-distance pattern, and analysis of neighborhood size using spatial autocorrelation indicated gene flow frequently occurred over distances of up to 100 km. However, analysis of sex-specific spatial autocorrelation and analysis of mitochondrial haplotype distributions failed to detect any evidence of sex-biased gene flow. Finally, our analyses reveal decreasing genetic diversity with increasing latitude, consistent with patterns of post-glacial recolonization of the Rocky Mountains.

Bighorn sheep gut microbiomes associate with genetic and spatial structure across a metapopulation

Studies in laboratory animals demonstrate important relationships between environment, host traits, and microbiome composition. However, host-microbiome relationships in natural systems are understudied. Here, we investigate metapopulation-scale microbiome variation in a wild mammalian host, the desert bighorn sheep (Ovis canadensis nelsoni). We sought to identify over-represented microbial clades and understand how landscape variables and host traits influence microbiome composition across the host metapopulation. To address these questions, we performed 16S sequencing on fecal DNA samples from thirty-nine bighorn sheep across seven loosely connected populations in the Mojave Desert and assessed relationships between microbiome composition, environmental variation, geographic distribution, and microsatellite-derived host population structure and heterozygosity. We first used a phylogenetically-informed algorithm to identify bacterial clades conserved across the metapopulation. Members of genus Ruminococcaceae, genus Lachnospiraceae, and family Christensenellaceae R7 group were among the clades over-represented across the metapopulation, consistent with their known roles as rumen symbionts in domestic livestock. Additionally, compositional variation among hosts correlated with individual-level geographic and genetic structure, and with population-level differences in genetic heterozygosity. This study identifies microbiome community variation across a mammalian metapopulation, potentially associated with genetic and geographic population structure. Our results imply that microbiome composition may diverge in accordance with landscape-scale environmental and host population characteristics.

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.

The genetic legacy of 50 years of desert bighorn sheep translocations

Conservation biologists have increasingly used translocations to mitigate population declines and restore locally extirpated populations. Genetic data can guide the selection of source populations for translocations and help evaluate restoration success. Bighorn sheep (Ovis canadensis) are a managed big game species that suffered widespread population extirpations across western North America throughout the early 1900s. Subsequent translocation programs have successfully re-established many formally extirpated bighorn herds, but most of these programs pre-date genetically informed management practices. The state of Nevada presents a particularly well-documented case of decline followed by restoration of extirpated herds. Desert bighorn sheep (O. c. nelsoni) populations declined to less than 3,000 individuals restricted to remnant herds in the Mojave Desert and a few locations in the Great Basin Desert. Beginning in 1968, the Nevada Department of Wildlife translocated ~2,000 individuals from remnant populations to restore previously extirpated areas, possibly establishing herds with mixed ancestries. Here, we examined genetic diversity and structure among remnant herds and the genetic consequences of translocation from these herds using a genotyping-by-sequencing approach to genotype 17,095 loci in 303 desert bighorn sheep. We found a signal of population genetic structure among remnant Mojave Desert populations, even across geographically proximate mountain ranges. Further, we found evidence of a genetically distinct, potential relict herd from a previously hypothesized Great Basin lineage of desert bighorn sheep. The genetic structure of source herds was clearly reflected in translocated populations. In most cases, herds retained genetic evidence of multiple translocation events and subsequent admixture when founded from multiple remnant source herds. Our results add to a growing literature on how population genomic data can be used to guide and monitor restoration programs.

Genetic assessment of a bighorn sheep population expansion in the Silver Bell Mountains, Arizona

Background

The isolated population of desert bighorn sheep in the Silver Bell Mountains of southern Arizona underwent an unprecedented expansion in merely four years. We hypothesized that immigration from neighboring bighorn sheep populations could have caused the increase in numbers as detected by Arizona Game and Fish Department annual aerial counts.

Methods

We applied a multilocus genetic approach using mitochondrial DNA and nuclear microsatellite markers for genetic analyses to find evidence of immigration. We sampled the Silver Bell Mountains bighorn sheep before (2003) and during (2015) the population expansion, and a small number of available samples from the Gila Mountains (southwestern Arizona) and the Morenci Mine (Rocky Mountain bighorn) in an attempt to identify the source of putative immigrants and, more importantly, to serve as comparisons for genetic diversity metrics.

Results

We did not find evidence of substantial gene flow into the Silver Bell Mountains population. We did not detect any new mitochondrial haplotypes in the 2015 bighorn sheep samples. The microsatellite analyses detected only one new allele, in one individual from the 2015 population that was not detected in the 2003 samples. Overall, the genetic diversity of the Silver Bell Mountains population was lower than that seen in either the Gila population or the Morenci Mine population.

Discussion

Even though the results of this study did not help elucidate the precise reason for the recent population expansion, continued monitoring and genetic sampling could provide more clarity on the genetic demographics of this population.