Genetic variation within and relatedness among wood and plains bison populations.

There are two recognized subspecies of bison, wood (Bison bison athabascae) and plains (Bison bison bison) bison. The establishment of most bison populations from a small number of individuals has raised concerns about their genetic variation. To this end, 11 bison populations were surveyed with 11 microsatellite loci in order to calculate genetic variation and genetic distances. Mean number of alleles ranged between 3.18 at Antelope Island State Park (Utah) and 6.55 at Wood Buffalo National Park (Alberta and Northwest Territories). Mean heterozygosity ranged from 0.295 at Antelope Island State Park to 0.669 at Custer State Park (South Dakota). The amount of genetic variability present in the bison populations as measured by mean number of alleles and overall probability of identity was found to correlate with the number of founders for all sampled populations. The G-test for heterogeneity revealed some evidence for the existence of subpopulations at Wood Buffalo National Park, however very small genetic distances between these subpopulations suggest that nuclear material from the plains bison introduced into Wood Buffalo National Park has diffused throughout the park. Genetic distances between the sampled populations were generally larger between than within the two bison subspecies.     

Reproductive success of bison bulls (Bison bison bison) in semi-natural conditions

Sexual size dimorphism has been related to a high variance in male reproductive success. Research on American bison (Bison bison bison), a species that shows moderate sexual dimorphism, has put forward the assumption that under wild conditions the largest part of the female herd is bred by a limited number of males. Thus far, this hypothesis has never been supported by genetic data. The aim of this study is therefore to test the hypothesis of extreme male reproductive variance among bison through the determination of the reproductive success of the bulls in private herds. We analysed genetic paternity in four private herds (n=19, 33, 39 and 54) kept under semi-natural conditions. By analysing blood, hair and tissue samples, using 8-10 polymorphic microsatellites, the reproductive success of the bulls was quantified. Additional genetic data were gathered through a survey distributed among bison breeders with private herds over the world. Results show a highly differential reproductive success for bison males in private herds kept under semi-natural conditions. In each study group, a single male sires at least 70% of the calves. In the survey groups, a single male sires 81-100% of the calves. Only one survey group displayed a deviating pattern showing a more evenly distribution of paternity (28.57, 33.33 and 38.10%) among three same aged subadult males.     

Genetic Diversity among Bacillus anthracis Soil Isolates at Fine Geographic Scales

Environmental samples were collected from carcass sites during and after anthrax outbreaks in 2000 and 2001 in the bison (Bison bison) population within Wood Buffalo National Park and the Hook Lake Region north of Wood Buffalo National Park. Bacillus anthracis spores were isolated from these samples and confirmed using phenotypic characterization and real-time PCR. Confirmed B. anthracis isolates were typed using multiple-locus variable-number tandem repeat analysis (MLVA15) and single-nucleotide-repeat analysis (SNRA). B. anthracis isolates split into two clades based on MLVA15, while SNRA allowed some isolates between carcass sites to be distinguished from each other. SNRA polymorphisms were also present within a single carcass site. Some isolates from different carcass sites having the same SNRA type had divergent MLVA types; this finding leads to questions about hierarchical typing methods and the robustness of the fine-scale typing of Bacillus anthracis.     

Post-bottleneck mtDNA diversity in a free-living population of European bison: implications for conservation

A free-living population of European bison Bison bonasus in the Białowieża Primeval Forest originated from only seven founder animals after a severe bottleneck that occurred at the beginning of the 20th century. Consequently, the contemporary population of the species is characterized by low genetic diversity. We studied a total of 195 individuals (127 males and 68 females). A 1429 bp fragment of mitochondrial DNA (mtDNA) including the D-loop region was analyzed in 87 individuals and revealed only three distinct haplotypes. Nucleotide ( π ) and haplotype ( H _d) diversity values were estimated for the European bison and were compared with π and H _d estimated from three individuals of American bison Bison bison . Very low diversity values were found in the European bison in comparison with the diversity values found in the American bison. The low mtDNA variability in the European bison is in concordance with theoretical expectations for a species that has undergone a severe and recent bottleneck. A management strategy for the preservation of the rare and very rare haplotypes present in the Białowieża population of the European bison is discussed. Furthermore, all 195 individuals were investigated for heteroplasmy involving these three haplotypes, in order to detect a possible association between heteroplasmy and the incidence of males affected by posthitis , a disease that affects the male reproductive organs, leading to necrotic lesions. Heteroplasmy was found in 15 females, in 17 males affected by posthitis and in 11 non-affected males, and no significant association was found.     

Genetic Analysis of the Henry Mountains Bison Herd

Wild American plains bison (Bison bison) populations virtually disappeared in the late 1800s, with some remnant animals retained in what would become Yellowstone National Park and on private ranches. Some of these private bison were intentionally crossbred with cattle for commercial purposes. This forced hybridization resulted in both mitochondrial and nuclear introgression of cattle genes into some of the extant bison genome. As the private populations grew, excess animals, along with their history of cattle genetics, provided founders for newly established public bison populations. Of the US public bison herds, only those in Yellowstone and Wind Cave National Parks (YNP and WCNP) appear to be free of detectable levels of cattle introgression. However, a small free-ranging population (~350 animals) exists on public land, along with domestic cattle, in the Henry Mountains (HM) of southern Utah. This isolated bison herd originated from a founder group translocated from YNP in the 1940s. Using genetic samples from 129 individuals, we examined the genetic status of the HM population and found no evidence of mitochondrial or nuclear introgression of cattle genes. This new information confirms it is highly unlikely for free-living bison to crossbreed with cattle, and this disease-free HM bison herd is valuable for the long-term conservation of the species. This bison herd is a subpopulation of the YNP/WCNP/HM metapopulation, within which it can contribute significantly to national efforts to restore the American plains bison to more of its native range.     

Parasites and diseases of bison in Canada IV. Serologic survey for brucellosis in bison in northern Canada

Serum samples collected from 2,365 free-roaming hybrid bison (Bison bison bison x Bison bison athabascae) in Wood Buffalo National Park and adjacent areas in the Northwest Territories were tested for brucellosis during the period 1959 to 1974. A positive reaction was obtained in 739 (31.2%) of the animals tested. The overall effect of brucellosis on this free-roaming bison population is unknown. The authors also dealt with some of the actual and possible consequences of the disease in this population.     

Genetic status of the European bison Bison bonasus after extinction in the wild and subsequent recovery

• 1 The European bison Bison bonasus went through a severe bottleneck and became extinct in the wild 90 years ago. The lowland subspecies B. b. bonasus is the only one of three original subspecies that exists today. The entire species derives from only 12 founders, including a bull of the Caucasian subspecies B. b. caucasicus. Due to its presence among founders, there are two geographically separated genetic lines of European bison: the pure lowland (Bia?owie?a) line and the hybrid lowland‐Caucasian line.
• 2 The lowland line of the European bison originates from only seven founders with an extremely varying genetic contribution. Approximately 80% of the genes in contemporary populations come from just two founders.
• 3 A variety of genetic markers (mtDNA, microsatellites, single nucleotide polymorphism microchips) were applied to studies of the level of depletion of genetic variability in European bison.
• 4 The lowland line of the European bison, the most extensively studied, shows very low levels of genetic variation, and has just half the microsatellite heterozygosity of the closely related American bison Bison bison. The effective population size (N_e) for the highly genetically homogenous lowland line in the Polish part of the Bia?owie?a Forest is estimated to be 23.5, far less than the census population size of 450.
• 5 The average inbreeding level in lowland bison is almost 50%, although no signs of inbreeding depression have been observed. In contrast, inbreeding effects have been noticed in the lowland‐Caucasian line, which has a much lower average inbreeding level (28%). In spite of the apparently high fitness of the lowland bison, the lack of genetic variation and high level of inbreeding may present substantial threats in the future, especially in the context of potential epizootics.

     

Fecal androgens of bison bulls during the rut

The influence of sex hormones is a key proximate factor underlying male reproductive behavior in mammals. Effective conservation policies for the remaining purebred plains bison (Bison bison bison) herds require knowledge of the physiology underlying bison reproductive biology. We used fecal steroid analysis to characterize androgen levels in adult bison bulls before, during, and after the rut, and to examine androgen levels of bulls differing in reproductive status, age, and mating success. Fieldwork was carried out at the Fort Niobrara National Wildlife Refuge in north-central Nebraska. All adult bison in the herd were individually known by unique brands. Fecal samples were collected during 2003 from bulls during pre-rut (June), rut (July-August), and post-rut (September), and behavioral observations focused on reproductive status and mating success during the rut. Matched sample data indicated that androgen levels (ng/g feces) of bulls peaked during the rut, doubling from pre-rut to rut and then declining by 75% during post-rut. Dominant bulls that tended (guarded) cows maintained higher androgen levels than bulls that were not tending. There was a positive correlation between bull age (associated with mating success) and androgens, with higher androgen levels in prime-aged bulls compared with younger bulls. Nonetheless, there was no correlation between mating success (measured by number of copulations observed) and androgen level. This suggests that while androgens may provide the proximate motivation to compete for matings, other factors determine the mating success of bison bulls.     

Phylogenetic relationships among the European and American bison and seven cattle breeds reconstructed using the BovineSNP50 Illumina Genotyping BeadChip

Here we present the first attempt to use the BovineSNP50 Illumina Genotyping BeadChip for genome-wide screening of European bison Bison bonasus bonasus (EB), two subspecies of American bison: the plains bison Bison bison bison (PB), the wood bison Bison bison athabascae (WB) and seven cattle Bos taurus breeds. Our aims were to (1) reconstruct their evolutionary relationships, (2) detect any genetic signature of past bottlenecks and to quantify the consequences of bottlenecks on the genetic distances amongst bison subspecies and cattle, and (3) detect loci under positive or stabilizing selection. A Bayesian clustering procedure (STRUCTURE) detected ten genetically distinct clusters, with separation among all seven cattle breeds and European and American bison, but no separation between plain and wood bison. A linkage disequilibrium based program (LDNE) was used to estimate the effective population size (N _e) for the cattle breeds; N _e was generally low, relative to the census size of the breeds (cattle breeds: mean N _e = 299.5, min N _e = 18.1, max N _e = 755.0). BOTTLENECK 1.2 detected signs of population bottlenecks in EB, PB and WB populations (sign test and standardized sign test: p = 0.0001). Evidence for loci under selection was found in cattle but not in bison. All extant wild populations of bison have shown to have survived severe bottlenecks, which has likely had large effects on genetic diversity within and differentiation among groups.     

The effect of ancient DNA damage on inferences of demographic histories

The field of ancient DNA (aDNA) is casting new light on many evolutionary questions. However, problems associated with the postmortem instability of DNA may complicate the interpretation of aDNA data. For example, in population genetic studies, the inclusion of damaged DNA may inflate estimates of diversity. In this paper, we examine the effect of DNA damage on population genetic estimates of ancestral population size. We simulate data using standard coalescent simulations that include postmortem damage and show that estimates of effective population sizes are inflated around, or right after, the sampling time of the ancestral DNA sequences. This bias leads to estimates of increasing, and then decreasing, population sizes, as observed in several recently published studies. We reanalyze a recently published data set of DNA sequences from the Bison (Bison bison/Bison priscus) and show that the signal for a change in effective population size in this data set vanishes once the effects of putative damage are removed. Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution.     

Preliminary assessment of reproductive technologies in wood bison (Bison bison athabascae): implications for preserving genetic diversity

Since the high prevalence of bovine tuberculosis and brucellosis in free-ranging wood bison in the Canadian north poses a threat to nearby healthy bison populations, commercial bison and cattle ranches, and potentially to humans, there is considerable impetus to salvage the genetics of infected bison and maintain a disease-free herd. In that regard, there is a great need to develop appropriate reproductive technologies. Therefore, the objective of this study was to develop protocols to produce and cryopreserve wood bison embryos (based on protocols used for cattle). Cumulus oocyte complexes (COC) aspirated from ovaries recovered after slaughter were matured in vitro, and fertilized with either frozen-thawed semen or chilled epididymal spermatozoa. Although both sources of spermatozoa resulted in acceptable rates of fertilization (64.4%, n=45; 89.2%, n=28, respectively) and cleavage (75.0%, n=40; 92.5%, n=40), production of morulae (7.5%, n=40; 25.0%, n=40) and blastocysts (7.5%, n=40; 10.0%, n=40) was low. Morulae- and blastocyst-stage embryos were frozen-stored by vitrification. To our knowledge, this is the first report regarding the in vitro production and cryopreservation of bison embryos for genetic recovery of diseased wood bison. These techniques have substantial potential for conserving and managing the genetic diversity of wild bison, and may also have important management implications for genetic salvage of diseased bison populations in North America.     

DNA fingerprinting and genetic diversity of the European bison (Bison bonasus), American bison (Bison bison), and gray Ukrainian cattle (Bos taurus)

To describe genetic variability and population diversity in domesticated populations of American bison (Bison bison), aurochs (Bison bonasus), and gray Ukrainian cattle (Bos taurus) different variants of DNA fingerprinting technique (utilizing the M13 phage DNA, (TTAGGG)4 synthetic oligonucleotide, and three arbitrary primers as hybridization probes) were used. Several parameters characterizing polymorphism and genetic diversity levels in each population (species) were evaluated on the basis of the profiles obtained. Dendrograms reflecting similarities between individual animals were constructed. Genetic variability of minisatellite and telomeric markers observed in the gray Ukrainian cattle flock was higher than that in aurochs and bisons. Comparison of the intrapopulation similarity (S) and gene diversity (H) indices along with the analysis of clusters in the dendrograms showed that the relatedness between the aurochs individuals was much higher than between the individual animals in the bison and gray Ukrainian cattle flocks. Furthermore, the gray Ukrainian cattle flock was represented by more distant relatives than the bison flock. It is suggested that reduced genetic variability and the appearance of deviant genotype observed in the two bison lines under selection, resulted from close inbreeding and the founder effect. The diagnostic value and efficacy of utilization of different molecular markers for estimation of genetic diversity and relatedness in domesticated animal populations is discussed.     

Genes of the extinct Caucasian bison still roam the Białowieża Forest and are the source of genetic discrepances between Polish and Belarusian populations of the European bison,Bison bonasus

European bison (Bison bonasus) populations from both the Polish (PL) and the Belarusian (BY) sides of the Bia?owie?a Forest represent the Lowland genetic line (LB line) – progeny of the Lowland bison (Bison bonasus bonasus) that inhabited western, central, and south‐eastern Europe in historical times. During the species recovery, one of the founders was a descendant of the extinct Caucasian bison (Bison bonasus caucasicus) and its descendants formed the other genetic line – Lowland–Caucasian (LC). There have been justified suspicions that LB European bison in the former Soviet Union had undergone cross‐mating with the LC line. We performed a comparative genetic analyses on European bison from the BY and PL parts of the Bia?owie?a Forest, the LC line and extinct Caucasian bison, based on a set of 19 microsatellite markers and 1512 bovine single nucleotide polymorphism (SNP) markers, polymorphic in at least one of the studied populations. Although genetic variability (mean allele number and expected heterozygosity) for both populations were similar, the F_ST jack‐knifing and principal component analyses PCA revealed highly significant differences between PL and BY bison from the Bia?owie?a Forest. Examining DNA of the extinct Caucasian bison revealed that at least part of the genetic variants found in the BY, but not the PL, population were of Caucasian origin. The results indicate that the contemporary population of European bison from the BY part of the Bia?owie?a Forest should not be regarded as a LB line. The results also suggest that the actual global population size of the LB line European bison is only a half of its official status. Consideration of the presented results are crucial in determining management actions and policy decisions in order to conserve LB line bison within the Bia?owie?a Forest – its natural refuge. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 752–763.     

Small population size and extremely low levels of genetic diversity in island populations of the platypus, Ornithorhynchus anatinus

Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (H(E)= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed.     

Genetic characteristics and prognosis of the existence of the European bison free-living population created in the "Orlovsky Poles'e" National Park

We present preliminary data on genetic aspects of preserving viability of the free-living population of European bison (Bison Bonasus L.) created in the Orlovskoe Poles'e National Park.     

Resistance to malignant catarrhal fever in American bison (Bison bison) is associated with MHC class IIa polymorphisms

The Rhadinovirus ovine herpesvirus-2 (OvHV-2) is the most common causative agent of malignant catarrhal fever (MCF) in clinically susceptible ruminants including cattle and bison. American bison (Bison bison) are highly susceptible to clinical MCF. Nevertheless, approximately 20% of bison on ranches or in feedlots become infected with the virus without developing clinical disease. Defining the genetic basis for differences in susceptibility between bison could facilitate development of improved control strategies for MCF. One genetic region that influences susceptibility to infectious diseases is the major histocompatibility complex (MHC). In this study, a Bison bison (Bibi) DRB3 oligonucleotide microarray was used to type 189 bison from 10 herds where MCF outbreaks had occurred. Binary logistic regression was used to classify DRB3 alleles as resistant (R), susceptible (S) or neutral (N). Animals were reclassified using six DRB3 genotype categories: N/N, N/R, N/S, R/S, R/R and S/S. Analysis of homogeneity across herds showed that there was a herd effect. Consequently, a penalized logistic regression model was run with herd and genotype categories as the explanatory variables. The R/R genotype was associated with resistance to MCF (P = 0.0327), while the S/S genotype was associated with clinical MCF (P = 0.0069). This is the first evidence that MHC class IIa polymorphism is associated with resistance or susceptibility to OvHV-2-induced MCF.     

MHC-DRB3 variation in a free-living population of the European bison, Bison bonasus

MHC genes play a crucial role in pathogen recognition and are the most polymorphic genes in vertebrates. Loss of variation in these genes in bottlenecked species is thought to put their survival at risk. We examined variation at the MHC II DRB3 locus in the European bison, Bison bonasus, a species that has undergone an extreme bottleneck: the current population originated from only 12 founders. We also tested for the association of DRB3 genes with the incidence of posthitis, a disease affecting the reproductive organs of bulls and posing a new threat to the survival of the species. We found very limited MHC diversity, with only four alleles segregating in a sample of 172 individuals from a free‐ranging Białowieża population. The alleles were highly divergent and revealed the hallmark of positive selection acting on them in the past, that is, a significant excess of nonsynonymous substitutions. This excess was concentrated in putative antigen‐binding sites, suggesting that selection was driven by pathogens. However, we did not observe departures from Hardy–Weinberg equilibrium, an indicator of strong ongoing selection. Neither have we found a significant association between DRB3 alleles or genotypes and susceptibility to posthitis. Alleles conferring resistance to males may have been lost during the extreme bottleneck the species had undergone.     

Genetic population substructure in bison at Yellowstone National Park

The Yellowstone National Park bison herd is 1 of only 2 populations known to have continually persisted on their current landscape since pre-Columbian times. Over the last century, the census size of this herd has fluctuated from around 100 individuals to over 3000 animals. Previous studies involving radiotelemetry, tooth wear, and parturition timing provide evidence of at least 2 distinct groups of bison within Yellowstone National Park. To better understand the biology of Yellowstone bison, we investigated the potential for limited gene flow across this population using multilocus Bayesian clustering analysis. Two genetically distinct and clearly defined subpopulations were identified based on both genotypic diversity and allelic distributions. Genetic cluster assignments were highly correlated with sampling locations for a subgroup of live capture individuals. Furthermore, a comparison of the cluster assignments to the 2 principle winter cull sites revealed critical differences in migration patterns across years. The 2 Yellowstone subpopulations display levels of differentiation that are only slightly less than that between populations which have been geographically and reproductively isolated for over 40 years. The identification of cryptic population subdivision and genetic differentiation of this magnitude highlights the importance of this biological phenomenon in the management of wildlife species.     

Effects of Prescribed Burning on Herbaceous and Woody Vegetation in Northern Lowland Meadows

Abstract Spring burning of sedge‐grass meadows in the Slave River Lowlands (SRL), Northwest Territories, Canada was applied between 1992 and 1998 to reduce shrub encroachment and enhance Bison bison (bison) habitat, although the impact of fire on preferred bison forage was unknown before management. In the summer of 1998 we conducted a study in the Hook Lake area of the SRL to test the effect of burn frequency (unburned, burned once, or burned three times since 1992) on herbaceous plant community composition and Salix spp. L. (willow) shrub vigor. Plant species abundance, litter biomass, soil pH, and depth of the organic soil horizon were measured in 300 1‐m² quadrats nested within 30 1,000‐m² plots in both burned and unburned dry meadows. To test the relationship between frequency and willow vigor, all willow shrubs within the plots were assigned a vigor score from I (dead) to IV (flourishing). The spring burns appear to have reduced willow vigor; however, shrub survival remained high (76%) on the most frequently burned meadows. Ordination plots resulting from canonical correspondence analysis suggest that multiple spring burns influenced plant community composition in dry meadow areas and that less palatable bison forage species (e.g., Carex aenea Fern. and Juncus balticus L.) were correlated with a regime of three spring burns. Our results suggest that frequent spring fires in the Hook Lake area have only a small negative effect on willow cover but may reduce the abundance of primary bison forage plants compared with less frequently burned meadows.     

Safety of revaccination of pregnant bison with Brucella abortus strain RB51

From December 1998 through February 1999, a study was conducted in a Brucella-infected bison herd to evaluate the safety of booster vaccination of adult bison (Bison bison) with 6 x 10(9) colony forming units (CFU) of Brucella abortus strain RB51 (SRB51) that had previously been vaccinated as yearlings with 1 x 10(10) CFU of SRB51. Abortions or other adverse effects were not observed after SRB51 booster vaccination. At 10 wk after adult vaccination, pregnant and nonpregnant bison (n = 65) were randomly selected for bacteriologic sampling of targeted maternal tissues during abattoir processing. Fetal tissues were also sampled in pregnant bison. The SR351 recovered from tissue samples of eight of 48 pregnant bison and none of 17 nonpregnant bison. In three of the eight culture-positive bison, SRB51 was recovered from fetal tissues. In three additional bison, one pregnant and two nonpregnant, B. abortus biovar 1 field strain was recovered from internal iliac or supramammary lymphatic tissues. Results of this study suggest the possibility that the SRB51 vaccine can be safely used to booster vaccinate pregnant bison in a Brucella-infected bison herd. Our data also reaffirms the potential for B. abortus field strains to persist in bison until attainment of reproductive age, despite extensive use of vaccination and serologic testing.