Barplot from STRUCTURE analysis of Theodore Roosevelt National Park horses and nine domestic breeds found in North America according to the following abbreviations: CAND, Canadian Horse; THBD, Thoroughbred; TNWH, Tennessee Walker; COPF, Colombian Paso Fino; ANDA, Andalusian; SADB, American Saddlebred; BELG, Belgian Draft; QUAH, Quarter Horse; ARAB, Arabian.

<p>Note: K = 3 (denoted with asterisk) was deemed the best result based on ΔK evaluation (insert).</p

Genetic diversity and origin of the feral horses in Theodore Roosevelt National Park

<div><p>Feral horses in Theodore Roosevelt National Park (TRNP) represent an iconic era of the North Dakota Badlands. Their uncertain history raises management questions regarding origins, genetic diversity, and long-term genetic viability. Hair samples with follicles were collected from 196 horses in the Park and used to sequence the control region of mitochondrial DNA (mtDNA) and to profile 12 autosomal short tandem repeat (STR) markers. Three mtDNA haplotypes found in the TRNP horses belonged to haplogroups L and B. The control region variation was low with haplotype diversity of 0.5271, nucleotide diversity of 0.0077 and mean pairwise difference of 2.93. We sequenced one mitochondrial genome from each haplotype determined by the control region. Two complete mtDNA sequences of haplogroup L were closely related to the mtDNA of American Paint horse. The TRNP haplotype B did not have close matches in GenBank. The phylogenetic test placed this sequence in a group consisting of two horses from China, one from Yakutia, and one from Italy raising a possibility of historical transportation of horses from Siberia and East Asia to North America. Autosomal STR loci were polymorphic and indicated that the TRNP horses were distinctly different from 48 major horse breeds. Heterozygosity, mean number of alleles, and other measures of diversity indicated that TRNP herd diversity was below that observed for most other feral herds and domestic breeds. Both mtDNA and STRs demonstrated that the existing genetic data sets of horses are insufficient to determine the exact origins of the TRNP horses. However, measures of nuclear and mitochondrial diversity have elucidated management needs. It is recommended that new genetic stock be introduced and that adaptive management principles are employed to ensure that unique mitochondrial lineages are preserved and genetic diversity is increased and maintained over time.</p></div

Comparison of genetic diversity between the Theodore Roosevelt National Park horse herd, other feral herds, and selected domestic breeds.

<p>Comparison of genetic diversity between the Theodore Roosevelt National Park horse herd, other feral herds, and selected domestic breeds.</p

Restricted Maximum Likelihood tree of nuclear genetic relationships Theodore Roosevelt National Park horses in comparison to 46 domestic breeds and Przewalski Horse (used as an outgroup).

<p>Numbers at split represent probability based on bootstrapping.</p

Barplot of K = 11 STRUCTURE result for Theodore Roosevelt National Park horses and nine domestic breeds according to the following abbreviations: CAND, THBD, TNWH, COPF, ANDA, SADB, BELG, QUAH, and ARAB (Abbreviations same as Fig 4).

<p>Note: presented to demonstrate that at the highest possible resolution, park horses still form their own genetic cluster.</p

PCR primers additionally designed to improve the amplification of three mtDNA sections.

<p>PCR primers additionally designed to improve the amplification of three mtDNA sections.</p

The mtDNA diversity statistics in the feral horse populations.

<p>The mtDNA diversity statistics in the feral horse populations.</p

Bayesian inference phylogenetic tree demonstrating the phylogenetic relationship of mitochondrial genomes of three mtDNA lineages found in the TRNP horses, and the mtDNAs of 84 modern horses.

<p>The donkey mitochondrial genome sequence (NC_001788) used as an outgroup is not displayed. Numbers shown by the Roman numeral I indicates the clades with the highest posterior probability value. The color scale refers to the clades with the posterior probabilities between 0.5 and 1.</p

Genetic variation of the 5’ portion of the mtDNA control region in horses living in Theodore Roosevelt National Park.

<p>The sequences were aligned with the horse reference mtDNA sequence (GenBank accession number X79547). Numbers show transitions.</p

Principal Coordinates Plot of nuclear genetic relationships for horses at Theodore Roosevelt National Park in comparison to select domestic breeds.

<p>ACRD, American Cream Draft; AKTK, Akhal Teke; ANDA, Andalusian; ARAB, Arabian; ASTR, Asturcon; BELG, Belgian Draft; BRCR, Brazillian Criollo; CAMP, Campolino; CAND, Canadian; CASP, Caspian; CHCR, Chilean Criollo; CLYD, Clydsedale; COPF, Colombian Paso Fino; DLPY, Dales Pony; FLPY, Fell Pony; GALI, Galiceno; GARO, Garrano; HAFL, Haflinger; HANO, Hanoverian; HLPY, Highland Pony; HOLS, Holstein; KRYZ, Kyrgyztan; LUSI, Lusitano; MOFT, Missouri Fox Trotter; MONG, Mongolian Horse; MORH, Morgan Horse; PANT, Pantaniero; PERC, Percheron; PERU, Peruvian Paso; PRPF, Puerto Rican Paso Fino; QUAH, Quarter Horse; RKMH, Rocky Mountain Horse; SADB, American Saddlebred; SEFR, Selle Francais; SHIR, Shire; SHPY, Shetland Pony; STBD, Standardbred; SUFK, Suffolk Punch; THBD, Thoroughbred; TNWH, Tennessee Walking Horse; TRNP, Theodore Roosevelt National Park; TURK, Turkoman; VECR, Venezuelian Criollo; WELP, Welsh Pony; YAKT, Yakut.</p