Diversity and antigenic potentials of Mycoplasmopsis bovis secreted and outer membrane proteins within a core genome of strains isolated from North American bison and cattle.

Mycoplasmopsis bovis is a worldwide economically important pathogen of cattle that can cause or indirectly contribute to bovine respiratory disease. M. bovis is also a primary etiological agent of respiratory disease in bison with high mortality rates. A major challenge in the development of an efficacious M. bovis vaccine is the design of antigens that contain both MHC-1 and MHC-2 T-cell epitopes, and that account for population level diversity within the species. Publicly available genomes and sequence read archive libraries of 381 M. bovis strains isolated from cattle (n = 202) and bison (n = 179) in North America were used to identify a core genome of 575 genes, including 38 that encode either known or predicted secreted or outer membrane proteins. The antigenic potentials of the proteins were characterized by the presence and strength of their T-cell epitopes, and their protein variant diversity at the population-level. The proteins had surprisingly low diversity and varying predictive levels of T-cell antigenicity. These results provide a reference for the selection or design of antigens for vaccine testing against strains infecting North American cattle and bison.

Genetic Re-assessment of Population Subdivision in Yellowstone National Park Bison.

Yellowstone National Park is home to the only plains bison population that has continually existed as wildlife, on the same landscape, through the population bottleneck of the late 19th century. Nevertheless, by the early 1900s, only 23 wild bison were known to have survived poaching. Salvation efforts included the addition of 18 females from Montana and 3 bulls from Texas to augment this population. A century later, nuclear microsatellite-based population level assessment revealed two genetically distinct bison sub-populations. However, in 2016 an analysis of mitochondrial haplotypes showed the two founding lineages were distributed throughout the park. This study is designed to delineate any current sub-structure in the Yellowstone bison population by strategically sampling the two major summer breeding herds and the two major winter ranges. Population level metrics were derived using the same microsatellite loci as the original study along with a newly developed set of highly informative bison specific Single Nucleotide Polymorphisms (SNPs). Our analyses reveal that the modern bison in Yellowstone National Park currently consist of one interbreeding population, comprised of two subunits.

A case of mortality in a re-introduced European bison associated with severe pneumonia caused by Dictyocaulus viviparus.

BACKGROUND: Dictyocaulosis is a parasitic disease caused by pulmonary nematodes from genus Dictyocaulus affecting various ungulate hosts. It can cause verminous bronchopneumonia and for heavily infected individuals, fatal outcomes can occur. CASE PRESENTATION: The study describes the case of a male European bison which died three months after relocation from Slovakia to one of the reintroduction areas in Nucșoara village, Fagaraș Mountains, Romania. Necropsy revealed the presence of pulmonary nematodes in the respiratory tract. Morphology and molecular diagnosis was performed and Dictyocaulus viviparus was identified. CONCLUSION: Rigorous health monitoring is essential to assure the success of reintroduction programs, understanding and preventing infectious diseases and limiting their impact on population health.

Effects of management outweigh effects of plant diversity on restored animal communities in tallgrass prairies.

A primary goal of ecological restoration is to increase biodiversity in degraded ecosystems. However, the success of restoration ecology is often assessed by measuring the response of a single functional group or trophic level to restoration, without considering how restoration affects multitrophic interactions that shape biodiversity. An ecosystem-wide approach to restoration is therefore necessary to understand whether animal responses to restoration, such as changes in biodiversity, are facilitated by changes in plant communities (plant-driven effects) or disturbance and succession resulting from restoration activities (management-driven effects). Furthermore, most restoration ecology studies focus on how restoration alters taxonomic diversity, while less attention is paid to the response of functional and phylogenetic diversity in restored ecosystems. Here, we compared the strength of plant-driven and management-driven effects of restoration on four animal communities (ground beetles, dung beetles, snakes, and small mammals) in a chronosequence of restored tallgrass prairie, where sites varied in management history (prescribed fire and bison reintroduction). Our analyses indicate that management-driven effects on animal communities were six-times stronger than effects mediated through changes in plant biodiversity. Additionally, we demonstrate that restoration can simultaneously have positive and negative effects on biodiversity through different pathways, which may help reconcile variation in restoration outcomes. Furthermore, animal taxonomic and phylogenetic diversity responded differently to restoration, suggesting that restoration plans might benefit from considering multiple dimensions of animal biodiversity. We conclude that metrics of plant diversity alone may not be adequate to assess the success of restoration in reassembling functional ecosystems.

Emergence of Mycobacterium orygis-Associated Tuberculosis in Wild Ruminants, India.

Tuberculosis caused by Mycobacterium orygis was detected in 2 spotted deer from a wildlife sanctuary in western India and an Indian bison from a national park in central India. Nationwide surveillance is urgently required to clarify the epidemiology of the Mycobacterium tuberculosis complex at the human-livestock-wildlife interface.

Comparative analysis of functional diversity of rumen microbiome in bison and beef heifers.

IMPORTANCE: Ruminants play a key role in the conversion of cellulolytic plant material into high-quality meat and milk protein for humans. The rumen microbiome is the driver of this conversion, yet there is little information on how gene expression within the microbiome impacts the efficiency of this conversion process. The current study investigates gene expression in the rumen microbiome of beef heifers and bison and how transplantation of ruminal contents from bison to heifers alters gene expression. Understanding interactions between the host and the rumen microbiome is the key to developing informed approaches to rumen programming that will enhance production efficiency in ruminants.

Sarcocystis cruzi (Hasselmann, 1923) Wenyon, 1926: redescription, molecular characterization and deposition of life cycle stages specimens in the Smithsonian Museum.

Currently, 7 named Sarcocystis species infect cattle: Sarcocystis hirsuta, S. cruzi, S. hominis, S. bovifelis, S. heydorni, S. bovini and S. rommeli; other, unnamed species also infect cattle. Of these parasites of cattle, a complete life cycle description is known only for S. cruzi, the most pathogenic species in cattle. The life cycle of S. cruzi was completed experimentally in 1982, before related parasite species were structurally characterized, and before the advent of molecular diagnostics; to our knowledge, no archived frozen tissues from the cattle employed in the original descriptions remain for DNA characterization. Here, we isolated DNA from a paraffin-embedded kidney of a calf experimentally infected with S. cruzi in 1980; we then sequenced portions of 18S rRNA, 28S rRNA, COX1 and Acetyl CoA genes and verified that each shares 99­100% similarity to other available isolates attributed to S. cruzi from naturally infected cattle. We also reevaluated histological sections of tissues of calves experimentally infected with S. cruzi in the original description, exploiting improvements in photographic technology to render clearer morphological detail. Finally, we reviewed all available studies of the life cycle of S. cruzi, noting that S. cruzi was transmitted between bison (Bison bison) and cattle (Bos taurus) and that the strain of parasite derived from bison appeared more pathogenic than the cattle strain. Based on these newfound molecular, morphological and physiological data, we thereby redescribed S. cruzi and deposited reference material in the Smithsonian Museum for posterity.

A serological survey of pathogens associated with the respiratory and digestive system in the Polish European bison (Bison bonasus) population in 2017-2022.

BACKGROUND: The European bison (Bison bonasus) is a near threatened species and requires health monitoring. The aim of the present study was to determine the prevalence of antibodies to pathogens known to cause respiratory and digestive illness in ruminants. RESULTS: In the studied 328 European bison, the highest seroprevalence was observed for Bovine herpesvirus-1 (BoHV-1) (50.27%), Bovine Coronavirus (BCoV) (26.36%), and Bluetongue Virus (BTV) (12.83%). For Mycoplasma bovis strains and Bovine Viral Diarrhea Virus (BVDV), positive results were rare. Interestingly, a higher prevalence of BTV antibodies was noted in the northeastern populations and older animals. CONCLUSIONS: Our findings indicate that the Polish European bison population appears to have considerable contact with BoHV-1; however, this does not appear to be of great significance, as clinical symptoms and post-mortem lesions are rarely noted in Polish European bison population. The high seroprevalence of BTV in the north-east of Poland is an ongoing trend, also noted in previous studies. It is possible that European bison may perpetuate the virus in this region. This is the first report of antibodies for BCoV in European bison.

Endobiotic Ciliates from the Rumen of the European Bison Bison Bonasus (Linnaeus, 1758) from the Vologda Oblast of Russia.

The fauna of endobiotic ciliates of the rumen of the European bison Bison bonasus from the Vologda oblast of Russia was investigated. In the studied bisons, 12 species of trichostomatids (Trichostomatia, Litostomatea) were found, ten of which were from the family Ophryoscolecidae and two species were from the family Isotrichidae. A high similarity of ciliate faunas in the rumen of different bison individuals in the studied population was noted. A comparative analysis of data on the species diversity and number of endobiotic ciliates in the rumen of various representatives of the genus Bison from different habitats was carried out.

The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation.

Dietary DNA metabarcoding enables researchers to identify and characterize trophic interactions with a high degree of taxonomic precision. It is also sensitive to sources of bias and contamination in the field and laboratory. One of the earliest and most common strategies for dealing with such sensitivities has been to remove all low-abundance sequences and conduct ecological analyses based on the presence or absence of food taxa. Although this step is now often perceived to be necessary, evidence of its sufficiency is lacking and more attention to the risk of introducing other errors is needed. Using computer simulations, we demonstrate that common strategies to remove low-abundance sequences can erroneously eliminate true dietary sequences in ways that impact downstream inferences. Using real data from well-studied wildlife populations in Yellowstone National Park, we further show how these strategies can markedly alter the composition of dietary profiles in ways that scale-up to obscure ecological interpretations about dietary generalism, specialism, and composition. Although the practice of removing low-abundance sequences may continue to be a useful strategy to address research questions that focus on a subset of relatively abundant foods, its continued widespread use risks generating misleading perceptions about the structure of trophic networks. Researchers working with dietary DNA metabarcoding data-or similar data such as environmental DNA, microbiomes, or pathobiomes-should be aware of drawbacks and consider alternative bioinformatic, experimental, and statistical solutions.

Three-dimensional characteristic of fungiform papillae and its taste buds in European bison (Bison bonasus), cattle (Bos taurus), and Bison bonasus hybrid.

BACKGROUND: Our recent macro- and scanning electron microscopic study of tongue conducted on domesticated cattle, wild living European bison, and Bison bonasus hybrid revealed various spatial arrangement and number of gustatory and mechanical papillae between parental species and their hybrid. Furthermore, scanning electron microscopy analysis of gustatory papillae indicated the variable distribution of fungiform papillae (Fu) over the surface of the tongue, which could be significant in differentiated taste perception during feeding in studied wild living and domesticated husbandry ruminants. To specify the detailed microstructure of Fu papillae with connective tissue cores (CTC) and intraepithelial taste buds system, the first time the three-dimensional computer-aided analysis of serial histoslides resulted in the rendering of 3D reconstructions of Fu papillae. RESULTS: The comparative analysis of 3D models Fu papillae conducted in six areas of lingual mucosa of each tongue revealed information about, microstructural diversity of Fu papillae in studied ruminants. The estimation of number and density of Fu papillae on tongues, rate of protrusion of papillae over mucosa, and a number of taste buds per papilla allowed to state the ventral surface of the lingual apex and posterolateral surfaces of the lingual torus as regions important in taste perception, as in the preselection of taken food, as well in the analysis of food during rumination, respectively. On the 3D models were observed three structural types of CTC of different distribution on the tongue in studied species. The quantitative data of the number of taste buds on Fu papillae have regional functional differences in the taste system important in feeding and veterinary practice. Moreover, our analysis determined specific features in examined hybrid and showed similarities of some studied features with cattle, i.e., maternal species. CONCLUSIONS: The 3D reconstruction method used for the first time in the field of study of the lingual papillae and taste buds system can be considered as an innovative and effective tool in assessing of the microstructures of Fu papillae, and it could be suitable for further studies of taste system structures in normal and pathological condition.

Acute-phase protein concentrations in serum of clinically healthy and diseased European bison (Bison bonasus) - preliminary study.

BACKGROUND: This is the first report describing levels of APPs in European bison. Serum concentration of acute phase proteins (APPs) may be helpful to assess general health status in wildlife and potentially useful in selecting animals for elimination. Since there is a lack of literature data regarding concentration of APPs in European bisons, establishment of the reference values is also needed. METHODS: A total of 87 European bison from Polish populations were divided into two groups: (1) healthy: immobilized for transportation, placing a telemetry collar and routine diagnostic purposes; and (2) selectively culled due to the poor health condition. The serum concentration of haptoglobin, serum amyloid A and α1-acid-glycoprotein were determined using commercial quantitative ELISA assays. Since none of the variables met the normality assumptions, non-parametric Mann-Whitney U test was used for all comparisons. Statistical significance was set at p < 0.05. Statistical analyses were performed using Statistica 13.3 (Tibco, USA). RESULTS: The concentration of haptoglobin and serum amyloid A was significantly higher in animals culled (euthanised) due to the poor condition in respect to the clinically healthy European bison. The levels of α1-acid-glycoprotein did not show statistical difference between healthy and sick animals. CONCLUSIONS: Correlation between APPs concertation and health status was proven, therefore the determination of selected APPs may be considered in future as auxiliary predictive tool in assessing European bison health condition.

Migrating bison engineer the green wave.

Newly emerging plants provide the best forage for herbivores. To exploit this fleeting resource, migrating herbivores align their movements to surf the wave of spring green-up. With new technology to track migrating animals, the Green Wave Hypothesis has steadily gained empirical support across a diversity of migratory taxa. This hypothesis assumes the green wave is controlled by variation in climate, weather, and topography, and its progression dictates the timing, pace, and extent of migrations. However, aggregate grazers that are also capable of engineering grassland ecosystems make some of the world's most impressive migrations, and it is unclear how the green wave determines their movements. Here we show that Yellowstone's bison (Bison bison) do not choreograph their migratory movements to the wave of spring green-up. Instead, bison modify the green wave as they migrate and graze. While most bison surfed during early spring, they eventually slowed and let the green wave pass them by. However, small-scale experiments indicated that feedback from grazing sustained forage quality. Most importantly, a 6-fold decadal shift in bison density revealed that intense grazing caused grasslands to green up faster, more intensely, and for a longer duration. Our finding broadens our understanding of the ways in which animal movements underpin the foraging benefit of migration. The widely accepted Green Wave Hypothesis needs to be revised to include large aggregate grazers that not only move to find forage, but also engineer plant phenology through grazing, thereby shaping their own migratory movements.

Widespread male sex bias in mammal fossil and museum collections.

A recent study of mammoth subfossil remains has demonstrated the potential of using relatively low-coverage high-throughput DNA sequencing to genetically sex specimens, revealing a strong male-biased sex ratio [P. Pecnerová et al., Curr. Biol. 27, 3505-3510.e3 (2017)]. Similar patterns were predicted for steppe bison, based on their analogous female herd-based structure. We genetically sexed subfossil remains of 186 Holarctic bison (Bison spp.), and also 91 brown bears (Ursus arctos), which are not female herd-based, and found that ∼75% of both groups were male, very close to the ratio observed in mammoths (72%). This large deviation from a 1:1 ratio was unexpected, but we found no evidence for sex differences with respect to DNA preservation, sample age, material type, or overall spatial distribution. We further examined ratios of male and female specimens from 4 large museum mammal collections and found a strong male bias, observable in almost all mammalian orders. We suggest that, in mammals at least, 1) wider male geographic ranges can lead to considerably increased chances of detection in fossil studies, and 2) sexual dimorphic behavior or appearance can facilitate a considerable sex bias in fossil and modern collections, on a previously unacknowledged scale. This finding has major implications for a wide range of studies of fossil and museum material.

Drivers of human-megaherbivore interactions in the Eastern and Western Ghats of southern India.

The global effort to protect megaherbivore populations is largely dependent on how human-wildlife conflict is identified, prioritized, and remedied. We examined the socio-ecological and landscape-scale factors determining spatial patterns of human-megaherbivore (Asian elephant Elephas maximus and gaur Bos gaurus) interactions across sixteen Forest Divisions in Tamil Nadu, India. Using a systematic grid-based design, we conducted questionnaire-based surveys of 1460 households at the human-wildlife interface adjacent to Protected Areas, Reserve Forest and Fringe Areas. We specifically collected information on elephant and gaur conflict incidents (e.g., human death/injuries, property damage, and crop-raiding), cropland type, extent of crop area and area lost to crop-raiding, from each household. We found that human-elephant conflict increased with percentage of crop cover, diversity of major and minor crops grown, proximity to water source, flat terrain, and lower rates of precipitation. Human-gaur conflict was greatest with a high diversity of major crops, proximity to water source, moderate precipitation, and more undulating terrain. We identified ca. 7900 km2 hotspot area of contiguous high-intensity elephant conflict. For gaur, we identified high-frequency conflict hotspot areas covering ca. 625 km2, which were patchily distributed, highly localised, and attributed mostly to the recent changing land-use patterns. Our findings will help policymakers and park managers in developing landscape-scale human-wildlife conflict mitigation plans in the identified conflict hotspots.

Jointly Inferring the Dynamics of Population Size and Sampling Intensity from Molecular Sequences.

Estimating past population dynamics from molecular sequences that have been sampled longitudinally through time is an important problem in infectious disease epidemiology, molecular ecology, and macroevolution. Popular solutions, such as the skyline and skygrid methods, infer past effective population sizes from the coalescent event times of phylogenies reconstructed from sampled sequences but assume that sequence sampling times are uninformative about population size changes. Recent work has started to question this assumption by exploring how sampling time information can aid coalescent inference. Here, we develop, investigate, and implement a new skyline method, termed the epoch sampling skyline plot (ESP), to jointly estimate the dynamics of population size and sampling rate through time. The ESP is inspired by real-world data collection practices and comprises a flexible model in which the sequence sampling rate is proportional to the population size within an epoch but can change discontinuously between epochs. We show that the ESP is accurate under several realistic sampling protocols and we prove analytically that it can at least double the best precision achievable by standard approaches. We generalize the ESP to incorporate phylogenetic uncertainty in a new Bayesian package (BESP) in BEAST2. We re-examine two well-studied empirical data sets from virus epidemiology and molecular evolution and find that the BESP improves upon previous coalescent estimators and generates new, biologically useful insights into the sampling protocols underpinning these data sets. Sequence sampling times provide a rich source of information for coalescent inference that will become increasingly important as sequence collection intensifies and becomes more formalized.

Comparative cognition in three understudied ungulate species: European bison, forest buffalos and giraffes.

BACKGROUND: Comparative cognition has historically focused on a few taxa such as primates, birds or rodents. However, a broader perspective is essential to understand how different selective pressures affect cognition in different taxa, as more recently shown in several studies. Here we present the same battery of cognitive tasks to two understudied ungulate species with different socio-ecological characteristics, European bison (Bison bonasus) and forest buffalos (Syncerus caffer nanus), and we compare their performance to previous findings in giraffes (Giraffa camelopardalis). We presented subjects with an Object permanence task, Memory tasks with 30 and 60 s delays, two inference tasks based on acoustic cues (i.e. Acoustic inference tasks) and a control task to check for the use of olfactory cues (i.e. Olfactory task). RESULTS: Overall, giraffes outperformed bison and buffalos, and bison outperformed buffalos (that performed at chance level). All species performed better in the Object permanence task than in the Memory tasks and one of the Acoustic inference tasks (which they likely solved by relying on stimulus enhancement). Giraffes performed better than buffalos in the Shake full Acoustic inference task, but worse than bison and buffalos in the Shake empty Acoustic inference task. CONCLUSIONS: In sum, our results are in line with the hypothesis that specific socio-ecological characteristics played a crucial role in the evolution of cognition, and that higher fission-fusion levels and larger dietary breadth are linked to higher cognitive skills. This study shows that ungulates may be an excellent model to test evolutionary hypotheses on the emergence of cognition.

A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus.

Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.

Serological evidence for historical and present-day exposure of North American bison to Mycoplasma bovis.

BACKGROUND: Mycoplasma bovis causes mastitis, otitis, pneumonia and arthritis in cattle and is a major contributor to bovine respiratory disease complex. Around the year 2000, it emerged as a significant threat to the health of North American bison. Whether healthy bison are carriers of M. bovis and when they were first exposed is not known. To investigate these questions we used a commercially available ELISA that detects antibodies to M. bovis to test 3295 sera collected from 1984 through 2019 from bison in the United States and Canada. RESULTS: We identified moderately to strongly seropositive bison from as long ago as the late 1980s. Average seroprevalence over the past 36 years is similar in the United States and Canada, but country-specific differences are evident when data are sorted by the era of collection. Seroprevalence in the United States during the pre-disease era (1999 and prior) was significantly higher than in Canada, but was significantly lower than in Canada during the years 2000-2019. Considering individual countries, seroprevalence in the United States since the year 2000 dropped significantly as compared to the years 1985-1999. In Canada the trend is reversed, with seroprevalence increasing significantly since the year 2000. ELISA scores for sera collected from free-ranging bison do not differ significantly from scores for sera from more intensively managed animals, regardless of the era in which they were collected. However, seroprevalence among intensively raised Canadian bison has nearly doubled since the year 2000 and average ELISA scores rose significantly. CONCLUSIONS: Our data provide the first evidence that North American bison were exposed to M. bovis many years prior to the emergence of M. bovis-related disease. Patterns of exposure inferred from these results differ in the United States and Canada, depending on the era under consideration. Our data further suggest that M. bovis may colonize healthy bison at a level sufficient to trigger antibody responses but without causing overt disease. These findings provide novel insights as to the history of M. bovis in bison and will be of value in formulating strategies to minimize the impact of mycoplasmosis on bison health and production.

Pathogens with potential impact on reproduction in captive and free-ranging European bison (Bison bonasus) in Poland - a serological survey.

BACKGROUND: The European bison is an endangered species, and as such it is extremely important to monitor herds for pathogens which can lead to reproductive failure. The aim of the present study was to determine the current prevalence of antibodies to pathogens known to potentially influence reproduction in European bison. Serum samples from 183 bison, originating from different parts of Poland, were tested using commercial ELISA tests for antibodies to Chlamydia spp., Coxiella burnetti, Leptospira interrogans, Neospora caninum and Toxoplasma gondii; the findings were compared between captive and main free-ranging herds, and with regard to the influence of demographic factors such as age and sex. The prevalence of seropositivity was also checked with regard to location and the animal species sharing it. RESULTS: Chlamydia spp. antibodies were present in 48 out of 130 (36.9%) tested samples. Coxiella burnetii was found in one sample out of 178 (0.58%). N. caninum in 36 out of 172 (20.9%) and T. gondii in 23 out of 172 (13.4%). No sample was positive for leptospirosis. Neither sex nor age appeared to have a significant effect on the occurrence of antibodies to the identified species. The prevalence of Chlamydia spp. in the samples varied significantly according to location; however, similar frequency ranges were observed between free ranging and captive herds. In contrast, antibodies to N. caninum were more common in free-ranging herds than captive herds, with the highest frequency observed in the Bieszczady Mountains. CONCLUSIONS: Chlamydia spp., N. caninum and T. gondii might have a similar impact on the reproductive potential of European bison as they have on cattle. The high occurrence of antibodies to N. caninum in bison from the Bieszczady Mountains may be associated with the relatively high density of the wolf population in the area.