I sampled the eastern portion of the Fort Apache Indian Reservation from June 19 to August 8 in 2008 and from May 6 to June 19 in 2009. I used scat detection dogs to find wolf (Canis lupus baileyi) scat on the Fort Apache Indian Reservation during 2008 and 2009. My population size estimate of the wolf population was 19 individuals (95% CI = 14 - 58; SE = 8.30) during 2008 and 2009. My study also used DNA analyses to obtain an accurate assessment of Mexican wolf diet and, compare prey remains in Mexican gray wolf scat with prey remains in two other sympatric carnivore species (coyote, C. latrans, and puma, Puma concolor). Percent biomass of prey items consumed by Mexican wolves included 89% for elk, 8% for mule deer, and 3% for coyote. Percent biomass of prey items consumed by pumas was 80% for elk, 12% for mule deer, 4% for turkey, and 4% for fox. I included an ethnographic feature to my research. My study showed evidence of shared knowledge about the wolf within Western Apache culture. My data fit the consensus model based upon the large ratio between the first and second eigenvalues. I provided a literature review of how traditional ecological knowledge has enhanced the field of conservation biology but also the challenges of collecting and incorporating it with western science. Lastly, I provide an historical perspective of wolves throughout Arizona, an assessment of their historical abundance, and document a possible mesocarnivore release. Between 1917 and 1964, 506 wolves, 117,601 coyotes, 2,608 mountain lions, 1,327 bears, 19,797 bobcats, and 21 jaguars were killed by PARC agents, bounty hunters, and ranchers as reported in U.S. Bureau of Biological Survey Annual Reports in Arizona. The relationship between the numbers of coyotes and wolves destroyed was investigated using Pearson correlation coefficient. There was a negative correlation between the numbers of wolves and coyotes destroyed in Arizona between 1917 and 1964 (r = -0.40; N = 46; p = 0.01) suggesting a possible mesopredator release of coyotes with the extirpation of the wolf in Arizona.

The genetic diversity and phylogeography of brown bear maternal lineages have been studied extensively over the last two decades. In this study the genetic diversity and maternal phylogeography of non-invasively sampled 35 brown bears, including 5 captive individuals were reported from Turkey. In addition to the optimization of DNA extraction from hair, faeces and old skin samples and their PCRs, Bayesian phylogenetic analyses based on a 269 bp long piece of bear mitochondrial DNA were conducted and 14 novel haplotypes belonging to three major lineages were revealed. The most widespread lineage was found to be the &ldquo / Eastern&rdquo / clade 3a, while geographically more restricted &ldquo / Western&rdquo / and &ldquo / Middle Eastern&rdquo / lineages were reported for the country for the first time. A specimen from the Taurus range (southern Turkey) was shown to be closely related to the presumably extinct bears in Lebanon. Moreover, a unique novel lineage that appears to have split early within the Middle Eastern clade was defined. Despite limited sampling, this study demonstrates a high level of mitochondrial diversity in Turkish brown bears, extends the ranges of both European and Middle Eastern clades into Turkey, and identifies a new divergent lineage of possibly wider historical occurrence while demonstrating the significance of non-invasive genetic sampling for such analysis.

This study looked at the efficacy of using woodland caribou fecal pellets as a source of DNA to identify sampled animals and estimate population demographics. Fecal pellet samples were collected using systematic surveys of woodland caribou ranges in Jasper National Park, Alberta and the North Interlake region, Manitoba. Collection of pellet samples took place when snow was present to allow for tracking and location of caribou cratering areas and to obtain good quality DNA. DNA was amplified at ten polymorphic loci and one sex-specific primer. To estimate population size (N ̂) and population growth rate (λ), mark-recapture models were used. Model assumptions were evaluated and tested by stratifying available samples based on herd and gender information. In using the Mh (jackknife) model, the population sizes for south Jasper National Park were estimated at 125 animals in 2006-2007 (95% CI: 114, 143), 91 animals in 2007-2008 (95% CI: 83, 105) and 134 animals in 2008-2009 (95% CI: 123, 152); comparable to the mark-resight population estimates calculated over the same sampling periods. Genetic diversity indices for the different herds in Jasper National Park presented a lower genetic diversity for the smaller Maligne and Brazeau herds when compared to the larger Tonquin and A La Peche herds. Use of population assignment tests on samples collected in Jasper National Park indicated considerable admixture between the different herds despite earlier telemetry work demonstrating strong herd fidelity. The North Interlake population was estimated at 134 animals (95% CI: 122,151) in 2006-2007 and 106 animals (95% CI: 97, 121) in 2007-2008. Using data collected between 2005 and 2008, population growth rate for North Interlake was estimated at 0.83 (90% confidence interval: 0.65, 1.02). As a λ below 1 indicates a declining population, continue monitoring of the North Interlake herd is highly recommended. This studied clearly showed that the sampling of fecal DNA is a reliable and noninvasive alternative to monitoring woodland caribou population sizes and trends in the boreal and mountain regions.

This study looked at the efficacy of using woodland caribou fecal pellets as a source of DNA to identify sampled animals and estimate population demographics. Fecal pellet samples were collected using systematic surveys of woodland caribou ranges in Jasper National Park, Alberta and the North Interlake region, Manitoba. Collection of pellet samples took place when snow was present to allow for tracking and location of caribou cratering areas and to obtain good quality DNA. DNA was amplified at ten polymorphic loci and one sex-specific primer. To estimate population size (N ̂) and population growth rate (λ), mark-recapture models were used. Model assumptions were evaluated and tested by stratifying available samples based on herd and gender information. In using the Mh (jackknife) model, the population sizes for south Jasper National Park were estimated at 125 animals in 2006-2007 (95% CI: 114, 143), 91 animals in 2007-2008 (95% CI: 83, 105) and 134 animals in 2008-2009 (95% CI: 123, 152); comparable to the mark-resight population estimates calculated over the same sampling periods. Genetic diversity indices for the different herds in Jasper National Park presented a lower genetic diversity for the smaller Maligne and Brazeau herds when compared to the larger Tonquin and A La Peche herds. Use of population assignment tests on samples collected in Jasper National Park indicated considerable admixture between the different herds despite earlier telemetry work demonstrating strong herd fidelity. The North Interlake population was estimated at 134 animals (95% CI: 122,151) in 2006-2007 and 106 animals (95% CI: 97, 121) in 2007-2008. Using data collected between 2005 and 2008, population growth rate for North Interlake was estimated at 0.83 (90% confidence interval: 0.65, 1.02). As a λ below 1 indicates a declining population, continue monitoring of the North Interlake herd is highly recommended. This studied clearly showed that the sampling of fecal DNA is a reliable and noninvasive alternative to monitoring woodland caribou population sizes and trends in the boreal and mountain regions.

The United States Fish and Wildlife Service (USFWS) expressed the need to develop appropriate management strategies for apparently high-density, growing black bear populations in the Roanoke-Neuse-Tar-Cape Fear ecosystem in coastal North Carolina and Virginia. In order to provide the scientific information necessary to develop these strategies, I investigated population densities and genetic structure of black bears at 3 national wildlife refuges [Great Dismal Swamp (GDSNWR), Pocosin Lakes (PLNWR), and Alligator River (ARNWR)]. Density estimates were derived from DNA samples collected noninvasively at each of the 3 refuges for 2 consecutive summers. Hair samples were analyzed for individual identification using 6-7 microsatellite markers. Estimated densities were some of the highest reported in the literature and ranged from 0.56-0.63 bears/km2 at GDSNWR to 0.65-1.12 bears/km2 at ARNWR to 1.23-1.66 bears/km2 at PLNWR. Sex ratios were male-biased in all areas of all refuges. Genetic variability and structure of bears at these refuges was assessed using 16 microsatellite markers for 40 bears from each refuge. Genetic variability of the 3 refuge populations was substantially high compared to other bear populations in North America, with observed heterozygosities ranging from 0.6729 at GDSNWR to 0.7219 at ARNWR. FST and DS values were relatively low (0.0257-0.0895 and 0.0971-0.3640, respectively), indicating movement of bears and gene flow across the landscape is adequate to prevent high levels of genetic differentiation and structure among the refuge bears. Genetic statistics at GDSNWR indicate that this population is isolated to some degree by geography (i.e., the Albemarle Sound) and encroaching urban development (i.e., the towns of Suffolk and Chesapeake). ARNWR has the potential to become isolated in the future if movement corridors to the south of the refuge are not maintained. Harvest of bears is likely warranted at PLNWR and ARNWR, though extreme caution must be taken the first few seasons as hunter success will be extremely high. Further research is needed to determine population growth rates, reproductive parameters, and survival rates at all 3 refuges, particularly if a hunting season will be established and maintained in these areas. Methods for regularly monitoring bear populations at these refuges also should be incorporated into biological programs, as bears comprise a significant component of the ecosystem at these refuges and cannot be ignored when outlining management goals. / Master of Science

In this thesis, molecular genetic methods were used to study a threatened species, the Eurasian otter. Estimates of population size and population dynamics parameters were obtained, the genetic effects of a restocking program was evaluated, and a population viability analysis was conducted to assess which demographic parameters are most important for the future viability of an otter population. Many of the studies were based on noninvasive genetic sampling of faeces. In the genetic evaluation of the restocking program, it was found that the released otters had contributed to subsequent generations. However, the effects were to a large degree limited to the near surroundings of the release areas. Comparison of two census methods, snow-tracking and noninvasive genetic census based on faeces, showed that approximately only half of the otters detected with the genetic census were found with the snow-tracking census. It is recommended to combine these two methods to obtain the most reliable estimates of population size. A short-term study on population dynamics in otters showed that apparent survival was higher in females than in males and that the rate of addition was also high and likely influenced by migration. The population viability analysis incorporated both genetics and demography and revealed that survival to first reproduction was the most crucial demographic parameter affecting the viability of the study population. This result suggests that conservation efforts should be focused on protocols that enhance the survival prospects of young females. Environmental stochasticity was also found to have large effects on the probability of extinction of this population.

Recent improvements in genetic analyses have paved the way in using molecular data to answer questions regarding evolutionary history, genetic structure, and demography. Key deer are a federally endangered subspecies assumed to be genetically unique (based on one allozyme study), homogeneous, and have a female-biased population of approximately 900 deer. I used 985bp of the mitochondrial cytochrome b gene and 12 microsatellite loci to test two hypotheses: 1) if the Moser Channel is a barrier to gene flow, I should expect that Key deer are differentiated and have reduced diversity compared to mainland deer and (2) if isolation on islands leads to a higher probability of extinction, I should expect that Key deer exhibit a small population size and a high risk of extinction. My results indicate that Key deer are genetically isolated from mainland white-tailed deer and that there is a lack of genetic substructure between islands. While Key deer exhibit reduced levels of genetic diversity compared to their mainland counterparts, they contain enough diversity of which to uniquely identify individual deer. Based on genetic identification, I estimated a census size of around 1,000 individuals with a heavily skewed female-biased adult sex ratio. Furthermore, I combined genetic and contemporary demographic data to generate a species persistence model of the Key deer. Sensitivity tests within the population viability analysis brought to light the importance of fetal sex ratio and female survival as the primary factors at risk of driving the subspecies to extinction.

Abstract Wild populations of large carnivores in Europe were almost wiped out during the last centuries. Nowadays, the number of brown bears in North and Eastern Europe has increased, and the current situation suggests that these populations have recovered or are in the process of recovery. Knowledge of the population genetic consequences of demographic recovery in large carnivores, especially across national borders and on broader geographical scales, is still limited. In this study, we collected 3,757 fecal and hair samples as well as 881 tissue samples from brown bears across Northern Europe, with a focus on the Finnish population and neighboring areas, to investigate the population structure, connectivity, and genetic diversity on a spatial as well as a temporal scale. Bayesian clustering analysis of the population structure suggested the division of brown bears in Northern Europe into several genetic clusters, and the subdivision of the Finnish population into a northern and southern subpopulation. The estimation of gene flow pointed to better connectivity of the bears between Southern Finland and Western Russia, while migration between Scandinavia and Northern Finland as well as between Scandinavia and Southern Finland/Western Russia appeared to be restricted. Genetic clusters identified in Finland, Russia and Northern Norway displayed high genetic diversity, which was among the highest reported in wild brown bears. Recovery of the Finnish population has been accompanied by a detected range expansion towards the north, while genetic differentiation between clusters has decreased and genetic diversity has increased in the southern population, suggesting expansion from the south. Our results demonstrated that the immigration of bears from Russia still plays a major role in the Finnish bear population; however, connectivity between the Finnish-Russian population and Scandinavian bears appears to be restricted and should be improved, as well as regularly monitored. / Tiivistelmä Suurpetojen luonnonpopulaatiot hävisivät Euroopasta melkein kokonaan viimeisten vuosisatojen aikana. Ruskeakarhujen määrä on viime aikoina kasvanut Pohjois- ja Itä-Euroopassa, ja karhupopulaatiot ovat toipuneet tai toipumassa. Tieto demografisen toipumisen geneettisistä seurauksista populaatioissa on varsin rajoittunutta etenkin laajemmassa maantieteellisessä mittakaavassa, yli valtiorajojen. Keräsimme tätä tutkimusta varten 3757 uloste- ja karvanäytettä ja 881 kudosnäytettä Suomesta ja sen lähialueilta. Tarkoituksenamme oli kartoittaa Pohjois-Euroopan karhupopulaatioiden geneettistä rakennetta ja monimuotoisuutta, sekä populaatioiden välisiä yhteyksiä huomioiden ajallinen ja maantieteellinen ulottuvuus. Bayesiläisen ryhmittelyanalyysin perusteella Pohjois-Euroopan karhut jakaantuvat useaan geneettiseen ryhmään. Suomen populaatiossa erottuivat eteläinen ja pohjoinen alapopulaatio. Analyysit geenivirran määrästä osoittivat, että Etelä-Suomen ja Länsi-Venäjän karhupopulaatiot ovat yhteneväisemmät, kun taas migraatio Skandinavian ja Pohjois-Suomen sekä Etelä-Suomen ja Länsi-Venäjän välillä vaikuttaisi olevan rajoittunutta. Suomesta, Venäjältä ja Pohjois-Norjasta tunnistetut alaryhmät olivat geneettisesti hyvin monimuotoisia, ja muuntelu oli korkeampaa kuin koskaan aiemmin karhuilla havaittu. Suomen karhupopulaation toipuessa ja levitessä pohjoiseen, geneettinen erilaistuminen maan sisällä on vähentynyt ja eteläisen alapopulaation monimuotoisuus kasvanut. Tämä viittaa populaation laajentumiseen etelästä käsin. Tulosten perusteella karhujen tulomuutto Venäjältä on yhä tärkeää Suomen populaatiolle. Suomen ja Venäjän karhupopulaatioiden yhteyttä Skandinavian karhupopulaatioihin tulisi seurata ja parantaa.