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No description available.

Only 40 years ago, just three individuals made the journey from Finland/Russia to found the current wolf population in the southwest of Sweden. This population, that to this date descends from less than 10 founders, has a substantial increased extinction risk due to inbreeding. Several previous studies have used SNPs to monitor the level of inbreeding and homozygosity in the population, as well as measure immigration and the inflow of new genetic material. This study uses both short- and long-read data to discover structural variants (SVs) and small indels in the population, so that they may be used to extend the analyses and provide more insight into the current state of the Scandinavian wolf population. After the calling of the SVs, strict filtering and manual curation were applied to the data, thereby removing many false positive calls and increasing confidence in the remaining SVs. Short-read and long-read SV-callers found 31,800 and 57,821 SVs respectively, with relatively little overlap between the two sets. By far, the most common SV-types were deletions and insertions, at about 30,000 each with varying length ranging from a 50 base pairs to several tens of Mbp. Analyses on the data, such as PCAs and parent-offspring trio analyses, reveal high-confidence calls and consistent results between SV-types and SV-callers, as well as a low estimated genotyping error rate. PCAs performed on the SVs resembled those performed on SNPs, which strengthens the credibility of the identified variants. Finally, this study suggests several alternative steps for possible improvement to the dataset, along with some proposals for subsequent research topics that may use the variants discovered in this study.

Food webs consist of a combination of bottom-up (resource-driven) and top-down (predator-driven) effects. The strength of these effects depends on the context in which they occur. I investigated food web (trophic) relationships between wolf (Canis lupus) predation, elk (Cervus elaphus) herbivory, aspen (Populus tremuloides Michaux) recruitment, and fire. The study setting, in the central portion of the Crown of the Continent Ecosystem, spans the US/Canada border and encompasses Glacier National Park (GNP), Montana and Waterton Lakes National Park (WLNP), Alberta. I stratified my observations across three spatially distinct areas, the North Fork Valley, in the western portion of GNP; the Waterton Valley, in the eastern portion of WLNP; and the Saint Mary Valley, in the eastern portion of GNP. All valleys are elk winter range (low-lying grasslands with patches of aspen). The valleys have three different observed wolf population levels (Saint Mary: low; Waterton: moderate; North Fork: high), which represent three levels of long-term predation risk (the probability of an elk encountering a wolf). Ecological characteristics (e.g., climate, soils, elevation, plant associations) are comparable among valleys. Fire has occurred in 90% of the North Fork. My objective was to examine the relative influence of bottom-up (fire) and top-down (predation risk) factors and the context-dependence of these relationships via data gathered during a three-year time span. I found complex elk responses to bottom-up and top-down factors that could influence habitat use by elk. Pellet transect data demonstrated that elk exhibited the same risk reduction behavior at all wolf population levels, even at very low levels. Predation risk variables that provided impediments to detecting or escaping wolves had a similar and negative influence on occurrence of elk (pellet piles), regardless of wolf population density. Fire had a negative effect on elk density and a positive effect on wolf density (per scat piles) in aspen communities where a high wolf population existed. Aspen cover, which may be riskier than open grassland, also had a negative effect on elk density, except at very high wolf levels without fire. The risk of wolf predation alone did not drive elk behavior. Conversely, focal animal (elk vigilance behavior) data suggested a positive relationship between wolf population and elk vigilance. However, when I deconstructed vigilance, elk demonstrated complex, context-dependent adaptive behavior in response to the long-term risk of predation by wolves. Commonly identified drivers of elk vigilance (group size, impediments to wolf detection and escape) appeared to be important drivers at an intermediate level of long-term predation risk (e.g., Waterton). These drivers ceased to function in this manner when the long-term predation risk level increased (The North Fork). At high levels of long-term predation risk, vigilance was high, but not driven by these common factors. In some cases, the relationship between vigilance and risk factors was reversed (e.g., group size). And at a low level of long-term predation risk (Saint Mary), elk did not respond to these drivers of vigilance. When I measured aspen demography (browse, recruitment), browse was lower in the North Fork, where there was a high wolf population, suggesting a top-down effect. However, I found low aspen recruitment in the absence of fire in all valleys, which indicates a bottom-up effect in that aspen is highly fire-dependent. Top-down predictors of aspen recruitment (e.g., plot position and stand size, which are related to predation risk) had no effect on browse levels regardless of wolf population level. In sum, the risk of wolf predation alone did not drive the food web relationships I observed. Bottom-up and top-down forces worked together in valleys that contained well-established wolf populations, and to a lesser degree in a valley with a low wolf population. Commonly used measures of predation risk responses (e.g., vigilance) reversed their relationship as the wolf population increased. Low aspen recruitment in the absence of fire demonstrates the importance of bottom-up effects. Bottom-up and top-down effects may be important joint engineers of aspen communities. My findings invite deeper inquiry into the interaction between bottom-up and top-down effects in large mammal systems. / Graduation date: 2012