<p>White croaker (<i>Genyonemus lineatus</i>) are a sentinel fish species for contamination due to their direct interaction with contaminated sediments through benthic foraging. White croaker within the Los Angeles and Long Beach Harbor exhibited hierarchical habitat selection: avoiding dredged areas while selecting for areas of high sediment total organic carbon (4.8&ndash;8.1%), high polychaete density (406&ndash;700 polychaetes/0.1 m²), and small sediment grain size (&lt;23.5 &micro;m). Model results suggest that these fish are moving into shallower waters at night to forage and may refuge more during the day to avoid predation. The predictive model for white croaker habitat use indicated three important areas of use within the LA-LB Harbor: Consolidated Slip, Inner LB Harbor, and Fish Harbor. The areas containing the most preferable habitat to white croaker are also areas of high sediment contamination, and thus are the likely locations where these fish are acquiring contaminants. </p>

<p> The federally threatened Delta Smelt has been cultured in a conservation hatchery since 2008 in response to significant declines in the wild. The refuge relies on accurate, efficacious, and repeatable molecular techniques to help maintain the population's overall genetic diversity and minimize inbreeding. We have created a panel of single nucleotide polymorphisms (SNPs) to support broodstock pedigree reconstruction and improve upon current genetic management with microsatellites. Properly implemented, a SNP panel is a more powerful, repeatable, and higher-throughput method. Its use will streamline the management of the captive Delta Smelt population, which is performed in near real-time throughout the spawning season (February - May). For the SNP discovery, we sequenced 27 broodstock samples from the 2012 spawn using restriction site associated DNA sequencing (RAD-seq). We then created a linkage map by genotyping three single pair crosses at 2317 newly discovered loci with RAD-seq. We successfully mapped 1123 loci and identified 26 linkage groups. Fluidigm SNPtype genotyping assays were developed for 104 mapped loci selected for minor allele frequency (>20%), neutrality (Hardy-Weinberg equilibrium), and marker location. Candidates for the genotyping panel were evaluated on a 96x96 Integrated Fluidic Circuit and tested for marker accuracy and ability to accurately assign parentage. When applied in conjunction with mating records, we found that a panel of 24 independent SNPs successfully assigned 100% of tested offspring if all samples were genotyped at a minimum of 18 loci.</p>

<p> In large, seasonally dynamic and spatially complex watersheds, the availability and relative importance of various food resources for stream fishes can be expected to vary substantially. While numerous studies have attempted to uncover the trophic linkages that support stream salmonids, much of these efforts have occurred at small scales that disregard variability of food resources inherent in lotic systems. This study aimed to determine large-scale patterns in the contributions of freshwater, terrestrial, and marine-derived food resources to juvenile Chinook and Coho salmon (<i>Oncorhynchus tshawytscha</i> and <i>O. kisutch</i>) in the large, glacially influenced Susitna River, Alaska. I quantified diet patterns both spatially, across different macrohabitat types positioned along a 169-km segment of the river corridor, and temporally, from June to October, using stable isotope and stomach content analyses. To further resolve energy pathways from basal carbon sources to juvenile salmon, I determined the relative roles of terrestrial organic matter and freshwater periphyton food sources to aquatic benthic invertebrate diets. The latter analysis showed that invertebrate consumers were more reliant on freshwater periphyton than on terrestrial organic matter. Bayesian stable isotope mixing models indicated that juvenile salmon in the middle Susitna River were, in turn, largely supported by freshwater invertebrate prey regardless of spatial and temporal context. The relative contribution of marine-derived prey (salmon eggs) to juvenile salmon diets was greatest in the fall within tributary mouth and off-channel macrohabitats during both years of the study. Terrestrial invertebrate prey contributions were generally greatest during mid-summer within all macrohabitat types sampled, however this pattern varied across years. No upstream to downstream diet pattern was apparent from the data. These results underscore the importance of freshwater energy pathways for sustaining juvenile Chinook and Coho salmon in the Susitna River and provide further spatial and temporal context for the importance of pulsed marine and terrestrial prey subsidies. As Pacific salmon stocks continue to decline, management and mitigation efforts should operate on knowledge gained from studies that encompass the large-scale spatial and temporal variability inherent in riverine landscapes.</p>

<p> Gamefish populations in North America are experiencing increasingly elevated recreational fishing pressures; however, the impacts of current fishing regulations have not been evaluated for most marine species. Mandatory catch and release often results from size and bag limits with the assumption of fish survival and recovery with minimal sublethal effects. Depending on the intensity and duration of the stressor, acute stress from angling and handling can have deleterious physiological and behavioral impacts with consequences for fish health and fitness. We evaluated the short-term sublethal effects of angling-related stressors on kelp bass, <i>Paralabrax clathratus</i>, one of the most popular gamefish in southern California. Collaborating with recreational anglers to capture fish using standard hook and line practices, we evaluated biochemical responses and recovery by collecting blood samples at different time points after capture (10-120 min), after fish were released and some were recaptured (3h to 186 d). Blood cortisol, glucose, and lactate were significantly elevated and steadily increased in the hour following capture and holding (p &lt; 0.001). Fish caught, released, and recaptured after varying time at liberty were found to have returned to basal levels in &lt; 24 h (p > 0.05). Physiological stress responses were positively correlated with angling and handling duration, but negatively correlated with increasing fish size (p &lt; 0.05), suggesting that larger individuals may be more resilient to capture stress. Likewise, kelp bass exhibited no signs of cumulative or chronic stress from repetitive angling/recapture events and recovered to basal levels in &lt;24 h (p > 0.05). Kelp bass were also tagged with acoustic accelerometer transmitters and tracked to evaluate fine-scale behavioral effects of angling stress on their normal diel movement and activity. Reduced frequency of high acceleration movements (i.e. rapid feeding strikes) was observed for 33 h post-release, followed by recovery and evidence of elevated feeding behavioral activity. Rate of movement and area use size showed high individual and temporal variation; however, reduced movement immediately after release steady increased to normal levels over the first 10 h post-release. There was no discernable effect of angling on area use size, but areas of high relief substratum may be important refuge habitat for angled kelp bass during recovery. By integrating physiological and behavioral endpoints for kelp bass to standard angling induced stress we conclude that this species is able to recover in &lt;24 h; however, smaller individuals may be more susceptible to predation during this recovery period. Based on these findings, it is likely that kelp bass may still fair well under current size and bag limits.</p><p>

abstract: Phosphorus (P), an essential nutrient for growth of all organisms, is often in limited biological supply for herbivore consumers compared to other elements, such as carbon (C). Ecological stoichiometry studies have assessed responses of filter-feeding zooplankton from the genus Daphnia to single and multi-species food resources that are P-limited, finding decreased growth as a result to changes in metabolic processes and feeding behavior. Conversely, recent laboratory studies have shown that P-rich algal food resources also result in decreased growth rates for Daphnia, though the possible mechanisms behind this maladaptive response is understudied. Moreover, no published study tests the existence of the “stoichiometric knife edge” hypothesis for low C:P under field conditions. To address this lack of information, I measured growth rate as well as respiration and ingestion rates for D. magna, D. pulicaria, and D. pulex that were fed natural lake seston experimentally enriched with different levels of PO43-. I found heterogeneous effects of high dietary P across Daphnia species. Growth rate responses for D. magna were strong and indicated a negative effect of high-P, most likely as a result to decreased ingestion rates that were observed. The seston treatments did not elicit significant growth rate responses for D. pulex and D. pulicaria, but significant responses to respiration rates were observed for all species. Consumer body stoichiometry, differences in seston C:P for each experiment, or differential assimilation by producer types may be driving these results. My study suggests that the stoichiometric knife edge documented in laboratory studies under low C:P conditions may not operate to the same degree when natural seston is the food source; diet diversity may be driving complex nuances for consumer performance that were previously overlooked. / Dissertation/Thesis / Masters Thesis Biology 2015

<p> An understanding of the spatial and temporal diversity of benthic invertebrates is necessary to understand, manage, and protect freshwater habitats. Benthic invertebrates are important components of aquatic ecosystems and are frequently used in bioassessment and biomonitoring programs. Benthic invertebrates can also play a role in nutrient cycling in lentic environments through bioturbation activities. This dissertation uses a range of techniques and analyses to understand the arrangement of benthic invertebrate diversity in Upper Klamath Lake, Oregon, and several watersheds in northern southern California. </p><p> Upper Klamath Lake (UKL) is a large, shallow, naturally eutrophic lake that has experienced declines in water quality, which has led to annual cyanobacterial blooms of <i>Aphanizomenon flos-aquae</i>. Benthic invertebrates can increase autochthonous nutrient cycling through benthic bioturbation activities. In order to better understand the role that benthic invertebrates play in UKL, I studied the density, taxonomic richness, and species composition of benthic invertebrate assemblages in three geographic regions (north, central, and south) and three habitats (littoral, open-water and trench) across UKL. I also characterized sediment composition and water quality at each collection site and determined which environmental variables correlated with differences in benthic invertebrate composition. This research is located in Chapters 1 and 3 of this dissertation. </p><p> Like benthic invertebrates in UKL, the mayfly <i>Baetis tricaudatus </i> is an abundant and ecologically important organism of freshwater ecosystems. Despite its widespread distribution, <i>B. tricaudatus</i> cannot be consistently and accurately identified and belongs to a species group known to have cryptic species diversity. While previous studies have examined the spatial distribution of this diversity, none have studied the temporal distribution. To better understand the temporal arrangement of diversity at the cytochrome oxidase subunit 1 (CO1) mitochondrial gene region, I collected <i> B. tricaudatus</i> specimens from 3 sites over 4 years and used haplotype networks to visualize diversity. Because my results were different than those from other studies on the same taxon, for my final chapter I analyzed <i> Baetis rhodani</i> group COI sequences from northern and southern California using Bayesian phylogenetic analyses and haplotype networks. This research contributes to our understanding of genetic diversity, which is an important component to biodiversity.</p><p>

Degradation of aquatic ecosystems is an unfortunate consequence of industrialization, urbanization and general societial activity. The health of biological communities in these systems is subject to chemical stressors including emerging contaminants and legacy compounds that inevitably transit from land-based ecosystems into aquatic habitats. Fish have been utilized as preferred vertebrate sentinels of these systems for decdes; however, base-line data regarding disease, immune responses, endocrine function and other physiological responses is often not experimentally qualified prior to field application. Here, the presence of estrogen receptors (ERs) in channel catfish ( Ictalurus punctatus) leukocytes is demonstrated. Estrogens affect the responsiveness of channel catfish peripheral blood leukocytes (PBLs) to mitogens in vitro. The ERs, ERα and ERβ2, are differentially expressed depending on leukocyte lineage, phenotype, and state of activation. Estrogens are likely involved in the regulation of immune responses in vivo, and estrogenic endocrine disrupting chemicals may directly impact leukocyte function. Additionally, laboratory studies established a better understanding of immune and endocrine responses to polychlorinated biphenyl (PCB) exposure in brown bullheads (Amieurus nebulosus) and Atlantic salmon (Salmo salar). This legacy compound clearly modulated the immune response in both species, and likely predisposes these animals to disease. Interestingly, short-term short-duration exposures to environmentally relevant concentrations during early development can have long-term effects on T-cell populations of the immune system in salmon. These laboratory studies facilitated the interpretation of data collected from a multi season field study in the Ashtabula River where PCB contamination is thought to have negative impacts on resident biota. This applied field study utilized brown bullheads and largemouth bass (Micropterus salmoides ) collected from the Ashtabula River and a reference site, Conneaut Creek. Histological, immunological, allometric and endocrine biomarker endpoints provided strong evidence that fish from the Ashtabula River are biologically different than those from the reference site. Data also emphasized the advantage of a multi-tier, multi-species, multi-season sampling approach. The biological data were supported by body burden chemical analysis. Lastly, two diseases of bullheads resulting from Edwardsiella ictaluri and Henneguya gurlei were descrbed, and further the understanding of infectious diseases of this sentinel fish.^

Biogeographic barriers have limit the movement of organisms, leading to speciation and shaping the development of unique regional biotas. Human-aided circumvention of biogeographic barriers, however, has increased the connectivity of isolated biotas, while changes in climate have been altering species geographic ranges, restructuring ecological networks, modifying ecological niche arrangements and increasing the frequency and intensity of natural pulse disturbances. In this context, examination of some of the most fundamental processes underlying the patterns of species diversity and community structure across biogeographical scales is therefore vital, especially as humans increasingly modify these relationships established over the course of geological history. The latitudinal diversity gradient is the most well-established and predominantly studied biogeographic diversity pattern on Earth. Higher tropical biodiversity with a decline towards higher latitudes occur in both hemispheres and has been observed for various systems including terrestrial, freshwater and marine. In my dissertation, I explored latitudinal variation in factors that can inform and modify fundamental ecological principles such as coexistence, community stability, and resistance. I studied communities of marine invertebrates across over 7000 km of continuous coastal habitat spanning 47-degree latitudinal range on the Eastern North and Central Pacific coast, from tropical Panama to subarctic Alaska. Experiments were based on the manipulation of recently recruited or adult communities of sessile marine invertebrates, such as barnacles, marine worms and encrusting colonial organisms. These organisms inhabit coastal ecosystems across continental scales and can colonize artificial substrates such as hull of commercial vessels that travel across oceans serving as vectors for marine biological invasions. Among my three aims I was able to: (1) examine how the complementarity of ecological niches varies from the tropics to subarctic among recruiting taxa, and how the differentiation of these recruitment pulses through time help inform coexistence across large spatial scales; (2) document distinct resilience responses to pulse disturbances between lower and high latitude sites, while exploring the interplay between compositional and functional recovery in biological communities; and finally, (3) implement a novel component to pre-existing models to predict probability of biological invasions based on the distinct pressures of propagule introduction, environmental similarity between donor and recipient regions, and the potential for biotic resistance. My dissertation yields empirical evidence of processes varying with latitude, advancing our knowledge in some of the most fundamental questions in classic and contemporary ecology. Large-scale documentation of the mechanisms and processes that maintain global patterns of biodiversity are uppermost in the design of global conservation strategies, especially in a more connected world. / Biology

Understanding the relationship between heterogeneity, biodiversity and ecosystem function is an active focus of ecological research that has direct applications to the formulation of sustainable, science-based, watershed conservation plans. Here, I applied ecological theory on heterogeneity to the expansion of North American beaver to test hypotheses about physical habitat and fish biodiversity at a riverscape scale. To test these hypotheses (Chapter 4), I first addressed two methodological issues (Chapter 2, 3). By evaluating three types of gear at three levels of effort in a randomized block design over 4 replicate days, I show that 10 minnow traps, 2 hoop nets and 20 m of electrofishing captured most fish species within a 30-m sampling area (Chapter 2). Multiple statistical measures provided similar information, therefore I used general indices (richness, diversity), ecological guilds (flow based), and select multivariate analyses (DCA) to summarize fish communities (Chapter 3). I used these methodological insights to test ecological hypotheses by collecting habitat and fish data at all beaver dams (n = 15) and select control sites (n = 9) in Fish Brook, a coastal watershed in northeastern Massachusetts. From these data, I gained six basic and applied insights. First, beaver dams were distributed throughout the stream network. Second, at a local scale, beaver dams created more habitat heterogeneity than control sites. Specifically, beaver dams created four types of habitat alterations based on upstream-downstream differences in stream width, depth, velocity, and substrate. Third, richness and diversity of fish species around beaver dams were linked to habitat heterogeneity. Fourth, the mechanisms by which beaver dams altered fish biodiversity were mediated through habitat changes at the beaver dam patch boundary. Upstream of the dam macrohabitat guilds occupied the lentic areas, while below dams, fluvial fish guilds used shallow, faster water. Fifth, fluvial species responded the most dramatically to these habitat changes. Finally, in a system depauperate of lotic habitat, fluvial habitats created below beaver dams provided an important refuge for native stream fish. These source areas can increase resiliency and maintaining them may be useful for sustainable watershed conservation plans in these types of systems.

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