Neotoma magister previously was regarded as a subspecies of Neotoma floridana. Evidence from analyses of variation in mtDNA, allozymes, and morphology indicates that N. magister is a highly distinct lineage (Hayes and Harrison 1992, Hayes and Richmond 1993, Edwards and Bradley 2001). Baker et al. (2003) and Musser and Carleton (in Wilson and Reeder 2005) recognized N. magister and N. floridana as distinct species. Baker et al. (2003) used the name "Appalachian Woodrat."

This species is endemic to the United States of America, where it has a large range. However, it is a microhabitat specialist, dependent on rocky areas, and it has experienced declines in many parts of its range with a significant percentage of its historical range no longer occupied. Although quantitative data supporting the contention that this species has declined 30% over a 10 year period are not available, it is easy to argue by inference of the shrinking of its overall distribution and the loss of important populations throughout its range that it is very probable that this level of decline has occurred.

The species has undergone precipitous range wide declines, being extirpated from New York state and with entire populations lost in New Jersey, Pennsylvania, Ohio, Maryland, and Indiana (Wilson and Ruff 1999). It is a specialist of talus and boulder field habitats and is largely distributed in metapopulations. These declines have serious implications for the maintenance of gene flow and dispersal.

Numerous technical documents since the 1999 publication show continued declines in range and abundance. The state of West Virginia State Wildlife Action Plan (2015 West Virginia State Wildlife Action Plan; wvdnr.gov) lists Neotoma magister as a Priority 1 Species in Greatest Need of Concern. The NatureServe codes list the species as S3 (subnational Vulnerable) and G3/G4 (globally Vulnerable to Apparently Secure).

The website of the Pennsylvania Game Commission focused on this species (Allegheny Woodrat; pa.gov - accessed 11/03/2024) lists it as threatened in Pennsylvania, due to loss of habitat, resources (chestnut and oaks), and disease (Raccoon roundworm parasite). There has also been loss of its preferred habitat resulting in increased fragmentation of metapopulations.

The state of Virginia has similar concerns, listing it as a Species of Concern with a Moderate Conservation Level and placing it in its listing of Mammals of Greatest Conservation Need (Wildlife Action Plan | Virginia DWR - accessed 11/03/2024).

This indicates declines and losses of populations throughout the range of the species. This species is listed as Near Threatened. Although it has a large range, it has experienced declines in many parts of its range with a significant percentage of its historical range no longer occupied. A reduction of close to 30% over the last ten years is suspected, making it close to qualifying for Vulnerable under criterion A2c. It is recommended that this species be assessed again within the next 3–4 years.

The range for this species extends throughout the Appalachian Mountains (Castleberry et al. 2006). It extends from western Connecticut, southeastern New York, northern New Jersey, and northern Pennsylvania southwestward through western Maryland, Tennessee, Kentucky, West Virginia, and northern and western Virginia (from the Blue Ridge westward) to northeastern Alabama (observed in several cave systems) and northwestern North Carolina (Hall 1981), with isolated populations north of the Ohio River in southern Ohio (where recent surveys failed to locate this species; W. Peneston pers. comm., cited by Mengak 2002) and southern Indiana (Whitaker and Hamilton 1998). Although Hall (1981) showed Neotoma magister in the northwestern corner of Georgia, the Tennessee River is generally accepted as the southern range limit.

Through the survey of distribution in the Appalachian Mountains (Gooley et al. 2018), from 2011–2015, organic signs of this species (latrines, fresh scat, fresh food caches, or maintained stick-nests) were a determining factor of their presence in the outcrop regions of the Northeastern and Midwestern United States. This specific survey took place in western Shawnee National Forest. Overall it has been determined that the presence of N. magister has increased in Southeastern Illinois, eastward into away from its remnant populations, once considered isolated.

The total adult population size is unknown but likely is much larger than 10,000. Populations are localized and generally quite small (less than ten), apparently exhibiting a typical metapopulation structure. For example, in Pennsylvania the Allegheny Woodrat population consists of 78 disjunct metapopulations (Butchkoski 2004). This species is represented by a very large number of occurrences or subpopulations (probably more than 200). The number of occurrences or subpopulations with good viability probably is substantially smaller than the total number of extant occurrences.

Populations in the northeastern United States have declined, while those in the southern portion of the range appear to have remained relatively stable. However, woodrats appear to be rare in Tennessee (Kennedy and Harvey 2001), and few specimens have been reported from Alabama, where present status is poorly known.

The species has disappeared from Connecticut, New York, most of eastern Pennsylvania, and all but one site in New Jersey. This decline has apparently been occurring for many years. Early sources (e.g., Newcombe 1930) remarked on the woodrat's decreasing range and abundance, and the most recent reports from Connecticut date from the 1930s (Goodwin 1935). Such a decline might be expected in the wake of human settlement, but in recent decades, woodrat decline has been dramatic in New York, New Jersey, Pennsylvania, and Maryland. Apparent extirpation has occurred in at least 100 sites in northern Virginia (Buhlmann pers. comm., 1992).

Since the late 1960s woodrats in Pennsylvania have disappeared from sites where they once occurred, particularly in eastern and northwestern Pennsylvania; surveys of more than 360 sites from which woodrats have been reported yielded 20 metapopulations, but five of these metapopulation areas no longer support woodrats, and seven of them have fewer active colonies than in the past (C. Fergus, no date; www.pgc.state.pa.us, accessed April 2006). The species has disappeared from the southeastern portion of Pennsylvania and has declined in much of the rest of the state; at present, populations exist throughout much of Pennsylvania's south-central and southwestern counties, with a few remnant populations in eastern counties; mapped distribution indicates that the species no longer occurs in roughly half of the historically occupied range (Pennsylvania Game Commission website, woodrat information last updated in 2006).

In New Jersey, several populations have been extirpated for at least 20 years; the single known remaining population has been relatively stable in recent years, based on trapping results in 1999–2001 (New Jersey Division of Fish and Wildlife).

Woodrats were documented throughout their historical range in southeastern New York as recently as the mid-1960s, when they appeared to occupy all available habitat; those populations were extirpated by 1987; currently, the only woodrats in the state are immigrants that occasionally occupy a small patch of habitat on the New York-New Jersey border (this is the northern extreme of the habitat for the last remaining New Jersey woodrat population) (New York State Comprehensive Wildlife Conservation Strategy, 2005 revised draft). Reintroductions attempted in the early 1990s were unsuccessful.

This species may be represented by only one population in Ohio, or possibly it is extirpated; recent surveys failed to locate woodrats there (W. Peneston pers. comm., cited by Mengak 2002).

In Maryland, woodrat populations have been in decline for over two decades and continue to decline (Dan Feller, Maryland Natural Heritage Program pers. comm., cited by New York State Comprehensive Wildlife Conservation Strategy 2005 draft).

In the early 1980s, extant populations in Indiana were reported from 20 sites (18 bluffs, two caves) adjacent to the Ohio River; in 1991–1992, live trapping surveys at 17 sites yielded a total of 101 woodrats at 12 (11 bluffs, one cave) of the 17 sites (Johnson 2002). Abundance in Indiana appears to have declined in recent decades. Population density for six sites in Indiana averaged 27.5/km of cliff habitat during the early 1980s (Cudmore 1985). During the 1990s density averaged about 11 individuals/km at 12 Indiana sites (Johnson et al. 1997).

Woodrat populations in the core of the range in West Virginia (Castleberry 2000), Virginia (Mengak 2000), and Kentucky (Thomas 1998) currently appear to be secure.

Cudmore (1983) estimated population densities of 8.3 to 71.9 woodrats per 1,000 m of cliff along the Ohio River in Indiana. According to Burt and Grossenheider (1976), populations of 5–8 adults per hectare are probably high.

In Illnois, there was an increase in the amount of debris that was being built up into the river as aftermath of the 2009 derecho.

Typical habitat is rocky cliffs and talus slopes. These woodrats make midden mounds and stick piles among rocks, but secluded nest sites generally are not within stick houses (see Hayes and Harrison 1992).

Throughout its range, this species is associated with extensive rocky areas such as outcrops, cliffs, talus slopes with boulders and crevices, and caves. It occasionally uses abandoned buildings but generally avoids humans. It generally occurs at higher elevations (to about 1,000 m) and is rarely found in lowlands or open areas. Because it is a habitat specialist, geographic range portrayals grossly exaggerate its true distribution. For example, the global range map shows approximately 40% of the land surface of Pennsylvania as included in Allegheny woodrat distribution, when in fact the Pennsylvania surface rock habitat currently occupied by woodrats covers less than one percent (0.77%) of the state (Hassinger pers. comm.).

In southern New York, New Jersey, and adjacent Pennsylvania, woodrat habitat "consists of extensive boulder fields at the base of ridges with rock outcrops. These talus slopes consist of large boulders (10-20 ft. [3-6 m] across) piled in several layers. Neotoma lives among the cave like spaces formed by the piled boulders" (Sciascia 1990).

Referring to the mountainous area of Pennsylvania, Merritt (1987) wrote, "limestone caves, rocky cliffs and accumulations of residual sandstone boulders marked by deep crevices with underground galleries represent favored habitat." Hall (1985) pointed out that good habitat is found "specifically at water gaps where cliff faces and boulder piles are usually abundant." Unpublished data from Pennsylvania Natural Diversity Inventories (eastern and western offices) make frequent references to woodrat occurrences in sandstone, limestone, or shale outcrops and cliffs, usually with crevices or abundant boulders; also solution caves and abandoned limestone quarries and mines. Associated forest is varied, including cove hardwoods, hemlock-birch, oak-pine, and various combinations of oaks, maples, hickories, beech, and yellow poplar (tulip-tree). Grape, mountain laurel, rhododendron and ferns are frequently mentioned.

In West Virginia, woodrats are common in caves, rock shelters, outcrops with deep crevices, and riverbanks with an abundance of sandstone rocks and boulders.

"In Maryland, this species is found predominately in cliffs, caves and rocky areas in the three western-most counties, and along cliffs of the Potomac River to the vicinity of Washington, D.C." (Feldhammer et al. 1984). In western Maryland "Pottsville Sandstone outcrops [provide] massive, blocky boulders and extensive cliffs with numerous crevices and miniature cave-like situations" (Thompson 1984).

In Indiana, extant populations are restricted primarily to south-facing limestone bluffs on the Ohio River, where there are den sites in the rock and dense red-cedar (Cudmore 1983, Scott Johnson pers. comm.).

In Kentucky, "cliffs with deep crevices, caves, or large boulders piled in such a way as to form numerous retreats and shelters are favored" (Barbour and Davis 1974). In Tennessee, "rocky cliffs, caves and fissures or tumbled boulders on the sides of mountains are the preferred habitat" (Hamilton 1943), and in North Carolina it is "rocky places and abandoned buildings at elevations above 3,000 ft (900 m)" (Adams 1987). Castleberry et al. (2001) suggest that forest clearcutting has minimal impact on woodrat movements, home range, and habitat use, as long as sufficient intact forest is retained adjacent to colonies. They mention, however, that harvesting methods that selectively remove important mast-producing tree species may represent the greatest threat from forest management.

A large house of sticks, leaves, and miscellaneous debris is built, usually within a cave, crevice, or other well-protected place. This may be a mound like a muskrat house (typical construction in the range of other subspecies), but is more often open, giving the impression of a large bird's nest (Poole 1940). Outside diameter is about 35-60 cm (Patterson 1933) and the inner cavity is about 12 cm across (Poole 1940). The nest is lined with shredded bark of grape, red cedar, hemlock, or basswood, grass, fur, rootlets, and sometimes feathers (Poole 1940, Merritt 1987).

Woodrats are basically solitary and unsociable, frequently fighting one another. Each lives alone in its house, except when breeding and raising young. Poole (1949) found "a great deal of individuality" in temperament, behaviour, food preferences, etc., among his captive Allegheny woodrats. When upset, woodrats may chatter their teeth or stomp their hind feet (Wiley 1980).

Near the nests are found piles of sticks and trash called middens. Part of the materials found in woodrat houses and middens appears to be cached food in the form of nuts, seeds, berries, cuttings of vegetation, and mushrooms. But there may also be miscellaneous bits of trash, including rags, bits of metal, bones, pieces of glass, paper, etc. Newcombe (1930) and Poole (1940) compiled lists of such materials. The function of this compulsive collecting is unknown.

Though solitary and territorial, woodrats most often occur in clusters due to patchiness of the rock outcrop, talus, and cave habitat, and conform to the concept of a metapopulation (Hassinger et al. 1996). Home ranges are small, 0.26-0.6 ha (Wright and Hall 1996); usually less than about 90 m across (Burt and Grossenheider 1976). Poole (1940) reported movements of 183 m and 92 m by two woodrats in Pennsylvania. Foraging movements, while often focused within rock habitat, may extend beyond the protection of rocks up to 160 m from the den site (Wright and Hall 1996). Den shifts tend be less than 100 m with a median of 40 m (Wright 1998), and woodrats, particularly females, often live their entire lives in the same outcrop (Feller, pers. obs., 1998). There are reports of large unidirectional movements of displaced woodrats, e.g., 1 km and 4 km (McGowan 1993), as well as naturally dispersing individuals, 0.3-1 km (McGowan 1993), 1 km (Feller, pers. obs., 1995), and up to 6 km (Wright pers. comm., 1998). While woodrats can travel long distances between patches, as distances increase, the chance of successful emigration between patches is likely to decrease, particularly in the absence of protective rock crevices. Barriers to dispersal are not clearly known, as woodrats have been documented to traverse seemingly inhospitable terrain, including roads, small streams, and small fields, though movements are largely within rock habitat (Feller, pers. obs.; Mengak pers. comm., 1998; Wright pers. comm., 1998). However, woodrats display unwary behaviour when crossing roads (Feller, pers. obs.), and road kills have been documented (Feller pers. obs.,1993; McGowan 1993).

Predators include owls, skunks, weasels, foxes, raccoons, bobcats and large snakes. Humans have been killing woodrats for thousands of years - first for food, and much later out of prejudice, because of a resemblance to European rats.

White-footed mice compete with woodrats for food (Rainey 1956), and in Indiana, opossums, raccoons and turkey vultures may compete for den sites (Cudmore 1983). Woodrats support many ecto- and endoparasites, including fleas, ticks, mites, chiggers, botflies, nematodes, and tapeworms (Cudmore 1985). Bubonic plague (Schwartz and Schwartz 1959) and rabies (Dowda et al. 1981) have been reported in wild woodrats. Woodrats are primarily vegetarian, and food preferences vary widely among individuals. Leaves, twigs, fruits, and seeds of many plants are eaten. They are primarily nocturnal.

Possibly widespread deforestation and habitat fragmentation contributed to the initial decline of the species, isolating populations and eliminating dispersal and travel corridors (Sciascia pers. comm., 1994). Deforestation and associated reduction/elimination of food resources currently may be a threat to some local woodrat populations. Causes of the continuing decline are not yet fully understood, but some hypotheses have been offered. Probably the explanation lies in a combination of these and other factors that may differ locally in importance (Linzey 1990).

Parasitism by the raccoon roundworm (Baylisascaris procyonis) has been identified as a significant cause of mortality and a probable major factor in the decline in several states (McGowan 1993; Hicks pers. comm., 1994; Johnson et al. 1997; LoGiudice 2000, 2006; Smyser et al. 2012b). Although rarely fatal to raccoons, infestation may cause cerebrospinal nematodiasis in other species and has caused declines in some populations (Kazacos 1983). New York released and monitored woodrats in formerly occupied areas and all the animals died (50 total, including the released adults and their progeny); 11 of the 13 recovered carcasses were infected by the roundworms (McGowan 1993; Hicks pers. comm., 1994). Stone observed that woodrat decline in New York coincided with a marked increase in raccoon numbers (Linzey 1990). Hayes (unpublished research proposal) suggested that woodrats may be especially vulnerable for two reasons: 1) among other novel items, woodrats are known to carry back to their nests the faeces of other animals, which might include raccoon scats contaminated with B. procyonis eggs, and 2) a "relatively long generation time increases the probability that individuals will become infested prior to reproduction." Both of these reasons recently have been documented (McGowan pers. comm., 1994). Additionally, McGowan (pers. comm., 1994) found that woodrats may colonize areas where an infected woodrat has recently died, thus perhaps maintaining spread of the parasite.

Hall (1988) noticed a correlation between the spread of the gypsy moth (Lymantria dispar) and loss of woodrats in Pennsylvania. "There is a possibility that acorns make up a significant part of the food supply of the species in Pennsylvania. Acorns may be important as a winter food source since they can be stored for long periods of time. Studies conducted by the Pennsylvania Game Commission show that acorn production drops to zero for several years following defoliation. Gypsy moth infestation has resulted in considerable mortality of oaks, especially along the poorer soils of rocky ridge tops. These are the areas where many rocky sites are found, which are ideal woodrat habitats." In support of his argument, Hall noted that at three other sites where woodrats survived, other winter food sources were available.

In a similar theory, McGowan (pers. comm., 1994) speculated that the 1930-1940s permanent loss of the American chestnut (Castanea dentata) may be a factor. This chestnut was extremely hardy and a bountiful producer of mast, and its previous distribution essentially mirrors the historic distribution of the woodrat. Loss of this stable and predictable food source may have led to the continuing woodrat population decline (LoGiudice 2006; Smyser et al. 2012b).

Nawrot and Klimstra (1976) argued that the disappearance of a similar species, N. floridiana illinoensis, was likely due to two unusually severe winters. "Despite a tolerance of Neotoma to many environmental conditions, severe winter weather appears to be a major factor in sudden woodrat population declines. Fitch and Rainy (1956) recorded a drastic decline in Neotoma floridianaabundance in Kansas after two winters of below-average temperatures and prolonged snow and ice cover. Significantly, this decimated population was unable to make substantial gains and continued to decline gradually for several years." Weather also has been proposed as a factor in Neotoma magister decline, a view that is supported by the fact that the decline has been in the northern part of the range. Records in Pennsylvania and West Virginia over the past thirty years indicate "below normal" temperatures in critical months accompanying the observed shrinkage in range (Linzey pers. comm., 1994).

In some areas, including caves popular with spelunkers, human disturbance has been implicated in the disappearance of woodrat populations (e.g., Kirkland 1986). These woodrats do seem to avoid areas of human habitation or heavy human use, but many sites where they have disappeared are remote and rarely visited by people.

Habitat is generally inaccessible and undesirable for development, but strip mining of coal and limestone is a potential threat in many areas. Monty and Feldhamer (2002) stated that increased predation by great horned owls has been proposed as a threat, but owl predation seems highly unlikely as a reason for the decline. Populations often are small and isolated, hence highly susceptible to extirpation (Mengak pers. comm., 1994). disruption of genetic connectivity within metapopulations may also be a factor (LoGiudice 2006; Smyser et al. 2012b).

Management guidelines resulting in the protection of Allegheny woodrat habitats are needed throughout the range. In particular, attention needs to be given to maintaining dispersal corridors among isolated populations. Continuing research on causes of the decline is also needed.

Examples of protected occurrences include those in the Great Smoky Mountains National Park, Falls Ridge (a TNC preserve in Virginia), and the Deam Nature Preserve in Indiana. Many populations receive fairly good de facto protection in numerous areas with inaccessible cliffs and caves. Many additional occurrences are in state game areas and national forests and parks; these may afford some protection.

Range-wide surveys are needed to better determine status and trends. Areas with woodrats should be protected from excessive human traffic. Mining and logging operations should not be permitted in areas with woodrat populations.