Within-guild dietary discrimination from 3-D textural analysis of tooth microwear in insectivorous mammals

Resource exploitation and competition for food are important selective pressures in animal evolution. A number of recent investigations have focused on linkages between diversification, trophic morphology and diet in bats, partly because their roosting habits mean that for many bat species diet can be quantified relatively easily through faecal analysis. Dietary analysis in mammals is otherwise invasive, complicated, time consuming and expensive. Here we present evidence from insectivorous bats that analysis of three-dimensional (3-D) textures of tooth microwear using International Organization for Standardization (ISO) roughness parameters derived from sub-micron surface data provides an additional, powerful tool for investigation of trophic resource exploitation in mammals. Our approach, like scale-sensitive fractal analysis, offers considerable advantages over twodimensional (2-D) methods of microwear analysis, including improvements in robustness, repeatability and comparability of studies. Our results constitute the first analysis of microwear textures in carnivorous mammals based on ISO roughness parameters. They demonstrate that the method is capable of dietary discrimination, even between cryptic species with subtly different diets within trophic guilds, and even when sample sizes are small. We find significant differences in microwear textures between insectivore species whose diet contains different proportions of ‘hard’ prey (such as beetles) and ‘soft’ prey (such as moths), and multivariate analyses are able to distinguish between species with different diets based solely on their tooth microwear textures. Our results show that, compared with previous 2-D analyses of microwear in bats, ISO roughness parameters provide a much more sophisticated characterization of the nature of microwear surfaces and can yield more robust and subtle dietary discrimination. ISO-based textural analysis of tooth microwear thus has a useful role to play, complementing existing approaches, in trophic analysis of mammals, both extant and extinct

Experimental evaluation of koala scat persistence and detectability with implications for pellet-based fauna census

Establishing species distribution and population trends are basic requirements in conservation biology, yet acquiring this fundamental information is often difficult. Indirect survey methods that rely on fecal pellets (scats) can overcome some difficulties but present their own challenges. In particular, variation in scat detectability and decay rate can introduce biases. We studied how vegetation communities affect the detectability and decay rate of scats as exemplified by koalas Phascolarctos cinereus: scat detectability was highly and consistently dependent on ground layer complexity (introducing up to 16% non-detection bias); scat decay rates were highly heterogeneous within vegetation communities; exposure of scats to surface water and rain strongly accelerated scat decay rate and finally, invertebrates were found to accelerate scat decay rate markedly, but unpredictably. This last phenomenon may explain the high variability of scat decay rate within a single vegetation community. Methods to decrease biases should be evaluated when planning scat surveys, as the most appropriate method(s) will vary depending on species, scale of survey and landscape characteristics. Detectability and decay biases are both stronger in certain vegetation communities, thus their combined effect is likely to introduce substantial errors in scat surveys and this could result in inappropriate and counterproductive management decisions

Snowshoe Hare and Forest Structure Relationships in Western Wyoming

Snowshoe hares (Lepus americanus) are a critically important prey species for Canada lynx (Lynx canadensis). Determination of snowshoe hare distribution and abundance is needed in western Wyoming for lynx conservation. We used linear regression to examine the correlations between snowshoe hare density, as determined by mark-recapture estimates, and fecal pellet plot counts on both uncleared and annually cleared plots on the Bridger-Teton National Forest, western Wyoming. We found significant correlations between hare density estimates and fecal pellet counts for both uncleared and annually cleared pellet counts; however the relationship was much stronger for annually cleared pellet counts. Adjusting the buffer size by omitting hard habitat edges (not used by hares) around the trapping grids improved correlations between hare density and fecal pellet counts further. We recommend pellet counts from annually cleared plots be used when precise estimates of snowshoe hare abundance are required. Though precision is sacrificed when using uncleared plots, they are useful as a coarse index of habitat use by hares. The derived regression equations should be used to identify foraging habitat for lynx in western Wyoming. In addition to snowshoe hares, in western Wyoming red squirrels (Tamiasciurus hudsonicus) and grouse (Bonasa umbellus and Dendragapus obscurus) are used by Canada lynx. Whether young forests or older multi-storied forests contain more snowshoe hares, red squirrels, and grouse in western Wyoming is currently unknown. We estimated snowshoe hare density, and indexed red squirrel and forest grouse abundance in 3 classes of 30-70-year-old lodgepole pine (Pinus contorta) and 4 classes of mature multi-storied forest with a spruce (Picea engelmannii)-fir (Abies lasiocarpa) component. We recorded landscape and forest structure characteristics to understand how these influence lynx prey abundance. Overall, snowshoe hares, red squirrels, and forest grouse were more abundant in multi-storied forests than young forests. Forest attributes that predicted prey abundance were often more prevalent in multi-storied forests. Results from this study suggest that multi-storied forests with a spruce-fir component were disproportionately important to snowshoe hares, red squirrels, and forest grouse in western Wyoming. Canada lynx conservation efforts should focus on maintaining, enhancing, and promoting multi-storied forests in this region

Evaluating the winter diet of a reintroduced herd of elk in the Cumberland Mountains, Tennessee, using next-generation sequencing techniques

A distinct subspecies of elk (Cervus canadensis), the North American elk (C. canadensis canadensis), once inhabited portions of the southeastern United States, including Tennessee, until their extirpation in the mid 1800s. From 2000 to 2008, 201 Manitoban elk were reintroduced on the North Cumberland Wildlife Management Area (NCWMA). A year-long food habits study using histological analysis of plant material from feces was completed for the NCWMA elk from 2003 to 2004 and has since aided managers in their landscape planning. Since then, more elk have been released onto the area, food plots have been established throughout the NCWMA, and the population has had approximately 20 years to establish itself on the landscape. Thus, a reevaluation of dietary habits is warranted. We collected 357 groups of fecal pellets from 68 set openings within the 79,318 ha NCWMA weekly from February to April of 2019 for a winter fecal diet analysis using next-generation sequencing techniques, also referred to as metabarcoding. Metabarcoding is a non-invasive methodology that has proven to be more effective in identifying herbivore diets than previously used methods. We conducted DNA extractions, a two-step polymerase chain reaction protocol, and completed library preparation of the samples using the Illumina MiSeq sequencing protocol to isolate the plant DNA from the other genetic material in the scat. A bioinformatical analysis was then conducted to determine what plants were identified from sequencing. Statistical analyses performed include calculating proportions for the genera detected from sequencing, determining if specific plants were used differently by males and females from specific genetic groups on the NCWMA, investigating alpha and beta diversity of sample sequences, and assessing the use of forage classes by elk during the winter of 2019. The results from this study will further inform managers of the dietary habits of the reintroduced NCWMA herd and assist them in future habitat management

Developing Microbial Biomarkers to Non-invasively Assess Health in Wild Elk (Cervus canadensis) Populations

The composition of the intestinal bacterial community (intestinal microbiome) of mammals is associated with changes in diet, stress, disease and physical condition of the animal. The relationship between health and the microbiome has been extensively demonstrated in studies of humans and mice; this provides strong support for its potential utility in wildlife. When managing elk (Cervus canadensis), federal and state agencies currently must rely on invasive sampling and coarse demographic data on which to base their decisions. By developing microbiome-based biomarkers that vary as a function of elk body condition and disease (i.e. microbial biomarkers), we hope to provide managers with the ability to monitor direct impacts from environmental stressors on individual animals and the herd. This approach, once established, represents a low cost, non-invasive sampling method based simply on fecal pellet collection in the field and intestinal microbiome analysis in the lab. Montana Fish, Wildlife and Parks collected the scat and linked body condition metrics from four GPS collared populations in Montana in winter 2014, using helicopter teams and invasive sampling methods. We analyzed 111 individual wild elk fecal microbiomes using Illumina MiSeq sequencing of partial 16S-rRNA gene amplicons. Using the QIIME pipeline and a floating search feature selection algorithm (SFFS) with linear discriminate analysis (LDA) and leave-one-out cross validation (CV) we were able to elucidate informative patterns in bacterial taxa presence and abundance by comparing them to various measured body conditions and geographic locations of elk sampled. Microbial biomarkers provide potential for managers to routinely obtain fine scale non-invasive health metrics from scat samples obtained in the field for species of concern

ESTIMATING TIGER (\u3ci\u3ePANTHERA TIGRIS\u3c/i\u3e) PREY DENSITY USING CAMERA TRAPS AND FECAL ACCUMULATION RATES

The conservation of tiger populations requires the preservation of their prey. Assessing prey populations is therefore important, but challenges arise due to the elusive nature of many prey species. We used two indirect methods to estimate the density of sika deer (Cervus nippon), an elusive tiger prey species, in the Sikhote-Alin Biosphere Reserve in the Russian Far East. The fecal accumulation rate (FAR) is widely used and provides estimates of ungulate density based on the accumulation of fecal pellet groups in previously cleared plots. More recently, the random encounter model (REM) was developed to estimate population density from the rates of contact between study animals and camera traps. Its use is controversial because of questions on how to define an encounter, estimate daily travel distance, and adjust for herds. The goal of this project was to compare density estimates from the two techniques and assess whether and when REM could replace FAR in such surveys. Detectability of the study animals was similar for both methods, but the FAR technique yielded a much higher density estimate, 13.97 ± 2.74 standard error (SE) sika deer km-2 than did the REM method 4.91± 1.76 (SE) sika deer km-2, which was closer to expectation based on previous studies. Both methods required estimates from outside studies: of defecation rates for FAR and of average travel distances for REM. REM also required an assumption on group sizes which were likely underestimated in the camera images. Our analysis suggests theoretical considerations and practical adjustments that must be made to both methods when estimating population density. We also propose integrating the two techniques by using the camera traps over cleared plots to estimate defecation rates directly from the study population. Overcoming challenges like these is vital to designing effective conservation plans for tigers and their prey

POPULATION ABUNDANCE AND GROWTH OF ELK (CERVUS CANADENSIS) IN WESTERN NORTH CAROLINA

In an effort to restore extirpated elk to their previous range, 52 elk were reintroduced to Great Smoky Mountains National Park (GRSM) in North Carolina during 2001 and 2002. Since their reintroduction, elk numbers have increased and their range has extended beyond GRSM boundaries. My primary research objectives included estimating population abundance, apparent survival, per capita recruitment, and population growth rate of elk in North Carolina. I used spatially explicit capture-recapture (SECR) models based on fecal DNA to identify individual elk and estimate population abundance and growth in the region. Technicians and I walked a series of transects throughout the region over 3 winter field seasons (2020–2022) and collected elk pellets encountered along these transects. These data were incorporated into both closed and open population SECR models to estimate elk densities, abundance, and population vital rates over the three-year period. The top performing single-sex closed SECR models for males and females estimated density separately by year and as a function of the scaled distance to primary field with densities decreasing as the distance to field increased. The total realized abundance estimates of combined males and females in the study area were 179 elk (95% CI = 149–215) in 2020, 220 elk (95% CI = 188–256) in 2021, and 240 elk (95% CI = 207–279) in 2022. The top open population SECR model estimated both apparent survival (φ [phi]) and population growth rate as functions of sex and year. Mean φ [phi] for males were 0.682 (95% CI = 0.317–0.908) for 2020-21 and 0.339 (95% CI = 0.152–0.596) for 2021-22. Mean φ [phi] for females were 0.953 (95% CI = 0.830–1.000) for 2020-21 and 0.829 (95% CI = 0.601–1.000) for 2021-22. Mean population growth rate estimates (λ [lambda]) for females were 1.559 (95% CI = 1.162–2.091) for 2020-21 and 1.122 (95% CI = 0.876–1.437) for 2021-22. Mean λ [lambda] for males were 1.127 (95% CI = 0.806–1.575) for 2020-21 and 0.811 (95% CI = 0.566–1.163) for 2021-22. This population likely could support limited sport hunting; continued monitoring is recommended

Capture-recapture of white-tailed deer using DNA sampling from fecal pellet-groups

Reliable density estimates of game and keystone species such as white-tailed deer (Odocoileus virginianus) are desirable to set proper management strategies and for evaluating those strategies over time. However, traditional methods for estimating white-tailed deer density have been inhibited by behavior, densely forested areas that can hamper observation (detection), and invalid techniques of estimating effective trapping area. We wanted to evaluate a noninvasive method of mark-recapture estimation using DNA extracted from fecal pellets as the individual marker and for gender determination, coupled with a spatial detection function to estimate density (Spatially Explicit Capture-Recapture, SECR). We collected pellet groups from 11 to 22 January 2010 at randomly selected sites within a 1-km2 area located on Arnold Air Force Base in Coffee and Franklin Counties, Tennessee. We searched 702 plots (10–m radius), collecting 352 pellet-group samples on 197 of the plots. We sent samples to Wildlife Genetics International (Nelson, British Columbia) for genetic analysis. One gender and 6 microsatellite markers with heterozygosity \u3e0.80 were selected for genotyping individuals. Fifteen samples (4%) were not suitable for analysis, 2 (1%) showed evidence of \u3e2 alleles per marker (mixture of DNA), and 114 (32%) failed to provide genotypes during testing. We assigned individual identity and gender to 223 (63%) of the samples which consisted of 39 individuals (18M:21F). We used Program DENSITY (SECR) to fit a model of the detection process to estimate density unbiased by edge effects and incomplete detection. Time of sampling had the largest effect on capture probabilities. Calculated total deer density was 6.2 (SE = 1.39) deer/km2. Buck to doe ratio was 1:1.75 based on density by gender (2.3 (SE = 0.85) bucks; 4.08 (SE = 1.10) does). We also evaluated whether fewer samples could be used to estimate density with similar measures of precision. Standard error increased from 1.39 for total sample analysis to 1.99 when we evaluated 50% of total samples, and 3.09 when we evaluated 20% of samples. We found DNA sampling from pellet groups provided deer density and sex ratio estimates useful for deer management decisions and reduces the risk of overestimating deer density, common in traditional methods

Wildlife Food Habits And Habitat Use On Revegetated Stripmine Land In Alaska

Thesis (Ph.D.) University of Alaska Fairbanks, 1984Food habits and habitat utilization of wildlife species on revegetated stripmine spoils in interior Alaska were studied from 1980 through 1982. Current reclamation techniques were beneficial for tundra voles, short-eared owls and marsh hawks. Caribou, Dall sheep, red fox, coyote, wolf, arctic ground squirrel, waterfowl, and various raptorial birds derived partial benefit from the reclaimed areas. The seeded grasses functioned as minor items in the diets of herbivores while reclaimed sites served as hunting areas for the various carnivores and raptors. Moose, showshoe hare, red-backed voles, willow ptarmigan and most nongame birds were adversely impacted by the reclaimed areas. Woody vegetation and its associated attributes such as cover and food were the essential habitat component missing from the reclaimed areas. Stripmining and reclamation procedures currently practiced in interior Alaska result in the formation of 'islands' of grassland interspersed throughout the natural habitat. The availability of undisturbed habitat adjacent to small sized, seeded areas, has made it possible for wildlife to take advantage of the reclaimed sites and still have sufficient amount of natural food and cover available with which to meet the nutritional and habitat needs of the animal. The detrimental effects of current reclamation procedures increase as the amounts of land disturbed by mining become very large. Present reclamation procedures create grasslands on disturbed sites. As the size of the disturbed area and subsequent areas of revegetation increases, the resulting loss of native forage and habitat will be very detrimental to the local wildlife. This adverse effect could be ameliorated if reseeded areas are interspersed with trees and shrubs. If recreating wildlife habitat is the major goal of reclamation, it is recommended that the creation of a diverse vegetative structure should be considered as important as the establishment of a ground cover