Limits...
Mitochondrial Genome Analysis Reveals Historical Lineages in Yellowstone Bison

View Article: PubMed Central - PubMed

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.

No MeSH data available.


Related in: MedlinePlus

TCS network tree of North American bison, based on all polymorphic sites.Each dash represents one single nucleotide difference between two neighboring haplotypes. The numbers in the parentheses after the name of each haplotype denote the number of bison belonging to each haplotype. Roman numerals I and II represent the two clades in this analysis. Animals with a wHap and EINP prefix denote wood bison haplotypes, while YNPHap, Templeton, and bHap17 denote Yellowstone bison. S6 and S9 are two historic bison sampled in or near the modern day Yellowstone National Park.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5120810&req=5

pone.0166081.g002: TCS network tree of North American bison, based on all polymorphic sites.Each dash represents one single nucleotide difference between two neighboring haplotypes. The numbers in the parentheses after the name of each haplotype denote the number of bison belonging to each haplotype. Roman numerals I and II represent the two clades in this analysis. Animals with a wHap and EINP prefix denote wood bison haplotypes, while YNPHap, Templeton, and bHap17 denote Yellowstone bison. S6 and S9 are two historic bison sampled in or near the modern day Yellowstone National Park.

Mentions: The analyses of all 65 plains and wood bison from across North America based on the combined data from Douglas et al. [14] and this study revealed 30 different haplotypes with a total of 120 polymorphic sites. Forty-six of these sites were synonymous, 37 were non-synonymous, and 37 were polymorphic sites in tRNA- and rRNA-coding regions. The only genes with no nucleotide differences between the 65 bison were the ND4L protein-coding gene, and the tRNA-Val, tRNA-Gln, tRNA-Met, tRNA-Tyr, tRNA-His, tRNA-Ser, tRNA-Glu, and the tRNA-Pro genes. The Templeton-Crandall-Singh (TCS) network tree (Fig 2 and Fig 3) identified two distinct clades of haplotypes separated by 10 polymorphisms unique to every member of each clade. Due to the large constraint on the mitochondrial genome, non-synonymous mutations in protein-coding genes that cause a change in the amino acid sequence are deemed especially important. In an attempt to reduce the noise in the tree in Fig 2, and to see if the clear divide between the two clades is still supported, a second tree only considering the 37 non-synonymous mutations was created (Fig 3). This tree disregards all nucleotide differences in tRNA and rRNA genes, as well as all synonymous changes in the 13 protein-coding genes in the mitochondrial genome.


Mitochondrial Genome Analysis Reveals Historical Lineages in Yellowstone Bison
TCS network tree of North American bison, based on all polymorphic sites.Each dash represents one single nucleotide difference between two neighboring haplotypes. The numbers in the parentheses after the name of each haplotype denote the number of bison belonging to each haplotype. Roman numerals I and II represent the two clades in this analysis. Animals with a wHap and EINP prefix denote wood bison haplotypes, while YNPHap, Templeton, and bHap17 denote Yellowstone bison. S6 and S9 are two historic bison sampled in or near the modern day Yellowstone National Park.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5120810&req=5

pone.0166081.g002: TCS network tree of North American bison, based on all polymorphic sites.Each dash represents one single nucleotide difference between two neighboring haplotypes. The numbers in the parentheses after the name of each haplotype denote the number of bison belonging to each haplotype. Roman numerals I and II represent the two clades in this analysis. Animals with a wHap and EINP prefix denote wood bison haplotypes, while YNPHap, Templeton, and bHap17 denote Yellowstone bison. S6 and S9 are two historic bison sampled in or near the modern day Yellowstone National Park.
Mentions: The analyses of all 65 plains and wood bison from across North America based on the combined data from Douglas et al. [14] and this study revealed 30 different haplotypes with a total of 120 polymorphic sites. Forty-six of these sites were synonymous, 37 were non-synonymous, and 37 were polymorphic sites in tRNA- and rRNA-coding regions. The only genes with no nucleotide differences between the 65 bison were the ND4L protein-coding gene, and the tRNA-Val, tRNA-Gln, tRNA-Met, tRNA-Tyr, tRNA-His, tRNA-Ser, tRNA-Glu, and the tRNA-Pro genes. The Templeton-Crandall-Singh (TCS) network tree (Fig 2 and Fig 3) identified two distinct clades of haplotypes separated by 10 polymorphisms unique to every member of each clade. Due to the large constraint on the mitochondrial genome, non-synonymous mutations in protein-coding genes that cause a change in the amino acid sequence are deemed especially important. In an attempt to reduce the noise in the tree in Fig 2, and to see if the clear divide between the two clades is still supported, a second tree only considering the 37 non-synonymous mutations was created (Fig 3). This tree disregards all nucleotide differences in tRNA and rRNA genes, as well as all synonymous changes in the 13 protein-coding genes in the mitochondrial genome.

View Article: PubMed Central - PubMed

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.

No MeSH data available.


Related in: MedlinePlus