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.     

Differential introgression of uniparentally inherited markers in bison populations with hybrid ancestries

Historical hybridization between Bison bison (bison) and Bos taurus (cattle) has been well documented and resulted in cattle mitochondrial DNA (mtDNA) introgression, previously identified in six different bison populations. In order to examine Y chromosome introgression, a microsatellite marker (BYM-1) with non-overlapping allele size distributions in bison and cattle was isolated from a bacterial artificial chromosome (BAC) clone, and was physically assigned to the Y chromosome by fluorescence in situ hybridization. BYM-1 genotypes for a sample of 143 male bison from 10 populations, including all six populations where cattle mtDNA haplotypes were previously identified, indicated that cattle Y chromosome introgression had not occurred in these bison populations. The differential permeability of uniparentally inherited markers to introgression is consistent with observations of sterility among first generation hybrid males and a sexual asymmetry in the direction of hybridization favouring matings between male bison and female cattle.     

Conservation genomics: disequilibrium mapping of domestic cattle chromosomal segments in North American bison populations

Introgressive hybridization is one of the major threats to species conservation, and is often induced by human influence on the natural habitat of wildlife species. The ability to accurately identify introgression is critical to understanding its importance in evolution and effective conservation management of species. Hybridization between North American bison (Bison bison) and domestic cattle (Bos taurus) as a result of human activities has been recorded for over 100 years, and domestic cattle mitochondrial DNA was previously detected in bison populations. In this study, linked microsatellite markers were used to identify domestic cattle chromosomal segments in 14 genomic regions from 14 bison populations. Cattle nuclear introgression was identified in five populations, with an average frequency per population ranging from 0.56% to 1.80%. This study represents the first use of linked molecular markers to examine introgression between mammalian species and the first demonstration of domestic cattle nuclear introgression in bison. To date, six public bison populations have been identified with no evidence of mitochondrial or nuclear domestic cattle introgression, providing information critical to the future management of bison genetic resources. The ability to identify even low levels of introgression resulting from historic hybridization events suggests that the use of linked molecular markers to identify introgression is a significant development in the study of introgressive hybridization across a broad range of taxa.     

The polymorphism of proteins, RAPD-PCR and ISSR-PCR markers in European and American bison and cattle

The comparative analysis of genetic differentiations between three species of Bovinae--Bos taurus, Bison bonasus, Bison bison with the use of different types of molecular-genetic markers--genetical-biochemical (35 loci) and DNA markers (RAPD-PCR, ISSR-PCR) was carried out. It was shown, that the evaluation of interspecies genetic interrelations was connected more with the determined molecular-genetic markers (loci), included in analysis, than with the marker's belonging to certain type (protein polymorphism, variability of DNA repeat distributions).     

Host defense function in neutrophils from the American bison (Bison bison)

Selected host defense functions of neutrophils isolated from American bison (Bison bison) were characterized and compared with those of cattle (Bos taurus). Bison neutrophils had a robust chemotactic response to both IL-8 and LTB(4), with maximal responses occurring at 10(-7) M (IL-8) and 10(-8) M (LTB(4)). The magnitude of the chemotactic response to IL-8 was similar in bison and bovine neutrophils (except at 10(-7) M IL-8, where bison had a stronger response). In response to LTB(4), bison neutrophils had a much stronger chemotaxis at both 10(-8) and 10(-7) M than did bovine cells. Production of reactive oxygen species (ROS) in response to phorbol myristate acetate (PMA) and opsonized zymosan (OpZ) was similar between bison and bovine neutrophils. However, the production of ROS in bison neutrophils stimulated with OpZ was primarily intracellular, while extracellular release of ROS was evident in bovine neutrophils stimulated with OpZ. Like bovine neutrophils, bison neutrophils did not generate a respiratory burst in response to fMLF. Granules prepared from bison neutrophils had potent direct killing action on the Gram-negative bacteria Escherichia coli but failed to kill the Gram-positive bacteria Staphylococcus aureus and, at intermediate doses, actually had a permissive effect for this bacteria. Thus, bison neutrophils have potent host defense capabilities similar in quality to those of bovine neutrophils; however, unique differences are present, which may allow bison neutrophils to respond to the distinct immunological challenges that bison encounter.     

Validation of 15 microsatellites for parentage testing in North American bison, Bison bison and domestic cattle

Fifteen bovine microsatellites were evaluated for use in parentage testing in 725 bison from 14 public populations, 178 bison from two private ranches and 107 domestic cattle from five different breeds. The number of alleles per locus ranged from five to 16 in bison and from five to 13 in cattle. On average, expected heterozygosity, polymorphism information content (PIC) and probability of exclusion values were slightly lower in bison than in cattle. A core set of 12 loci was further refined to produce a set of multiplexed markers suitable for routine parentage testing. Assuming one known parent, the core set of markers provides exclusion probabilities in bison of 0.9955 and in cattle of 0.9995 averaged across all populations or breeds tested. Tests of Hardy-Weinberg and linkage equilibrium showed only minor deviations. This core set of 12 loci represent a powerful and efficient method for determining parentage in North American bison and domestic cattle.     

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.     

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.     

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.     

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.     

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.

     

Seasonal Shifts in Diet and Gut Microbiota of the American Bison (Bison bison)

North American bison (Bison bison) are becoming increasingly important to both grassland management and commercial ranching. However, a lack of quantitative data on their diet constrains conservation efforts and the ability to predict bison effects on grasslands. In particular, we know little about the seasonality of the bison diet, the degree to which bison supplement their diet with eudicots, and how changes in diet influence gut microbial communities, all of which play important roles in ungulate performance. To address these knowledge gaps, we quantified seasonal patterns in bison diet and gut microbial community composition for a bison herd in Kansas using DNA sequencing-based analyses of both chloroplast and microbial DNA contained in fecal matter. Across the 11 sampling dates that spanned 166 days, we found that diet shifted continuously over the growing season, allowing bison to take advantage of the seasonal availability of high-protein plant species. Bison consumed more woody shrubs in spring and fall than in summer, when forb and grass intake predominated. In examining gut microbiota, the bacterial phylum Tenericutes shifted significantly in relative abundance over the growing season. This work suggests that North American bison can continuously adjust their diet with a high reliance on non-grasses throughout the year. In addition, we find evidence for seasonal patterns in gut community composition that are likely driven by the observed dietary changes.     

Polymorphism of bovine microsatellite DNA sequences in the lowland European bison

Investigations of genetic polymorphism of microsatellite DNA sequences were conducted in 22 individuals of the European bisonBison bonasus (Linneaus, 1758) from Bia?owie?a Primeval Forest. For this purpose 27 cattle microsatellite primer pairs were used. Among the 27 microsatellite markers examined, an amplification product was obtained for 21 loci. This rendered it possible to identify total of 40 alleles in the bison population tested. In addition, eight loci were proved to be monomorphic. A majority of the 40 alleles identified was identical with the alleles identified at the corresponding loci in cattle. Only two alleles seem to be specific for the European bison. The value of heterozygosity for the examined loci in bison population from Bia?owie?a was low and ranged from 0.13 to 0.53. Hence, the polymorphism information content was low as well. Based on our results the microsatellite DNA markers identified in cattle may be used to analyse the genetic structure of the population of European bison.     

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 seasonal fertility of North American bison (Bison bison) bulls

The objective of this study was to determine the presence and magnitude of seasonal fluctuations in semen quality and other reproductive indices in bison bulls. Testicles from 288 commercially slaughtered bison bulls were collected monthly over a 1-year period. Carcass and testicle weight were determined and measurements of seminiferous tubule lumen, diameter, and epithelial thickness were made. Sperm cell morphology and defects were described and quantified using epididymal semen from each testicle. Twenty-one Plains (Bison bison bison) and Wood bison (Bison bison athabascae) breeding bulls, averaging 6.0 years of age (range 2.5-8.0), from three farms were selected for semen collection and evaluation on the basis of producer co-operation. Semen was collected by electro-ejaculation on four seasonal occasions during a 12-month period. Ejaculate quality was judged on the basis of volume, density, gross and individual motility, morphology, live/dead ratio, and concentration. Sperm cell morphologies were evaluated microscopically and classified according to criteria used for bovine semen. Fecal testosterone was measured at each semen collection using a commercial competitive binding radioimmunoassay. There was an increase in carcass weights over the study period and testis weights were moderately correlated (r=0.44) with carcass weights. However, mean testes weights were heavier (P<0.05) in the summer than in winter, spring, or fall periods. There were no differences in the proportion of normal and abnormal epididymal sperm between seasons but there were seasonal changes in the testicular parenchyma. Seminiferous tubule and lumen diameter, and epithelial thickness were greatest (P<0.05) in summer. Live bulls gained weight between April and November, but lost weight over the winter. Normal sperm cell percentages as well as individual sperm cell motility in electro-ejaculated sperm samples were higher (P<0.05) at the pre-breeding collection relative to other collections, but no change in sperm cell concentrations occurred over the study period. Fecal testosterone concentrations were highest at the pre-breeding period (June) but decreased (P<0.05) in each subsequent collection to reach their lowest levels in the April. While many changes in seen characteristics were not significant, overall results indicate the presence of some reproductive seasonality and increased testicular capacity in the summer breeding season. Bulls showing marginal semen quality in the winter but otherwise carrying desirable genetic traits may warrant another evaluation in late spring prior to being culled from a breeding program.     

Sperm characteristics in plains (Bison bison bison) versus wood (Bison bison athabascae) bison

The objective was to compare sperm characteristics between the two subspecies of North American bison, plains bison (Bison bison bison) and wood bison (Bison bison athabascae). Frozen-thawed ejaculated sperm from age-matched plains (n = 3) and wood (n = 2) bison were evaluated for morphometry, motility, viability, protein profile, and in vitro fertilization characteristics. Sperm morphometry and motility were assessed with computer-based systems, viability was assessed with SYBR-14 and propidium iodide, and fertilizing ability was determined using a heterologous in vitro fertilization system (using bovine oocytes). For plains versus wood bison, there were significant differences for head width (4.76 ± 0.22 vs 4.71 ± 0.19 μm; mean ± SD), head area (35.64 ± 1.91 vs 34.72 ± 2.64 μm²), head perimeter (23.61 ± 0.68 vs 23.31 ± 0.98 μm), midpiece length (14.58 ± 0.4 vs 14.36 ± 0.51 μm), midpiece width (0.81 ± 0.06 vs 0.79 ± 0.07 μm), and tail length (46.61 ± 2.15 vs 45.98 ± 2.08 μm). However, there was no significant difference in head length (overall, 9.04 ± 0.37 μm), progressive motility (41.16 ± 8.39%), or viability (41.58 ± 5.58%). Based on two-dimensional gel electrophoresis, 93 out of 113 protein spots were similar in their expression patterns. Furthermore, we inferred that differences in sperm biometry between these subspecies did not affect in vitro fertilization percentage (overall, 82.62 ± 12.13%). Based on these findings, we concluded that plains bison were an appropriate research model for developing reproductive technologies for wood bison.     

Effectiveness of bovine microsatellites in resolving paternity cases in American bison, Bison bison L.

A set of 33 cattle microsatellite primer pairs was tested with the DNA of American bison from a captive population in Belgium and evaluated for usefulness in parentage testing. Two primer sets did not amplify and three were monomorphic. Among the polymorphic markers, the number of alleles ranged from two to nine. Heterozygosity, polymorphism information content (PIC) and probability of exclusion (PE) values were low by comparison with those obtained with the same markers in cattle. Two methods of estimating PE were used, one which assumed equal allele frequencies between parental sexes and another which took into account differences in allele frequencies between parental sexes. An internationally accepted set of nine microsatellites gives cumulative PE values of 0·98 and 0·97, respectively, for the two methods. The potential of this marker set to identify bison × cattle hybrids is discussed. Because bison and cattle have a common ancestor, these microsatellites are a useful way to establish genetic distances and can lead to the construction of phylogenetic trees.     

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.     

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.