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Whole genome sequences (WGS) of 185 North American Thoroughbred horses were compared to quantify the number and frequency of variants, diversity of mitotypes, and autosomal runs of homozygosity (ROH). Of the samples, 82 horses were born between 1965 and 1986 (Group 1); the remaining 103, selected to maximize pedigree diversity, were born between 2000 and 2020 (Group 2). Over 14.3 million autosomal variants were identified with 4.5-5.0 million found per horse. Mitochondrial sequences associated the North American Thoroughbreds with 9 of 17 clades previously identified among diverse breeds. Individual coefficients of inbreeding, estimated from ROH, averaged 0.266 (Group 1) and 0.283 (Group 2). When SNP arrays were simulated using subsets of WGS markers, the arrays over-estimated lengths of ROH. WGS-based estimates of inbreeding were highly correlated (r > 0.98) with SNP array-based estimates, but only moderately correlated (r = 0.40) with inbreeding based on 5-generation pedigrees. On average, Group 1 horses had more heterozygous variants (P

Six foals with interstitial pneumonia of undetermined etiology from Southern California were analyzed by viral metagenomics. Spleen, lung, and colon content samples obtained during necropsy from each animal were pooled, and nucleic acids from virus-like particles enriched for deep sequencing. The recently described equine copiparvovirus named eqcopivirus, as well as three previously uncharacterized viruses, were identified. The complete ORFs genomes of two closely related protoparvoviruses, and of a bocaparvovirus, plus the partial genome of a picornavirus were assembled. The parvoviruses were classified as members of new ungulate protoparvovirus and bocaparvovirus species in the Parvoviridae family. The picornavirus was classified as a new species in the Salivirus genus of the Picornaviridae family. Spleen, lung, and colon content samples from each foal were then tested for these viral genomes by nested PCR and RT-PCR. When present, parvoviruses were detected in both feces and spleen. The picornavirus, protoparvovirus, and eqcopivirus genomes were detected in the lungs of one animal each. Three foals were co-infected with the picornavirus and either a protoparvovirus, bocaparvovirus, or eqcopivirus. Two other foals were infected with a protoparvovirus only. No viral infection was detected in one animal. The complete ORFs of the first equine protoparvoviruses and bocaparvovirus, the partial ORF of the third equine picornavirus, and their detection in tissues of foals with interstitial pneumonia are described here. Testing the involvement of these viruses in fatal interstitial pneumonia or other equine diseases will require larger epidemiological and/or inoculation studies.

In Modoc County, located in northeastern California, there is a high elevation sage-steppe rangeland ecosystem heavily populated by wild horses and managed primarily by the United States Forest Service (USFS) called the Devil's Garden Plateau. Wild horses have significantly exceeded (roughly 2,000 horses) appropriate management levels (206-402 horses) in recent years and expanded their range outside of the designated territory (258,000 acres) and onto private and tribal lands (nearly 500,000 acres). Increased pressure from wild horses on the multiple use mandate of Forest Service lands have put strains on livestock, wildlife, and the local rural economy. The Modoc National Forest has decreased grazing by roughly 5,000 AUMs (animal unit months) on the Devil’s Garden Plateau due to excessive wild horse use. Each lost AUM results in a decrease of $57.43 - $144.70 of income to Modoc County. Three helicopter gathers in recent years have removed over 1,500 horses from the Devil’s Garden Plateau. Due to the extensive collaboration between the USFS, Modoc National Forest, and local partners, many of these horses have found new homes. This was done by using a tiered pricing approach and offering sales with limitations for older and unadoptable horses. The addition of a robust social media campaign run by volunteers has created a brand for the Devil’s Garden Plateau horses and educated the public on the declining range condition and horse health. Although good progress is being made to gather and place horses in private care, more diverse management solutions may be needed in the future.

Mushroom is a unique coat color phenotype in Shetland Ponies characterized by the dilution of the chestnut coat color to a sepia tone and is hypothesized to be a recessive trait. A genome wide association study (GWAS), utilizing the Affymetrix 670K array (MNEc670k) and a single locus mixed linear model analysis (EMMAX), identified a locus on ECA7 for further investigation (Pcorrected = 2.08 × 10-10). This locus contained a 3 Mb run of homozygosity in the 12 mushroom ponies tested. Analysis of high throughput Illumina sequencing data from one mushroom Shetland pony compared to 87 genomes from horses of various breeds, uncovered a frameshift variant, p.Asp201fs, in the MFSD12 gene encoding the major facilitator superfamily domain containing 12 protein. This variant was perfectly concordant with phenotype in 96 Shetland Ponies (P = 1.15 × 10-22), was identified in the closely related Miniature Horse for which the mushroom phenotype is suspected to occur (fmu = 0.02), and was absent in 252 individuals from seven additional breeds not reported to have the mushroom phenotype. MFSD12 is highly expressed in melanocytes and variants in this gene in humans, mice, and dogs impact pigmentation. Given the role of MFSD12 in melanogenesis, we propose that p.Asp201fs is causal for the dilution observed in mushroom ponies.

A unique eye color, called tiger-eye, segregates in the Puerto Rican Paso Fino (PRPF) horse breed and is characterized by a bright yellow, amber, or orange iris. Pedigree analysis identified a simple autosomal recessive mode of inheritance for this trait. A genome-wide association study (GWAS) with 24 individuals identified a locus on ECA 1 reaching genome-wide significance (Pcorrected = 1.32 × 10-5). This ECA1 locus harbors the candidate gene, Solute Carrier Family 24 (Sodium/Potassium/Calcium Exchanger), Member 5 (SLC24A5), with known roles in pigmentation in humans, mice, and zebrafish. Humans with compound heterozygous mutations in SLC24A5 have oculocutaneous albinism (OCA) type 6 (OCA6), which is characterized by dilute skin, hair, and eye pigmentation, as well as ocular anomalies. Twenty tiger-eye horses were homozygous for a nonsynonymous mutation in exon 2 (p.Phe91Tyr) of SLC24A5 (called here Tiger-eye 1), which is predicted to be deleterious to protein function. Additionally, eight of the remaining 12 tiger-eye horses heterozygous for the p.Phe91Tyr variant were also heterozygous for a 628 bp deletion encompassing all of exon 7 of SLC24A5 (c.875-340_1081+82del), which we will call here the Tiger-eye 2 allele. None of the 122 brown-eyed horses were homozygous for either tiger-eye-associated allele or were compound heterozygotes. Further, neither variant was detected in 196 horses from four related breeds not known to have the tiger-eye phenotype. Here, we propose that two mutations in SLC24A5 affect iris pigmentation in tiger-eye PRPF horses. Further, unlike OCA6 in humans, the Tiger-eye 1 mutation in its homozygous state or as a compound heterozygote (Tiger-eye 1/Tiger-eye 2) does not appear to cause ocular anomalies or a change in coat color in the PRPF horse.

The depredation of feral horses by mountain lions is usually a rare phenomenon and only a few cases have been documented in scientific literature. While such reports indicate that mountain lions are easily capable of killing feral horses, these studies have focused solely on the feral horses and have neglected to consider the mountain lion’s perspective (i.e., movement patterns, prey choice). Today, feral horses have created an artificial prey base for mountain lions, and even if natural ungulate species were not present, mountain lions appear to survive and flourish while consuming feral horses. During a feral horse behavior study conducted in 2005, a resident mountain lion in the Virginia Mountain Range was deemed responsible for several feral horse deaths, with most of the carcasses found being young foals or juvenile horses. A large live trap was developed and was strategically placed in a mountain lion travel corridor where the depredated horse carcasses were found. Bait in the live trap was changed on a weekly basis to prevent spoilage. The trap was set from October through December 2006 and monitored each morning. A 7-yearold, 60-kg female lion was caught in the trap after 3 months of trapping efforts. It was tranquilized, weighed and measured, and fitted with a satellite GPS collar. The satellite collar gave 4 locations per night. Based on the those GPS locations, we determined the lion had depredated on many feral horses, and it continued to range in the same area, even though other native wildlife species, such as mule deer, were in low densities. We monitored her progress until October 2007 to determine overall movement patterns and prey choice.

Controlling fertility of feral horses through the use of long-acting contraceptives or sterilization approaches has been championed as a reasonable and humane solution for addressing overpopulation problems in several western states. However, methods to accomplish long-term contraceptive efficacy of horses following a single treatment have been lacking. In fall 2002 and spring 2003, we initiated a study to compare the long-term efficacy of a single-shot contraceptive vaccine directed at gonadotropin releasing hormone (GonaCon™) to that of a single-shot vaccine directed at the zona pellucida (SpayVac) and to the use of intrauterine contraceptive devices (IUD). Both vaccines were administered with AdjuVac™, an adjuvant developed at the National Wildlife Research Center. The objectives of the study were to determine: 1) 3-year efficacy for preventing pregnancy, 2) whether the contraceptive effects are reversible, and 3) whether there are contraindications. The Nevada Department of Agriculture provided the feral mares, which were maintained at the Nevada State Penitentiary, Carson City, facility. Mares were dewormed and given health vaccinations annually. Eight untreated control mares were compared to 12 mares treated with SpayVac, 16 mares treated with GonaCon™, and 15 mares treated with copper-containing IUDs. Only 25% (2/8) of the control mares were not pregnant or infertile in the first year. All mares in the SpayVac group were infertile, and 94% (15/16) were infertile in the GonaCon™ group during the first breeding season. In Year 2, 80% (10/12) of the SpayVac-treated mares and 60% (9/15) of the GonaCon™-treated mares were infertile. In Year 3, 80% of the SpayVac mares and 53% (8/15) of the GonaCon™-treated mares were infertile. For IUD-treated mares, 80% (12/15) were infertile after Year 1, but only 29% (4/14) and 14% (2/14) were infertile after Years 2 and 3, respectively. For IUD mares that were infertile, it was possible to visualize the IUD by ultrasonography, leading us to conclude that mares that became pregnant had lost their IUDs. For mares given SpayVac, uterine edema was commonly observed. In Years 2 and 3, antibody titers for SpayVac were progressively lower compared to titers observed in Year 1.

To date, management and research on feral horses have been strongly influenced by concerns and priorities of the general public. Due to outcry from numerous interest groups, research and management of feral horses have tended to be autecological, focused on individuals rather than populations, and addressing potential competition between horses and cattle, thus largely ignoring questions addressing roles that feral horses may play in arid and semiarid ecosystems. Management can never satisfy all desires of all interest groups, and research rarely can give answers so definitive that further questions will not arise. However, as we attempt to demonstrate, both management and research can help shape and inform public opinion through numerous means. Because feral horses have been one of the most contentious management issues of the last 100 years, it is critical that managers and investigators address both immediate and long-term concerns in their work. Honest communication of results and associated levels of uncertainty, along with rigorous testing of alternative explanations, are essential in issues having high levels of sociopolitical interest. Continued use of relevant, well-planned investigations in concert with thoughtful management may help define the future role the feral horse will play as "an integral part of the system of public lands" in the western United States.

"Feral" is defined. For each of the principal species of feral mammals in California, we note the broad ecological implications they have on the environment and the potential or actual management approaches being followed. The main emphasis of this paper, and all of the slides shown, was on how wild horses and burros, two controversial feral species, are managed in California and in other western states. The feral pig is about to become the number one big game animal in California, and muskrats (Ondatra zibethica (L.)), which were introduced or escaped into the Sacramento Valley--hence locally feral--are the state's number one furbearer. Except for these species, the other feral mammals are, for the most part, much less desirable.