Managing Genetic Diversity and Extinction Risk for a Rare Plains Bison (Bison bison bison) Population

The Ruminant Telomere-to-Telomere (RT2T) Consortium

Telomere-to-telomere (T2T) assemblies reveal new insights into the structure and function of the previously 'invisible' parts of the genome and allow comparative analyses of complete genomes across entire clades. We present here an open collaborative effort, termed the 'Ruminant T2T Consortium' (RT2T), that aims to generate complete diploid assemblies for numerous species of the Artiodactyla suborder Ruminantia to examine chromosomal evolution in the context of natural selection and domestication of species used as livestock.

When Theory Meets Practice: Balancing Genetic Diversity and Behaviour When Choosing Founders for a Recently Reintroduced Bison (Bison bison) Herd in Banff National Park, Canada

The tragic decline of plains bison (Bison bison bison) in North America is well known. By the turn of the 20th century, plains bison, once numbering in the tens of millions, were extirpated from the wild in Canada. Banff National Park, AB, Canada, is within the original range of bison in North America, and still contains suitable habitat for the species. In 2017, we used measures of genetic diversity, as well as age and reproductive status, to select 16 plains bison for reintroduction to an unoccupied corner of their former historic range in Banff National Park. However, five of the preferred founders from this genetically diverse group needed to be substituted for less ideal candidates when aggressive behavior was observed, which could have compromised animal welfare during translocation. The level of genetic diversity in the founding population was therefore lower than if all proposed founders had been used, although the difference was not substantial. As expected, adults in this small, reintroduced herd had lower observed heterozygosity and number of alleles than the larger source herd, but expected heterozygosity was higher, likely a result of preferentially choosing individuals with rare alleles. Another substantial contribution to genetic diversity was in unborn fetuses: sired by males that were not translocated, the calves born a few months later provided a boost to the genetic diversity of this small founder herd. Where opportunities allow, the inclusion of pregnant females can significantly increase the genetic diversity of small founder populations. When compared to other founded herds of bison, the techniques described here have ensured that the newly established Banff NP herd is one of the most diverse bison herds in Canada, despite its relatively small number of founders.

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.

Production of embryos and a live offspring using post mortem reproductive material from bison (Bison bison bison) originating in Yellowstone National Park, USA

Bison from Yellowstone National Park (YNP) have an important genetic history. As one of the few wild herds of bison with no evidence of cattle DNA introgression and a large enough population to maintain genetic diversity, they are considered a conservation priority for the species. Unfortunately, there is a high prevalence of the zoonotic disease brucellosis in the herd. Part of the management strategy for controlling the disease and herd size in YNP is to remove bison from the population during the winter migration out of the park. This interagency management cull provides an opportunity to collect a large number of oocytes from a wild bison population for genetic banking and research purposes. During the winters of 2014-2018, which is the nonbreeding season for bison, oocytes were collected post mortem and used to determine the effects of donor reproductive maturity and pregnancy status on oocyte quality and in vitro fertilization (IVF) outcomes, and to demonstrate the feasibility of producing healthy offspring. Cumulus oocyte complexes (COCs) were placed into an in vitro embryo production (IVP) system, and on days 7, 7.5, and 8 of in vitro culture (Day 0 = day of in vitro fertilization) embryos were assessed for developmental stage and quality prior to vitrification. Embryos were then stored in liquid nitrogen until the breeding season when a subset were warmed, cultured for 6 h, evaluated for survival, and transferred to healthy bison recipients. There were no significant differences in the ability of recovered COCs to support blastocyst development based on female reproductive maturity or pregnancy status (juvenile 79/959 (8.2%) vs sexually mature 547/6544 (8.4%); non-pregnant 188/2302 (8.2%) vs pregnant 556/6122 (9.1%)). Following the transfer of 15 embryos to 10 recipients, one healthy female calf was born. This work demonstrates that live offspring can be generated from COCs collected from YNP bison post mortem in the non-breeding season, and that gamete recovery can be a valuable tool for conservation of valuable genetics for this species while mitigating diseases like brucellosis.