Ectotherms, including sharks, behaviorally thermoregulate in order to optimize physiological processes. Juvenile sharks often utilize estuaries, which can provide warm water temperatures that increase metabolism and facilitate growth. Both the California Horn Shark (Heterodontus francisci) and the Leopard Shark (Triakis semifasciata) occupy estuaries of southern California as juveniles and represent contrasting activity levels; horn sharks are relatively sedentary while leopard sharks are more active and mobile. The primary aim of this study was to better understand the relationship of behavioral thermoregulation and metabolism in response to temperature in these two species. The objectives were threefold: 1) identify the temperatures juveniles prefer, 2) assess the sensitivity of metabolism (Q10) to temperature via measurements of oxygen consumption, and 3) compare these results between species, sex, and seasonal acclimation treatments. Using a shuttlebox, this study showed juvenile horn sharks and leopard sharks have comparable thermal preferences and temperature ranges. Respirometry trials at different temperatures showed both species exhibited increasing metabolic rates with increasing temperature, and leopard sharks exhibited higher metabolic rates than horn sharks across all temperatures. However, horn sharks exhibited a higher overall Q10 suggesting their metabolism has greater thermal dependence. Underlying acclimation to seasonal temperatures did not appear to have an effect on any of these parameters. Horn sharks likely target environments (i.e., day-time resting places) closer to their preferred temperature and more stable in temperature fluctuation than leopard sharks. Lab-based determination of physiological and behavioral responses to temperature are important in understanding habitat usage during vulnerable life stages.

Signals are evolved to help animals communicate and thereby maximize their inclusive fitness. To increase the efficiently of communication, selection favors animals that are able to increase the effectiveness or amplify their signals over evolutionary time. Relatively few studies of signal amplification have been conducted on fishes although fishes include many species whose behavior is well-known. The Sarcastic Fringehead (Neoclinus blanchardi, Teleostei) exhibits an extreme version of a common aggressive display, the “gaping display” in which an open mouth is presented toward an opponent. This species has extremely long maxillae that are flared laterally during the display. In this study, display behaviors of three live specimens and 14 videos of N. blanchardi were observed, described, and analyzed. The comparative anatomy of N. blanchardi and the related species N. uninotatus and N. stephensae, were examined to document the structures related to the unusual gaping display. Fluorescence of the buccopalatal membrane was investigated. Finally, geometry morphometry, including the truss network system and thin-plate spline, and PCA were used to study the evolution of the maxilla under the heterochrony framework. The results show that the unusual gaping display is used for intraspecific territorial defense. Three main morphological modifications related to amplification of this display are enlargement of the buccopalatal membrane, enlargement of the adductor mandibulae muscle complex, and lengthening of the maxilla. The elongate maxilla of N. blanchardi evolved via acceleration (faster growth compared to outgroups) and hypermorphosis (continued growth to a larger body size), both forms of peramorphosis. All of these characters play a role in the amplification of the gaping display in N. blanchardi.

It is widely accepted that mesopelagic fishes are very abundant and maintain a high global biomass, but there exists a high degree of uncertainty in these biomass estimates. These fishes carry out all of their life stages in the water column and many undergo daily vertical migrations from the depths of the mesopelagic to the surface waters at night, returning to depth at dawn. This migratory behavior is one of the ecological factors that complicates our abilities to confidently evaluate the biomass of this group of fishes. Assessing the habitat use throughout ontogeny of mesopelagic fishes is a critical first step in understanding their role in the ecosystem. Additionally, the onset of diel vertical migration is relatively known for these fishes. Furthermore, larval fish identification is difficult and time consuming, and is often resolved only to the family level due to lack of taxonomic knowledge of species-specific ELH stages. Larval fishes

undergo profound changes during the early life history stages, therefore it is plausible that the earliest stages respond to environmental perturbations very differently than the later stages.

This dissertation is an examination of the importance of ontogenetic stage-specific investigation of larvae relative to habitat use. I describe the vertical distribution of ELH stages of the common mesopelagic fish species off central California by analysis of repeated tows of a discrete depth sampler, collected with a 1m2 MOCNESS from the same station during both day and night. I determined that common species of mesopelagic fish larvae off central and southern California exhibit differences in their diel distributions and that there are substantially more species of mesopelagic fish larvae below the epipelagic zone. Investigation using a larger sample set of MOCNESS data collected in central and southern California confirmed that mesopelagic fish larvae are more deeply distributed than previously realized. The patterns suggested that DVM begins in the larval stages for some species, which is much earlier in development than previously described for species in this geographic region. I then describe the ontogenetic changes in abundance and horizontal distribution of common species of mesopelagic fish larvae affected by the extreme El Nino event in 1997-1998 followed by the La Nina in the California Cooperative Oceanic Fisheries Investigations (CalCOFI). The results indicated that within the CalCOFI sampling area, mesopelagic fish species with an affinity for warm water conditions had a higher larval abundance and were closer to shore during the El Niño, and were less abundant and farther offshore during the La Niña. The opposite pattern was generally observed for mesopelagic fishes with an affinity for cold water conditions. Additionally, I discovered that the mesopelagic fish larval abundance in the CalCOFI region is dominated by the earliest stages of the larval period.

Finally, I discuss the conclusions of this dissertation that highlight the importance of ontogenetic habitat use patterns of mesopelagic fishes. Given their high global abundance, importance in the oceanic food web, and the potential for fisheries exploitation, this is an essential first step towards a reliable biomass assessments of mesopelagic fishes.

This project compiled current and historical records of fishes occurring in the vicinity of the San Diego-La Jolla Ecological Reserve (SDLJER), and assessed the effects of the Reserve on the abundance, diversity and population structure of resident fishes. This was accomplished by collection of quantitative data within the Reserve, immediately adjacent to the Reserve, and at site relatively distant from the Reserve that is not part of any marine reserve and subject to more intense fishing pressure. These assessments included transect surveys of densities and size distributions of conspicuous fishes. This study provides critical, but heretofore absent, baseline data for population monitoring of fishes in the Reserve and adjacent rocky-reef and kelp-forest communities in the San Diego region. In addition, records of fishes recorded within the vicinity of the SDLJER were compiled from the Scripps Institution of Oceanography Marine Vertebrate Collection in order to provide a detailed list of the ichthyofauna recorded in and around the Reserve.

The overall goal of this project was to develop the necessary infrastructure to permit species identification of California marine fishes using molecular sequence data. This involved the following efforts. 1) Compilation of an up-to- date list of marine fish species occurring in and around California. 2) Collecting and archiving in the Marine Vertebrate Collection, Scripps Institution of Oceanography, tissues and voucher specimens of California marine fish species. 3) Development of a standardized protocol for molecular identification of fishes, including sample preparation/DNA extraction, DNA amplification via polymerase chain reaction (PCR) and DNA sequencing, using three mitochondrial gene sequences (cytochrome b, 16S ribosomal DNA, cytochrome oxidase 1). 4) Making sequence data available on-line permitting remote comparison of sequence data with reference sequences from known species.

Studying evolutionary change with respect to the development of morphological traits in an organism can give insight on the evolutionary development and diversification of those traits, as well as valuable information about how these characteristics contribute to behavior. The Longjaw Mudsucker (Gillichthys mirabilis, Gobiidae) has been studied extensively for its ability to occupy low oxygen environments, yet few studies research the ontogeny of its elongate jaw as it relates to a unique gaping display behavior. Members of the Gillichthys genus exhibit this territorial defense behavior during mating months and G. mirabilis possess exceptionally long maxillae that are laterally flared during its gaping display. The elongate maxilla and associated buccopharyngeal membrane amplifies the aggressive gaping display of G. mirabilis and also increases surface area for gas exchange during aerial respiration. In this study, the maxillae of G. mirabilis, Gillichthys seta, and the outgroup species Eucyclogobius newberryi were examined and analyzed in an ontogenetic size series using digitized landmarks and caliper measurements. With these features, principal component analysis was used to study evolution in the maxilla of these three species under the heterochrony framework. Sexual dimorphism in the maxilla and body shape-space were also investigated to observe sexual trait selection and body shape correlation. The results show the maxilla of G. mirabilis evolved via acceleration (increased growth rate) and hypermorphosis (continued growth), two forms of peramorphosis. These results give us a start in understanding the evolutionary progression of the Longjaw Mudsucker and the potential connection of its elongated maxillae with its gaping display.