Genomic evaluation of hybridization in historic and modern North American Bison (Bison bison)

Abstract

During the late nineteenth century North American bison underwent a significant population bottleneck resulting in a reduction in population size of over 99% and a species-level near-extinction event. Factors responsible for this destruction included indiscriminate killing, loss of access to suitable habitat, and diseases. At the nadir of this population crash, very few wild plains bison survived and were restricted to Yellowstone National Park, USA and a small number of wild wood bison remained in Wood Buffalo National Park, Canada. However, most surviving bison in the late 1800’s were maintained by cattle ranchers in private herds where hybridization between bison with various breeds of domestic cattle was often encouraged. Over the last 20 years, the legacy of this introgression has been identified using mitochondrial DNA and limited nuclear microsatellite analyses. However, no genome-wide assessment has been performed, and some herds were believed to be free of introgression based on current genetic testing strategies. Herein, we report detailed analyses using whole genome sequencing from nineteen modern and six historical bison, chosen to represent the major lineages of bison, to identify and quantitate signatures of nuclear introgression in their recent (within 200 years) history. Both low and high coverage genomes provided evidence for recent introgression, including animals from Yellowstone, Wind Cave, and Elk Island National Parks which were previously thought to be free from hybridization with domestic cattle. We employed multiple approaches, including one developed for this work, to identify putative cattle haplotypes in each bison genome. These regions vary greatly in size and frequency by sample and herd, though we detected domestic cattle introgression in all bison genomes tested. Since our sampling strategy spanned across the diversity of modern bison populations, these finding are best explained by multiple historical hybridization events between these two species with significant genetic recombination over the last 200 years. Our results demonstrate that whole genome sequencing approaches are required to accurately quantitate cattle introgression in bison.

Possible origins and implications of atypical morphologies and domestication-like traits in wild golden jackals (Canis aureus)

“…These findings suggest that the particular morphology of Jackie might be due to ancient introgressions of domestic dog alleles, that were almost completely eroded after a few backcrossing generations, leaving traces of dog ancestry only at particular genomic regions or in linkage with multiple or particular coat colour and other morphologically associated genes, and thus not detectable at the few uniparental and autosomal loci we analysed. Future genome-wide studies, based on ancestral chromosomal block reconstruction methods 49 , 50 could help identify possible dog-derived regions along Jackie's genome, potentially the reason for the observed morphological anomalies, as previously conducted in North American grey wolves to detect a functional 3-bp melanistic deletion along chromosome 16, presumably introgressed via historical admixture with dogs 51 , 52 , or in North American bison ( Bison bison ) populations to identify cattle haplotypes introgressed in their genomes over the last 200 years 53 .…”

Using Pet Food as the Subject to Investigate the Effectiveness of Whole-Genome Sequencing in the Authentication of Highly Processed Complex Food

“…In the simulation test, only limited number of the reads (∼0.2%) in the in silico datasets of each species have been mapped to the other genome (Table ). The gene introgression between bison and cattle in North America has been clarified in recent research . It is possible that the beef sample we used here was from a species with genetic variants originating from gene introgression which has been accumulated to a certain level during propagation.…”

“…The gene introgression between bison and cattle in North America has been clarified in recent research. 40 It is possible that the beef sample we used here was from a species with genetic variants originating from gene introgression which has been accumulated to a certain level during propagation. This observation indicated that in a practical test, the choice of reference genomes in a read mapping-based analysis would impact both the identification and quantification of an ingredient.…”

Evolution of immunogenetic components encoding ultralong CDR H3

“…3 and 6 ). Thus, it is feasible that the presence of these gene segments in bison is a consequence of cattle introgression following hybridization between bison and cattle in the late 1800s (Stroupe et al 2022 ). However, we located ultralong-encoding IGHV in all members of the Bos and Bison group, including Bos frontalis , which is evolutionary older than bison, and Bos primigenius , the ancestor to extant taurine ( Bos taurus ) and zebu ( Bos indicus ) cattle that went extinct in the early 1600 s (Zeyland et al 2013 ).…”