Dr Meredith Hudes-Lowder: Biostatistician

Historical perspective

Free-roaming horse herds in the West are combinations of domestic lineages, not unique taxa. Peer-reviewed studies and federal reports indicate that U.S. free-roaming herds are formed from various breeds and sources, including ranch stock and tribal herds. For instance, a genetic analysis of Theodore Roosevelt National Park, a well-documented example, reveals that Western rangelands have historically received horses from diverse origins and breeds (Thomas, 2024). Horses in the park likely originated from multiple sources, a typical pattern for U.S. feral herds.

The National Academies’ review of BLM genetics lists a few herds with evidence of old Spanish bloodlines, such as those in the Cerbat Mountains of Arizona, the Pryor Mountains of Montana, and Sulphur in Utah. Salt River is not on this list, highlighting that it is not a distinct genetic population that needs specific preservation. National Park Service sites consistently describe free-roaming horses as non-native, feral descendants of domestic stock, not as a separate wildlife species.

“Extinction” is not the right term; the real risk is local extirpation. By definition, extinction refers to the worldwide loss of a species, whereas extirpation denotes the disappearance of a species from a particular area, even as it continues to exist elsewhere. If a local herd disappears, that means it has been extirpated, not extinct. Looking at horses: the domestic species Equus caballus is plentiful, with about 6.65 million domestic horses in the U.S. (2023 American Horse Council) and around 73,000 free-roaming horses and burros on BLM lands (2025). A local decline at Salt River cannot result in species-level “extinction.”

If genetic health is the concern, it can be addressed without exaggerating census numbers. Standard conservation practice for feral herds involves monitoring diversity and, if necessary, introducing outside genetic stock. This is precisely what peer-reviewed studies suggest when diversity is low, such as in TRNP. In other words, genetic viability is managed through breeding contributions and gene flow, not by claiming a unique lineage at Salt River.

In summary, the Salt River herd is a historical grouping of formerly domestic horses, not a unique taxon. Federal reports recognize only a few Spanish-lineage herds elsewhere. Using accurate terminology, the worst-case biological outcome is local extirpation, not extinction. Even local genetic risks are manageable with standard tools, such as monitoring and, if needed, introductions.

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Introduction: The genetic problem we’re solving

The Salt River Herd’s long-term health depends on maintaining enough genetic diversity to adapt to drought, disease, and habitat change. The single best indicator of how fast diversity erodes is adequate population size (Ne)—the number of animals that actually pass genes to foals—rather than the raw headcount (N) (Waples et al., 2013; Nunney, 1993). In free-ranging, polygynous horses, Ne is usually lower than N because a few stallions sire a disproportionate share of foals, and age/sex structure is uneven (Waples et al., 2013; Nunney, 1993). Modern conservation guidance therefore manages to set Ne targets explicitly—keep Ne ≳ 50 to limit short-term inbreeding and push higher when possible for long-term adaptability—rather than working to census alone (Frankham et al., 2014a, 2014b). We will treat genetic diversity as a routine management outcome and show it on the same dashboard as foaling rate and habitat metrics (Hoban et al., 2021; Andersson et al., 2022).

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What determines genetic viability (and why headcount isn’t enough)

Who breeds matters more than who is present. A manager-friendly relation explains why male monopolies depress Ne:

Here, Nm and Nf are the numbers of breeding stallions and mares, respectively (Waples et al., 2013; Nunney, 1993). If only a few stallions dominate paternity, Ne stays low no matter how many mares are on the landscape. Genetic drift then chips away at diversity every generation, which is why holding Ne near or above ~50 measurably slows loss across horse-length timeframes (Frankham et al., 2014a). Conversely, spreading reproduction across more stallions and enough mares lifts Ne at the same census size. For example, moving from roughly 12 breeding stallions/35 breeding mares (Ne ≈ 36) to ~20 breeding stallions/40 breeding mares (Ne ≈ 53) crosses the short-term safety threshold without increasing total herd size—purely by broadening who contributes (Waples et al., 2013).

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What can we do to maintain the genetic health of the Salt River?

Measure smart, noninvasively. We will establish a genetic baseline using fecal DNA (fresh, air-dried in paper bags), then re-sample every two years. Labs will pre-screen extracts by qPCR, use replicate genotyping, and track error rates to ensure reliability (King et al., 2018; Hausknecht et al., 2010). Routine outputs: Ne (linkage-disequilibrium estimators), heterozygosity, allelic richness, and—when blood/tissue SNPs are available—runs of homozygosity (ROH) to detect recent inbreeding (Colpitts et al., 2022; Andersson et al., 2022).

Manage breeding probabilities (without assigning mates).

Broaden stallion contribution: use contraception and removal priorities to prevent a few males from monopolizing paternity; the goal is ~18–22 effective breeding stallions alongside ~35–40 breeding mares, which typically yields Ne ≈ 50–55 at N ≈ 100 (Waples et al., 2013; Nunney, 1993).

Rotate contraception by lineage: keep contraception on standard lines; off for 1–2 seasons for under-represented lines so their foals enter the crop (Nuñez et al., 2017).

Pick the right tool, measure the tradeoffs: PZP often extends receptive behavior and increases mare band-switching (lower mare fidelity), reshuffling who breeds (Nuñez et al., 2009; Nuñez et al., 2010; Madosky et al., 2010; Jones & Nuñez, 2019). GnRH immunocontraception (e.g., GonaCon-type) can suppress fertility with no deleterious breeding-season behavioral effects when implemented carefully (Ransom et al., 2014). We will track mare band-change rates and the number of effective breeding stallions alongside genetic metrics to adjust dosing in real-time (King et al., 2021; Nuñez et al., 2017; Jones et al., 2020).

Avoid genetically biased removals: when removals/adoptions are required, retain animals carrying rare alleles or representing under-sampled lines. Use pedigree-aware tools such as PMx where pedigrees exist, or molecular kinship rules where they do not (Lacy et al., 2011; Putnam & Ivy, 2014).

Use “natural” gene flow when available: occasional 5–10% cross-boundary inflow from neighboring jurisdictions (e.g., Fort McDowell Yavapai Nation; Salt River Pima–Maricopa Indian Community) is not guaranteed but has occurred; when newcomers appear, document immediately, pause contraception on immigrant mares, and avoid removing immigrant stallions until they’ve contributed foals—this raises NmN_mNm​ and lowers variance in family size, boosting Ne (King et al., 2018; Waples et al., 2013; Nunney, 1993).

If trends still slip: implement small, screened genetic rescue (a few unrelated immigrants over several years) using standard outbreeding-risk safeguards (Frankham et al., 2011; Frankham et al., 2014a, 2014b).

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Refuting the “low numbers = extinction” claim “

Too few horses means inevitable extinction” is incorrect because extinction risk is not determined by census size alone. What matters genetically is Ne, which we can measure and manage. A herd of ~100 can maintain a population of 50 or more when reproduction is spread across around 20 stallions and 35–40 mares (Waples et al., 2013; Nunney, 1993). Ongoing noninvasive monitoring lets us detect drift or inbreeding early and adjust contraception/removals accordingly (King et al., 2018; Andersson et al., 2022). If needed, even small gene flow—natural cross-boundary movement or a carefully screened introduction—has repeatedly improved diversity and fitness in small populations (Frankham et al., 2011; Frankham et al., 2014a, 2014b). The cautionary case is closed, isolated systems like Sable Island, which persist at modest size but accumulate ROH and inbreeding over time—underscoring that management plus occasional gene flow, not inflated census, is the remedy (Plante et al., 2007; Colpitts et al., 2022; Colpitts, 2024). In short: a well-managed, moderately sized Salt River Herd can remain genetically viable without overshooting ecological limits, provided we monitor Ne and act on the results. Why genetics matter. 

Genetic diversity is crucial for a free-roaming herd’s ability to adapt to internal and external forces. It helps maintain options when weather, disease, or habitat conditions change. The most useful measure for tracking how quickly this capacity declines is effective population size (Ne). This number represents the animals that actually pass genes to foals. In free-ranging horses, Ne is often lower than the total number of horses. This occurs because a few stallions sire many foals and there is an uneven distribution of age and sex classes (Waples et al., 2013; Nunney, 1993). Modern recommendations set clear Ne targets. Keep Ne at or above 50 to reduce short-term inbreeding and increase it when possible for long-term adaptation. Genetic diversity should be a routine management goal, not an afterthought (Frankham et al., 2014a, 2014b; Hoban et al., 2021; Andersson et al., 2022).

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What drives Ne, the number of reproducing horses?

Ne relies on who breeds, not just who is present. There is a practical connection between Ne and the number of breeding males and females. This highlights the negative impact of male monopolies: 

So, if only a few stallions (Nm) dominate offspring production, Ne remains low regardless of how many mares (Nf) foal (Waples et al., 2013; Nunney, 1993). Genetic drift reduces variation with each generation. Keeping Ne at or above about 50 significantly slows this decline across generations (Frankham et al., 2014a). The expected decrease in heterozygosity due to drift is given by:

 

Short-term bottlenecks have a significant impact because the harmonic mean influences long-term Ne: 

Variance in family size, such as a few stallions producing many foals, further lowers Ne like this: 

(Nunney, 1993; Waples et al., 2013).   

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How to measure all of this without roundups. 

Fresh fecal pellets contain enough sloughed cells for individual identification and population-genetic studies. Air-drying these pellets in paper bags often yields better results than using ethanol for PCR, especially in arid areas (King et al., 2018). Accuracy improves if labs pre-screen DNA extracts using qPCR to filter out low-quality samples and implement replicate genotyping with negatives to minimize errors (Hausknecht et al., 2010). Aside from classic measures such as heterozygosity and allelic richness, it can also include user-friendly indicators on dashboards to keep non-genetic audiences informed about progress (Andersson et al., 2022; Hoban et al., 2021). We plan to include this in our Salt River Horse Registry Database^tm or other similar monitoring programs at other management areas. When blood or tissue samples are available, genome-wide SNPs allow for the calculation of runs of homozygosity (ROH) and a genomic inbreeding fraction: 

This is sensitive to recent inbreeding and small Ne (Colpitts et al., 2022). Cases from Sable Island illustrate this pattern. Early microsatellite studies described diversity within a closed herd. Later ROH mapping showed significant genomic markers of drift and inbreeding. A recent dissertation links those genomic trends to demographics and ecology, with clear implications for management (Plante et al., 2007; Colpitts et al., 2022; Colpitts, 2024). Small and isolated herds on Greek islands demonstrate how geography and history can rapidly lead herds to different genetic baselines. This means that goals and strategies should consider the local context (Katsoulakou et al., 2023).  

Total round costs of Genetic Analysis

Two ready-to-use budgeting scenarios

A grant could be obtained for the studies

A) Baseline genetics (Salt River–style), n = 80 fecal samples

• Extraction (80× $16) ≈ $1,280. fees.oregonstate.edu
• qPCR prescreen (plate-based; modest line item). PMC
• Microsat PCR + fragment analysis + scoring (assume $60–$120 per successful sample) → $4,800–$9,600. The University of Alabama at Birmingham and Texas A&M University-Corpus Christi
• Baseline lab subtotal ≈ $6.1k–$11.0k (add reporting/PI time as needed).
  (If you outsource end-to-end to a wildlife genetics provider, expect a single per-sample quote that folds these in.)

B) Monitoring cycle, n = 50 fecal samples

• Extraction ≈ $800. fees.oregonstate.edu
• Microsat + scoring (assume $60–$120 each) → $3,000–$6,000. The University of Alabama at BirminghamTexas and A&M University-Corpus Christi
• Monitoring lab subtotal ≈ $3.8k–$6.8k.

If you add hair/blood SNP arrays on a handled subset, reagent list prices start at $35 per array (processing extra) and require high-quality DNA; plan $100–$200+ per sample all-in for service providers. Use arrays to map relatedness/ROH, but rely on microsats for routine fecal rounds. Neogen and Thermo Fisher Scientific

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Contraception, social structure, and genetics. 

Contraception can support genetic goals, but different methods can affect social structure, which impacts the equations above through Nm and Vk. PZP prevents fertilization and is associated with more extended periods of receptivity and increased band-switching (lower mare fidelity). This reshuffle mating opportunities and often increases male competition (Nuñez et al., 2009; Nuñez et al., 2010; Madosky et al., 2010; Jones & Nuñez, 2019; Jones et al., 2020). GnRH immunocontraception, like GonaCon-type programs, acts higher up the endocrine pathway. Field studies indicate reliable fertility suppression without adverse behavioral effects during the breeding season when applied carefully. However, any handling or culling can still change behavior and should be monitored (Ransom et al., 2014). Recent research also shows how habitat and social conditions influence actual breeding (King et al., 2025) and how social instability may increase female aggression, altering breeding opportunities (Nunez & Adelman, 2025). In practice, select a mix of contraception that aligns with dart access and desired group stability. Monitor mare band-change rates and the number of effective breeding stallions while tracking genetic metrics to allow for adjustments (Nuñez et al., 2017; King et al., 2021).  

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Potential cross-boundary inflow (Fort McDowell Yavapai Nation; Salt River Pima–Maricopa Indian Community). 

Occasional inflows of 5–10% new horses from nearby areas can happen, but they are not guaranteed. These inflows should be considered opportunistic, natural genetic rescue—a benefit to plan for but not rely on. Even a small number of newcomers can reduce drift and refresh rare alleles if those animals breed (Waples et al., 2013; Nunney, 1993; Frankham et al., 2014a). When and if newcomers are identified, follow these steps:

(1)   Document immediately with photo IDs and microchips if possible. Collect fecal DNA within 24–48 hours (King et al., 2018; Hausknecht et al., 2010);

(2)   Let them breed by pausing contraception on immigrant mares for one or two seasons and avoiding removal of immigrant stallions while proceeding with other removals. This increases Nm and lowers Vk, raising Ne;

(3)   Maintain contraception on well-represented resident lines to favor under-represented (including immigrant) lineages in producing foals (Frankham et al., 2014a; Nuñez et al., 2017);

(4)   Follow regular biosecurity and welfare checks

(5)   Re-estimate your metrics (Ne, heterozygosity, allelic richness, ROH; plus mare band-switching if PZP is utilized) in the next cycle (King et al., 2018; King et al., 2021).

Because space use influences gene flow, maintaining corridors and functional band ranges increases the chances that rare movements will occur and impact genetic diversity (King et al., 2021; King et al., 2025). Use standard outbreeding-risk safeguards to minimise risks—such as the same species, similar environments, and evidence of historical connectivity (Frankham et al., 2011).  

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Action plan (measure → interpret → act → re-measure). 

• Baseline this year. Gather fecal genotypes from most animals (for N ~100–150, aim for ~80 unique individuals). Link genetic IDs to photo IDs or microchips (King et al., 2018). 

• Every 2 years. Sample 40–60 unique individuals. Report Ne, heterozygosity, allelic richness, and, when available, ROH. If PZP is widely used, also report mare band-change rates (King et al., 2018; Nuñez et al., 2009; King et al., 2021). 

• Triggers. Green: Ne ≥ 50 and diversity stable—continue rotations. Yellow: Ne 35–49 or 5–10% diversity decline over 4 years—widen male participation (rotate contraception off under-represented mares; keep it on standard lines) and revisit removals to avoid losing rare lines. Red: Ne < 35 or fast-rising ROH—treat natural inflow as first-line genetic rescue. If this is insufficient, plan a small, screened introduction (Frankham et al., 2014a, 2014b; Andersson et al., 2022; Hoban et al., 2021; Colpitts et al., 2022; Colpitts, 2024). 

• During required removals/adoptions. Avoid choices biased by genetics: use molecular relatedness and allelic value to retain individuals from rare lines and reduce male monopolies. Use PMx to minimize mean kinship when pedigrees exist. When they do not, kinship-based molecular rules generally outperform random selection (Lacy et al., 2011; Putnam & Ivy, 2014). 

• Context matters. Larger, less dense ranges support more bands and lower male monopolies. In contrast, closed systems, such as Sable Island, and small islands, like those in Greece, accumulate inbreeding more quickly and require earlier, more cautious genetic intervention (Plante et al., 2007; Colpitts et al., 2022; Katsoulakou et al., 2023).    

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References

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Colpitts, J. (2024). Causes and consequences of variation in genomic diversity in Sable Island feral horses (Doctoral dissertation). University of Saskatchewan.

Colpitts, J., McLoughlin, P. D., & Poissant, J. (2022). Runs of homozygosity in Sable Island feral horses reveal the genomic consequences of inbreeding and divergence from domestic breeds. BMC Genomics, 23(1), 501. https://doi.org/10.1186/s12864-022-08729-9

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