Mexican Wolf Research Articles

Ecological and social drivers of Mexican Wolf home range size across spatiotemporal scales

Ecological and social drivers of Mexican Wolf home range size across spatiotemporal scales

The importance of livestock in the diet of Mexican wolf Canis lupus baileyi in northwestern Mexico

The reintroduction of the Mexican wolf in the wilds of northwestern Mexico has allowed us to address its trophic ecology and elucidate conflicts with livestock producers: their main mortality factor. Our objective was to determine the feeding habits of wolves in Mexico, as well as the quantity and frequency of livestock predation in relation to seasonal and individual variables, through the analysis of genetically identified scats. During 2012–2022 we collected 1171 Mexican wolf scats. We extracted and sequenced DNAm and identified individuals and their sex using microsatellite analysis. We washed the scat and separated the undigested components for taxonomic identification. We estimated the frequency of prey items, the biomass it contributed to the diet, and compared prey consumption between sexes and between the birth and dispersal seasons. We constructed generalized linear models to identify the relationship between livestock presence in the diet and dietary prey richness with respect to environmental and individual variables. We identified 68 wolves that had consumed 30 species of vertebrates. Of these, white‐tailed deer (36.12%), diversionary feeding (22.79%), and cattle (25.56%) had the highest contribution to biomass. The ingestion of items was independent of the sex of the wolves but was dependent on the season. The presence of deer and diversionary feeding decreased the likelihood of cattle being ingested but also decreased the richness of items of wild species in the wolf diet. Wolves in northwestern Mexico fed mainly on large prey available in the reintroduction area, including livestock. As wolves consume livestock, it increases the risk of retaliatory actions from ranchers. Our results serve as a basis for the implementation of strategies to reduce human–wolf conflicts and set a baseline for coexistence in northwestern Mexico.

An evaluation of potential inbreeding depression in wild Mexican wolves

AbstractEstimates of the influence of inbreeding on the fitness of wild animals can guide genetic conservation in rare species. Conservation genetics is important in Mexican wolves (Canis lupus baileyi) because the current population descended from 7 founders and mean inbreeding is relatively high. As an endangered subspecies, Mexican wolves are actively managed using select conflict avoidance measures and by placing captive‐born foster pups into wild litters. We obtained data on inbreeding coefficients of wolf pups and adults based on a pedigree dating to 1957 and data on reproduction for wild wolf packs during 1998–2022. We estimated trends in inbreeding coefficients and the associations between dam, sire, and pup inbreeding coefficients and pup recruitment to age 9 months, and assessed 3 components of recruitment: probability of producing a litter, number of pups produced, and recruitment conditional on successful reproduction. We generated estimates using generalized linear mixed models and bootstrapped estimates of confidence intervals. Mean inbreeding coefficients were high (0.227, SD = 0.047) in the wild population, but we detected no significant evidence of an increase during 2010–2022. Overall, the net associations of dam, sire, and pup inbreeding coefficients with our primary fitness metric, pup recruitment to age 9 months, did not differ from zero. While high inbreeding coefficients are a concern for the long‐term recovery of the subspecies, the stable level of inbreeding, lack of evidence for inbreeding depression, high pup production (5.1 pups/litter, SD = 1.64), and rapid population growth (384% increase from 2010–2022) indicate that inbreeding has not prevented rapid progress towards recovery goals under current management practices.

Behavioral trade-offs and multitasking by elk in relation to predation risk from Mexican gray wolves.

Predator non-consumptive effects (NCE) can alter prey foraging time and habitat use, potentially reducing fitness. Prey can mitigate NCEs by increasing vigilance, chewing-vigilance synchronization, and spatiotemporal avoidance of predators. We quantified the relationship between Mexican wolf (Canis lupus baileyi) predation risk and elk (Cervus canadensis) behavior. We conducted behavioral observations on adult female elk and developed predation risk indices using GPS collar data from Mexican wolves, locations of elk killed by wolves, and landscape covariates. We compared a priori models to determine the best predictors of adult female behavior and multitasking. Metrics that quantified both spatial and temporal predation risk were the most predictive. Vigilance was positively associated with increased predation risk. The effect of predation risk on foraging and resting differed across diurnal periods. During midday when wolf activity was lower, the probability of foraging increased while resting decreased in high-risk areas. During crepuscular periods when elk and wolves were most active, increased predation risk was associated with increased vigilance and slight decreases in foraging. Our results suggest elk are temporally avoiding predation risk from Mexican wolves by trading resting for foraging, a trade-off often not evaluated in behavioral studies. Probability of multitasking depended on canopy openness and an interaction between maternal period and predation risk; multitasking decreased prior to parturition and increased post parturition in high-risk areas. Openness was inversely related to multitasking. These results suggest adult female elk are altering the type of vigilance used depending on resource availability/quality, current energetic needs, and predation risk. Our results highlight potentially important, but often-excluded behaviors and trade-offs prey species may use to reduce the indirect effects of predation and contribute additional context to our understanding of predator-prey dynamics.

An Ecoregional Conservation Assessment for Forests and Woodlands of the Mogollon Highlands Ecoregion, Northcentral Arizona and Southwestern New Mexico, USA

The Mogollon Highlands, Arizona/New Mexico, USA, spans a large biogeographical region of 11 biotic communities, 63 land cover types, and 7 ecoregions. This 11.3 M ha region has high levels of beta diversity across topo-edaphic gradients that span deserts to mountain tops. The main stressors affecting the region’s forests and woodlands include climate change, livestock grazing, and frequent mechanical removals of large amounts of forest biomass for fire concerns. We present an ecoregion conservation assessment for robust conservation area design that factors in appropriate wildfire response to protect communities from increasing threats of climate-induced wildfires spreading into urban areas. We focused mainly on maintaining connectivity for endangered focal species (grizzly bear (Ursus arctos horribilis) and Mexican wolf (Canis lupus baileyi)) along with protecting mature and old-growth (MOG) forests, Piñon (Pinus spp.)–Juniper (Juniperus spp.) Woodlands, and riparian areas. Over half the region is managed by federal agencies where new protected areas can be integrated with tribal co-management and prescribed burning, defensible space, and home hardening to protect communities from the growing threat of climate-induced wildfires. However, just 9% of the study area is currently protected, and even with the inclusion of proposed protected areas, only 24% would be protected, which is below 30 × 30 targets. The potential grizzly bear habitat, wolf habitat connectivity, and MOG forests (1.6 M ha (14.2%) of the study area; 18% protected) are concentrated mainly in the central and eastern portions of the MHE. There were 824 fires (2 to 228,065 ha) from 1984–2021, with 24% overlapping the wildland–urban interface. Regional temperatures have increased by 1.5 °C, with a 16% reduction in precipitation and stream flow since 1970 that under worst-case emission scenarios may increase temperatures another 3 to 8 °C by the century’s end. The unique biodiversity of the MHE can be better maintained in a rapidly changing climate via at least a three-fold increase in protected areas, co-management of focal species with tribes, and strategic use of fuel treatments nearest communities.

Mexican Wolf Hunting! Epidemiological Report on Mexican Lupus Nephropathy in Pediatric Age

Mexican Wolf Hunting! Epidemiological Report on Mexican Lupus Nephropathy in Pediatric Age

Factors influencing timing of puberty in Mexican gray wolves (Canis lupus baileyi)

Abstract The reintroduced population of Mexican gray wolves (Canis lupus baileyi) continues to rely on a carefully managed captive breeding program. Although success of that program depends on detailed knowledge of reproductive processes, age of puberty has not been determined. This study assessed male puberty status (presence of sperm in ejaculates), maintained in nine US facilities, during their first breeding season. Variables possibly associated with puberty were also evaluated. There was a significant effect of body weight, testis size, facility latitude, and date of collection, whereas a statistical trend was found for age and inbreeding coefficient. Social factors, including being housed with sire, had no effect. Over half the males in their first breeding season were producing sperm, although in some cases sperm quality was poor, suggesting possible infertility. Although there was no minimum body weight associated with presence of sperm, likelihood increased with increasing body weight, highlighting a possible critical role for nutrition. The trend for sperm production in males collected later in the breeding season and at lower latitudes suggests that later collections, especially at higher latitudes, might reveal a higher percentage of pubertal males. These results have potential implications for breeding program management and introduce the possibility that more wild gray wolves than previously thought might produce sperm during their first year, even if they do not sire young.

Kill rates on native ungulates by Mexican gray wolves in Arizona and New Mexico

AbstractMexican gray wolf (Canis lupus baileyi) reintroduction began in 1998 in Arizona, USA, with 11 individuals initially; wolves from this population dispersed into New Mexico, USA, the following year. Numbers of wolves have steadily increased (≥241 individuals in Dec 2022) and the size of the recovery area has expanded in both states. Understanding kill rates is fundamental to the recovery and management of Mexican wolves to properly maintain a healthy and sustainable population of wolves and their prey species. We used global positioning system (GPS) cluster analysis to locate kill sites and estimate kill rates on native ungulate prey taken in the recovery area by 10 Mexican wolf groups during winter (15 Feb–15 Mar) and 8 wolf groups during summer (15 Jun–15 Jul) in 2015–2017. Elk (Cervus canadensis) composed 94% of the native ungulates documented at Mexican wolf kill sites (n = 139); the remaining 6% were mule deer (Odocoileus hemionus; n = 9). Two‐thirds of all wolf‐killed native ungulates were elk calves. We estimated kill rates as ungulate biomass killed/wolf/day. From combined results for all years, we estimated that each Mexican wolf killed on average 9.0 ± 5.4 kg (±95% CI) of ungulate biomass per day during winter and 7.8 ± 6.2 kg during the summer. Our estimates of kill rates could be overestimated if Mexican wolves obtained a substantial amount of their biomass from scavenging, particularly during 4 months of hunting seasons (Sep–Dec) not captured in winter and summer. Using data from the first 2 years of the study (2015, 2016), we developed a logistic regression model to predict probability of an elk kill occurring at a GPS cluster as a function of hours spent by a collared wolf at that GPS cluster and size of the wolf group. Applying this model to the final year of the study (2017) resulted in similar numbers of predicted (n = 16.1 and 27.2 in winter and summer, respectively) and observed numbers (n = 15 and 26) of elk kills. Additionally, the demographic composition of the 2017 elk kills closely matched that of the previous 2 years. The results of this study indicate similar predation patterns of Mexican wolves to those of wolves in northern locations and can help wildlife managers plan for potential effects from a larger population of wolves across a broad area in Arizona and New Mexico.

Factors affecting the recovery of Mexican wolves in the Southwest United States

Abstract Recovering and maintaining large carnivore populations is a global conservation challenge that requires better knowledge of the factors affecting their populations, particularly in shared landscapes (i.e. non‐protected areas where people occupy and or utilize the land). The Mexican wolf (Canis lupus baileyi) is an endangered wolf subspecies being recovered on shared landscapes in the Southwest United States and Mexico. We used data from the U.S. program to model population growth, evaluate the impact of management removal and illegal killing relative to other demographic factors, and test hypotheses about factors influencing rates of management removal and illegal killing. From 1998 to 2019, the population growth averaged 12% per year. Rates of natural reproduction, illegal killing and other mortality remained consistent over the 22 years; while releases, translocations and management removals varied markedly between two time periods, phase 1:1998–2007 and phase 2:2008–2019. The number of wolves removed for conflict management was higher during phase 1 (average ~ 13 per year, rate = 24.8%) than phase 2 (average of ~5 per year, rate = 5.2%). This decrease in management removal resulted in the wolf population resuming growth after a period of population stagnation. Two factors influenced this decrease, a change in policy regarding removal of wolves (stronger modelling support) and a decrease in the number of captive‐reared adult wolves released into the wild (weaker modelling support). Illegal mortality was relatively constant across both phases, but after the decrease in management removal, illegal mortality became the most important factor (relative importance shifted from 28.2% to 50.1%). Illegal mortality was positively correlated with rates of reintroduction and translocation of wolves and negatively correlated with the rate of management removal. Synthesis and applications. Using management removal to reduce human–carnivore conflict can have negative population impacts if not used judiciously. Recovering and maintaining carnivore populations in shared landscapes may require greater tolerance of conflict and more emphasis on effective conflict prevention strategies and compensation programs for affected stakeholders.

Camera trapping as a method for estimating abundance of Mexican wolves

AbstractEstimating wildlife abundance, particularly for rare and elusive species, is challenging because of time, cost, and methodological constraints. The Mexican wolf (Canis lupus baileyi), a federally‐listed endangered subspecies of gray wolf, is currently monitored using ground and aerial methods to obtain a minimum known population count. As the Mexican wolf population has grown and expanded, the time and cost required to monitor the subspecies has increased. We investigated the efficacy of camera trapping for estimating Mexican wolf abundance by comparing the accuracy, precision, and cost of camera trapping to those obtained with current monitoring techniques. Between 1 November 2019 and 31 July 2020, we collected 13,317 photos of wolves from 124 camera traps in Arizona where Mexican wolves were known to occur, excluding tribal lands. We used a spatial mark‐resight analysis to estimate abundance for both winter (November 2019 through February 2020) and summer (April through July 2020) seasons, with and without the assistance of global positioning system (GPS) telemetry data to identify individual wolves. Combined with GPS data, camera trapping provided a summer abundance estimate ( = 50, 95% CI = 37–64) that was 14% lower than the 2019 minimum known population count (N = 59), but included the minimum known population count in the 95% confidence interval. The summer no telemetry abundance estimate was 27% below the minimum known population count ( = 43, 95% CI = 30–56). During winter, abundance estimates obtained from camera trapping (no telemetry: = 33, 95% CI = 15–52; telemetry: = 45, 95% CI = 28–62), were much lower than the 2019 Mexican wolf minimum known population count (winter: N = 62), but included the minimum known population count in the 95% confidence interval for the winter telemetry dataset. A cost comparison indicated that the first‐year camera trapping equipment expenses were 1.7 times the equipment cost of the current method and that camera trapping equipment expenses in subsequent years were equivalent to the equipment cost of the current method, and required at least 1.4 times the labor hours. We provide recommendations to potentially improve Mexican wolf abundance estimates and minimize camera trapping expenses. The results of our project may help managers make appropriate decisions for their population monitoring needs, while considering budget, staffing capabilities, precision, and accuracy.

Endocranial volume increases across captive generations in the endangered Mexican wolf

Endangered animals in captivity may display reduced brain sizes due to captive conditions and limited genetic diversity. Captive diets, for example, may differ in nutrition and texture, altering cranial musculature and alleviating constraints on cranial shape development. Changes in brain size are associated with biological fitness, which may limit reintroduction success. Little is known about how changes in brain size progress in highly managed carnivoran populations and whether such traits are retained among reintroduced populations. Here, we measured the endocranial volume of preserved Mexican wolf skulls across captive generations and between captive, wild, and reintroduced populations and assessed endocranial volume dependence on inbreeding and cranial musculature. Endocranial volume increased across captive generations. However, we did not detect a difference among captive, wild, and reintroduced groups, perhaps due to the variability across captive generations. We did not find a relationship between endocranial volume and either inbreeding or cranial musculature, although the captive population displayed an increase in the cross-sectional area of the masseter muscle. We hypothesize that the increase in endocranial volume observed across captive generations may be related to the high-quality nutrition provided in captivity.

Behavioral Changes Related to Stress in a Mexican Gray Wolf (Canis lupus baileyi) Pack

Stress is an interesting combination of biological responses to adverse environmental factors. Stress responses can be adaptive as a way individuals respond to potential life threats or situations potentially reducing reproduction success. Normally, it produces a change in an individual’s priorities directing energy to solve immediate situations instead of long-term investments. In this work we report a two stress inducing situations for Mexican wolf packs at the old Wildlife Research Center (CIVS) of San Cayetano, México. In the first one, an attempt to provide artificial dens within the enclosure occurred just prior to the parturition date for the litter. The dam changed the described normal wolf-mother behavior giving birth in a small depression instead of a den and moving the puppies several times until they died, post-mortem analysis reveals that death of one pup was due to a pneumonia. In the second case accidental separation of one of the yearling females produced changes in behavioral patterns in the family pack, including increased exploratory, passing, watching, and smelling behaviors in comparison to the time when the entire pack was together. These two study cases document the behavioral responses to a stress situation.

Living on the Edge: A Transnational Perspective on the Mexican Wolf and Its Near-Extinction

Living on the Edge: A Transnational Perspective on the Mexican Wolf and Its Near-Extinction

Are wild wolves southpaws? Including potential conservation implications

Lateralization, or a left-right bias in behavior (e.g., handedness), was originally thought to exclusively exist in humans, but is now known to be widespread. Lateralization can exist at the individual or group level. In dogs (Canis lupus familiaris), tests of paw preference have produced inconsistent results. Because wolves (C. l.) differ genetically, morphologically, and behaviorally from dogs, I was interested in assessing them for lateralization. I examined lateralization (right versus left) of the foot captured (a step test analog) of wild wolves (n = 93) trapped for radiocollaring purposes in the Superior National Forest, Minnesota from 2011 – 2017 and 2019. No support was found for lateralization, and sex and age class were not significant predictors of which foot was captured. Because many mammals demonstrate lateralization, and because population-level lateralization is thought to convey increased social cohesion, it is surprising that wild wolves did not demonstrate population level lateralization. This step test analog may not have been an appropriate measure (as lateralization is task dependent) and / or wolf lateralization may exist at the individual level, but not the population level. Future work on wolf lateralization at both the individual and population levels examining pawedness via multiple tasks while accounting for potential confounding factors (such as different rearing conditions and methods) could provide clarification. Examining potential trade-offs between the costs and benefits of lateralization that these highly social animals may incur would be very interesting in terms of evolution and in comparison with dogs. Furthermore, because lateralization has been connected to emotional functioning and animal welfare, baseline lateralization data from wild wolves may inform captive wolf management and conservation, including the captive breeding programs for endangered Mexican wolves (C. l. baileyi) and red wolves (C. rufus) and other programs (e.g., educational facilities).

Editorial 2022

Editorial 2022

Assessing spontaneous howling rates in captive wolves using automatic passive recorders

ABSTRACT We studied the spontaneous vocal behaviour of captive wolves at the International Wolf Center (IWC) in Minnesota (spring 2019 and winter 2020), and the Centro del Lobo Ibérico Félix Rodríguez de la Fuente (CLIFRF) in Spain (winter 2020). We used AudioMoth recording devices to record wolf howling 24 h/day. We identified 412 solo howl series and 403 chorus howls and found differences between wolves at the two centres. Vocal rates for North American wolves at the IWC (7.8 chorus howls/day in spring and 4.8 chorus howls/day in winter) were higher than rates obtained for Iberian wolves from CLIFRF (3.8 chorus howls/day in winter). Howling rates obtained in our study were similar to those obtained for captive Mexican wolves and greater than those reported for wild wolves. Hourly distribution of howling was also different between centres. The greatest howling activity identified at IWC was at pre-sunrise, while at CLIFRF the peak occurred at sunset. Weather conditions had little influence on the vocal behaviour of the captive wolves we studied. We show the potential of passive recorders to study topics of animal acoustic communication, such as vocal rates and temporal patterns, that have not been deeply addressed due to technological constraints.

Using hybridization capture to obtain mitochondrial genomes from forensically relevant North American canids: Assessing sequence variation for species identification

The majority of DNA casework processed by forensic laboratories focuses on human samples, but material from canids (dogs, wolves, coyotes) can also be encountered. Undomesticated canids can be the center of forensic investigations in the U.S. since some species are endangered. As many wolf species are similar morphologically, identification in the field by wildlife officers is not always straight-forward, making molecular based-approaches ideal. While some published methods using mitochondrial DNA targets can discriminate among Canis species, they are either not compatible with highly degraded samples or cannot differentiate closely related sub-species. Although some U.S. laboratories regularly perform veterinary/wildlife casework including canid identifications, their validated methods and reference genetic databases are not publicly available. We aimed to assess the utility of alternative regions in the mitochondrial genome for discriminating among canid species, including the complete genome. To achieve this, we utilized a commercial hybridization capture panel composed of biotinylated RNA “baits” designed for the domestic dog to enrich canid mitochondrial genomes for next-generation sequencing. We used this panel to successfully sequence complete mitochondrial genomes for 51 samples, representing four U.S. forensically relevant canids (coyote, wolf, Mexican wolf, dog). While the complete mitochondrial genome permitted discrimination, we also assessed previously published mitochondrial DNA targets (n, 5) for resolution and identified four alternate ∼200 bp fragments from ND1, ND5, COI and CYTB genes that could help resolve canids. The utility of these alternate regions should be assessed in future studies using forensic-type samples representing canids from diverse geographic areas, prior to casework implementation.

One of these wolves is not like the other: morphological effects and conservation implications of captivity in Mexican wolves

AbstractMaintaining animal populations in captivity can be a useful way to conserve species, especially those that are extinct in the wild or endangered in their native habitats. These animals could be reintroduced into the wild from captivity if conditions improve. However, captive populations of endangered species are often established with few wild‐caught individuals and are maintained in novel habitats, conditions which may make these populations prone to morphological divergence. Changes in cranial morphology, in particular, may limit reintroduction success because these morphological changes may alter cranial functionality related to capturing and consuming prey. To assess whether unintentional morphological changes occur in captivity, we examined the crania and mandibles of 275 specimens of wild, captive and reintroduced Mexican wolvesCanis lupus baileyi. We detected significant differences in skull size and shape among these populations. Captive specimens displayed the greatest overall shape variation and were significantly differentiated from the wild population in regions of the skull that are essential to cranial functionality. The reintroduced population displayed the narrowest trait distribution, with cranial morphology that grouped consistently with the captive morphotype. The small number of individuals of the founding population along with the increased variation in cranial morphology among captive Mexican wolves suggests that morphological changes in captivity may be related to genetic changes such as genetic drift or relaxed selection. This study helps to define the changes that may occur in captivity, the potential mechanisms behind these shifts, and the ways in which morphological variation in captive populations may impact conservation initiatives.

A sliver of the past: The decimation of the genetic diversity of the Mexican wolf.

The endangered Mexican wolf (Canis lupus baileyi) is known to carry exceedingly low levels of genetic diversity. This could be (i) the result of long-term evolutionary patterns as they exist at the southernmost limit of the species distribution at a relatively reduced effective size, or (ii) due to rapid population decline caused by human persecution over the last century. If the former, purifying selection is expected to have minimized the impact of inbreeding. If the latter, rapid and recent declines in genetic diversity may have resulted in severe fitness consequences. To differentiate these hypotheses, we conducted comparative whole-genome analyses of five historical Mexican wolves (1907-1917) and 18 contemporary Mexican and grey wolves from North America and Eurasia. Based on whole-genome data, historical and modern Mexican wolves together form a discrete unit. Moreover, we found that modern Mexican wolves have reduced genetic diversity and increased inbreeding relative to the historical population, which was widespread across the southwestern United States and not restricted to Mexico as previously assumed. Finally, although Mexican wolves have evolved in sympatry with coyotes (C. latrans), we observed lower introgression between historical Mexican wolves and coyotes than with modern Mexican wolves, despite similarities in body size. Taken together, our data show that recent population declines probably caused the reduced level of genetic diversity, but not the observed differentiation of the Mexican wolves from other North American wolves.

Unveiling the Fecal Microbiota in Two Captive Mexican Wolf (Canis lupus baileyi) Populations Receiving Different Type of Diets.

Simple SummaryThe Mexican wolf (Canis lupus baileyi) is an endangered canine. Both Mexico and the United States are currently collaborating to reproduce and reintroduce individuals to their original habitats. However, keeping these wolves in captivity represents a great commitment to meet their basic needs. Diet is a determining factor that is closely related to health and reproductive fitness. The type of diet that is fed to canines in captivity must provide the required nutrients for their development and welfare. The study of the fecal microbiota is a non-invasive way to establish the abundance and diversity of bacterial communities to determine if they are in a healthy condition. We analyzed data from two captive populations of Mexican wolves (i.e., northern and central Mexico) receiving different type of diets (Michilia population: mainly kibble vs. Ocotal population: mainly raw meat). The operational taxonomic units (OTUs) in Michilia resulted in 204 genera and 316 species, while in Ocotal there were 232 genera and 379 species. In the Michilia, dominance of bacteria that degrade carbohydrates was observed (related to kibble diet). In contrast, the Ocotal microbiota was dominated by protein-degrading bacteria (related to raw meat diet). The main outcomes generated in this study should help to enhance the welfare of the captive Mexican wolves to increase its numbers.The Mexican wolf (Canis lupus baileyi) was once distributed in southern United States and northern Mexico. It is an endangered subspecies detached from the gray wolf, and likely exemplifies one of the original migration waves of C. lupus into the new world. This is a canine whose individuals survive in specialized facilities, zoos, and museums as part of captive-breeding programs. In order to contribute to the improvement of the management of this species and favor its long-term conservation in Mexico, we aimed to evaluate the diversity and abundance of the fecal bacterial microbiota in two populations exposed to different types of diet: (1) Michilia (23° N, 104° W); kibble daily and raw meat sporadically, and (2) Ocotal (19° N, 99° W); raw meat daily and live animals periodically. Next generation sequencing (V3-V4 16S rRNA gene) by Illumina was implemented. The operational taxonomic units (OTUs) in Michilia resulted in 9 phyla, 19 classes, 34 orders, 61 families, 204 genera, and 316 species, while in Ocotal there were 12 phyla, 24 classes, 37 orders, 69 families, 232 genera, and 379 species. Higher estimated Chao1 richness, Shannon diversity, and core microbiota were observed in Ocotal. Differences (p < 0.05) between populations occurred according to the Bray–Curtis beta diversity index. In the Michilia, dominance of bacteria that degrade carbohydrates (Firmicutes, Lachnospiraceae, Blautia, Clostrodium, Eisenbergiella, Romboutsia, and Ruminococcus) was observed; they are abundant in kibble diets. In contrast, the Ocotal microbiota was dominated by protein-degrading bacteria (Fusobacteria, Fusobacteriaceae, and Fusobacteria), indicating a possible positive relation with a raw meat diet. The information generated in this study is fundamental to support the implementation of better management plans in the two populations considered here, as well as in different facilities of southern United States and Mexico, where this subspecies is kept in captivity for conservation purposes.