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Ecology and evolution2024; 14(4); e11197; doi: 10.1002/ece3.11197

Population genomics provide insight into ancestral relationships and diversity of the feral horses of Theodore Roosevelt National Park.

Abstract: Theodore Roosevelt National Park (TRNP) manages a herd of feral horses () which was present on the landscape prior to the establishment of the park. The population presents a unique scenario in that it has experienced fairly intensive and well-documented management since the park's establishment, including herd size reductions, intentional introduction of diversity, and subsequent attempts to remove introduced lineages. This provides an interesting case study on the genetic effects of diverse evolutionary forces on an isolated feral population. To explore the effects of these forces and clarify the relationship of this feral herd with other horses, we used genome-wide markers to examine the population structure of a combined dataset containing common established breeds. Using the Illumina Equine 70k BeadChip, we sampled SNPs across the genome for 118 TRNP horses and evaluated the inbreeding coefficient and runs of homozygosity (RoH). To identify breed relationships, we compared 23 representative TRNP samples with 792 horses from 35 different breeds using genomic population structure analyses. Mean of TRNP horses was 0.180, while the mean for all other breeds in the dataset was 0.116 (SD 0.079). RoH analysis indicates that the TRNP population has experienced recent inbreeding in a timeframe consistent with their management. With Bayesian clustering, PCA, and maximum likelihood phylogeny, TRNP horses show genetic differentiation from other breeds, likely due to isolation, historical population bottlenecks, and genetic drift. However, maximum likelihood phylogeny places them with moderate confidence (76.8%) among draft breeds, which is consistent with the known history of breeds used on early North Dakota ranches and stallions subsequently introduced to the park herd. These findings will help resolve speculation about the origins of the herd and inform management decisions for the TRNP herd.
© 2024 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
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Publication Date: 2024-04-01 PubMed ID: 38571790PubMed Central: PMC10985374DOI: 10.1002/ece3.11197Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research article investigates the genetic relationships and diversity of wild horses in Theodore Roosevelt National Park using population genomics, providing insight into their ancestral ties and how management practices have influenced their genetic composition.

Introduction and Background

  • The research was conducted on the feral horses of Theodore Roosevelt National Park (TRNP), which have been there since before the foundation of the park. These horses provide a unique case study due to the intensive and documented management they’ve had since the park’s establishment.
  • The management practices include reductions in herd size, intentional insertion of diversity, and later efforts to remove certain lineages introduced.
  • The article explores both the effects of these management practices and the genetic ramifications of a range of evolutionary forces on this isolated wild horse population.

Methodology

  • The researchers used genome-wide markers to study the population structure of the horses. These markers included a dataset of common, established breeds for comparison.
  • A total of 118 TRNP horses were examined using the Illumina Equine 70k BeadChip, which samples SNPs (single nucleotide polymorphisms) across the genome.
  • The team evaluated the inbreeding coefficient and checked for runs of homozygosity (RoH) to determine if inbreeding had occurred in recent times.
  • For a detailed breed comparison, 23 representative TRNP samples were compared with 792 horses from 35 different breeds using genomic population structure analyses.

Findings

  • The average inbreeding coefficient of the TRNP horses was found to be 0.180, whereas the mean for all other breeds in the dataset was lower at 0.116. This suggested the occurrence of inbreeding among the TRNP horses.
  • RoH analysis further supported this indication of recent inbreeding, with the timeframe aligning with the history of the park’s management.
  • Through the use of Bayesian clustering, PCA, and maximum likelihood phylogeny, the TRNP horses displayed genetic differentiation from other breeds because of isolation, previous population bottlenecks, and genetic drift effects.
  • However, these analyses placed the TRNP horses, with a moderate level of confidence (76.8%), among draft breeds. This aligns with the known history of breeds that were on early ranches in North Dakota and stallions that were later introduced into the park’s herd.

Conclusion

  • The research study’s findings contribute valuable information on the origins of the TRNP horses.
  • The data collected can help inform and guide future management decisions regarding the feral herd in the park.

Cite This Article

APA
Thompson MA, McCann BE, Rhen T, Simmons R. (2024). Population genomics provide insight into ancestral relationships and diversity of the feral horses of Theodore Roosevelt National Park. Ecol Evol, 14(4), e11197. https://doi.org/10.1002/ece3.11197

Publication

Ecology and evolution
ISSN: 2045-7758
NlmUniqueID: 101566408
Country: England
Language: English
Volume: 14
Issue: 4
Pages: e11197
PII: e11197

Researcher Affiliations

Thompson, Melissa A
  • Department of Biology University of North Dakota Grand Forks North Dakota USA.
  • Theodore Roosevelt National Park National Park Service Medora North Dakota USA.
McCann, Blake E
  • Theodore Roosevelt National Park National Park Service Medora North Dakota USA.
Rhen, Turk
  • Department of Biology University of North Dakota Grand Forks North Dakota USA.
Simmons, Rebecca
  • Department of Biology University of North Dakota Grand Forks North Dakota USA.

Conflict of Interest Statement

The authors declare no conflict of interest.

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Citations

This article has been cited 1 times.
  1. Luštrek B, Šimon M, Turk K, Bogičević S, Potočnik K. Comparing Genomic and Pedigree Inbreeding Coefficients in the Slovenian Lipizzan Horse as a Case Study for Small Closed Populations. Animals (Basel) 2025 Sep 23;15(19).
    doi: 10.3390/ani15192774pubmed: 41096369google scholar: lookup
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