The genus Albula includes marine fish species, commonly called bonefish, that occur in tropical coastal ecosystems worldwide. Their association to nearshore marine environments makes bonefish especially vulnerable to habitat loss and overharvest. Artisanal fisheries often harvest bonefish, although, in certain areas, bonefish support lucrative catch-and-release recreational fisheries. Bonefish are largely understudied compared to other economically significant fish species, and the presence of cryptic species within the Albula genus has further complicated the establishment of conservation measures. In particular, there is no detailed biological information available on bonefish from the Red Sea despite the unregulated harvest of bonefish that occurs there. To facilitate the establishment of management and contribute to the overall knowledge of Albula biology, I assessed the genetic diversity, growth, and seasonal reproduction of bonefish in Saudi Arabia. Based on samples collected from local fish markets and coastal waters, my findings provide the first genetically verified records of A. glossodonta in the Red Sea and A. oligolepis in the northwest Indian Ocean. Moreover, my results indicate a genetically distinct Red Sea population of A. glossodonta that reaches smaller sizes than documented for the species in the Pacific Ocean and exhibits distinct seasonal spawning activity over the winter months. This information enables fishery managers to make informed decisions regarding bonefish size limits and seasonal colures around peak spawning activity. My results may become increasingly relevant as the potential for lucrative recreational fisheries for Albula glossodonta will likely increase with the ambitious Red Sea tourism development plans.

Bonefish (Albula spp.) support an economically important sport fishery, yet little is known regarding the reproductive biology of this genus. Analysis of oocytes histology and sex hormone levels was conducted on wild female bonefish sampled during and outside the spawning season in Grand Bahama, Central Andros, and South Andros, The Bahamas to assess reproductive state. Bonefish are commonly found along shallow water flats, or in pre-spawn aggregations (PSA) during spawning months. 17β-estradiol levels suggest vitellogenic consistency between habitats. However, fish are more reproductively developed at PSA based on the occurrence of larger, more prevalent vitellogenic oocytes and evidence of final maturation. Variability in hormone levels and spawning readiness existed between Grand Bahama and Andros PSAs, suggesting peak spawning may differ by region. Findings from this study will contribute baseline data to the captive bonefish restoration project at Harbor Branch Oceanographic Institute and to the limited ecological data regarding bonefish reproduction. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2018. / FAU Electronic Theses and Dissertations Collection

Relying on field research to complete the life history for certain fish species can be inadequate, but laboratory research can be used to fill these gaps. These gaps exist for Bonefish (Albula spp.), a tropical marine fish and popular sportfish. In this study, aquaculture techniques were applied to Bonefish in a captive setting at Harbor Branch Oceanographic Institute (HBOI) and Cape Eleuthera Institute (CEI) to induce spawning and describe early ontogeny. Photothermal manipulations and hormone injections were used to induce gonad maturation and spawning, which was achieved once at CEI and is the first record of hormone-induced spawning for Bonefish. From that spawn, egg and larval development were recorded and described through 26 hours and 56 hours respectively, representing the first record of these early life stages for Bonefish. This work expands upon what is known about Bonefish reproductive biology and will be useful for management and future captive research. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2018. / FAU Electronic Theses and Dissertations Collection

Florida’s recreational bonefish fishery generates substantial economic benefits to the region; however, the resource has never been adequately assessed to determine standard benchmarks for sustainability. The situation offered a unique opportunity to address unresolved issues in sustainability for a valuable recreational fishery that is almost exclusively catch and release. The goal of this dissertation was three-fold: (1) to develop a comprehensive framework for conducting rigorous stock assessments on recreational catch-and-release fisheries; (2) to apply these methods to the Florida bonefish fishery to compare results against internationally-recognized sustainable fishery benchmarks; and, (3) provide recommendations for longer-term assessment strategies and management efforts. Due to the dearth of available bonefish information, existing literature were synthesized and new quantitative data and models concerning bonefish demographics (i.e. growth, survivorship) and population dynamics were developed. Data for age-and-growth were collected with a focus on both small (< 100 mm FL) and large (>650 mm FL) bonefish which had been under-sampled in previous research. A two-stage growth model was developed that allowed predictions of size-at-age over the complete life history of the species. Evidence from multiple analyses suggested a single species of bonefish in the Florida fishery. A mail survey of bonefish captains (guides) acquired baseline statistics on the south Florida bonefish fishery. Fleet fishing effort is mostly concentrated in the northern Florida Keys (Biscayne Bay to Islamorada) and reflects to some extent bonefish spatial population abundance. The majority of the respondents indicated the stock had declined over the past few decades. A sized-based mortality estimator was used to determine mortality. Changes in current population size from 2003-2010 were determined from a visual survey. Historical stock size was inferred from a relative abundance index from standardized tournament catch rates. Annual trends of the mortality estimates implied a stable population that is not declining which contrasts with the index of abundance and visual survey results. Both the index of abundance and visual survey displayed overall declining trends in recent years. Bonefish movements were determined from anchor tag and acoustic telemetry. Anchor tagging data were analyzed to evaluate movements, stock size structure and mortality. Results revealed no significant relationships between distance moved and days at large or days at large and length at tagging; however, significant individual movements (>100 kilometers) were recorded. Use of acoustic telemetry showed frequent movements around the barrier islands, schooling behavior, and a possible spawning effect with movements to offshore reef habitats. Stock status was addressed with two different classes of assessment models: REEFS, a length-based model which estimated the stock as moderately exploited with the current fishing mortality rate less than the maximum sustainable yield fishing mortality rate; and a “catch-free” age-structured model which indicated a large stock decline over the past 40 years with the stock currently bordering an overfished benchmark. The age-structured model was assumed to be the most robust method because it incorporated the majority of the research data (age and growth, selectivity, mortality, visual survey, CPUE standardization, vessel effort). In conclusion, the stock’s productivity has been significantly reduced over the past 50 years due to fishing, but also degradation of key prey populations, habitats, and water quality, resulting in a current bonefish population that is bordering an overfished state. Recommendations are provided for improving future stock assessments and management approaches. The assessment framework and quantitative methods and models developed here are broadly applicable to bonefish stocks around the world.

Bonefish (Albula spp.) support an economically important catch-and-release recreational fishery, as well as artisanal harvesting, in The Bahamas. Little is known about the large-scale movement patterns of bonefish, yet such information is essential for proper species conservation and management. I used acoustic telemetry to determine large-scale movement patterns of bonefish around Andros, Bahamas, in conjunction with presumed spawning migrations. I conclude that bonefish travel long distances from shallow flats to pre-spawning aggregation sites in proximity to off-shore reef locations. Off-shore movement to deeper reef locations occurs around both new and full moons. This study has also confirmed anecdotal reports that the North Bight is an important spawning migration corridor for bonefish. This information is critical for the protection of bonefish and identifies important habitats (e.g. migration corridors and pre-spawning aggregations) on Andros that warrant protection from coastal degradation or fishing pressures.

Bonefish (Albula spp.) support valuable recreational and artisanal fisheries worldwide. Declining stocks have been reported at multiple localities, potentially jeopardising numerous multimillion-dollar industries. In particular, tourism generated through bonefish fly fishing contributes considerably to the economies of many isolated tropical islands and atolls. However, despite their economic value, little is known about bonefish in the Indian Ocean. This study aimed to contribute to the understanding of bonefish ecology in the Indian Ocean by (1) reviewing the bonefish literature to identify knowledge gaps; (2) evaluating the postrelease survival of acoustically tagged bonefish and; (3) quantifying the spatial and temporal movements of bonefish at a near-pristine and predator rich atoll in the Seychelles. A review of published literature on bonefish indicated that despite considerable biological and ecological research in the Pacific and Atlantic oceans, virtually no research has been conducted in the Indian Ocean. To help address this research gap, an acoustic telemetry study was initiated at the remote St. Joseph Atoll, within an existing array of 88 automated datalogging acoustic receivers. Thirty Albula glossodonta were surgically implanted with Vemco V13 acoustic transmitters in May 2015 and tracked for a period of one year. Only 10% of the tagged bonefish were detected for more than two weeks. A comparison of the final 100 hours of movement data from fish that were detected for less than two weeks to fish detected for longer periods revealed distinct differences. These included differences in area use patterns and significant differences in the average daily distance moved, speed of movement and residency index. This suggested that mortality in the form of post-release predation was high (90%) with tagged fish detected for less than two weeks being preyed upon by sharks. The three surviving bonefish were tracked for 210 to 367 days. These individuals remained in the atoll and showed high use of the marginal habitats between the shallow sand flats and the deeper lagoon. Water temperature, diel cycle and tide were significant predictors of bonefish presence in the lagoon. The high post-release predation of bonefish has implications for the management of this and other Albula species. Despite these fisheries being catch-and-release, bonefish fishing may be unsustainable due to the high post-release mortality, particularly in areas that are rich in predators. Therefore, protected areas or limitations on fishing effort need to be considered.

Local ecological knowledge (LEK) is a useful method to capture environmental or resource changes when there is an absence of biological data. Since the bonefish fishery is data limited, this study aims to understand the trend of bonefish decline over the last 40 years using LEK and to assess whether varying fisher experience and fisher type would influence perception of bonefish decline. Semi-structured surveys and key informant interviews were conducted to collect LEK data. Along with perceiving an overall decline (p

The burgeoning frequency of genome sequencing in recent years is a testament to both the improvements in sequencing technologies and the utility of genomic analyses for biological discovery. The rapid proliferation in technological advancements and availability of complementary data types and techniques has obfuscated the optimal process of genome assembly and raised the barrier to entry to unprecedented levels. In this dissertation, we describe the genome assemblies performed for several marine teleosts and discuss the algorithms and applications required for genome assembly, including some of our specific contributions to the genome assembly and annotation space. In Chapter 1 and Chapter 2, we review the taxonomy, life history, and biogeography of the Roundjaw Bonefish (Albula glossodonta) and describe its genome assembly. The genome assemblies with some analyses are described for the Bluefin (Caranx melampygus) and Giant (Caranx ignobilis) Trevallies in Chapter 3 and Chapter 4, respectively. Chapter 5 and Chapter 6 define and assess algorithms for the annotation of simple sequence repeats in genomic sequences. Publicly available annotations of carbapenem-resistance plasmids were epidemiologically analyzed in Chapter 7. The resiliency of phylogenetic trees to the removal of taxa is explored with a new nodal stability metric and algorithm, TANOS, in Chapter 8. Finally, in Chapter 9, a review of and commentary on vertebrate genome assembly is presented with recommendations for new projects. The aim of this dissertation, and the final chapter in particular, is to explore genome assembly methods and reduce the barrier to entry for new entrants.