The vast majority of rivers in the developed world are affected by human alteration, which in turn negatively affects the species that rely on these highly diverse and species rich areas to survive. Homogenization of previously heterogenic areas due to a change in water discharge and the substrate availability in the rivers is often regarded as the main reason for the loss of species richness in rivers and the riparian zone. Because of this, there are a lot of restoration projects which main goal is to increase heterogeneity. The goal of this thesis is to compare hydrology and geomorphology variables between four types of reaches with high flow velocity (rapids in free-flowing reaches, rapids with regulated flow, impounded reaches and reaches in outlet channels below hydropower plants). In this thesis I wanted to find out how changes in geomorphology and hydrology affect fish species richness, riparian vegetation richness and aquatic vascular plants species richness. The result show that both fish species richness and riparian vegetation species richness are negatively affected by the changes in geomorphology and hydrology. There was no significant difference for aquatic vascular plants when comparing the regulation types. The most altered reach type, outlet channels, had significantly fewer fish species compared to the less altered reach type, impounded reaches. Outlet channels also had less riparian vegetation cover compared to all other regulation types, and fewer riparian vegetation species compared to both free-flowing reaches and impounded reaches. In conclusion, hydropower plants and timber floating have both negatively impacted the riverine ecosystem, and in turn caused a decrease in species richness for fish and riparian plants. The reaches studied in this thesis will continue to be altered and the species richness and species composition will change from an ecosystem that relied on the natural flow regime to an ecosystem more used to the flow regime created by the hydropower plants.

The Sacramento San Joaquin Delta has been highly altered by human activity since the mid-1800s from mining, agriculture, dredging, and urbanization. Did the resulting modifications to channel width, depth, and length alter tidal range in the Sacramento San Joaquin Delta? In this study, archival tidal records were evaluated at many stations throughout the San Francisco Bay and Delta, with a focus on San Francisco, Rio Vista, Sacramento, and Stockton daily, monthly, and annual tidal ranges. Monthly and seasonally averaged tidal ranges were analyzed to determine seasonal changes. In addition, tidal range was compared to daily Delta discharge to consider the effects of river flow. Results show that the spatial pattern of tidal amplitude through the San Francisco Bay and Delta system have changed since the mid-nineteenth century and the changes are consistent with human and climate change impacts on the Delta landscape. There is a general 7% increase in mean annual tidal range in San Francisco from 1860 to 2018. In Stockton, mean annual tidal range increased from 0.6 meters to 0.9 meters between 1908 and the 1930s but decreased approximately 9% from the 1930s to 2011. Mean annual tidal range in Sacramento increased from zero to 0.5 meters between 1890 and the late 1930s and then decreased by 50% through the early 2000s to approximately 0.25 meters. Lower tidal ranges in the early 1900s are consistent with the effects of hydraulic mining. Increased tidal ranges in the mid-20th century are consistent with dredging throughout the system. Recent decreases in tidal ranges are consistent with wetland restoration, increased water storage, and further modifications to the geometry and management of the Delta. A peak river flow shift from late spring/early summer to early spring has contributed to increased tidal range between February and June by 0.1 and 0.6 meters in San Francisco and Stockton, respectively. In Sacramento, the least decrease in tidal range between 1939 and the present occurred during spring months, due to the decrease in river discharge during this period. Tides have recorded the history of environmental change within the highly altered San Francisco Bay and Sacramento San Joaquin system. While not as notable as similarly altered systems, the changes described here were most significant in Sacramento where mean annual tidal range has ranged between zero and 0.5 meters since 1890 and, for any discharge below 1,000 cubic meters per second, mean daily tidal range is higher from 1938 to 1939 than from 1997 to 2018. Change in tidal range implies potential change in tidal velocities, salinity intrusion dynamics, and flood risk within the system, especially in Sacramento.

In 2004, I initiated a year-long study to investigate the food habits of burrowing owls (Athene cunicularia). Burrowing owls have been found in a variety of human-altered landscapes; however, little is known about burrowing owl food habits in urban landscapes. Burrowing owl food habits during the non-breeding season are also largely undocumented, despite increasing concern over the survival of overwintering burrowing owls. Differences in prey consumption between reproductive and non-reproductive owls during the breeding season have not yet been examined. I collected pellets over a 12 month period at four study sites affected by different levels of human alteration in the southern San Joaquin Valley of California. Data was collected at four study sites representing natural (Wind Wolves), semi-natural (Allensworth Ecological Reserve), agricultural (Friant Kern Canal), and urban (Bakersfield) landscapes. Invertebrates, primarily ground dwelling insects, were the most commonly consumed prey type, found in 96% of all pellets examined. Among vertebrates, mammals were the most commonly consumed (18.5% of all pellets). Shannon-Weiner diversity indices identified differences in prey diversity consumed between seasons within each site and between sites within seasons, except during the breeding season where diversity was the same at all sites. The diversity indices at Wind Wolves (natural site) and Bakersfield (urban site) were the same, while the diversity indices at Allensworth Ecological Reserve (semi-natural site) and Friant Kern Canal (agricultural site) were the same. Binary logistic regression was used to determine if consumption of individual prey types varied by site, season, and a site/season interaction. Mammals were consumed in greater proportions during the breeding season at most sites compared to other seasons. The proportion of pellets containing mammals during the breeding season decreased as the level of human-alteration increased, with mammal consumption highest at Wind Wolves (60.0%) and lowest at Bakersfield (13.1%). Consumption of several insect categories differed by site and/or season (Coleoptera, Dermaptera, and Orthoptera), but overall consumption of insects was not different by either factor. To assess differences in prey consumption between reproductive and non-reproductive owls, pellets collected during the 2005 breeding season were classified as having come from a nest burrow or a non-nest burrow based on positive identification of reproduction. Shannon-Weiner diversity indices and binary logistic regression were calculated for this data set. No differences were detected in overall diversity or in the proportional consumption of individual prey categories. The results of this study indicate that burrowing owls have a highly variable diet and may have sufficient ecological plasticity to allow them to adjust their food habits to the prey species available in human-altered landscapes. However, the implications of altered food habits on burrowing owl fitness in heavily disturbed landscapes, particularly urban landscapes, needs further study.