Mitochondrial Genome Analysis Reveals Historical Lineages in Yellowstone Bison

Abstract

Yellowstone National Park is home to one of the only plains bison populations that have continuously existed on their present landscape since prehistoric times without evidence of domestic cattle introgression. Previous studies characterized the relatively high levels of nuclear genetic diversity in these bison, but little is known about their mitochondrial haplotype diversity. This study assessed mitochondrial genomes from 25 randomly selected Yellowstone bison and found 10 different mitochondrial haplotypes with a haplotype diversity of 0.78 (± 0.06). Spatial analysis of these mitochondrial DNA (mtDNA) haplotypes did not detect geographic population subdivision (FST = -0.06, p = 0.76). However, we identified two independent and historically important lineages in Yellowstone bison by combining data from 65 bison (defined by 120 polymorphic sites) from across North America representing a total of 30 different mitochondrial DNA haplotypes. Mitochondrial DNA haplotypes from one of the Yellowstone lineages represent descendants of the 22 indigenous bison remaining in central Yellowstone in 1902. The other mitochondrial DNA lineage represents descendants of the 18 females introduced from northern Montana in 1902 to supplement the indigenous bison population and develop a new breeding herd in the northern region of the park. Comparing modern and historical mitochondrial DNA diversity in Yellowstone bison helps uncover a historical context of park restoration efforts during the early 1900s, provides evidence against a hypothesized mitochondrial disease in bison, and reveals the signature of recent hybridization between American plains bison (Bison bison bison) and Canadian wood bison (B. b. athabascae). Our study demonstrates how mitochondrial DNA can be applied to delineate the history of wildlife species and inform future conservation actions.

De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification

“…The reference bison (aka Templeton) has a well-documented history, showing that it originated from YNP. This bison was utilized in a collaborative research project on brucellosis (Forgacs et al, 2016). When sampled, he was being managed as part of a brucellosis-free herd on a private ranch in Montana.…”

Genetic variation of the mitochondrial DNA control region across plains bison herds in USA and Canada

“…While opportunities for comparison among mtDNA studies of bison have been limited due to designation of haplotypes mostly based on restriction sites and low quality of some mtDNA sequences [10], partial control region sequences [11] or the lack of the control regions in the mitochondrial genome sequences [19], we were able to compare the mtDNA control region haplotypes in our study with the complete control region sequences of bison mitochondrial…”

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

“…One library was sequenced under the CanSeq150 project using the same workflow at the Sequencing Facility of The Center for Applied Genomics (TCAG) in the Hospital for the Sick Kids. Existing whole-genome DNA sequencing data from a further 14 bison (Forgacs et al, 2016) was included in the analysis. The resulting data set includes plains (n = 26) and wood (n = 13) bison ( Table 1).…”