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

Genetic Diversity of Wisent Bison bonasus Based on STR Loci Analyzed in a Large Set of Samples

Wisent Bison bonasus is an example of a species saved from extinction and reintroduced into nature after a few decades of captive breeding. There were only twelve founders of the Lowland–Caucasian line (LC) and even fewer (seven out of twelve) of Lowland (LB) animals. The genetic diversity in studies based on pedigree or markers is very low. In this paper, we present a summary of the long-term genetic monitoring conducted for the worldwide population of European bison. We summarized the long-term genetic monitoring studies conducted on the worldwide population of wisents to date. We genotyped 2227 wisents from two genetic lines (LC and LB) and different populations at ten microsatellite loci. We found low polymorphism, with only 2.7 alleles per locus, and much lower values of observed heterozygosity (0.380 and 0.348 in the LC and LB lines, respectively) than expected heterozygosity. The difference between the lines is only noticeable in allele proportions, so the number of markers is not enough to distinguish the two genetic lines. We also present the genetic distance among four free-roaming populations that are geographically close to each other. We found that the genetic distance of one of them is larger than that of the others, which could be the effect of genetic drift.

Analysis of the Genetic Diversity of the European Bison (Bison bonasus) Population in Lithuania

The European bison is a species well known for its low genetic variability due to historical bottleneck incidents. Restoration of the European bison population in Lithuania began at the end of the 20th century, and the Lithuanian population was re-established with ten individuals from the Prioksko-Terrasny reserve in Russia and one free-roaming individual captured in Lithuania. This research focused on the genetic diversity and genetic structure of European bison in Lithuania based on microsatellite markers and mtDNA sequences. The results of the microsatellite analysis revealed that the Lithuanian population (n = 34) has a different genetic structure to individuals in Poland (n = 16), Germany (n = 10), and Sweden (n = 6). The analysis of the mtDNA sequences showed a low level of variation, with two haplotypes observed in the Lithuanian bison population. H1 was more frequent and was also found in Poland, Romania, and Russia. The results of this investigation show that individuals should be continuously genetically monitored, registering their migrations and relocations for the successful management of the species in Lithuania.

Genealogical analysis of European bison population revealed a growing up population despite very low genetic diversity

In 1919, the European bison population became extinct in the wild. The rescue of the lowland subspecies and the whole species was achieved mainly thanks to individuals from the Białowieża Forest (Polish-Belarusian border). There are currently two breeding lines—the lowland (purebred B. b. Bonasus) founded by 7 individuals and the lowland-Caucasian (hybrids of B. b. Bonasus and B. b. caucasicus) founded by 12 individuals. This genealogical study was conducted on 15,071 individuals recorded in the pedigree book between 1881 and 2020. Its objective was to determine the level of genetic variability and inbreeding almost 100 years after the rescue measures were initiated. The completeness of the pedigree of the reference population was 77% in the fifth generation backwards. A maximum of 23 generations can be traced back in the pedigree. The average inbreeding coefficient and the mean average relatedness of the reference population were very high, about 17% and 16% respectively. No significant amount of new inbreeding was discovered. The reference population has lost 9.11% of the total genetic diversity compared to the population of founders. A male of the Caucasian subspecies Kaukasus was discovered among the ancestors of the lowland lineage reference population. The effective population size calculated based on the increase in inbreeding was 23.93 individuals, based on complete generations equivalent it was 16.1 individuals. Wright’s F-statistics showed very small differences in genotypic frequencies between individuals within the two lineages in the reference population (FIS = 0.10), between individuals and the total population (FIT = 0.04) and low differentiation between lineages (FST = 0.06). The population of the European bison from the Białowieża Forest is generally very uniform but still shows good fitness.

In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))-Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

New data on the genetic diversity of European bison Bison bonasus (Linnaeus, 1758) in Belarus

The paper presents data on the assessment of the genetic diversity of five subpopulations of the European bison (Bison bonasus) in Belarus — from the National Park “Belovezhskaya Pushcha”, the National Park “Pripyatsky”, the Osipovichi district (Mogilev area), SEI “Berezinsky Biosphere Reserve” and the Grodno region. In general, the work includes 30 samples of muscle tissue from the collection of Gene bank of wild fauna in SSPA “SPC NAS of Belarus on Bioresources” (Minsk, Belarus). Microsatellites were used as markers to assess genetic diversity, structure, and search for signs of a sharp decline in the size of bison subpopulations in the past. A total of 11 microsatellite markers were used, recommended by the Food and Agriculture Organization of the United Nations for cattle research. The analysis of B. bonasus subpopulation from the NP “Pripyatsky” showed signs of passing through the genetic bottleneck. All studied subpopulations are characterized by a similarly low genetic diversity level in all analyzed indicators (mean number of alleles, allelic diversity, observed and expected heterozygosity). The expected heterozygosity (He) for the three subpopulations from the NP “Belovezhskaya Pushcha”, the NP “Pripyatsky” and from the Osipovichi district ranged from 0.37 to 0.39. For the studied subpopulations, the values of the fixation index were negative. The assessment of the presence of genetic structuring between the subpopulations of bison from the NP “Belovezhskaya Pushcha”, the NP “Pripyatsky” and from the Osipovichi district based on the values of such indexes as Fst and DJost which showed no signs of genetic differentiation, which is also confirmed by principal coordinates analysis (PCoA). The European bison conservation in Belarus has required tremendous efforts in the past. So far, even though the impressively large population size reached in Belarus, B. bonasus status still should not be considered as stable, which is closely linked to aspects of its overall low genetic diversity. Our research confirmed the low genetic variability of Belarusian subpopulations. Therefore, the more extensive research concentrated on identifying genetic diversity is necessary to ensure the beneficial control of gene flow and register a potential correlation of unfavorable gene variants with possible inbreeding depression. These attempts are required to lay the groundwork for the management and protection of the European bison in Belarus.

Complex Admixture Preceded and Followed the Extinction of Wisent in the Wild

Retracing complex population processes that precede extreme bottlenecks may be impossible using data from living individuals. The wisent (Bison bonasus), Europe’s largest terrestrial mammal, exemplifies such a population history, having gone extinct in the wild but subsequently restored by captive breeding efforts. Using low coverage genomic data from modern and historical individuals, we investigate population processes occurring before and after this extinction. Analysis of aligned genomes supports the division of wisent into two previously recognized subspecies, but almost half of the genomic alignment contradicts this population history as a result of incomplete lineage sorting and admixture. Admixture between subspecies populations occurred prior to extinction and subsequently during the captive breeding program. Admixture with the Bos cattle lineage is also widespread but results from ancient events rather than recent hybridization with domestics. Our study demonstrates the huge potential of historical genomes for both studying evolutionary histories and for guiding conservation strategies.