Neotoma Magister Research Articles

Genetic Evidence of Allegheny Woodrats (Neotoma magister) in Alabama: Continued Existence at the Southern Extent of its Range

Genetic Evidence of Allegheny Woodrats (Neotoma magister) in Alabama: Continued Existence at the Southern Extent of its Range

A RANGE-WIDE ECTOPARASITE SURVEY FOR ALLEGHENY WOODRATS (NEOTOMA MAGISTER).

Allegheny woodrats (Neotoma magister) are karst-specializing rodents that are rare or in conservation need in many states within their current range. Parasitism and habitat fragmentation have been suggested as primary reasons for declining populations. The presence, prevalence, and impact of ectoparasites, including fleas, ticks, and bots, is not fully understood rangewide. We collected Allegheny woodrat ectoparasites across 8 states in their range, identifying parasites via morphological and genetic means. Across contributions from 8 states, we discovered 2 woodrat-specific fleas parasitizing Allegheny woodrats: Orchopeas pennsylvanicus (all contributing states, n = 228) and Epitedia cavernicola (Indiana only, n = 9). The former was a new state record in New Jersey and Ohio. Woodrat specialists Ixodes woodi were morphologically identified as the dominant tick species (n = 38), and our contributions to genetic databases may ease confusion in future efforts. Three generalist species of ticks representing 8 individuals were identified as Dermacentor variabilis, Amblyomma americanum, and Ixodes scapularis. Only 2 bot fly species were recognized in Allegheny woodrats: 1 squirrel bot (Cuterebra emasculator) and 10 individuals of Cuterebra sp. not genetically conspecific to any known eastern U.S. rodent bot. The host specificity for fleas is not surprising, given that previous small-scale surveys and ticks primarily appear to be a mix of genus-specific (Ixodes woodi) and generalist species. There remains uncertainty with bots via morphological and genetic analyses. Our survey presents a wide-ranging baseline survey for Allegheny woodrats across their range, emphasizing the diversity (or specificity) of parasite groups for this species. An understanding of Allegheny woodrats and the health impact of ectoparasites is imperative because they face myriad challenges rangewide, especially considering the bot-driven demise of 1 woodrat in our study. Ectoparasites can have a marked impact on already-declining woodrat populations across their range and should not be overlooked in future surveys.

Attempted Predation of Live-Captured Neotoma magister (Allegheny Woodrat) by Strix varia (Barred Owl) and Buteo jamaicensis (Red-Tailed Hawk) in Kentucky

Attempted Predation of Live-Captured Neotoma magister (Allegheny Woodrat) by Strix varia (Barred Owl) and Buteo jamaicensis (Red-Tailed Hawk) in Kentucky

Observation of an Interaction between an Allegheny Woodrat (Neotoma magister) and a Timber Rattlesnake (Crotalus horridus) in Pennsylvania

Neotoma magister (Allegheny Woodrat) is a threatened species in Pennsylvania and listed as Endangered in 4 of 5 bordering states. Declining food resources, genetic isolation, habitat fragmentation, disease, and increasing predator populations are considered the primary threats to Allegheny Woodrat populations. Herein, we share an observation captured on a wildlife camera of an adult woodrat displaying agonistic behavior toward a small Crotalus horridus (Timber Rattlesnake).

Activity Patterns of Allegheny Woodrats (Neotoma magister) and Two Potential Competitors in Virginia

Neotoma magister (Allegheny Woodrat) is a nocturnal, emergent rock-habitat specialist (i.e., inhabits rocky outcrops, boulderfields, and caves). Woodrat populations have declined range-wide due to habitat fragmentation, endoparasites, and interspecific competition. We estimated the diel activity curves of Allegheny Woodrats and assessed the effects of habitat type (exposed rock habitat/cave-exterior vs. cave-interior) and season (spring, summer, and fall) on curve shape. We also investigated the effect of 2 granivorous competitors' presence and activity curves (Peromyscus spp. and Tamias striatus [Eastern Chipmunk]) on woodrat activity. Additionally, we investigated whether the presence or absence of Procyon lotor (Raccoon), a primary carrier of Baylisascaris procyonis (Raccoon Roundworm), significantly affects the presence or absence of Allegheny Woodrats. We used remote-detecting cameras to document the diel cycles of Allegheny Woodrats and 2 competitors across 83 sites in western Virginia and 2 sites in West Virginia from 2017 to 2022. For 13,002 recorded events, we detected woodrats at 36 of 85 sites (3778 camera events). We observed a higher proportion of daytime activity by woodrats within cave interiors than cave exteriors. Allegheny Woodrat activity curves differed among seasons, with the greatest differences observed between summer and fall and with ∼80% activity overlap. These activity curves differed significantly when co-occurring with versus not co-occurring with a competitor. Additionally, Allegheny Woodrats showed an inverse activity rate with Peromyscus spp. Thus, our results suggest that competition avoidance via temporal partitioning occurs between these species. Allegheny Woodrats and Raccoons occurred together more often than expected suggesting the presence of woodrats is currently not reduced by the presence of Raccoons. Our remote-detecting camera data help elucidate relationships of Allegheny Woodrats with presumptive competitors, and open avenues for further investigation in Virginia.

A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population

BackgroundAllegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, the abundance of Allegheny woodrats has declined throughout the species’ range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small, genetically depauperate subpopulation in New Jersey, woodrats were translocated from a genetically robust population in Pennsylvania (PA) in 2015, 2016 and 2017. Herein, we assess the efficacy of these translocations to restore genetic diversity within the recipient population.ResultsWe designed a novel 134 single nucleotide polymorphism panel, which was used to genotype the six woodrats translocated from PA and 82 individuals from the NJ population captured before and after the translocation events. These data indicated that a minimum of two translocated individuals successfully produced at least 13 offspring, who reproduced as well. Further, population-wide observed heterozygosity rose substantially following the first set of translocations, reached levels comparable to that of populations in Indiana and Ohio, and remained elevated over the subsequent years. Abundance also increased during the monitoring period, suggesting Pennsylvania translocations initiated genetic rescue of the New Jersey population.ConclusionsOur results indicate, encouragingly, that very small numbers of translocated individuals can successfully restore the genetic diversity of a threatened population. Our work also highlights the challenges of managing very small populations, such as when translocated individuals have greater reproductive success relative to residents. Finally, we note that ongoing work with Allegheny woodrats may broadly shape our understanding of genetic rescue within metapopulations and across heterogeneous landscapes.

Comparison of Two Detection Methods for a Declining Rodent, the Allegheny Woodrat, in Virginia

Abstract Allegheny woodrats Neotoma magister are an imperiled small mammal species most associated with emergent rock habitats in the central Appalachian Mountains and the Ohio River Valley. The monitoring of populations and their spatiotemporal distributions typically has relied on labor-intensive livetrapping. The use of remote-detecting cameras holds promise for being an equally or more effective method to determine species presence, although trap-based captures permit the estimation of other parameters (e.g., survival, population size, site fidelity). In 2017, 2018, and 2020 we compared standard livetrapping with paired cameras for determining site occupancy of Allegheny woodrats in the central Appalachian Mountains of western Virginia. We further examined the influence of baited vs. unbaited cameras at several sites of confirmed occupancy in 2019. We observed that the detection probability using cameras was approximately 1.7 times that of live traps. Also, detection probability at baited camera traps was 1.3–2.0 times that of unbaited camera traps. Estimates of occupancy ranged from 0.44 to 0.49. Our findings suggest that the use of baited remote-detecting cameras provides a more effective method than livetrapping for detecting Allegheny woodrats. Our study provides a framework for the development of a large-scale, long-term monitoring protocol of Allegheny woodrats with the goals of identifying changes in the distribution of the species and quantifying local extinction and colonization rates at emergent rock outcrops and caves throughout the species' known distribution.

Allegheny woodrat occupancy across western Virginia, United States

The Allegheny woodrat Neotoma magister, a rock outcrop habitat specialist, has suffered drastic reductions in geographic range over the past 40 years. Previous research has examined habitat characteristics at varying spatial scales, but none have used occupancy modeling to examine trends over time. Therefore, we used presence/absence data from live trapping to assess environmental variables likely to influence Allegheny woodrat occupancy and detection patterns at a regional scale across western Virginia, USA, from 2009 to 2011. We observed a shift in occupancy and detection rates across years with a peak in 2009, a decline in 2010 and apparent recovery in 2011. We found significant isolation by distance effect influencing woodrat occupancy across the region, with occupancy linked to sites in closer proximity to other occupied locations. Occupancy increased in oak and hickory forests, suggesting woodrat occurrence increases in forest types with a higher abundance of hard and soft mast‐producing species. We found variable effects of elevation over time, with higher occupancy at higher elevations in 2009 but at lower elevations in 2010, which may be explained by variation in winter severity and mast abundance across years. Allegheny woodrat management should include activities to promote and retain mast‐producing species at higher elevations to offset potential subpopulation contractions during harsh winters.

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Reproductive success of captive-reared Allegheny Woodrats (Neotoma magister) released into genetically depauperate populations

Habitat fragmentation and degradation have led to a proliferation of small and isolated populations that are vulnerable to genetic erosion. Reduction in habitat and concomitant declines in population connectivity can expediate the collapse of species that exist as natural metapopulations. In recent years, Allegheny woodrats (Neotoma magister) have experienced local extirpations and declines in genetic diversity across their range due to disease-related mortality, reduced food availability, and disruption of connectivity among subpopulations. In response, we developed a captive-breeding program to facilitate genetic management of isolated woodrat populations in Indiana. Between 2010 and 2012, 27 captive-reared individuals were released to four sites with declining woodrat abundance. We used 99 single nucleotide polymorphisms and 11 microsatellite loci to genotype sympatric woodrats from the four sites, sampled before and after the release of captive-reared individuals, to: (1) evaluate the post-release reproductive success of captive-reared individuals and (2) characterize changes in genetic diversity. A minimum of five of the 27 captive-reared woodrats produced at least 20 offspring, 11 of which were sired by a single male. One site exhibited increased abundance by the end of the monitoring period, although genetic variability decreased. Two sites experienced population declines in concert with fluctuating genetic variability. The last site showed comparable abundance at the beginning and end of the monitoring period, with an increase in observed heterozygosity. Our results indicate that captive-reared woodrats were, in some cases, able to reproduce in the wild, interbreed with residents and increase genetic diversity and abundance among small, isolated subpopulations.

Effects of Prescribed Fire on Site Occupancy of Allegheny Woodrats (Neotoma magister) in a Mixed-Oak Forest in South-Central Pennsylvania

Prescribed fire has increasingly been used to manage and restore eastern oak (Quercus spp.) forests. Fire has the potential to influence habitat use by forest-dwelling small mammals, including species of conservation concern such as the Allegheny woodrat (Neotoma magister). Thus, an understanding of how Allegheny woodrats respond to habitat changes caused by fire is of increasing importance. We investigated the effects of prescribed fire on a population of Allegheny woodrats in a mixed-oak forest in south-central Pennsylvania. We surveyed 18 rock outcrops for Allegheny woodrats using remote game cameras in September–October 2019. We fit single-season occupancy models in Program PRESENCE to examine the effects of site covariates related to burn history (burned or unburned) and burn frequency (number of burns), topography, and vegetation structure and composition on occupancy (Ψ) of Allegheny woodrats while accounting for imperfect detection (p). In 252 camera trap-nights, we recorded 356 detections of Allegheny woodrats at 50% of sites surveyed. Top-ranked occupancy models (ΔAICc ≤ 2) indicated that Allegheny woodrat occupancy was positively related to burn frequency, overstory tree species richness, and elevation; however, the effects of these covariates were not significant. Our results suggest that low-intensity prescribed fire implemented at moderate (3–5 y) return intervals in oak forests is unlikely to impact Allegheny woodrat populations, but the effects of more frequent and intense fires remain unknown. Additional studies are needed to determine how Allegheny woodrats respond to post-fire vegetation regrowth and recovery over time.

The Prevalence of the Raccoon Roundworm, Baylisascaris procyonis, in Allegheny Woodrat Habitat in the Mid-Atlantic Region, U.S.A.

Baylisacaris procyonis is a roundworm that is tolerated by its primary host, raccoons (Procyon lotor). However, this roundworm can be fatal to intermediate mammalian hosts and may be a contributing factor to population declines of the endangered, Allegheny woodrat (Neotoma magister). We used fecal flotation to determine the prevalence of B. procyonis eggs in raccoon scat found in locations that overlap with where woodrats persist in the mid-Atlantic. We determined that B. procyonis was present at two extant woodrat colonies in Maryland and Pennsylvania. We expect woodrat populations at these sites to decline, if the roundworm and other factors (e.g., forest fragmentation) are not alleviated.

The Prevalence of the Raccoon Roundworm, Baylisascaris procyonis, in Allegheny Woodrat Habitat in the Mid-Atlantic Region, U.S.A.

Baylisacaris procyonis is a roundworm that is tolerated by its primary host, raccoons (Procyon lotor). However, this roundworm can be fatal to intermediate mammalian hosts and may be a contributing factor to population declines of the endangered, Allegheny woodrat (Neotoma magister). We used fecal flotation to determine the prevalence of B. procyonis eggs in raccoon scat found in locations that overlap with where woodrats persist in the mid-Atlantic. We determined that B. procyonis was present at two extant woodrat colonies in Maryland and Pennsylvania. We expect woodrat populations at these sites to decline, if the roundworm and other factors (e.g., forest fragmentation) are not alleviated.

Bot Fly Parasitism of Allegheny Woodrats (Neotoma magister) in Virginia

The Allegheny woodrat (Neotoma magister) is a species of high conservation concern and relatively well-studied with respect to habitat use/associations, food habits, conservation genetics, and population trends. However, with the exception of raccoon roundworm (Baylisascaris procyonis) occurrence and etiology in woodrats, most disease and parasite ecology aspects for the woodrat are unknown. Herein, we examined the prevalence of bot flies (Cuterebra) over nearly three decades of woodrat surveys (1990–2018) in the central Appalachian Mountains of western Virginia. We use genetic analyses to identify recent bot fly specimen collections from a woodrat captured in 2017. Though highly variable from year to year, the overall prevalence of parasitism was low (typically < 4% of captures). As such, bot flies do not appear to be a widespread parasitic burden to Allegheny woodrats in Virginia. Genetic analysis of four collected bot fly larvae was inconclusive, as the genetic signature of these woodrat bots did not match any of the six bot species known to parasitize rodents and lagomorphs in the eastern United States. Further collections and genetic analyses will be needed to determine if the genetic database is incomplete or incorrect, or if our find is a new species of bot fly not yet taxonomically recognized.

Bot Fly Parasitism of Allegheny Woodrats (Neotoma magister) in Virginia

The Allegheny woodrat (Neotoma magister) is a species of high conservation concern and relatively well-studied with respect to habitat use/associations, food habits, conservation genetics, and population trends. However, with the exception of raccoon roundworm (Baylisascaris procyonis) occurrence and etiology in woodrats, most disease and parasite ecology aspects for the woodrat are unknown. Herein, we examined the prevalence of bot flies (Cuterebra) over nearly three decades of woodrat surveys (1990–2018) in the central Appalachian Mountains of western Virginia. We use genetic analyses to identify recent bot fly specimen collections from a woodrat captured in 2017. Though highly variable from year to year, the overall prevalence of parasitism was low (typically < 4% of captures). As such, bot flies do not appear to be a widespread parasitic burden to Allegheny woodrats in Virginia. Genetic analysis of four collected bot fly larvae was inconclusive, as the genetic signature of these woodrat bots did not match any of the six bot species known to parasitize rodents and lagomorphs in the eastern United States. Further collections and genetic analyses will be needed to determine if the genetic database is incomplete or incorrect, or if our find is a new species of bot fly not yet taxonomically recognized.

Observed Predation of Neotoma magister (Allegheny Woodrat) by Strix varia (Barred Owl) in Virginia

Neotoma magister (Allegheny Woodrat) is a Tier IV species of conservation concern in the Commonwealth of Virginia. Threats across its range include habitat fragmentation, parasites, and predation. Until now, predators have been suggested, but not confidently documented. Here, we use wildlife camera footage to document a predation event of an adult female Allegheny Woodrat by Strix varia (Barred Owl). This is the first documented predation event for this species. Our finding contributes to the growing knowledge of threats to Allegheny Woodrats within their range.

Historical Documentation of the Allegheny Woodrat (Neotoma magister) in Massachusetts

Although most summaries of the distribution of Neotoma magister (Allegheny Woodrat) do not include Massachusetts, there are 2 historical reports of the species' past occurrence there. Herein, we review those reports and provide details on a specimen from the Berkshire Mountains taken in 1958. No additional observations have been documented in Massachusetts over the subsequent 60 years. Recent efforts to confirm presence of woodrats at the Berkshire Mountains site and efforts in the past several decades to locate a population elsewhere in Massachusetts have been unsuccessful. We conclude that the Allegheny Woodrat historically occurred in Massachusetts, although available habitat was limited. Based on the available habitat and the documented patterns of decline in other portions of the Northeast, it is almost surely now extirpated from Massachusetts.

Natural and anthropogenic factors affecting Allegheny woodrat occupancy

The Allegheny woodrat (Neotoma magister) is a habitat specialist closely associated with rock habitats throughout the Appalachian region. Although genetic studies have examined gene flow and connectivity among rock habitats, estimates of initial occupancy, colonization, and local extinction based on field studies are not available. Therefore, we used data from camera surveys to examine site and landscape characteristics with the potential to influence Allegheny woodrat initial occupancy, colonization, and local extinction at Shenandoah National Park, Virginia, USA, from May to September 2015. We modeled these parameters relative to covariates using a multiseason occupancy modeling approach. We found that colonization of rock outcrops by Allegheny woodrats occurs across a range of human impact levels, supporting previous research that Allegheny woodrats are relatively tolerant of human disturbance, including the type of disturbances (e.g., rock climbing, hiking) that occur at rock outcrops on our study area and other protected areas within the range. We also found lower localized extinction rates in oak (Quercus spp.)–hickory (Carya spp.) than oak–pine (Pinus spp.) forests, likely because the diversity of mast-producing species and abundant understory vegetation in oak–hickory forests provide habitat conditions more conducive to woodrat persistence. Management efforts for Allegheny woodrats should focus on maintaining forests with a diversity of mast-producing species, which could include use of prescribed fire and monitoring and treatment programs to reduce effects of invasive insects and pathogens. © 2018 The Wildlife Society.

Influence of landscape heterogeneity on the functional connectivity of Allegheny woodrats (Neotoma magister) in Virginia

Allegheny woodrats (Neotoma magister) exist as groups of metapopulations due to their dependence on naturally disjunct rocky outcrops in the eastern United States. Severe demographic declines of Allegheny woodrats have occurred in many parts of the range due to a myriad of interacting processes, therefore identifying factors that help maintain the integrity of metapopulations is needed to guide conservation efforts. One factor considered critical to metapopulation persistence is maintaining functional connectivity. Therefore, our objective was to identify landscape factors that influence gene flow in Allegheny woodrats. We sampled 159 individuals from throughout the distribution in Virginia, genotyped them at 22 microsatellite loci, and modeled effects of land cover, roads, large rivers, and elevation on gene flow. The model that parameterized areas ≤ 750 m in elevation as a barrier to gene flow performed best among the tested models, which indicates that functional connectivity is highest in high elevation habitats. We found little evidence for anthropogenic factors influencing gene flow, but continued study across extant metapopulations is needed in more peripheral areas to evaluate if anthropogenic barriers impact functional connectivity. Overall, our study emphasizes the importance of considering elevation for maintaining functional connectivity of Allegheny woodrats in the face of ongoing demographic declines in the eastern United States.

Mitochondrial genome of an Allegheny Woodrat (Neotoma magister)

The Allegheny woodrat (Neotoma magister) is endemic to the eastern United States. Population numbers have decreased rapidly over the last four decades due to habitat fragmentation, disease-related mortality, genetic isolation and inbreeding depression; however, effective management is hampered by limited genetic resources. To begin addressing this need, we sequenced and assembled the entire Allegheny woodrat mitochondrial genome. The genome assembly is 16,310 base pairs in length, with an overall base composition of 34% adenine, 27% thymine, 26% cytosine and 13% guanine. This resource will facilitate our understanding of woodrat population genetics and behavioral ecology.