Mountains Bear DNA and Camera Survey: 2008‐2009

December 2010

Christopher Servheen, U.S. Fish and Wildlife Service, College of Forestry and Conservation, University of , Missoula, Mt 59812 [email protected] Fax: 406‐329‐3212 Rebecca Shoemaker, College of Forestry and Conservation, University of Montana, Missoula, Mt 59812 [email protected]

Bitterroot DNA Survey 2008‐2009 Final Report December 2010 BACKGROUND The grizzly bear (Ursus arctos horribilis) was listed as threatened under the Endangered Species Act in 1975. At that time, the Bitterroot ecosystem was identified as an area containing grizzly bears (41 FR 31734). After further investigation, in 1996, the US Fish and Wildlife Service determined that the best available scientific data indicated there was not a population of grizzly bears in the Bitterroot ecosystem (USFWS 1996). The Service released a supplemental chapter to its 1993 Grizzly Bear Recovery Plan detailing specific efforts in the Bitterroot ecosystem needed to achieve recovery. Following the recommendations of this supplemental Recovery Plan chapter, the Service initiated an environmental impact analysis (EIS) to assess the feasibility of implementing recovery actions in the Bitterroot ecosystem. The Record of Decision (ROD) was released in November 2000, with the selected alternative being, “Restoration of grizzly bears as a nonessential experimental population with citizen management.” (USFWS 2000). The ROD was never funded however it remains valid.

Until September 2007, it was widely accepted that there were no grizzly bears in the Bitterroot ecosystem. On September 3, 2007, a young male grizzly bear was mistakenly killed by a black bear hunter in the northern Bitterroot ecosystem of a few miles from the Idaho/Montana border. Using this bear’s unique genetic signature, we determined it originated in the Selkirk Ecosystem nearly 140 air miles away. After confirming the identity and origin of the grizzly bear, many questions were raised. For instance, does this single, male bear mean there is a population in the Bitterroot ecosystem or was he just a transient passing through? The Final EIS defined a population in the following way: “…verified evidence within the previous six years, consisting of photos within the area, verified tracks and/or sightings by reputable scientists or agency personnel, of at least two different female grizzly bears with young or one female seen with different litters in two different years in an area geographically distinct from other grizzly bear populations.” (USFWS 2000). The Endangered Species Act defines a 10(j) “non‐essential experimental” population as one that is “…wholly separate geographically from non‐ experimental populations of the same species.” To make an informed decision based on the best available science about whether the Bitterroot Ecosystem meets this definition and to

2 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 document the presence of any other grizzly bears in the Bitterroot Ecosystem; we surveyed the northern for grizzly bear presence using DNA barbed‐wire hair stations and motion‐ triggered digital cameras.

STUDY AREA The study area in 2008 consisted of the northern Bitterroot Mountains between U.S. Highway 12 and Interstate 90 in areas in both Idaho and Montana (Figures 1, 2, 3). The effort was focused in National Forest lands near the Kelly Creek drainage, where the grizzly bear was killed in 2007. These forests included the Clearwater National Forest (ID), the St. Joe District of the Idaho Panhandle National Forest (ID) and the Lolo National Forest (MT).

In 2009, we expanded our sampling effort to include 2 main study areas: 1) the Clark Fork Study Area, and 2) the Bitterroot Study Area (Figures 2, 3). The Clark Fork Study Area includes the northern Bitterroot Mountains of Montana south of the between St. Regis and the Idaho/Montana state line. Our sites were primarily located on the Kootenai (MT) and Lolo (MT) National Forests with 2 sites on the Coeur d’Alene District of the Idaho Panhandle National Forest (ID). The Bitterroot Study Area in 2009 was a continuation of our 2008 sampling effort in the northern Bitterroot Mountains between the Idaho/Montana state line and US Hwy. 12 in Idaho. This study area is within the Clearwater National Forest (ID) and the St. Joe District of the Idaho Panhandle National Forest (ID).

METHODS Sampling Strategy. In 2008, we placed as many hair stations as possible over the course of a short field season (July‐August). In doing so, ease of access (rock slides, snow banks, proximity to trails, etc.) influenced our site placement to allow us to put multiple sites out in a single day. We left these sites out for 1 sampling session (approximately 14 days), then removed them and re‐set them at a new location.

3 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 In contrast, in 2009, we had two different sampling periods. We sampled the Clark Fork Study Area in the early season (May‐June) while we sampled the Bitterroot Study Area during July‐ August (Figure 2). In the Clark Fork Study Area, we used a similar approach to 2008 and placed the maximum number of sites possible out for 14 day sessions, then moved these to new locations for the next sampling session. In the Bitterroot Study Area, we attempted to reduce the overall quantity of sites while improving the quality of sites. We re‐visited areas that were successful in photographing multiple bears and collecting bear hair in 2008, placed sites in large areas that lacked roads and trails, and attempted to select locations that were “natural movement areas” for wide‐ranging mammals. These included confluences of major or multiple drainages (e.g., Canyon Creek x Little N. Fk. Clearwater) and major mountain saddles (e.g., Pole Mountain saddle). For these 2009 Bitterroot Study Area sites, we collected hair and re‐baited them every 2 weeks so that they were on the landscape at the same location for periods ranging from 2‐6 weeks.

Site Selection. Our rationale for choosing sites was based on several factors. We consulted with local biologists, managers, and conservation officers from the Great Burn Study Group, the Idaho Department of Fish and Game, the Montana Department of Fish Wildlife and Parks, and the U.S. Fish and Wildlife Service (USFWS) to locate promising areas. Other macro‐site selection factors included natural movement areas such as saddles, drainages, finger ridges, and confluences; relative levels of human access; and landscape scale wind movement patterns. Micro‐site selection was based on availability of bear foods, proximity to trail junctions, proximity to creek confluences, landscape heterogeneity, wind dispersal, and proximity to water sources. Specific site locations were chosen on the ground by field crews trained to identify good quality grizzly bear habitat, foods, bear sign, and movement areas. Individual sites were placed at least 500m from any road or developed site and at least 100m from any trail.

Hair Collection. Collection of bear hair with barbed‐wire was based on protocols verified to be effective in snagging bear hair (see Woods et al. 1999, Kendall et al. 2009). At each station,

4 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 sites consisted of a non‐reward lure pile encircled by barbed wire. Lure piles were composed of local organic matter such as rotten logs and moss and were piled approximately 1m high and 1m wide and doused with approximately 2 liters of non‐reward lure solution. The barbed‐wire was >2m from the lure pile on all sides and 45cm above the ground. A cloth soaked in lure was hung above the site to disperse the lure scent further.

Motion triggered cameras were placed at as many sites as possible. We used Reconyx PC‐85 cameras because of their quick “trigger time” (time between a trigger event and photo being taken), long battery life, portability, and reliability. Because we had only 30 cameras, it was not possible to place cameras at all sites when more than 30 sites were out at a single time.

We attempted to revisit sites every 14 days to collect hair samples and re‐bait or dismantle the site but this sampling session time varied from 12‐16 days depending on logistics and scheduling. Each barb was treated as a single sample and collected in its own coin envelope. Both the barb and the tweezers used to collect samples were burned after collecting each sample to avoid cross‐contamination. Trees used as part of the corral, the ground below the barbed‐wire, and the lure pile were also checked for hair.

Genetic Analysis. All samples were transported to Wildlife Genetics International (WGI) in Nelson, B.C. by a USFWS employee under a CITES (Convention on International Trade in Endangered Species) permit. Samples were visually inspected initially and then screened for species identification using a sequence‐based mtDNA test. In the event that grizzly bear samples were detected, individual ID would be established using a standardized set of 7 microsatellite markers that are highly variable in grizzly bear populations in the lower‐48 States. Error‐checking followed a standard protocol (Paetkau 2003). If grizzly bear samples were identified, WGI would use an assignment test to determine where the bear came from based on its unique genetic signature (Paetkau et al. 1995; Waser and Strobeck 1998; Paetkau et al. 2004).

5 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 To assess the effectiveness of our 2009 Bitterroot Study Area sampling strategy, we genotyped a subset of black bear samples from sites to attempt to answer the following questions and inform future study designs: 1. For sites that were re‐baited, did we get different individuals in subsequent sessions or the same individual re‐visiting? 2. How far apart should sites be placed to avoid sampling the same individuals? 3. Which strategy was more successful? In the Bitterroot, did we get more individuals per site at sites that were re‐baited or sites that were only in one place for 2 weeks? 4. For our sites in the Clark Fork Study Area on different sides of I90, did we document any individuals on both sides of I90? 5. How does the estimated number of individuals based on photo data compare with the known number of individuals identified by genotype?

Photo Data Analysis. All photo data were uploaded using Reconyx software. Every photo was viewed and assigned a species and number of unique individuals. For black bears, we defined unique individuals as those that visited the site more than 6 hours apart or those that were visibly different if less than 6 hours apart. For 2009 photo data, we recorded the color phase of black bears, reproductive status of black bears accompanied by cubs or yearlings, and the day of the session that black bears were detected.

RESULTS During 2008 and 2009, we obtained 1,585 hair samples over 189 sampling sessions, none of which were from grizzly bears. Black bear and wolf photographs were well distributed across our study areas (Figures 4, 5, 6, 7) although black bear photos were much more common. Annual results are detailed below.

Hair Station Data 2008. From July 7, 2008 to September 6, 2008 a total of 68 sites were set up for a total of 952 trap nights (68 sites x 14 nights). We collected 422 non‐ungulate hair samples from 76 percent of the sites (52/68 sites) for an average of 6.2 hair samples per site. There

6 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 were also 2 scat samples submitted that were > 2 inches in diameter and warranted further analysis. Of the hair samples, 329 with suitable material (i.e., an adequate root based on visual inspection with a dissecting scope) were analyzed, identifying 0 grizzly bear samples, 279 black bear samples, and 6 dog or wolf samples. Forty one of these 329 samples failed to amplify due to low sample quality. The remaining 3 samples consisted of 1 probable black bear and 2 probable dogs/wolves. These samples produced mixed results during their first analysis and did not have enough original material for re‐analysis. The bear hair sample in question produced a “strong black bear result plus a weak grizzly bear peak” in the first analysis (Paetkau 2009). However, all 27 of the other samples collected at this site, including samples collected from barbs immediately adjacent to this sample were from black bears. According to WGI, “the best explanation for the ‘grizzly/black’ result is that it was a black bear hair with a touch of grizzly contamination from the lab” (Paetkau 2009). There were also no photos of grizzly bears at this site. After considering all of these factors, we concluded that this sample was from a black bear. Of the 2 scat samples submitted, 1 was from a black bear and 1 was of insufficient quality to amplify.

Camera Data 2008. From July 7, 2008 to September 6, 2008 we set cameras at 55 of the sites and received photos from 52 of them after 3 malfunctioned, for a total of 770 trap nights (52 sites x 14 nights). We captured 408 photos of animals in this time period with no grizzly bear photos. Of these 408 photos, 119 were photos of carnivores, 264 were ungulates, and 25 were small or unidentified animals (Table 1). The carnivore photos consisted of pictures of 83 different photos of black bears (Ursus americanus), 1 mountain lion (Puma concolor) photo, 7 wolf (Canis lupus) photos, 5 coyote (Canis latrans) photos, and 22 pine marten (Martes americana) photos. The ungulate photos consisted of 177 deer (Odocoileus spp.) photos, 33 elk (Cervus canadensis) photos, and 54 moose (Alces alces) photos. The remaining 25 photo captures were small mammals (Sciurus species, Lepus americanus, domestic dog) or unidentified.

7 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 Carnivore photo captures were spread across the sites in the following way: 63% (33/52 sites) of sites had photos of black bears, 2% (1/52 sites) had mountain lion photos, 11% (7/52 sites) had photos of wolves, 8% (5/52 sites) had photos of coyotes, and 29% (22/52 sites) had photos of pine marten.

Ungulate photo captures occurred at 75% (39/52 sites) of the sites. Sixty‐five percent (34/52 sites) of sites captured photos of deer species, 46% (24/52 sites) had photos of moose, and 25% (13/52 sites) had photos of elk.

Hair Station Data 2009. From May 18, 2009 to September 2, 2009 a total of 89 sites were set, with multiple re‐baits of certain sites, for a total of 1,705 trap nights. During this time, we collected 1,163 non‐ungulate hair samples: 803 in the Clark Fork Study Area and 360 in the Bitterroot Study Area. In the Clark Fork Study Area, we sampled from May 18 – July 8, 2009 for a total of 66 sites. We obtained non‐ungulate hair at 92.4% (61/66) of these sites, with an average of 12.2 samples per site. In the Bitterroot Study Area, we sampled from July 13 – September 2, 2009 for a total of 55 sessions in 23 different locations: 5 sites collected after 2 weeks, 4 sites collected after 4 weeks (and 1 re‐baiting), and 14 sites collected after 6 weeks (with 2 re‐baitings). The average length of time that sites were on the landscape in the Clark Fork Study Area was 14.2 days and 32.1 days in the Bitterroot Study Area. In the Bitterroot Study Area, we obtained non‐ungulate hair at 72.7% (40/55) of our sites, with an average of 6.6 samples per site.

Of 1,163 samples collected, 118 lacked suitable material for genetic testing, 12 were visually identified as ungulate hair, and 423 were removed from the sample based on photo data, barb location, sample quantity, and budget constraints. Of the remaining 610 samples, 586 produced black bear results, 6 produced non‐ursid results including 1 coyote, 4 wolves (or dogs = Canis lupus), and 1 elk; and 18 failed during species testing (Paetkau 2010).

8 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 In addition to species identification, we identified individual genotypes for a subsample of the black bear hair collected. Due to budget constraints, we selected 84 hair samples for individual genotyping based on the site’s location, sampling strategy, and sample quantity to answer our 5 research questions regarding study design, camera efficacy, and connectivity across I90. These 84 hair samples were obtained at 10 different sites (Figure 8). Of the 84 hair samples selected for genotyping, 11 failed and 73 were successful, with 32 individual black bears identified: 17 females and 15 males. While there were multiple samples from the same individual at sites, there were only 2 individuals that re‐visited the same site during different sessions and no individual was detected at multiple sites.

Once individual genotyping had been done, additional analyses were completed. The observed heterozygosity of the 32 individuals averaged across the 6 microsatellites used was 0.86 (Paetkau 2010). Additionally, a cluster analysis was performed to assess the genetic relatedness of our sample of black bears to other black bears in Idaho and Montana (Figure 9) (Paetkau 2010).

Camera Data 2009. From May 18, 2009 to September 2, 2009 we set cameras at 57 of the 66 Clark Fork sites and all 23 of the Bitterroot sites for a total of 1,537 camera trap nights. We captured 711 photos of animals in this time with no grizzly bear photos. Of these 711 photos, 308 were photos of carnivores, 328 were ungulates, and 75 were small or unidentified animals (Table 2). The carnivore photos consisted of 248 different photos of black bears (Ursus americanus), 9 mountain lion (Puma concolor) photos, 5 wolf (Canis lupus) photos, 22 coyote (Canis latrans) photos, 18 pine marten (Martes americana) photos, 4 bobcat (Lynx rufus) photos, and 2 skunk (Mephitis mephitis) photos. The ungulate photos consisted of 156 deer (Odocoileus spp.) photos, 144 elk (Cervus canadensis) photos, and 28 moose (Alces alces) photos. The remaining 75 photo captures were small mammals (Sciurus species, Lepus americanus) or unidentified.

9 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 Carnivore photo captures were spread across the sites in the following way: 83% (92/111 sessions) had photos of black bears, 7% (8/111 sessions) had mountain lion photos, 4% (4/111 sessions) had photos of wolves, 14% (16/111 sites) had photos of coyotes, and 11% (12/111 sessions) had photos of pine marten. Ungulate photo captures included deer species at 44% (49/111 sessions) of sites, elk at 36% (40/111 sessions) of sites, and moose at 19% (21/111 sessions) of sites.

For 2009 photo data, we recorded color phase, reproductive status of black bears with offspring, and the day(s) of each session that bears were detected. Overall, nearly 37% of black bears photographed were not black in color, instead ranging from blonde to brown (Table 3). In the Bitterroot Study Area, 7% (6/86) of black bears were with young, with 1.5 young on average. In the Clark Fork Study Area, 9% (14/162) of black bears were with young, with 1.9 young on average.

DISCUSSION We did not detect any grizzly bears in the study area during our sampling in 2008 or 2009. However, this survey cannot document absence in the survey area; it can only document the presence of a species (MacKenzie 2005). Thus, our results cannot be interpreted as documenting the absence of grizzly bears in the study area. Failing to detect a species could be caused by a number of different scenarios: 1) the species is absent; 2) the species is present but not during the spatial or temporal scale that was sampled; 3) the species is present but chose not to visit the sampling site; 4) the species is present, it visited the sampling site but did not leave any evidence (i.e., was not detected). Sampling design can be adjusted spatially and temporally to minimize the possibility of species being present but not detected. Because seasonal home ranges for female grizzly bears vary from 150‐250 km2 (60‐100 mi2) (Mace and Waller 1997), we tried to space our sites no more than 16 km (10 miles) apart in any given session and sample repeatedly throughout the season to maximize the probability that a grizzly bear would encounter a hair sampling station. We attempted to enhance our probability of documenting a grizzly bear within the study area by selecting optimal habitat characteristics on

10 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 both a macro‐ and micro‐site scale. We believe that these temporal and spatial considerations increased the probability of detection for grizzly bears.

Our success rate for obtaining bear hair (73‐92%) was comparable to success rates with similar methods in the Northern Continental Divide Ecosystem of Montana (79%) (Jeff Stetz, pers. comm.) and the Yaak River drainage of northwestern Montana (60%) (Mace and Chilton 2002). Within the Bitterroot Study Area, our success rate was comparable across years (76% in 2008; 73% in 2009). The average number of samples per site in the Bitterroot Study Area was similar in 2008 (6.2 samples per site) and 2009 (6.6 samples per site) but was higher in the Clark Fork Study Area (12.2 samples per site). These numbers are comparable to what was obtained in the 2004 survey in the Northern Continental Divide Ecosystem (8.1 samples per site) and are higher than the number obtained using these methods in the in 2009 (3.4 samples per site). The exact reasons for these differences in the number of hair samples per site are unclear but lower black bear density in each study area is a plausible explanation. While excessive wind or rain could lead to fewer samples being retained over the 2‐week sampling session, camera data indicate there were only 2 sites at which we obtained photos of a bear but did not get a hair sample. In comparison, there were 8 sites at which we obtained bear hair samples but no photos of bears. This seems to indicate that our sites were effective at obtaining hair samples from bears that visited.

Our inability to detect grizzly bears does not mean they are absent from the study area. Grizzly bear mortalities within or adjacent to the Bitterroot Study Area (n = 2) and the Clark Fork Study Area (n = 3) suggest grizzly bears at least occasionally use these areas. While our methods have been effective at detecting grizzly bears in other low density populations like that found in the Cabinet Mountains of northwest Montana (see Kasworm et al. 2008), the probability of detecting a grizzly bear is low. In Alberta, where there is a known population of grizzly bears including many radio‐collared animals, Boulanger et al. (2004) found that when bears are within 250m of hair sampling stations, there is a 37% chance they will not leave a hair sample, either because they did not enter the site or they did not leave a hair sample (Boulanger et al. 2004).

11 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 Furthermore, they found that capture probability at DNA hair stations was less than 5% if bears are greater than 1.69 km from a site (Boulanger et al. 2004).

To address the question of whether our 2009 Bitterroot Study Area sampling strategy was effective, we asked whether we were getting new individuals at each session and how many total individuals were identified. We found that sites that were out for 2 weeks (n = 4) identified 2.75 individuals on average whereas sites that were out for 3 sessions (n = 5) identified 4.2 individuals on average. However, when examining individual sampling sessions in the Bitterroot Study Area, there were fewer individuals identified in any given 2 week session (1st session = 1.6; 2nd session = 1.2; 3rd session = 1.8). These results should be interpreted cautiously due to low sample sizes and sample quantities such that some samples could not be amplified for individual identification. While we would expect a site that is on the landscape for 6 weeks to document more individuals than one that is only out for 2 weeks, this was an untested assumption. Although we cannot directly compare these data to determine which sampling strategy was more successful because they were on the landscape at different times, we demonstrated that re‐baiting optimal sites is an effective way to detect individuals. Also of interest, due to budget constraints, all of our single session sites were from the Clark Fork Study Area, where we experienced a much higher success rate obtaining bear samples at sites (92.4% vs. 73% in the Bitterroot Study Area). This further supports the idea that our strategy to re‐bait optimal sites was successful since we obtained more individuals on average even though we were sampling in a study area with a lower overall success rate.

There were only 2 of 32 individuals that re‐visited the same site in subsequent sessions. Both of these were females which have smaller home ranges and would be more likely to encounter a site more frequently than a male bear with a larger home range. This is further evidence that our sampling strategy was effective since we had very few repeat visits.

We did not document any individual bears at 2 different sites. Our sites in the Bitterroot Study Area were between 2.7 km (1.7 mi) and 22.5 km (14 mi) apart. This suggests that these distances are adequate to obtain samples from new individuals. We did, however, document 2

12 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 individuals that re‐visited the same site in subsequent sessions. Of 32 individuals identified, we consider this rate of re‐visits negligible, indicating our sampling design was optimal to detect new individuals during each session.

We did not document any individual bears on both sides of I90. We selected 4 sites with sufficient samples for genotyping: 2 north of I90 and 2 south of I90, all sampled during the same sampling session. Two of our sites were only 1.8 miles apart across I90. The fact that we did not document any of the same individuals on both sides of I90 is consistent with our other results in the Bitterroot Study Area where there is no potential fragmentation zone (i.e., I90 corridor). As such, these data do not suggest anything about whether I90 is an impediment to black bear movement. This was not an objective of our original study but was interesting to assess as part of our genotyping analysis.

When comparing the estimated number of individuals based on photo data with the known number of individuals based on genotyping, we found that photo data tends to inflate the number of individuals (Table 4). This is expected because we cannot decipher individuals with certainty using photo data and have to use a rule set instead. For example, at the Brimstone Creek site, photo data indicated 8 bears. This included 2 sets of females with 3 cubs of the year. Even though it was likely these 2 family groups were the same, we counted them separately because they visited the site 7 days apart.

Once individual genotyping had been done, additional analyses were completed. The observed heterozygosity (Ho = 0.86) was high. So high, in fact, that Wildlife Genetics International stated there was enough variability to identify individuals using only 2 markers (G10L and G10H) instead of the 6 normally used (Paetkau 2010). A cluster analysis revealed the genetic relatedness of our sample of black bears to other black bears in Idaho and Montana (Figure 9) (Paetkau 2010). Samples from our study area fell between samples from other study areas in Idaho and Montana, indicating a relatively contiguous black bear population across state lines.

13 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 The alignment with geography was excellent, with clustering closely reflecting longitude (Paetkau 2010).

Our two different methods for detecting bears (camera and hair sampling station) were both effective. The number of sites with pictures of bears in the Clark Fork Study Area (51 of 56 sessions = 91%) was similar to the number of sites with non‐ungulate hair samples (61 of 66 sessions = 92%). Similarly, in the Bitterroot Study Area, our camera success rate (76% (42 of 55 sessions)) was similar to our sample success rate (73% (40 of 55 sessions)). Only 2 of 103 sites with black bear photos were without a hair sample. In contrast, our photo data and hair samples for wolves were not similar at all. At the 4 sites where we obtained photos of wolves, we did not obtain any wolf hair samples whereas there were no photo detections of wolves or dogs at any of the sites where wolf/dog hair samples were obtained. Our results highlight the importance of using multiple methods concurrently to increase the likelihood of detection (Kasworm et al. 2005; Barr et al. 2006).

Photographic data demonstrate that bears visited hair sampling stations throughout the sampling session with a drop off in activity after Day 12 (Figure 10). This suggests the lure was effective at attracting animals throughout the sampling session.

Our photo data regarding species, color phase, and reproductive output are incomplete as they only reflect the 111 sessions containing cameras and those animals that entered the camera’s range (i.e., inside the wire near the center of site) and were detected. They are a product of our sampling methods and design. As such, they are not representative of any population but are useful anecdotally to compare across years and will establish a baseline of observed reproductive output for our study areas and our methods. The color phase information is relevant to grizzly bear conservation because mistaken identification kills by black bear hunters still occur. Our results highlight the importance of determining bear species based on more than color alone (Table 3).

14 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 Management & Research Implications: To promote grizzly bear expansion and occupancy in the Study Areas, we recommend managing human activities to limit the potential for disturbance (e.g., timber harvesting during winter); limiting and/or concentrating motorized human access such that there are large contiguous patches of secure, roadless habitat; implementing food storage regulations to limit the availability of attractants that could increase bear/human conflicts; and educating hunters and recreationists about how to identify grizzly bears and avoid conflicts.

A practical management implication of our research was the photo documentation of the many color phases of black bears in the area, which can make accurate species identification difficult. More than 25% of all black bears in the study area were not black‐colored (Table 3). This fact should be used at every opportunity to educate black bear hunters about the importance of properly identifying their targets.

An important research implication arising out of this study was documented by Wildlife Genetics International. They learned they can identify species using a single hair, and in 5 out of 6 trials, using a single hair without a root. This is relevant when considering sub‐sampling, collection protocols, and when attempting to detect a rare, wide‐ranging species.

15 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 LITERATURE CITED Barr, M.B., C.R. Anderson, D.S. Moody, and D.D. Bjornlie. 2006. Testing remote sensing cameras to count independent female grizzly bears with cubs of the year: Pilot study report 2006. Wyoming Game and Fish Department, Wyoming, USA.

Boulanger, J., G. Stenhouse, and R. Munro. 2004. Sources of heterogeneity bias when DNA mark‐recapture sampling methods are applied to grizzly bear (Ursus arctos) populations. Journal of Mammalogy 85:618‐624.

Kasworm, W.F., H. Carriles, T.G. Radandt, and C. Servheen. 2005. Cabinet‐Yaak grizzly bear recovery area 2004 research and monitoring progress report. USFWS, Libby, Montana, USA.

Kasworm, W.F., H. Carriles, T.G. Radandt, and C. Servheen. 2008. Cabinet‐Yaak grizzly bear recovery area 2007 research and monitoring progress report. US Fish and Wildlife Service, Libby, Montana, USA.

Kendall, K.C., J.B. Stetz, J. Boulanger, A.C. Macleod, D. Paetkau, and G.C. White. 2009. Demography and genetic structure of a recovering grizzly bear population. Journal of Wildlife Management 73:3‐17.

Mace, R.D. and T.L. Chilton. 2002. Montana black bear research project progress report for years 2000‐2002. Montana Department of Fish Wildlife and Parks, Kalispell, Montana, USA.

Mace, R.D. and J.S. Waller. 1997. Spatial and temporal interaction of male and female grizzly bears in northwestern Montana. Journal of Wildlife Management 61:39‐52.

MacKenzie, D.I. 2005. What are the issues with presence‐absence data for wildlife managers? Journal of Wildlife Management 69:849‐860.

Paetkau, D. 2003. An empirical exploration of data quality in DNA‐based population inventories. Molecular Ecology 12:1375‐1387.

Paetkau, D. 2009. Results summary report from David Paetkau, Wildlife Genetics International to Chris Servheen, U.S. Fish and Wildlife Service Grizzly Bear Recovery Coordinator.

Paetkau, D. 2010. Results summary report from David Paetkau, Wildlife Genetics International to Chris Servheen, U.S. Fish and Wildlife Service Grizzly Bear Recovery Coordinator.

16 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 Paetkau, D., W. Calvert, I. Stirling, and C. Strobeck. 1995. Microsatellite analysis of population structure in Canadian polar bears. Molecular Ecology 4:347‐354.

Paetkau, D., R. Slade, M. Burden, and A. Estoup. 2004. Genetic assignment methods for the direct, real‐time estimation of migration rate: a simulation‐based exploration of accuracy and power. Molecular Ecology 13:55‐65.

U.S. Fish and Wildlife Service. 1996. Bitterroot Ecosystem recovery plan chapter ‐ supplement to the grizzly bear recovery plan. Missoula, Montana, USA.

U.S. Fish and Wildlife Service. 2000. Grizzly bear recovery in the Bitterroot ecosystem. Final Environmental Impact Statement. Missoula, Montana, USA.

Waser, P.M., and C. Strobeck. 1998. Genetic signatures of interpopulation dispersal. Trends in Ecology and Evolution 13:43‐44.

Woods, J.G., D. Paetkau, D. Lewis, B.N. McLellan, M. Proctor, and C. Strobeck. 1999. Genetic tagging of free‐ranging black and brown bears. Wildlife Society Bulletin 27:616‐627.

17 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 Table 1. Photo data, 2008, Bitterroot Study Area. CARNIVORES black bear coyote marten mtn.lion wolf 84 5 22 1 7 119

UNGULATE/OTHER deer elk moose other* 177 33 54 25 289

GRAND TOTAL 408

* dog, snowshoe hare, squirrel, unknown

Table 2. Photo data, 2009, Clark Fork and Bitterroot Study Areas. CARNIVORES study area black bear bobcat coyote lion marten skunk wolf Bitterroots 86 0 11 5 12 0 4 118 Clark Fork 162 4 11 4 6 2 1 190

UNGULATE/OTHER study area deer elk moose other* Bitterroots 54 17 12 11 94 Clark Fork 102 127 16 64 309

GRAND TOTAL 711

* includes 34 hares, 1 porcupine, 5 birds, 33 rodents, and 2 unidentifiable animals.

18 Bitterroot DNA Survey 2008‐2009 Final Report December 2010 Table 3. Color phase of black bears obtained through photographic data, Clark Fork and Bitterroot Study Areas, 2009. # of black bears # of black bears Grand COLOR PHASE in Bitterroot % in Clark Fork % % Total Study Area Study Area

black 58 73% 84 58% 142 63%

blonde 3 4% 16 11% 19 8%

brown 9 11% 40 27% 49 22%

cinnamon 0 0% 2 1% 2 1%

mixed 9 11% 4 3% 13 6%

grand total 79 146 226

Table 4. Number of individuals detected at select sites using photo data versus genotyping.

# # individuals "individuals" site using using photo genotypes data Bostonian 3 5 Brimstone 3 8 Crow 3 4 Frost x Roaring 7 9 Hanacker 1 1 Isabella x Jug 4 4 Pole Mtn. saddle 3 7 Silver x Burke 4 4 Simmons 4 4

Avg. # "individuals" detected 3.6 5.1

19 Bitterroot DNA Survey 2008‐2009 Final Report December 2010

Figure 1. Distribution of DNA barbed‐wire hair stations, 2008, northern Bitterroot Mountains.

20 Bitterroot DNA Survey 2008‐2009 Final Report December 2010

Clark Fork Study Area

Bitterroot Study Area

Figure 2. Distribution of DNA barbed‐wire hair stations, 2009, Clark Fork Study Area and Bitterroot Study Area.

21 Bitterroot DNA Survey 2008‐2009 Final Report December 2010

Figure 3. Distribution of all DNA barbed‐wire hair station sites, 2008‐2009.

22 Bitterroot DNA Survey 2008‐2009 Final Report December 2010

Figure 4. Distribution of sites that had photos of black bears, 2008, northern Bitterroot Mountains.

Figure 5. Distribution of sites that had photos of black bears, 2009, Bitterroot Study Area. The green triangles are mountain locations on the Google Earth basemap.

23 Bitterroot DNA Survey 2008‐2009 Final Report December 2010

Figure 6. Distribution of sites that had photos of wolves, 2008, northern Bitterroot Mountains.

Orange = lion Blue = coyote Yellow = wolf White = wolf & coyote

Figure 7. Distribution of sites that had photos of wolves, coyotes, and lions, 2009, Bitterroot Study Area. The green triangles are mountain locations on the Google Earth basemap.

24 Bitterroot DNA Survey 2008‐2009 Final Report December 2010

Figure 8. Distribution of 10 hair station sites that were sub‐sampled for individual genotyping, 2009.

25 Bitterroot DNA Survey 2008‐2009 Final Report December 2010

Figure 9. Six‐locus clustering results from the program Genetix. Black bears from the Bitterroot and Clark Fork Study Areas (purple) fall squarely between bears from 10 other study areas in Idaho (yellow) and Montana (other colors). (Adapted from Paetkau 2010).

30

25

20 bears 15 of

# 10

5

0 0123456789101112131415 day detected

Figure 10. Sampling session days in which black bears were detected in both the Clark Fork and Bitterroot Study Areas based on photo data, Bitterroot Mountains, 2009.

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