Genetic variation and differentiation of bison (Bison bison) subspecies and cattle (Bos taurus) breeds and subspecies

A globally integrated structure of taxonomy to support biodiversity science and conservation

All aspects of biodiversity research, from taxonomy to conservation, rely on data associated with species names. Effective integration of names across multiple fields is paramount and depends on the coordination and organization of taxonomic data. We assess current efforts and find that even key applications for well-studied taxa still lack commonality in taxonomic information required for integration. We identify essential taxonomic elements from our interoperability assessment to support improved access and integration of taxonomic data. A stronger focus on these elements has the potential to involve taxonomic communities in biodiversity science and overcome broken linkages currently limiting research capacity. We encourage a community effort to democratize taxonomic expertise and language in order to facilitate maximum interoperability and integration.

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.

Buffalo on the Edge: Factors Affecting Historical Distribution and Restoration of Bison bison in the Western Cordillera, North America

The historic western edge of the bison (Bison bison) range and the ecological processes that caused its formation are frequently debated with important implications for bison restoration across North America. We test the hypothesis that a combination of bottom-up habitat suitability and top-down harvest pressure from Indigenous peoples were important processes in forming the western edge of bison distribution. Using 9384 historical journal observations from 1691–1928, we employ MaxEnt ecological niche modelling to identify suitable bison habitat across the Western Cordillera from bottom-up climatic, land cover, and topographic factors. We then use mixed-effect logistic regression to test if bison occurrence in journal records can be in part explained by the abundance of humans, wolves, or grizzly bears, in addition to MaxEnt-derived habitat suitability. We find support for our hypothesis because of the limited suitable habitat in the Rocky Mountains that likely prevented westward bison dispersal from their core habitat, and there was a negative relationship between bison occurrence and human harvest pressure. On this basis, we propose that intensive human harvest from large populations in the Western Cordillera, subsidized by other wildlife, salmon, and vegetation resources, is an underappreciated socioecological process that needs to be restored alongside bison populations. Co-managing bison with Indigenous peoples will also mitigate the adverse effects of overabundant bison populations and maximize the ecological and cultural benefits of bison restoration.

A Reference Genome Assembly of American Bison, Bison bison bison

Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison-Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ~13× more contiguous overall and ~3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC_bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.

Development of SNP-Based Genomic Tools for the Canadian Bison Industry: Parentage Verification and Subspecies Composition

Genomic technologies have been increasingly applied in livestock production due to their utility in production management and animal genetic improvement. The current project aimed to develop genomic resources for the Canadian bison industry, specifically a parentage verification tool and a subspecies composition tool. Both products stand to help with building and maintaining purebred and crossbred bison populations, and in turn bison conservation and production. The development of this genomic toolkit proceeded in two stages. In the single-nucleotide polymorphism (SNP) discovery and selection stage, raw sequence information from 41 bison samples was analyzed, and approximately 52.5 million candidate biallelic SNPs were discovered from 21 samples with high sequence quality. A set of 19,954 SNPs (2,928 for parentage verification and 17,026 for subspecies composition) were then selected for inclusion on an Axiom myDesign custom array. In the refinement and validation stage, 480 bison were genotyped using the custom SNP panel, and the resulting genotypes were analyzed to further filter SNPs and assess tool performance. In various tests using real and simulated genotypes, the two genomic tools showed excellent performance for their respective tasks. Final SNP sets consisting of 191 SNPs for parentage and 17,018 SNPs for subspecies composition are described. As the first SNP-based genomic toolkit designed for the Canadian bison industry, our results may provide a new opportunity in improving the competitiveness and profitability of the industry in a sustainable manner.

Development and Assessment of a Body Condition Score Scheme for European Bison (Bison bonasus)

Resettlement projects of the strongly threatened European bison (Bison bonasus) require a monitoring phase to assess both population status and habitat quality. Schemes of animal body condition scores (BCS) are robust tools to meet this requirement in practice. However, so far, no BCS scheme has been designed for European bison. Here, we suggest a body condition score scheme based on the extent of soft tissue around bony structures. The scoring system was developed with scores ranging from 1 (emaciated) to 5 (obese). Condition scores can be deduced after visually assessing the European bison both from the side and behind. Robustness of the scheme was evaluated: Unbiased people from different professional backgrounds were asked to assess the BCS of photographed semiwild European bison under field conditions and results were compared. Results demonstrate the suitability of the method. Nevertheless, variability of the results among assessors illustrates the necessity for training as well as for further research to validate the scheme as a true measure of physiological condition. We discuss the prospects and limits of a broad use of this scheme within the European bison community, and recommend the BCS scheme as a management tool.

Genetic variation and differentiation in parent-descendant cattle and bison populations

Genetic variation and differentiation at 32 microsatellite loci was quantified for parent-descendant cattle populations and parent-descendant bison () populations. We compared heterozygosity () and allelic richness () for 587 cattle of four breeds and three lines derived from them, and 188 bison in three pairs of parent-descendant populations. and were less in the Line 1 Hereford inbred cattle population than in the parent Hereford breed. and were intermediate in a composite population (CGC, derived from crossing Red Angus, Charolais, and Tarentaise) compared to the three parent breeds. Crossbreeding of Line 1 with CGC resulted in an F generation with increased and relative to Line 1 and CGC, followed by decreased and in 2 backcross generations to Line1. Three transplanted wild bison populations had smaller and than their respective parent populations. These data demonstrate that genetic variation reduced from founder effects or inbreeding can be restored with crossbreeding and gene flow.

Biobanking genetic resources: challenges and implementation at the USDA National Animal Germplasm Program

There is adequate infrastructure in the US to identify and acquire germplasm from the major beef and dairy cattle and swine breeds. However, when we venture outside these species, the same tasks become more difficult because of a lack of breed associations, databases that include genotypic and phenotypic data and low numbers of animals. Furthermore, acquisition of germplasm from non-cattle and non-swine species can be difficult because these animals are often not located near the National Animal Germplasm Program, which makes collection and preservation of the samples in a timely manner that much more complicated. This problem is compounded because not all preservation protocols are optimised for field collection conditions or for all types of germplasm. Since 1999, the USDA National Animal Germplasm Program has worked to overcome these obstacles by developing policies, procedures and techniques in order to create a germplasm repository for all agricultural species (wild and domesticated) in the US. Herein, we describe these activities and illustrate them via a case study on how our efforts collecting Navajo-Churro sheep have created a secure backup of germplasm and how we specifically overcome these issues as they relate to rare and minor breeds of agricultural species.

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.