Using Genetics to Assess Differentiation Among Raccoons in an Area with Variable Rabies Status in Alabama

The western spread of raccoon rabies in Alabama has been slow and even appears to regress eastward periodically. While the disease has been present in the state for over 30 years, areas in northwest Alabama are devoid of raccoon rabies. This variation resulting in an enzootic area of raccoon rabies primarily in southeastern Alabama may be due to landscape features that hinder the movement of raccoons (i.e., gene flow) among different locations. We used 11 raccoon-specific microsatellite markers to obtain individual genotypes to examine gene flow among areas that were rabies free, enzootic with rabies, or had only sporadic reports of the disease. Samples from 70 individuals were collected from 5 sampling localities in 3 counties. The landscape feature data were collected from geographic information system (GIS) data. We inferred gene flow by estimating FST and by using Bayesian tests to identify genetic clusters. Estimates of pairwise FST indicated genetic differentiation and restricted gene flow between some sites, and an uneven distribution of genetic clusters was observed. Of the landscape features examined (i.e., land cover, elevation, slope, roads, and hydrology), only land cover had an association with genetic differentiation, suggesting this landscape variable may affect gene flow among raccoon populations and thus the spread of raccoon variant of rabies in Alabama

Landscape Genetics of Raccoons (\u3ci\u3eProcyon lotor\u3c/i\u3e) Associated with Ridges and Valleys of Pennsylvania: Implications for Oral Rabies Vaccination Programs

Raccoons are the reservoir for the raccoon rabies virus variant in the United States. To combat this threat, oral rabies vaccination (ORV) programs are conducted in many eastern states. To aid in these efforts, the genetic structure of raccoons (Procyon lotor) was assessed in southwestern Pennsylvania to determine if select geographic features (i.e., ridges and valleys) serve as corridors or hindrances to raccoon gene flow (e.g., movement) and, therefore, rabies virus trafficking in this physiographic region. Raccoon DNA samples (n = 185) were collected from one ridge site and two adjacent valleys in southwestern Pennsylvania (Westmoreland, Cambria, Fayette, and Somerset counties). Raccoon genetic structure within and among these study sites was characterized at nine microsatellite loci. Results indicated that there was little population subdivision among any sites sampled. Furthermore, analyses using a model-based clustering approach indicated one essentially panmictic population was present among all the raccoons sampled over a reasonably broad geographic area (e.g., sites up to 36 km apart). However, a signature of isolation by distance was detected, suggesting that widths of ORV zones are critical for success. Combined, these data indicate that geographic features within this landscape influence raccoon gene flow only to a limited extent, suggesting that ridges of this physiographic system will not provide substantial long-term natural barriers to rabies virus trafficking. These results may be of value for future ORV efforts in Pennsylvania and other eastern states with similar landscapes

A Noninvasive Method to Detect Mexican Wolves and Estimate Abundance

Monitoring wolf abundance is important for recovery efforts of Mexican wolves (Canis lupus baileyi) in the Blue Range Wolf Recovery Area in Arizona and New Mexico, USA. Although radiotelemetry has been a reliable method, collaring and tracking wolves in an expanding population will be prohibitively expensive and alternative methods to estimate abundance will become necessary. We applied 10 canid microsatellite loci to 235 Mexican wolf samples, 48 coyote (C. latrans) samples, and 14 domestic dog (C. lupus familiaris) samples to identify alleles that provide reliable separation of these species. We then evaluated an approach for prescreening, noninvasively collected DNA obtained from fecal samples to identify Mexican wolves. We generated complete genotypes for only those samples identified as probable Mexican wolves. We used these genotypes to estimate mark–recapture population estimates of Mexican wolves and compared these to known numbers of wolves in the study area.We collected fecal samples during 3 sampling periods in 2007–2008 and used Huggins-type mark–recapture models to estimate Mexican wolf abundance. We were able to generate abundance estimates with 95% confidence for 2 of 3 sampling periods. We estimated abundance to be 10 (95% Cl = 6–34) during one sampling period when the known abundance was 10 and we estimated abundance to be 9 (95% CI = 6 –30) during the other sampling period when the known abundance was 10. The application of this noninvasive method to estimate Mexican wolf abundance provides an alternative monitoring tool that could be useful for long-term monitoring of this and other recovering populations. Published 2016. This article is a U.S. Government work and is in the public domain in the USA

A Noninvasive Method to Detect Mexican Wolves and Estimate Abundance

Monitoring wolf abundance is important for recovery efforts of Mexican wolves (Canis lupus baileyi) in the Blue Range Wolf Recovery Area in Arizona and New Mexico, USA. Although radiotelemetry has been a reliable method, collaring and tracking wolves in an expanding population will be prohibitively expensive and alternative methods to estimate abundance will become necessary. We applied 10 canid microsatellite loci to 235 Mexican wolf samples, 48 coyote (C. latrans) samples, and 14 domestic dog (C. lupus familiaris) samples to identify alleles that provide reliable separation of these species. We then evaluated an approach for prescreening, noninvasively collected DNA obtained from fecal samples to identify Mexican wolves. We generated complete genotypes for only those samples identified as probable Mexican wolves. We used these genotypes to estimate mark–recapture population estimates of Mexican wolves and compared these to known numbers of wolves in the study area.We collected fecal samples during 3 sampling periods in 2007–2008 and used Huggins-type mark–recapture models to estimate Mexican wolf abundance. We were able to generate abundance estimates with 95% confidence for 2 of 3 sampling periods. We estimated abundance to be 10 (95% Cl = 6–34) during one sampling period when the known abundance was 10 and we estimated abundance to be 9 (95% CI = 6 –30) during the other sampling period when the known abundance was 10. The application of this noninvasive method to estimate Mexican wolf abundance provides an alternative monitoring tool that could be useful for long-term monitoring of this and other recovering populations. Published 2016. This article is a U.S. Government work and is in the public domain in the USA

Estimating Population Size of Mexican Wolves Noninvasively (Arizona)

Monitoring wolf abundance is a significant problem confronting biologists coordinating the recovery of the Mexican wolf (Canis lupus baileyi) population in the Blue Range Wolf Recovery Area (BRWRA) in Arizona and New Mexico (Figure 1). Thus far, radiotelemetry has been a satisfactory method. However, collaring and tracking more wolves in the expanding population is expensive. The development of a cost-effective method to estimate Mexican wolf populations will assist the long-term management and recovery of wolves. We are attempting species and individual identification using DNA extracted from wolf scat because scat is both readily available and easy to collect (Putman 1984). Progress in contemporary molecular genetics has made noninvasive genetic sampling of an animal population possible (Goossens et al. 2000, Prugh et al. 2005). The ability to identify an individual through DNA amplification of a scat sample allows us to treat reoccurrences of a genotype in additional samples as marked recaptures. Mark-recapture models may then be used to estimate population size based on collected genotypes. We are currently developing appropriate laboratory, sampling, and field protocols to collect scat and conduct a genetic mark-recapture study of Mexican wolves in a portion of the BRWRA. We tested our ability to identify individual Mexican wolves in the lab by collecting scat and blood from eight captive wolves at the Sevilleta National Wildlife Refuge in New Mexico. We stored scat samples in 50-ml centrifuge tubes along with silica beads to act as a desiccant (1:4 scat to silica beads by volume), using filter paper barriers to prevent silica dust from embedding itself on the surface of the scat. We extracted DNA from surface scrapings of scat following the protocol for human DNA analysis from stool samples (QIAGEN 2007). We have successfully amplified 10 canid specific microsatellite markers (Ostrander et al. 1993) in the Sevilleta samples. These markers allowed us to obtain individual genotypes for all eight wolves. We are in the process of cross-checking genotypes obtained from scat against those obtained from blood. We have demarcated a compact study area within the BRWRA comprising approximately 2,500 km2 in the Apache Sitgreaves National Forest in Arizona. The Interagency Field Team, which coordinates the recovery project, is using radiotelemetry to monitor wolves in the study area and knows precisely how many wolves exist there. The study area is occupied by four packs (Paradise, Hawk’s Nest, Bluestem, and Rim) whose territories are contiguous with each other. Furthermore, there are no unoccupied regions within the study area that could be colonized during the duration of the study. Therefore, this study area presents us with an opportunity to use radiotelemetry estimates as a baseline to evaluate the precision and accuracy of our technique

Development of 10 Polymorphic Microsatellite Loci Isolated From The Mountain Beaver, \u3ci\u3eAplodontia rufa rufa\u3c/i\u3e (Rafinesque)

We developed 10 microsatellite markers for the mountain beaver, Aplodontia rufa rufa. In three populations of A. r. rufa, the number of alleles for these loci ranged from monomorphic to nine. Average observed heterozygosities in these populations ranged from 0.29 to 0.60. We also tested previously published markers from the endangered subspecies A. r. nigra in A. r. rufa populations

LACTATING NORTH AMERICAN BEAVERS (\u3ci\u3eCASTOR CANADENSIS\u3c/i\u3e) SHARING DENS IN THE SOUTHWESTERN UNITED STATES

During a radio-tracking study of North American beavers (Castor canadensis) in Arizona, we discovered three adult, lactating beavers using the same bank den at the same time. Two adult females 5.2 kmdownstreamalso were using the same den at the same time. For the first case, we documented use of communal dens by lactating adults on seven occasions during 68 days. For the second case, we documented communaluseof adenonthreeoccasionsduring 45days.Totest the hypothesis that these communal females were closely related,weusedeight autosomalDNAmicrosatellites.Two females in thefirstdenwere first-order relatives. However, the other communal females were unrelated to the females with which they shared the den.We conclude that communal denning, wheremultiple females raise one ormore litters in the same den, may have occurred in our study area and communal-denning partners are, in some cases, close kin