<p> Evolutionary biologists are supremely interested in the events that cause populations to diverge and speciate, and the mechanisms that maintain divergence over time. Here, I investigate the evolutionary history of a boreal bird species complex. Boreal bird species are co-distributed, diverged during the Pleistocene, and generally have patterns of genetic divergence that are consistent with a single &ldquo;boreal&rdquo; clade in northern and eastern North America. The Gray-cheeked Thrush species complex, however, shows a possible species break in eastern North America between the Bicknell&rsquo;s Thrush (<i> Catharus bicknelli</i>) and Gray-cheeked Thrush (<i>Catharus minimus </i>). Using population genetic and genomic analyses of the largest sampling to-date of either species, I find that the eastern break indeed coincides with a species-level divergence, although low levels of admixture in a few individuals and one probable hybrid hint at the possibility of occasional hybridization. Species distribution models (SDMs) of the Last Glacial Maximum revealed that divergence may have been maintained by residence in different late-Pleistocene refugia. However, because speciation occurred mid-Pleistocene, I examined the geographical context of divergence of the Bicknell&rsquo;s Thrush and Gray-cheeked Thrush using multivariate analyses and ecological niche modeling techniques of local-scale habitat data and broad-scale climate and tree species distributions. Local-scale habitat analyses reveal that the thrushes breed at sites with unique tree species composition, physiognomy (forest structure), and ground cover characteristics; furthermore broad-scale analyses reveal that niche divergence, rather than conservatism, was the predominant pattern for these species, suggesting that ecological divergence has played a role in their speciation. This dissertation supports the hypothesis that the Bicknell&rsquo;s Thrush and Gray-cheeked Thrush are distinctive species that breed in divergent local- and broad-scale niches and emphasizes that this species-level divergence seems unique among boreal bird species.</p>

<p> Culverts are ubiquitous in urban and natural environments, installed to provide road access and erosion control, but often impact fish movements in freshwater habitats. Effects of culverts on marine and estuarine fish are not well-studied. This study aimed to understand the potential impacts of a culvert, which connects a large tidal bay and a coastal lagoon, on the movements of several species of fish. Habitat characteristics of both sites were analyzed to better understand these movements, including water parameters, sediment characteristics, and zooplankton, benthic macroinvertebrate, and small fish communities. The two habitats differed in terms of temperature, salinity, dissolved oxygen, zooplankton abundance, and community composition of zooplankton, benthic macroinvertebrates, and small fish. The culvert and associated grate limited large fish from moving between the two habitats likely due to body size and other morphological characteristics. Removing this barrier and replacing it with an open channel would increase connectivity between these two habitats which could improve trophic quality in the lagoon habitat and increase functionality overall.</p><p>

<p> Information about population dynamics, life history variation, and connectivity patterns of threatened cutthroat trout (<i>O. clarkii</i> spp.) is critical for effective management and restoration. The Lahontan cutthroat trout (<i>O. c. henshawi;</i> LCT) is classified as threatened under the Endangered Species Act due to widespread extirpations across its range, and is at increased risk due to drought, habitat fragmentation, and climate change. This study was conducted in the Summit Lake Basin, NV (USA), which has a population of LCT that resides in Summit Lake and its tributary stream network. The objectives of this research were to (1) examine the population dynamics of stream- and lake-dwelling LCT in the context of drought, (2) quantify the amount of stream-resident versus adfluvial life histories in an adfluvial spawning tributary, and (3) identify the level of population connectivity between stream-resident and adfluvial components of the population. Chapter 1 shows that stream-dwelling trout were more resilient to drought disturbance and that drought refugia in the stream contribute to their resilience. Chapter 2 provides evidence for stream-residency in addition to high population connectivity across the lake and stream environments that is likely to increase in high flow years. While LCT and other cutthroat species have innate characteristics that allow them to persist in dynamic and harsh environments, this research highlights the importance of drought refugia and landscape connectivity to the long-term persistence and viability of co-occurring adfluvial and stream-resident fish.</p><p>