Clethrionomys Gapperi Research Articles

Small-Mammal Consumption of Hypogeous Fungi in the Central Adirondacks of New York

Abstract Small mammals are generally known to consume and disperse subterranean (hypogeous) fungi, but accounts for this behavior are lacking for the northeastern US. We report on the use of these fungi by a sample of small mammals from the central Adirondack Mountains of New York. We analyzed 57 fecal samples from Peromyscus maniculatus (Deer Mouse), Myodes gapperi (Southern Red-backed Vole), Tamias striatus (Eastern Chipmunk), and Blarina brevicauda (Short-tailed Shrew) to determine whether they were consuming fungi in the central Adirondack Mountains. We found that fecal samples from Eastern Chipmunk (n = 12), Southern Red-backed Vole (n = 14), Short-tailed Shrew (n = 14), and Deer Mouse (n = 17) contained Glomus spp. (arbuscular mycorrhizal fungi) spores (33.3%, 35.7%, 21.4%, and 17.6% of samples, respectively) and Russulaceae spores (66.6%, 35.7%, 7.14% and 5.9% of samples, respectively). One sample from an Eastern Chipmunk also contained Gautieria spores.

Woodland mouse and vole response to increased structural diversity following midrotation commercial thinning in spruce plantations

We assessed whether commercially thinning (CT) spruce (Picea spp.) plantations (40% basal area removal) can cause structural changes in fine woody debris (FWD) and understory vegetation to improve habitat quality for small rodents in northwestern New Brunswick, Canada. We created three contrasting environments (FWD rich – understory vegetation rich, FWD poor – understory vegetation rich, and FWD poor – understory vegetation poor) by establishing CT with debris retention (merchantable trunk removal), CT with all debris removed (full tree removal), and non-CT (plantation without CT) in six midrotation white spruce (Picea glauca (Moench) Voss) plantations. We live-trapped small mammals in each plantation during spring and summer of 2011 and 2012 and estimated animal density and survival with capture–recapture models. Southern red-backed vole (Myodes gapperi (Vigors, 1830)) density was two to three times greater in CT with debris retention than in either non-CT or CT with debris removal, and their survival rate was twice that in CT with debris removal. Woodland jumping mouse (Napaeozapus insignis (Miller, 1891)) density was two to five times greater in non-CT than in either CT treatment. Deer mice (Peromyscus maniculatus (Wagner, 1845)) did not show any treatment effect. Productivity and demographics were not affected by CT treatment for any species. We found evidence that midrotation spruce plantations are used differently by small mammal species based on stand condition and recommend that managers maintain plantations in CT and non-CT states.

Effects of Vegetation, Landscape Composition, and Edge Habitat on Small-Mammal Communities in Northern Massachusetts

In southern New England forests, small mammals provide essential contributions to ecosystem functioning via food-web interactions and seed dispersal. This region has been exposed to extensive habitat fragmentation due to residential and agricultural development, resulting in a considerable amount of edge habitat, in addition to naturally occurring landscape heterogeneity. Limited research has been conducted relating small-mammal species richness and abundance to different types of edge habitat in this region. Studies incorporating an analysis of variation in both fine-scale vegetation and coarse-scale landscape variation are even more limited. We compared small-mammal richness, total abundance, and abundance of Peromyscus maniculatus (Deer Mouse), Peromyscus leucopus (White-footed Mouse), Myodes gapperi (Red-backed Vole), Tamias striatus (Eastern Chipmunk), and Tamiasciurus hudsonicus (Eastern Red Squirrel) at developed-edge, wetland-edge, and forest-interior sites. We also measured vegetation and landscape variables to understand how variation in characteristics at different scales affected small-mammal measures. We selected 4 sites of each edge type and used Sherman live-traps during the summers of 2009–2010 to survey small-mammal populations (75 traps for 4 nights at 12 sites for 2 y = 7200 trap-nights). We did not find differences among edge types and interior forest for total abundance, richness, and abundance of the 5 small-mammal species with sufficient data for analysis. However, vegetation variables and landscape variables were significantly associated with small-mammal populations. Step-wise linear regression included vegetation variables for 4 of the 5 species, and various landscape scales were included in all analyses except abundance of Peromyscus adults. Patch size was included in 4 analyses (positive for total abundance, White-footed Mouse, and Red-backed Vole; negative for Eastern Chipmunk). We found conifer basal area to have a positive relationship with abundance of Peromyscus adults and Red-backed Voles, but a negative relationship with abundance of Peromyscus juveniles and Eastern Red Squirrels. Species abundance and richness of small-mammal communities and populations in northeastern Massachusetts were related to both fine-scale vegetation differences and coarse-scale landscape metrics, but these relationships were complex and scale-dependent.

General versus specific surveys: Estimating the suitability of different road-crossing structures for small mammals

The use of wildlife road-crossing structures (WCS hereafter) is less monitored for small mammals than for more emblematic species. Furthermore, because of the undeniable difficulty of small-mammal track identification, most biologists usually carry out general surveys without species recognition. We hypothesized that general surveys traditionally used for monitoring WRC by small mammals may be biased because the degraded habitats along roads are mainly used by generalist and not specialist species. For this reason, we compared the results of a general small-mammal survey with those from a species-specific one, focusing on 3 study species: 1 habitat generalist (North American deer mouse [Peromyscus maniculatus]), 1 forest specialist (southern red-backed vole [Myodes gapperi]), and 1 prairie specialist (meadow vole [Microtus pennsylvanicus]). We sampled along 4 types of WCS (overpasses, open-span underpasses, and both elliptical and box culverts) in Banff National Park (Canada), by placing footprint track tubes along the WCS, and as a reference in front of their entrances (mainly located in roadside grasslands) and in the surrounding woodlands. Using the traditional general survey, we did not detect significant differences in small-mammal presence among WCS and reference sites. In contrast, species-specific surveys showed that only the deer mouse (a generalist species) consistently used the WCS. The deer mice did not show preferences for any WCS type, whereas the specialist species (voles) used only overpasses. Therefore, general surveys used without species identification can underestimate the value of WCS for specialist small mammals, with relevant conservation implications. As a consequence, we recommend species-specific surveys of WCS suitability for small mammals. We also suggest improving the habitat (or at least the cover availability) in the WCS and along the space between them and the surrounding environments to increase WCS suitability for specialist species. © 2015 The Wildlife Society.

Cyclic dynamics of a boreal southern red-backed vole population in northwestern Quebec

In Fennoscandia, red-backed vole populations (Myodes spp.) often show regular fluctuations of abundance of 3- to 5-year periods. In contrast, only a few populations show evidence of cyclic fluctuations in North America. From 2001 to 2009, we livetrapped southern red-backed voles (Myodes gapperi) in 3 mature jack pine and 3 mature black spruce forest stands in the Muskuchii hills region, Quebec, Canada. We found that their density fluctuated (up to 41-fold) with a cyclical pattern and 4-year periods. Our study is the first to demonstrate cyclic dynamics in a southern red-backed vole population found in the boreal forest of North America. Regular pulse of food or heavy predation may be responsible for the fluctuations of southern red-backed voles. Furthermore, vole cycles may help elucidate the factors driving the irruptions of owls in the boreal forest.

Feeding ecology informs parasite epidemiology: prey selection modulates encounter rate with Echinococcus multilocularis in urban coyotes.

We investigated the role of urban coyote feeding ecology in the transmission of Echinococcus multilocularis, the causative agent of Alveolar Echinococcosis in humans. As coyotes can play a main role in the maintenance of this zoonotic parasite within North American urban settings, such study can ultimately aid disease risk management. Between June 2012 and June 2013, we collected 251 coyote feces and conducted trapping of small mammals (n = 971) in five parks in the city of Calgary, Alberta, Canada. We investigated E. multilocularis epidemiology by assessing seasonal variations of coyote diet and the selective consumption of different rodent intermediate host species. Furthermore, accounting for small mammal digestibility and coyote defecation rates we estimated the number of small mammal preys ingested by coyote and consequently, coyote encounter rates with the parasite. Dominant food items included small mammals, fruit and vegetation, although hare and deer were seasonally relevant. The lowest frequency of occurrence per scat of small mammals was recorded in winter (39.4 %), when consumption of deer was highest (36.4 %). However, highest encounter rates (number of infected hosts predated/season) with E. multilocularis (95% CI: 1.0 - 22.4), combined with the lack of predation on non-competent small mammal species, suggest that winter is the critical season for transmission and control of this parasite. Within the small mammal assemblage, voles (Microtus pennsylvanicus and Myodes gapperi) were the selected preys of urban coyotes and likely played a key role for the maintenance of the urban sylvatic life-cycle of E. multilocularis in Calgary.

Small Mammal Movements and Fire History: Testing the Long-Term Effects of the 1988 Huckleberry Mountain Fire

Fires are an important ecological force shaping biological communities in western North America. Fires change landscapes in ways which influence the relative abundance and activities of the organisms occurring in those habitats. Preliminary results from previous work suggest the stage of fire succession may influence individual movements on the landscape. As part of a long-term study of the 1988 Yellowstone fires along the John D. Rockefeller, Jr. Memorial Parkway, we set out to examine these patterns in more detail to (1) test whether the two dominant small mammal species were moving different distances based upon the stage of succession in a particular habitat, and (2) determine the role of habitat complexity, resource types, and species abundance in driving these patterns. Using movement distances from capture-recapture data and fluorescent powder tracking of individuals we compared movement distances and habitat usage between mid-succession and late-succession trapping grids for red-backed voles (Myodes gapperi) and deer mice (Peromyscus maniculatus). The results suggest deer mice, some of the first colonizers to burned habitat, are moving farther than red-backed voles, and move farther in burned habitats than in unburned habitats. Red-backed voles exhibit slightly, but not significantly, longer movements in burned habitats. Powder tracking results suggest habitat complexity, in particular the quantity of coarse woody debris, may partially explain the differences in movement patterns by burn history. These results are important for understanding the long-lasting impacts of fire history on population and community patterns.

Determinants of survival over 7 years for a natural cohort of sugar maple seedlings in a northern hardwood forest

The regeneration ecology of sugar maple (Acer saccharum Marsh.) has been impacted by acid rain leaching of base cations from the soils throughout much of its range. We tracked the survival and causes of death for a natural cohort of sugar maple seedlings across 22 sites in the Hubbard Brook Valley in New Hampshire, USA, where soil acidification has been documented. Survival over 7 years averaged 3.4%; however, significant differences in survival were observed among sites, which were classified into three main groups based on the shape of their survival curves. These site groups differed in position on the landscape, seedling nutrition and leaf size, and the prevalence of damage agents, but not in soil Ca. First-season mortality was high (71%), and the main damage agents were fungal infection (Rhizoctonia spp.) and caterpillar herbivory (Geometridae). Other principal causes of mortality in order of importance were winter injury, mechanical damage, and rodent (Myodes gapperi Vigors, 1830) tunneling, and all damage agents varied significantly in severity between years. This study highlights the importance of landscape-level variation in biotic factors for predicting sugar maple regeneration success. Predictions of sugar maple regeneration will require a better understanding of controls on initial seedling growth and the suite of biotic agents that damages seedlings.

Impact of non-native terrestrial mammals on the structure of the terrestrial mammal food web of Newfoundland, Canada.

The island of Newfoundland is unique because it has as many non-native terrestrial mammals as native ones. The impacts of non-native species on native flora and fauna can be profound and invasive species have been identified as one of the primary drivers of species extinction. Few studies, however, have investigated the effects of a non-native species assemblage on community and ecosystem properties. We reviewed the literature to build the first terrestrial mammal food web for the island of Newfoundland and then used network analyses to investigate how the timing of introductions and trophic position of non-native species has affected the structure of the terrestrial mammal food web in Newfoundland. The first non-native mammals (house mouse and brown rat) became established in Newfoundland with human settlement in the late 15th and early 16th centuries. Coyotes and southern red-backed voles are the most recent mammals to establish themselves on the island in 1985 and 1998, respectively. The fraction of intermediate species increased with the addition of non-native mammals over time whereas the fraction of basal and top species declined over time. This increase in intermediate species mediated by non-native species arrivals led to an overall increase in the terrestrial mammal food web connectance and generality (i.e. mean number of prey per predator). This diverse prey base and sources of carrion may have facilitated the natural establishment of coyotes on the island. Also, there is some evidence that the introduction of non-native prey species such as the southern red-backed vole has contributed to the recovery of the threatened American marten. Long-term monitoring of the food web is required to understand and predict the impacts of the diverse novel interactions that are developing in the terrestrial mammal food web of Newfoundland.

A Regional Study of Diversity and Abundance of Small Mammals in Ohio

The goal of this study was to obtain information on diversity, abundance, and distribution of non-volant small mammals in 4 major habitat types in each of 5 regions of Ohio. We trapped in 31 study areas, representing 39 counties, for 3 consecutive nights for a total of 38,400 trap nights. We established eight 100-m transects (each with 10 live traps, 20 snap traps, and 20 pitfall traps) per study area in woodland, oldfield, grassland-pasture, or restored prairie-wetland habitats. We captured fourteen species of small mammals (shrews and rodents <100 g in body mass), but 97% of the 2150 captured consisted of just 4 species: Microtus pennsylvanicus (Meadow Vole; 31%), Peromyscus leucopus (White-footed Mouse; 29%), Blarina brevicauda (Short-tailed Shrew; 21%), and Sorex cinereus (Masked Shrew; 16%). Regional differences in abundance of small mammals (captures/100 trap nights) and species diversity (H') were not significant (P > 0.05). Seven species of interest were captured in low numbers (<10) and 2 others, Reithrodontomys humulis (Eastern Harvest Mouse) and Myodes gapperi (Red-backed Vole), were not captured in the course of the 2-year study.

Spatial heterogeneity and temporal variations in Echinococcus multilocularis infections in wild hosts in a North American urban setting

Echinococcus multilocularis, the causative agent of human alveolar echinococcosis, has the potential to circulate in urban areas where wild host populations and humans coexist. The spatial and temporal distribution of infection in wild hosts locally affects the risk of transmission to humans. We investigated the spatial and temporal patterns of E. multilocularis infection in coyotes and rodent intermediate hosts within the city of Calgary, Canada, and the association between spatial variations in coyote infection and the relative composition of small mammal assemblages. Infection by E. multilocularis was examined in small mammals and coyote faeces collected monthly in five city parks from June 2012 to June 2013. Coyote faeces were analysed using a ZnCl2 centrifugation and sedimentation protocol. Infection in intermediate hosts was assessed through lethal trapping and post-mortem analysis. Parasite eggs and metacestodes were morphologically identified and molecularly confirmed through species-specific PCR assays. Of 982 small mammals captured, infection was detected in 2/305 (0.66%) deer mice (Peromyscus maniculatus), 2/267 (0.75%) meadow voles (Microtus pennsylvanicus), and 1/71 (1.41%) southern red backed voles (Myodes gapperi). Overall faecal prevalence in coyotes was 21.42% (n=385) and varied across sites, ranging from 5.34% to 61.48%. Differences in coyote faecal prevalence across sites were consistent with local variations in the relative abundance of intermediate hosts within the small mammal assemblages. Infections peaked in intermediate hosts during autumn (0.68%) and winter (3.33%), and in coyotes during spring (43.47%). Peaks of infections in coyote faeces up to 83.8% in autumn were detected in a hyper-endemic area. To the best of our knowledge, our findings represent the first evidence of a sylvatic life-cycle of E. multilocularis in a North American urban setting, and provide new insights into the complexity of the parasite transmission ecology.

The influence of environmental factors on the morphology of red-backed volesMyodes gapperi(Rodentia, Arvicolinae) in Québec and western Labrador

Geographical patterns of morphological variation in small mammals are often associated with environmental factors. The southern red-backed vole Myodes gapperi is a widespread and abundant small mammal in Canada, occurring in environments as diverse as mixed-wood forests and taiga. First upper molars and skulls from nine populations of southern red-backed voles distributed across three ecozones and approximately 10° of latitude were analysed by means of geometric morphometric techniques, and their relationships with environmental variables were examined. A weak, non-linear trend of size increase towards higher latitudes was observed in voles' skulls. Environmental variables appeared to be important drivers of shape differentiation among populations from the three distinct ecozones analysed. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 112, 204–218.

Voles, trees, and woody debris structures as habitat: Balancing forest crop protection and biodiversity

Relatively homogeneous early successional habitats develop after clearcutting and wildfire that voles of the genera Microtus and Myodes may colonize and generate population fluctuations. In these habitats, vole populations may reach pest status by their feeding on newly planted tree seedlings. Strategic management of excess woody debris into piles and windrows helps diversify new clearcuts by enhancing populations of forest-floor small mammals, including voles, and some of their predators.This study tested the hypotheses (H) that (H1) abundance of voles and incidence of feeding damage to tree seedlings will be higher in windrow than dispersed (conventional) sites of woody debris, and (H2) there will be a gradient of damage with the highest incidence immediately adjacent to windrows. A third hypothesis (H3) predicts that feeding damage to trees will increase in relation to windrow size. Microtus voles and red-backed voles (Myodes gapperi) were live-trapped for three years (2010–2012) in replicated sites with woody debris dispersed and in windrows at three study areas in the southern interior of British Columbia, Canada. Incidence of feeding damage and mortality to tree seedlings by voles was measured in all sites. Mean abundance of M. gapperi, Microtus, and total voles were all significantly (P ≤ 0.04) higher (up to 3.4 times) in windrow than dispersed sites, and hence the abundance part of H1 was supported. Mean annual percentage of trees damaged by voles was significantly (P ≤ 0.03) higher in windrow than dispersed sites over the two winters and for cumulative incidence of damage, and hence the tree damage part of H1 was supported. Mortality of trees followed this pattern but was not formally significant. Trees planted immediately adjacent to a windrow had significantly (P < 0.01) greater feeding damage than seedlings planted further away, and hence H2 was supported. There were significant linear relationships between mean percentage of trees killed (r = 0.67; P < 0.01) and mean number of total voles, and also with mean volume of woody debris per meter length of windrow (r = 0.98; P < 0.01). Thus, H3 was also supported. To minimize overall mortality of trees, it is likely worthwhile to not plant trees near windrows. Slightly reduced stocking (<5% net forest area) and potential loss of some trees to voles need to be balanced alongside biodiversity and conservation considerations provided by woody debris structures.

Responses of red-backed voles (Myodes gapperi) to windrows of woody debris along forest–clearcut edges

Context Southern red-backed voles (Myodes gapperi) disappear from clearcuts within the first year or two after harvest, at least in studies in coniferous and mixed forests of western North America. Post-harvest woody debris arranged in large piles and windrows supports populations of M. gapperi on clearcuts and may extend their persistence there. Aims To test the hypotheses (H) that for M. gapperi, (H1) population parameters of abundance, reproduction, and survival would be higher in windrow–forest than isolated windrow sites, and higher or similar to those in interior old forest sites; (H2) connectivity provided by windrow-forest structures will mitigate potential negative effects of clearcuts and abundance of M. gapperi will remain similar at the abrupt edge between forest and new clearcuts; and (H3) connectivity provided by windrow–forest structures will allow increased movements between both habitats. Methods Study areas were located in three forest ecological zones in southern British Columbia, Canada. Populations of M. gapperi were sampled from 2010 to 2012 in three types of habitats on new clearcuts: isolated windrows of woody debris, windrows attached to uncut old forest, and in uncut old forest. Key results Higher mean values of abundance and number of juvenile recruits of M. gapperi in the isolated windrow and windrow–forest sites than forest sites was contrary to our prediction for H1. In support of H2, we could not detect any differences in the mean number of captures among forest, edge and windrow sections of the windrow–forest sites, nor in the mean range length among the three habitat types. For H3, connectivity provided by windrow–forest structures may mitigate potential negative effects on abundance for M. gapperi at the abrupt edge between forest and new clearcuts. Conclusions and Implications Voles did not commonly move between the forest and windrow habitats, but did move readily within forest and within windrows. Substantial movement by M. gapperi within windrows suggested that this microtine will move along windrows and potentially use these paths of connectivity to cross clearcuts. If the prey base is present, windrow connectivity may enhance these open areas for small mustelids and other carnivores and help maintain abundance and diversity of some forest mammals on clearcuts.

Succession Effects on Mammal and Inverterbrate Communities 26 Years After the 1988 huckleberry Mountain Fire

Fires are an important and increasingly common driver of habitat structure in the intermountain West. Through an ongoing study of burned and adjacent unburned areas along the John D. Rockefeller, Jr. Memorial Parkway, we examine the long-term effects of the 1988 fire season on community assembly, succession, and ecological processes. We collected mark/recapture data on rodents, removal data for insectivorous mammals and invertebrates, and habitat measurements on four grids in 2014 and combined these results with previous survey data. In 2014, 4,800 trap nights yielded 13 species of small mammals, comprising 618 individuals. Macroarthropod abundance was higher on burned grids, but diversity was higher on unburned grids. In contrast, springtail (Collembola) diversity was higher on burned grids, but abundance was highest in unburned grids. Since the beginning of this long-term study, the total number of mammal species has increased across all sites, and relative abundance in burned areas has shifted from early successional species (Peromyscus maniculatus) to those more associated with old growth forests (such as Myodes gapperi). Other than in 1991, the burned grids have harbored more diverse small mammal communities than the unburned control grids. Significant, long-term differences in vegetation based upon burn history were observed, including different ground cover, less canopy cover, and more coarse woody debris in burned sites. This work provides a unique long-term picture of the interrelationships of small mammal and invertebrate communities and correlated habitat variables as these ecosystems undergo post-fire succession.

Safety from predators or competitors? Interference competition leads to apparent predation risk

Prey often react to predation risk by foraging preferentially in the safety of cover rather than in more risky open patches. Yet this pattern of patch use also can be caused by dominant interspecific competitors. We develop a simple theory of this form of apparent predation risk that describes the patch use of an optimal forager confronted with dominant individuals. The theory predicts that subordinate animals should increase their use of safe foraging patches as the density of nearby dominants increases. We tested the theory with meadow voles (Microtus pennsylvanicus) and southern red-backed voles (Myodes gapperi). We used dyadic encounters to confirm that meadow voles are dominant over red-backed voles. We then evaluated their respective foraging patterns in pairs of covered and open patches in 4 adjacent subgrids in an old-field enclosure. Subordinate redbacked voles foraged indifferently between covered and open patches when few meadow voles were present. Red-backed voles increased their use of both patches as the number of nearby meadow voles increased. Givingup densities were lowest, and harvesting efficiency highest, in covered patches when the number of nearby meadow voles was high. These results document competition between the 2 species and suggest that vigilance toward dominant meadow voles magnifies the risk experienced by red-backed voles in open patches. Investigators assessing foraging behavior between ‘‘safe’’ and ‘‘risky’’ patches might misinterpret the competitive effect as predation risk unless they 1st account for competition among foraging individuals.

Ticks (Acari: Ixodidae) on small mammals in Kootenay National Park, British Columbia, Canada.

Two hundred and ninety-one ticks (i.e., 185 larvae, 72 nymphs, and 34 adults) were removed from 153 small mammals comprising six species collected in Verdant Forest, Numa Forest, and Marble Canyon within Kootenay National Park, British Columbia, Canada. Morphological examination and molecular analyses (i.e., polymerase chain reaction-single-strand conformation polymorphism [PCR-SSCP] and DNA sequencing of the mitochondrial 16S rRNA gene) of the ticks revealed that most individuals were Ixodes angustus Neumann. All life cycle stages of I. angustus were found primarily on southern red-backed voles, Clethrionomys gapperi (Vigors). Two Dermacentor andersoni Stiles females were also found on these small mammals. The results of the molecular analyses also revealed that there were three 16S haplotypes of I. angustus and two 16S haplotypes of D. andersoni. A comparison of available sequence data suggests genetic divergence between I. angustus near the western and eastern limits of the species distributional range in North America. Additional studies are needed to determine whether there are genetic differences between I. angustus from North America, Japan, and Russia, and whether there is geographical variation in the ability of ticks to transmit pathogens to their mammalian hosts.

Red-Backed Vole Brain Promotes Highly Efficient In Vitro Amplification of Abnormal Prion Protein from Macaque and Human Brains Infected with Variant Creutzfeldt-Jakob Disease Agent

Rapid antemortem tests to detect individuals with transmissible spongiform encephalopathies (TSE) would contribute to public health. We investigated a technique known as protein misfolding cyclic amplification (PMCA) to amplify abnormal prion protein (PrPTSE) from highly diluted variant Creutzfeldt-Jakob disease (vCJD)-infected human and macaque brain homogenates, seeking to improve the rapid detection of PrPTSE in tissues and blood. Macaque vCJD PrPTSE did not amplify using normal macaque brain homogenate as substrate (intraspecies PMCA). Next, we tested interspecies PMCA with normal brain homogenate of the southern red-backed vole (RBV), a close relative of the bank vole, seeded with macaque vCJD PrPTSE. The RBV has a natural polymorphism at residue 170 of the PrP-encoding gene (N/N, S/S, and S/N). We investigated the effect of this polymorphism on amplification of human and macaque vCJD PrPTSE. Meadow vole brain (170N/N PrP genotype) was also included in the panel of substrates tested. Both humans and macaques have the same 170S/S PrP genotype. Macaque PrPTSE was best amplified with RBV 170S/S brain, although 170N/N and 170S/N were also competent substrates, while meadow vole brain was a poor substrate. In contrast, human PrPTSE demonstrated a striking narrow selectivity for PMCA substrate and was successfully amplified only with RBV 170S/S brain. These observations suggest that macaque PrPTSE was more permissive than human PrPTSE in selecting the competent RBV substrate. RBV 170S/S brain was used to assess the sensitivity of PMCA with PrPTSE from brains of humans and macaques with vCJD. PrPTSE signals were reproducibly detected by Western blot in dilutions through 10-12 of vCJD-infected 10% brain homogenates. This is the first report showing PrPTSE from vCJD-infected human and macaque brains efficiently amplified with RBV brain as the substrate. Based on our estimates, PMCA showed a sensitivity that might be sufficient to detect PrPTSE in vCJD-infected human and macaque blood.

Site occupancy and spatial co-occurrence of boreal small mammals are favoured by late-decay woody debris

Dwindling stocks of decaying coarse woody debris (CWD), as a result of forest management and growing interest for biofuels, may jeopardize the persistence of a broad spectrum of organisms such as small mammals. In this study, we quantified the effects of CWD in late-decay stages on the occupancy dynamics of small mammals in managed and unmanaged boreal forests. Probabilities of initial site occupancy, colonization, local extinction, and co-occurrence were modelled for five boreal small mammal species. Southern red-backed voles (Myodes gapperi Vigor) and southern bog lemmings (Synaptomys cooperi Baird) were more likely to occupy sites with high volumes of late-decay CWD early in the summer. The probability of local extinction for deer mice (Peromyscus maniculatus Wagner) slightly decreased with an increasing volume of late-decay CWD in harvested sites. Southern red-backed voles and meadow voles (Microtus pennsylvanicus Ord) co-occurred more often in old, uncut forests, as well as harvested sites with high volumes of late-decay CWD. These results suggest that cover provided by late-decay CWD benefited two small rodent species during early reproduction and increased persistence of deer mice later in the summer. Finally, we found that in addition to high live-tree basal areas, high late-decay CWD volume also favours local diversity of small mammals.

Bayesian models describing microhabitat associations of infrequently captured small mammals sampled under a complex hierarchical design

Knowledge about the relationship between habitat structure and abundance of a target species facilitates biodiversity conservation in managed forests. However, modeling the relationship for infrequent small mammal species in silvicultural experiments introduces the challenge of excessive zero counts and complex hierarchical sampling. A common solution has been to ignore infrequent species. The goal of this study was to model microhabitat associations of infrequently captured forest floor small mammal species with Bayesian models that accounted for subsampling and the blocking design of a large-scale variable-retention harvest experiment. Poisson, negative binomial and overdispersed Poisson Generalized Linear Mixed Models (GLMMs) were fitted to data for three small mammal species with different rates of capture. Shrew–mole (Neurotrichus gibbsii) and Keen’s deer mouse (Peromyscus keeni) were the two infrequent species and southern red-backed vole (Myodes gapperi) was the frequent species selected for modeling. Capture rate was predicted from variables representing vegetation structure, and results were compared to corresponding Generalized Linear Models (GLMs). GLMMs predicted stronger and sometimes contrary effects of vegetation structure with wider confidence intervals compared to GLMs. The overdispersed Poisson GLMM provided the most consistent and adequate fit to infrequent species. Capture rate of the shrew–mole was found to be negatively associated with tall shrub cover and coarse woody debris volume. Similarly, capture rate of Keen’s deer mouse was negatively associated with herb cover and coarse woody debris volume. Finally, captures of southern red-backed vole was associated negatively with herb cover and coarse woody debris volume but positively associated with vertical complexity of overstory vegetation. With correct GLMM specification, statistical inferences of habitat predictors were more reliable as autocorrelation between samples was properly accounted for and valid standard errors were estimated. Furthermore, the GLMMs in this study fitted capture rates of infrequent species well and produced admissible results on the association of these species to microhabitat features. Infrequent species need not be excluded from analysis; in fact, inclusion of these species is crucial to conservation of species diversity by designing silvicultural treatments that produce or protect suitable habitat.