My research in coastal Ecuador and the northern Gulf of Mexico (GOM) elucidated differences in value of shallow estuarine habitats for fishes and invertebrates. I focused on mangrove and tidal river habitats in Ecuador, and oyster reef, vegetated marsh edge, and nonvegetated bottom habitats in the GOM. Coastal Ecuador has lost 20-30% of mangrove wetlands over the past 30 years. Such habitat loss can impair the ecological functions of wetlands. In this study I identified the fish community of the remaining mangrove wetland in Rio Palmar, Ecuador. For comparison, an adjacent tidal river without mangroves, Rio Javita, was also sampled. I found that although Rios Palmar and Javita are characterized by relatively low fish-species richness compared to other tropical estuarine systems, they appear to provide important habitat for several economically- and ecologically-valued species. In the GOM, I examined the fish and invertebrate communities of adjacent oyster reef (oyster), vegetated marsh edge (VME), and nonvegetated bottom (NVB) habitats. Three main relationships emerged: 1) Oyster and VME provide habitat for significantly more species (as a measure of richness) relative to NVB; 2) Oyster and VME provide habitat for uncommon and rare species; and 3) Many of the species collected in multiple habitats occurred at higher abundances in oyster or VME habitat. Contrary to the current low value ranking of oyster habitat relative to other estuarine and salt marsh habitats, oyster provides high quality habitat for many species. Understanding how key species utilize estuarine habitats is critical for future conservation and management efforts. My research indicated that VME habitat may provide better foraging options for juvenile pinfish (Lagodon rhomboides), and together with corroborating evidence from other studies, suggest that VME provides a critical nursery function for juvenile pinfish, especially in estuaries where seagrass habitat is sparse or nonexistent. Additionally, I documented that juvenile white shrimp (Litopenaeus setiferus) select for oyster habitat because of higher food availability and not because of refuge needs from predation by blue crabs. Oyster habitat appears to provide a nursery function for juvenile white shrimp. Overall, my research demonstrated that structurally complex habitats, such as mangroves, VME, and oyster provide essential habitat at the community, population, and individual levels.

The self-sustaining status of Georgian Bay’s trophy muskellunge (Esox masquinongy) fishery is owed in part to the widespread distribution of high quality coastal wetlands used as nursery habitat. The specific wetland features that promote the recruitment of young-of-the-year (YOY) muskellunge in Georgian Bay have not been clearly defined, and without such information, it is unclear to what extent an unprecedented period of sustained low water-levels (c. 1999), and/or shoreline modifications, will continue to degrade the suitability of nursery habitats used by muskellunge throughout Georgian Bay. In this thesis, I use data from two years of intensive sampling in two embayments of northern Georgian Bay to statistically differentiate between wetlands that were found with and without YOY muskellunge. By doing so, I have provided the first quantifiable definition of suitable nursery habitat for muskellunge in Georgian Bay. Muskellunge nurseries have a structurally complex community of submersed aquatic vegetation (SAV; e.g. Potamogeton richardsonii) within the water column (≤ 1-m depth) and a fish community that had abundant suitable prey (e.g. Cypinid species) and a scarcity of early-life predators (e.g. Perca flavescens). Some key aspects of the SAV community were governed by wetland's bathymetry, and this relationship makes it possible to model the effect of changing water-level scenarios on habitat suitability. I translated these results into a management tool for fish management agencies by creating an Index of Nursery Habitat Suitability (INHS) that can be applied to other embayments in Georgian Bay to identify high quality early-life habitats for muskellunge. I developed two INHS models and applied them to an independent dataset from other regions of Georgian Bay, and found them to differentiate between sites that were known to be used by YOY muskellunge and those where YOY were absent. These were also able to track deterioration in habitat quality associated with the recent decade of low water levels. Both INHS models rely on variables based on robust ecological relationships known to favour YOY survivorship that can be readily collected by fish management agencies, and one INHS model does not require detailed information of the aquatic plant community. Both models were also designed to minimize the frequency of false negatives (suitable nursery sites misidentified as unsuitable) and false positives (unsuitable nursery sites misidentified as suitable). These INHS models should become an important tool that will complement harvest regulations to promote this economically and ecologically valuable, self-sustaining muskellunge population in Georgian Bay. / Thesis / Doctor of Philosophy (PhD) / The following Ph.D. describes how a period of sustained low water levels and shoreline modifications in Georgian Bay, Lake Huron, have impacted the coastal wetland habitat used by muskellunge during their early life. To counteract these adverse effects, the thesis provides a definition of the wetland features that promote the survival of young-of-the-year muskellunge in Georgian Bay. Included is a proposed management tool in the form of an Index of Nursery Habitat Suitability (INHS) for muskellunge that can be used to identify high-quality, early-life habitat of muskellunge. Furthermore, the INHS can be used to predict how the quality of this habitat responds to different water-level scenarios and to shoreline modification in Georgian Bay, and to guide rehabilitative efforts of degraded wetland habitat.

The Chandeleur Islands (Louisiana) contain nursery habitats for lemon sharks that provide abundant prey and protection from predation. Other local shark species (Atlantic sharpnose, bull, and blacktip sharks) co-occur with lemon sharks in the same region, including the nearby Biloxi Marshes. To better assess how lemon sharks use these nursery habitats, I measured diet and prey availability of young of the year and juvenile lemon sharks from 2009 to 2010. Young lemon sharks at the Chandeleur Islands have a relatively reduced diet breadth in comparison to those from nurseries in Bimini (Bahamas) and the Florida Keys. At the Chandeleur Islands, young lemon sharks appear to be opportunistically feeding on the most abundant prey items, resulting in high prey abundance and low diversity in their diet. Opportunistic feeding by young lemon sharks suggests minimal dietary overlap with other local shark species, resulting in minimal competition for resources.

Anecdotal evidence suggested that immature lemon sharks (Negaprion brevirostris) occur at the Chandeleur Islands in southeastern Louisiana. From May 2009 to August 2011, the Nekton Research Laboratory at the University of New Orleans regularly sampled habitats at the Chandeleur Islands to confirm the presence of immature individuals of this species. During these efforts, 147 immature lemon sharks (neonates, young-of-the-year, and juveniles) were collected. Each shark was PIT tagged and a tissue sample was taken for genetic analyses. Sizes ranged from 56 – 177 cm total length. Sharks showed a preference for sandy substrate and smaller individuals showed significant preference for shallow waters. Collection data for N. brevirostris were obtained from various locations around the Gulf of Mexico for comparison. Based on a review of current literature, collection data, and microsatellite analysis it was possible to classify the Chandeleur Islands as an elasmobranch nursery ground under the definition presented by Huepel et al. (2007). Current literature and high densities of N. brevirostris suggests that the Chandeleur Islands are the only area in the northern Gulf of Mexico where neonatal and YOY lemon sharks have been recorded. Results from a combination of SPOT 5 satellite tags, PIT tags, and FLOY tags show that immature N. brevirostris at the Chandeleur Islands remain in the vicinity of the islands for several months. The abundance of juvenile sharks across years provides evidence of continuous use of these islands as a pupping area. Genetic analysis supports this information with 7 of 15 mothers returning across years. The combination of this information indicates that the Chandeleur Islands are the northern- and western-most documented nursery ground for this species. Special care should be given to this habitat as CPUE for N. brevirostris decreased significantly during this research following the 2010 Deepwater Horizon disaster and subsequent oil prevention measures. Genetic research indicates a high level of inbreeding and genetic separation between the Chandeleur Islands population and other known populations in Florida, Belize, and the Bahamas.

In the Maritimes, only two striped bass spawning populations remain: the Miramichi River in New Brunswick and the Shubenacadie – Stewiacke system in Nova Scotia. The Shubenacadie – Stewiacke system is subjected to a well pronounced twice daily tidal bore which induces dramatic changes in water parameters and challenges pelagic life. This system will be subject to potential change through brine discharge, a by-product of the Alton Natural Gas Storage Project. . Examining the temporal distribution of mysids, striped bass eggs and larvae at a fixed location around the Alton Project site will provide baseline information on population structure and insights into how egg and larvae distributions change with respect to tidal cycles, temperature and salinity. Surface plankton net tows from the top 0.75m of the water column were used to collect mysids, striped bass eggs and larvae over 14 months over two years. Daily mean egg abundance surpassed 1000 eggs/m3 once in 2008. A decrease of 1.9 °C in water temperature at the Alton Project site coincided with a cessation of eggs, and presumably, spawning. Spawning resumed when temperatures surpassed 15 °C. In contrast, the largest spawning event of the 2009 season occurred as water temperatures decreased (14 to 12.7 °C). The 2009 spawning season was longer (49 days) than 2008 (31 days) by 18 days, and in both years spawning peaked within the last week of May and first week of June. Two large spawning events, over 4000 daily mean eggs/m3 apiece, were detected May 24 and June 2, 2009. Mysids were present in high numbers throughout May to November, with some tows greater than 14,000 individuals/m3 in June 2008 and August 2009. Over the length of the ebb tide, as salinity decreases, mysid abundance also decreased. Whereas, striped bass egg abundance was consistently lowest at high tide and increased progressively over about 300 minutes through the ebb tide. Both striped bass larvae and mysids displayed patchiness in their temporal distribution suggesting passive transport in the this system. In both 2008 and 2009, larvae were detected at the Alton Project site for 38 days. The colder temperatures and larger tidal range of 2009, coupled with large increase in rainfall during the larval season contributed to the over 30-fold lower abundance over that found in 2008. When abundance was related in concert with temperature and salinity, mysids were ever present at high abundances except on three occasions. Mysid abundance decreased when salinity dropped beneath 5 ‰ during both years, and in 2008 when temperatures were lower than 15 °C. Salinity was impacted according to a seven-day lag after rainfall in both years, although the minimum volume of rainfall and associated impact on salinity have yet to be described.

Southern flounder (Parlichthys lethostigma) is a recreationally and commercially important flatfish species found in the Gulf of Mexico, and recent analyses indicate that the northern Gulf of Mexico population is in decline. For proper management, knowledge of habitats used throughout the juvenile stage is needed. The aim of the current study is to examine habitat use of young-of-year (YOY) southern flounder in the Galveston Bay complex using habitat distribution models and acoustic telemetry. A set of habitat distribution models examined how habitat use changes during the first year of life. In addition, southern flounder were tagged with acoustic telemetry transmitters and monitored with a novel receiver array that allows for measurements of fine-scale movements. These movements were compared to habitat maps to examine habitat selection. Habitat distribution models determined that habitat requirements for southern flounder change with ontogeny and season. Newly settled southern flounder were most influenced by physicochemical parameters and the presence of seagrass beds. YOY southern flounder, however, showed increased occurrence at freshwater inlets during summer and fall months, and occurrence decreased at tidal inlets during the fall. Predictions of habitat suitability across the Galveston Bay complex indicate that the factors influencing occurrence of southern flounder change with season, ontogeny, and availability of suitable habitats. With acoustic telemetry, it was apparent that habitat use by southern flounder was nonrandom and influenced by benthic and other physicochemical conditions. Habitat analyses indicated that southern flounder used sand habitats more frequently than seagrass, oyster reef, or salt marsh habitats. Telemetry results also indicated that depth and water temperature were important determinants of habitat suitability for YOY southern flounder, with individuals preferring deeper and cooler regions of the water column in Christmas Bay. Both model and telemetry analyses indicate that habitat use by YOY southern flounder is dynamic across multiple spatial and temporal scales, with distributions and movements influenced strongly by ontogenetic changes in habitat associations, temporal and spatial variability in physicochemical conditions, and tidal cycles.

Successful management of bighorn sheep depends on understanding the mechanisms responsible for population growth or decline, habitat selection, and utilization distribution after translocations. We studied a declining population of desert bighorn sheep in the North San Rafael Swell, Utah to determine birthdates of neonates, demographics, limiting factors, population size, probable cause of death, production, and survival. We documented 19 mortalities attributed to a variety of causes including cougar predation (n = 10, 53%), bluetongue virus (n = 2, 11%), reproductive complications (n = 2, 11%), hunter harvest (n = 1, 5%), and unknown (n = 4, 21%). Annual survival of females was 73% (95% CI = 0.55—0.86) in 2012 and 73% (95% CI = 0.55—0.86) in 2013. Adult male survival was 75% in 2012 (95% CI = 0.38—0.94) and 88% (95% CI = 0.50—0.98) in 2013. Disease testing revealed the presence of pneumonia-related pathogens. The population increased from an estimated 127 in 2012 to 139 in 2013 (λ = 1.09). Lamb:ewe ratios were 47:100 in 2012 and 31:100 in 2013. Mean birthing dates were 21 May in 2012 and 20 May in 2013. Spatial separation from domestic sheep and goats, and aggressive harvest of cougars, may have aided in the recovery of this population after disease events. Second, we investigated the timing of parturition and nursery habitat of desert bighorn sheep in the North San Rafael Swell to determine the influence of vegetation, topography, and anthropogenic features on resource selection. We monitored 38 radio-tagged ewes to establish birthing dates. We documented birthdates of 45 lambs. We used collar-generated GPS locations to perform logistic regression within a model-selection framework to differentiate between nursery and random locations (n = 750 for each) based on a suite of covariates. The top model included elevation, slope, ruggedness, aspect, vegetation type, distance to trails, and distance to roads. We used these variables to create a GIS model of nursery habitat for the North San Rafael (desert bighorns) and the Green River Corridor (Rocky Mountain bighorns). Ewes showed preference for steep, north-facing slopes, rugged terrain, lower elevation, and avoidance of roads. Our model provides managers with a map of high probability nursery areas of desert and Rocky Mountain bighorns to aid in conservation planning and mitigate potential conflicts with industry and domestic livestock. Finally, we monitored 127 reintroduced female bighorn sheep in three adjacent restored populations to investigate if the size and overlap of habitat use by augmented bighorns differed from resident bighorns. The size of seasonal ranges for residents was generally larger than augmented females. However, there was a shift in utilization distribution in all three populations after augmentation. Overlap indices between resident and augmented sheep varied by source herd. These data will help managers understand the dynamics of home range expansion and the overlap between provenance groups following augmentations.

The common snook, Centropomus undecimalis, is an estuarine dependent sport fish that relies upon subtidal wetlands as nursery habitat. Despite the economic and recreational significance of this species, there are portions of its life history and biology that are poorly understood, particularly its early life history. Understanding juvenile snook use of wetland habitats is crucial given the rapid loss and degradation of these areas to anthropogenic impacts. Young-of-the-year snook were collected in pond and creek habitats of a single wetland system to assess early life ecology and habitat use. Proxies of habitat quality were used to determine which habitats within a small spatial scale were optimal for young-of-the-year snook recruitment. Results indicated that even on a very small spatial scale, differences in habitat use were apparent, whereby smaller snook initially recruited to pond habitats and dedicated all energy into growth. Upon reaching a size of at least 40 mm SL snook began an ontogenetic habitat shift and moved to the tidal creek habitat. There, snook began to store energy, thus becoming more robust. Stable carbon and nitrogen isotopic analyses confirmed the ontogenetic habitat shift and revealed that snook have high site fidelity within the pond and creek habitats. Stable isotopic analysis also indicated that YOY snook appear to feed at the third trophic level consuming neonatal poecilliids and shrimp, and ultimately rely on benthic microalgae and particulate organic matter as basal resources. Results of this study advance the knowledge of juvenile snook ecology and will likely have implications for resource managers who are responsible for preserving and restoring wetland habitats upon which juvenile snook rely.

Diet and movements in fishes are often logistically challenging to study. Trace element and stable isotope analyses have advanced these fields considerably, but are still constrained by methodological impediments, such as the tendency towards lethal sampling. Studying endangered fishes is particularly challenging as representative samples are difficult to obtain. However, the information gained from such studies is often critical to the recovery of endangered fishes as knowledge of life history attributes has the potential to greatly influence the success of management strategies. I tested the viability of using fin rays in fishes as a non-lethal approach to study diet and movement patterns over time. I then applied the methods I developed to study the life history of the critically endangered Goliath Grouper, Epinephelus itajara. Fin ray analyses have traditionally been used in age and growth studies, as well as in a limited number of projects that study the chemical constituents of the ray itself. Therefore, I first tested whether fin rays could be used as chronological recorders of chemical properties over time using a pseudo-experimental design. By using samples from various aquaria, I had documentation of the time of capture of every animal used. Based on the assumption that the otolith in fishes represents a conserved, chronological matrix, I compared trace element concentrations between the otolith and the fin ray of each individual. In addition I tested whether stable isotope values of δ13C and δ15N differed between the wild and captive life phases of each individual. Divalent ions and positively-charged transition metals (e.g., Fe, Co) in particular showed strong associations between the two structures, suggesting conservation of material. Stable isotope values of δ13C and δ15N differed between the wild and captive life phases in most of the fishes sampled, also suggestive of conserved matrices. I then tested and modeled the differences in δ15N values over time between the populations of Goliath Groupers on the west and east coasts of Florida. In general, individuals on the west coast had lower overall values and a larger difference between juvenile and adult values. The mechanism that caused the differences between coastal populations may have been an artifact of the environment, rather than different feeding behaviors. Last, I investigated different nursery habitats for Goliath Groupers in southwestern Florida. I characterized juvenile nurseries based on the chemical fingerprints of trace elements within the inorganic matrix of the fin rays. Groupings based on these fingerprints were surprisingly accurate and can be used to identify essential nursery habitat for the species in years to come. This research demonstrated the efficacy of novel techniques that were used to gather information on the life history of a critically endangered fish in the state of Florida. The results can be used to influence management strategies in the future, particularly with regard to nursery habitat use.

No description available.