Climate and land-use change have altered and continue to affect the diversity, composition, and distribution of freshwater organisms throughout the world. This is particularly true in arid and semi-arid regions, where aquatic organisms may experience more pronounced reductions in available habitat with declines in precipitation, increases in water demand, and habitat degradation through human land-use. However, documentation of changes in taxonomic assemblages over long-time periods has been rare because of the difficulty in obtaining historical occurrence data. This dissertation used data from previously published literature, a resurvey study, museum specimens, and enthusiast sightings to document changes in the occurrence rates and distribution of freshwater organisms throughout California over the past century.

Summary information regarding freshwater taxa known to occur in California did not previously exist in a central publication. I therefore conducted a review of several primary groups of stream organisms found in the Mediterranean region of California and statewide. For this work, I gathered data from a variety of literature sources and museum specimens to summarize species composition and endemism in the region, and to identify data gaps and conservation priorities for the examined groups. The remainder of this dissertation focuses largely on changes in Odonata species diversity, composition, and occurrence rates over time in California. This charismatic group was ideal for study of change over time because of their relatively low diversity, well-known taxonomy, and the existence of sufficient historical and current specimen records and more recent enthusiast sightings of odonates.

I conducted a resurvey of sites originally sampled for Odonata by Clarence H. Kennedy 1914-1915. This work involved surveys of odonates at 81 sites throughout central California and northwestern Nevada, 45 of which were directly comparable to Kennedy's original sites. I found that while site-level species richness has not changed significantly, assemblages have become more homogeneous across sites. Habitat generalists have generally expanded in the extent of their distribution while habitat specialists have declined. In examining current local and regional factors influencing the occurrence of Odonata species in this region, I found that species occurrence was higher during site visits with higher degree-days, especially for highly mobile groups, including dragonflies and migratory species. The probability of presence across species was lower in highly urban sites, particularly for habitat specialists. Overall, both regional and local factors influenced the occurrence of odonates in the study with implications for conservation.

A large component of this dissertation included development and analysis of a database of over 33,000 Odonata occurrence records throughout California over the past century. This database included specimen records from museums in California and large odonate collections elsewhere, as well as statewide enthusiast sightings from recent years. I noted that these unstandardized data contain biases with regards to uneven sampling effort, which must be addressed in analysis. Subsequent analyses of occurrence records before and after 1975 indicated that Odonata distribution may have generally shifted northwards with temperature warming and to lower minimum elevations in response to increased summer water-availability in low-elevation agricultural regions. Similar to results from the resurvey study, the museum specimen data indicated that highly mobile migratory species have increased while habitat specialists have declined. I concluded that a combination of sampling biases, species traits, and climate that have influenced the probability of detection of Odonata species over the last century.

An understanding of environmental responses to current and emerging problems and the capacity to forecast future threats requires appropriate indicators. The temporal scale of impact to animal health and species biodiversity can vary from centuries in the case climate change, to immediate, such as chemical spills. This dissertation uses genetics, physiology, and community ecology to understand current and emerging environmental threats and appropriate biomonitoring responses across a range of temporal scales.

Patterns of genetic diversity across a species range can suggest past glacial refugia and recolonization, dispersal barriers, and evidence of vulnerabilities to future change. However, population genetic structure and historical refugia among co-occurring species is not well characterized for many groups of aquatic organisms. Therefore, I compared phylogeographies of five, large bodied co-occurring aquatic insect species (four stoneflies: Calineuria californica, Hesperoperla pacifica, Pteronarcys californica, and Pteronarcys princeps and one caddisfly: Dicosmoecus gilvipes) across their ranges.

Widespread and persistent environmental contaminants may be monitored in the marine environment using top predators such as marine mammals. I sampled serum, inner blubber, and outer blubber and determined predictive equations between tissues for a suite of persistent organic pollutants in northern elephant seals (Mirounga angustirostris), which indicated strong relationships, particularly between serum and inner blubber POP concentrations.

Although benthic macroinvertebrate communities respond to natural environmental fluctuations they can still serve as indicators of acute anthropogenic stressors. Multiple years of macroinvertebrate sampling (2004, 2010-2013) in an urban creek quantified the community response to an accidental, 3000 L, oil spill using a Before-After Control-Impact approach. Taxa richness and sensitive taxa decreased immediately, but recovered one year later, likely aided by drift from upstream reference sites and winter rains. Additionally, I identified five indicator taxa that will enhance future biomonitoring efforts.

To better understand population dynamics and response to drought in seasonal wetlands, I investigated successional changes in macroinvertebrate occurrence and abundance in northern California. The early-season predator assemblage was dominated by dytiscid beetles and late-season by Lestes damselflies. The phenology of taxa and life history strategies may affect how macroinvertebrate populations respond to increased annual variation in hydroperiod as a result of future climate change.

Changes to hydrology, water chemistry, physical habitat, and the landscape surrounding aquatic ecosystems can have profound effects on their biological communities, potentially reducing important ecosystem services and functions provided to wildlife and humans. In this dissertation, I examine how environmental variables, human activities, and management practices have affected stream and wetland biota throughout Northern California.

The parasitic trematode Ribeiroia ondatrae has been shown to cause limb malformations in amphibian species through laboratory studies, but these small-scale experiments lacked important ecological co-factors that could alter parasite transmission rates and host susceptibility. Therefore, I conducted a multi-year, nested experiment at Hog Lake in Mendocino County to test host responses to Ribeiroia infection. The addition of Ribeiroia-infected snails to half of Hog Lake caused an increase in severe limb malformations in Pacific chorus frogs (Pseudacris regilla) and monitoring at different spatial scales revealed unique dose-response relationships because of ecological interactions and environmental co-factors. To determine if the parasite might contribute to population declines, I monitored juvenile and adult P. regilla at Hog Lake and a second wetland for four years. The consistently low (< 5%) malformation prevalence in adult frogs despite a generally high malformation prevalence (30-50%) in juvenile frogs confirmed that malformed amphibians do not survive to adulthood, indirect evidence that Ribeiroia may cause population declines. Multi-year surveys at 17 Northern California wetlands showed a strong dose-response relationship among the parasite and P. regilla malformation levels, providing evidence that Ribeiroia is an important cause of limb malformations in this region.

Effective conservation of wetland species depends on understanding how anthropogenic stress, natural environmental variables, and management activities affect biological communities. To identify which of these explanatory variables were most influential and determine the conservation value of created wetlands, I sampled amphibians and insects from a total of 49 stormwater ponds, stockponds, and natural ponds in Northern California. Overall, landscape variables (i.e., percent urban and natural, number of ponds within 1 km, and elevation) were associated with differences in macroinvertebrate community structure, but specific conductance and percent littoral vegetation present were important co-factors. Compared to natural ponds, stockponds supported the most similar invertebrate assemblages and greater amphibian species richness. Light cattle-grazing of areas surrounding natural ponds and stockponds was associated with increased amphibian richness, whereas the addition of exotic fishes was associated with mild differences in invertebrate populations. This research showed that stockponds are conservation resources for amphibians and invertebrates but that proper management is necessary to maximize this potential.

To objectively quantify the ambient condition of wetlands, ecologists use the plants and animals found in aquatic habitats as biological indicators. Because no biological indicator has been developed for wetlands in California, I designed an index of biotic integrity (IBI) to determine the ecological condition of the wetland based on macroinvertebrate community structure. Eight metrics that showed significant responses to urbanization, had adequate range, and lacked redundancy with each other were incorporated into the IBI. The IBI was successfully validated and showed no bias along natural gradients (e.g., ecoregion, elevation, and precipitation), except that non-perennial and perennial ponds did support slightly different communities, indicating that the IBI is applicable across this region.

Although biomonitoring data have been successfully used to quantity the ecological condition of perennial streams in many regions of California, no analysis tool (e.g., IBI) has been developed for the San Francisco Bay Area, a region which contains a large proportion of non-perennial streams. To identify least-disturbed reference sites in a highly urban region and examine how inter-site and temporal variability affect bioassessment data, I analyzed a large (> 400 sites) stream bioassessment dataset. I found that using geographic information system (GIS) watershed analysis and local physical habitat data were both necessary to identify least-disturbed reference sites. Among reference sites, the macroinvertebrate assemblages of perennial streams were different from non-perennial streams, a result which demonstrates the need for separate IBIs for these two habitat types. Interannual variability was moderate across 2000 to 2007, with index scores ranging from 10-15 out of 100 points, but some sites showed extreme variation of more than 50 points.

In summary, this dissertation shows that effective management of wetlands and streams can be accomplished with the use of biomonitoring data to infer ecological condition and that stockponds are valuable conservation resources when properly managed.

In this dissertation, I examined the occurrence of insecticides in streams in intensive soy production regions of South America, and their effects on invertebrate communities. Recently soy has become a major export crop in South America, and the insecticides used are highly toxic to aquatic invertebrates. I adapted the Species at Risk pesticide index (SPEARpesticides), which was developed in Europe to assess effects of pesticide contamination in agricultural streams. I then explored the relative importance of insecticides in comparison to other agricultural stressors, and the potential for riparian buffers to mitigate pesticide transport and impacts. My study sites were on small streams adjacent to agricultural fields in four soy production regions: two regions in the Argentine Pampas (La Plata-Magdalena and Arrecifes), and one region each in the Atlantic forest habitat of Brazil and Paraguay.

Commonly used insecticides were detected at high frequencies in all three countries, and pyrethroids insecticides were the most likely to occur at acutely toxic concentrations. Samples with highest toxicity were collected from streams with riparian buffer width less than 20 m, and buffer width was the most important predictor variable in explaining insecticide levels. I evaluated the toxicity of the four most commonly detected insecticides to Hyalella curvispina, a freshwater amphipod that is widespread in South America. The lowest LC50 values were found for the pyrethroid insecticides lambda-cyhalothrin and cypermethrin, followed by chlorpyrifos and alpha-endosulfan.

After adapting the SPEARpesticides index for local invertebrate communities in the Argentina streams, I found that SPEARpesticides was the only response metric that was significantly correlated with insecticide levels. Multiple regression showed that insecticide toxicity was the most important stressorin explaining variability in the SPEARpesticide index.

I then evaluated the relative importance of insecticides and other agricultural stressors on invertebrate communities in Atlantic Forest streams. Although buffer widths in Brazil streams were negatively correlated with insecticide concentrations, and had a moderate importance in mitigating effects on some sensitive taxa, insecticides had little importance in explaining variability in invertebrate communities. The forested riparian buffer zones are likely to have mitigated the effects of pesticides on stream invertebrate communities in these regions.

Human disturbance at global and local scales is profoundly impacting stream ecosystems in California. For example, climate change, which is considered a form of human disturbance in this dissertation, is causing notable increases in air temperature and decreases in precipitation in some regions of the state. These changes are outside the range of natural variability and are expected to intensify. Furthermore, these changes affect stream-water temperatures, stream-flow levels, and aquatic biota. Human disturbance at the local scale in California includes, but is not limited to, urbanization, the development and use of land for timber extraction and agriculture, and manipulation of habitats for recreation or for the preservation of endangered species.

I examined the impacts of global change and human disturbance on stream ecosystems in Northern California at a variety of sites and using a variety of biological and physical techniques. The sites were located in five California counties, including Lake, Marin, Napa, Siskiyou, and Sonoma. Monitoring and analytical techniques for benthic macroinvertebrates used both standard and novel approaches and metrics of biological assessment. Physical techniques included surveys of channel widths and longitudinal profiles, bankfull-channel estimates, flow measurements, pebble counts, fine-sediment measurements, and large-wood inventories, which were analyzed using a variety of geomorphological and hydrological approaches.

I found that: 1) the common metrics used in biological assessment will have continued applicability for biological assessment programs in Northern California and that a new metric for detecting climate-change effects could be developed; 2) stream-crossing reconstruction was causing increased patchiness of benthic-macroinvertebrate communities in the short term; 3) vineyard water-withdrawals were having an effect on stream communities that occurred after a threshold level of vineyard coverage and extent was reached; and 4) the addition of engineered, large-wood structures to streams for physical-habitat restoration increased pool frequency and caused changes in the benthic community, although the resulting levels of large wood in the channels were still lower than levels typically found in other regions of the northwestern United States.

The Geysers of Sonoma County, California, currently the larges geothermal energy field in the world, is expected to expand its electrical generating capacity considerably in the coming years. However, these future developments may result in watershed modification and potentially deleterious effects on aquatic biota due to the topography of the area. Analysis of the response of benthic populations and communities to past and ongoing geothermal energy development and operational practices was undertaken by means of an extensive six site sampling program on Big Sulfur Creek and a concentrated colonization study above, in, and below a heavily impacted tributary (Little Geysers Creek).

Differences in species diversity were noted among the six Big Sulfur Creek sites that were selected relative to the presence or absence of natural fumaroles or hot springs and the absence or stage of geothermal energy development. Distribution and colonization patterns of a population of sericostomatid caddisfly, Gumaga nigricula, and especially its dominance in high silt areas, suggest that both siltation and fumarole activity may select for certain populations.

The arrival of the Chinese mitten crab to the San Francisco Bay-San Joaquin Delta (Bay- Delta) ecosystem has been a source of widespread concern. This crab has spread from its native range, in China, to coastal ecosystems throughout Europe and, most recently, into North America. The Chinese mitten crab population in California has exploded within the last decade to cover hundreds of miles of the Bay-Delta and its tributaries. The Chinese mitten crab is a large, catadromous crab, moving from freshwater habitats where it spends its juvenile years to saltwater habitats in order to reproduce. In other countries into which this species has been introduced, the abundance and behavior of the crab has caused detrimental impacts to fisheries and loss of bank stability in areas where it burrows.

Through a grant from the Water Resources Center, we set out to examine the ecology, distribution, and economic and ecological impacts of the Chinese mitten crab in the fresh and saline waters of San Francisco’s South Bay. The Chinese mitten crab offers excellent opportunities to: 1) study the population dynamics of an invasive species; 2) examine differences and similarities for this organism between its native and new environments; and 3) use research findings to make recommendations for understanding and control of this organism.

From 1976-1983, a series of studies were undertaken at The Geysers K.G.R.A. in Sonoma and Lake Counties, California to evaluate the effects of geothermal energy development on aquatic biota at The Geysers. A major objective throughout the eight years of the research project has been to develop quantitative methods to analyze and monitor benthic communities. This report summarizes the methods used and presents examples of the data such approaches have produced.

Each report on a sampling approach contains: (1) a summary of the advantages and disadvantages of the device; (2) an illustration of the device; (3) a description of its use either at The Geysers or in pilot studies to test the appropriateness of its use at The Geysers; and (4) a sample data set.