Aquaculture and Fisheries Commons^™

West Coast Rock Lobster Resource Harvest Strategy, Department Of Primary Industries And Regional Development, Western Australia

Fisheries management papers

Harvest strategies for Western Australia’s (WA) aquatic resources are formal documents developed by the Department of Primary Industries and Regional Development (DPIRD, the Department) to support decision-making processes that ensure the outcomes are consistent with the principles of Ecologically Sustainable Development (ESD; Fletcher 2002a) and Ecosystem Based Fisheries Management (EBFM; Fletcher et al. 2012). Harvest strategies are a key component of all contemporary fishery management systems and a requirement for certification under the Marine Stewardship Council (MSC). The objectives of ESD are reflected in the objectives of the Fish Resources Management Act 1994 (FRMA) and the Aquatic Resources Management Act …

Comparison Of Dna Extraction Methods For The Detection Of Canned Tuna Species With Dna Mini-Barcoding, Aubrey J. Emmi, Biola Fatusin, Rosalee S. Hellberg

Food Science Faculty Articles and Research

Tuna is susceptible to species mislabeling due to its high demand, quick rate of production, and wide range of price points. DNA barcoding, a sequencing-based technique, allows for the detection of species mislabeling by targeting a standardized region of DNA. A mitochondrial control region (CR) DNA barcode has been found to be capable of species discrimination for tuna, but it is challenging to recover the entire DNA fragment from canned tuna. While a short fragment of CR, referred to as a “mini-barcode,” has shown some success with canned tuna species identification, more research is needed to improve identification rates. The …

South Coast Offshore Crustacean Resource Of Western Australia Harvest Strategy, Department Of Primary Industries And Regional Development, Western Australia

Fisheries management papers

Harvest strategies for aquatic resources in Western Australia (WA) that are managed by the Department of Primary Industries and Regional Development (DPIRD, the Department) are formal documents that ensures decision-making processes are consistent with the principles of Ecologically Sustainable Development (ESD; Fletcher 2002) and Ecosystem Based Fisheries Management (EBFM; Fletcher et al. 2012). The objectives of ESD are reflected in the objects of the Fish Resources Management Act 1994 (FRMA) and the Aquatic Resources Management Act 2016 (ARMA), which is anticipated replace the FRMA once enacted. At this point, the Fish Resources Management Regulations 1995 (FRMR) is also anticipated to …

Biodiversity Of Philippine Marine Fishes: A Dna Barcode Reference Library Based On Voucher Specimens, Katherine E. Bemis, Matthew G. Girard, Mudjekeewis D. Santos, Kent E. Carpenter, Jonathan R. Deeds, Diane E. Pitassy, Nicko Amor L. Flores, Elizabeth S. Hunter, Amy C. Driskell, Kenneth S. Macdonald Iii, Lee A. Weigt, Jeffrey T. Williams

Biological Sciences Faculty Publications

Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g., filets, fish meal); however, DNA reference libraries are incomplete, and public repositories for sequence data contain incorrectly identified sequences. During a nine-year sampling program in the Philippines, a global biodiversity hotspot for marine fishes, we developed a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 2,525 specimens representing 984 species. Specimens were primarily purchased …

Genome-Wide Analysis Of Acute Low Salinity Tolerance In The Eastern Oyster Crassostrea Virginica And Potential Of Genomic Selection For Trait Improvement, Alexandra J. Mccarty, Standish K. Allen Jr., Louis V. Plough

VIMS Articles

As the global demand for seafood increases, research into the genetic basis of traits that can increase aquaculture production is critical. The eastern oyster (Crassostrea virginica) is an important aquaculture species along the Atlantic and Gulf Coasts of the United States, but increases in heavy rainfall events expose oysters to acute low salinity conditions, which negatively impact production. Low salinity survival is known to be a moderately heritable trait, but the genetic architecture underlying this trait is still poorly understood. In this study, we used ddRAD sequencing to generate genome-wide single-nucleotide polymorphism (SNP) data for four F_{2 …}

Genomic Degeneration And Reduction In The Fish Pathogen Mycobacterium Shottsi, David T. Gauthier, Janis H. Doss, M. Lagatta, T. Gupta, R.K. Karls, F. D. Quinn

Biological Sciences Faculty Publications

Mycobacterium shottsii is a dysgonic, nonpigmented mycobacterium originally isolated from diseased striped bass (Morone saxatilis) in the Chesapeake Bay, USA. Genomic analysis reveals that M. shottsii is a Mycobacterium ulcerans/Mycobacterium marinum clade (MuMC) member, but unlike the superficially similar M. pseudoshottsii, also isolated from striped bass, it is not an M. ulcerans ecovar, instead belonging to a transitional group of strains basal to proposed “Aronson” and “M” lineages. Although phylogenetically distinct from the human pathogen M. ulcerans, the M. shottsii genome shows parallel but nonhomologous genomic degeneration, including massive accumulation of pseudogenes accompanied by proliferation of …

Otoliths Of South-Western Australian Fish: A Photographic Catalogue, Chris Dowling, Kim Smith, Elain Lek, Joshua Brown

Fisheries research reports

Due to the species-specific nature of otoliths and given they are often the only part of the fish preserved when fish die, otolith catalogues can be used in numerous applications, such as diet studies in fish eating animals, including pinnipeds, fish and sea birds; archaeological purposes such as reconstructing indigenous people’s diets from otoliths found in middens or evolutionary history of fish species by comparing fossilized otoliths. Given the unique mixture of subtropical and temperate fish, including many endemic species that occur off the southwest corner of WA having a catalogue for this area is extremely important for people working …

Age, Growth, And Mortality Of Atlantic Tripletail In The North-Central Gulf Of Mexico, Amanda E. Jefferson, Matthew B. Jargowsky, Meagan N. Schrandt, Pearce T. Cooper, Sean P. Powers, John Dindo, J. Marcus Drymon

University Faculty and Staff Publications

In the southeastern USA and the Gulf of Mexico (GOM), Atlantic Tripletail Lobotes surinamensis are increasingly targeted by recreational anglers, indicating that stock status should be assessed. A critical need for such assessments is age-specific data; however, previous studies have drawn conflicting conclusions regarding the most appropriate structure for aging. Moreover, growth parameters and mortality rates for GOM Atlantic Tripletail are unknown. Therefore, the goals of this study were to (1) evaluate sagittal otoliths and first dorsal spines as aging structures; (2) model combined and sex-specific growth; and (3) estimate mortality rates for GOM Atlantic Tripletail. From 2012 to 2019, …

Recent And Rapid Radiation Of The Highly Endangered Harlequin Frogs (Atelopus) Into Central America Inferred From Mitochondrial Dna Sequences, Juan P. Ramirez, Cesar A. Jaramillo, Erik D. Lindquist, Andrew J. Crawford, Roberto Ibanez

Biology Educator Scholarship

Populations of amphibians are experiencing severe declines worldwide. One group with the most catastrophic declines is the Neotropical genus Atelopus (Anura: Bufonidae). Many species of Atelopus have not been seen for decades and all eight Central American species are considered “Critically Endangered”, three of them very likely extinct. Nonetheless, the taxonomy, phylogeny, and biogeographic history of Central American Atelopus are still poorly known. In this study, the phylogenetic relationships among seven of the eight described species in Central America were inferred based on mitochondrial DNA sequences from 103 individuals, including decades-old museum samples and two likely extinct species, plus ten …

Status Of The Blackstripe (Fundulus Notatus) And Blackspotted (F. Olivaceus) Topminnows In The Ozark Uplands Of Central Missouri, Nathaniel Steffensmeier, Naznin Sultana Remex, Robert Hrabik, David D. Duvernell

Biological Sciences Faculty Research & Creative Works

The topminnow species Fundulus notatus and F. olivaceus have broadly overlapping geographic distributions that extend throughout much of the central and southern United States. In the northern portion of their respective ranges, in Missouri, the regional distributions of the two species coincide largely with recognized ecoregions. In the unglaciated southern half of Missouri, F. olivaceus is distributed throughout Ozark upland habitats while F. notatus is abundant in marginal large river and prairie habitats along the Ozark borders. An exception to this partitioning is the historical report of abundant F. notatus in the Bourbeuse and upper Meramec River drainages within the …

Biotechnological Application In Aquaculture And Its Sustainability Constraints, Olaganathan Rajee, Tang Kar Mun Alicia

Publications

The valuable nutritional and biochemical properties have made fisheries products one of the most vital high-quality protein sources for human consumption. Aquaculture has become the great alternative to substitute wild catches when the yield from fishing are no longer sufficient to sustain the massive food demand of the human population which is constantly burgeoning. However, aquaculture requires multidisciplinary approaches with holistic and environmental-friendly management measures to ensure its long term success and sustainability. Biotechnological applications have enhanced the effectiveness and cost-efficiencies of aquaculture by augmenting the productivity of aquaculture to meet global needs. Despite the benefits, the biotechnological application in …

Exploration Of Sonic Hedgehog Gene Expression In Fathead Minnows (Pimephales Promelas), Brooke Renee Greiner

Undergraduate Honors Theses

Pollutants, as a result of wastewater treatments, have been shown to have negative impacts on aquatic ecosystems. To better understand the possible consequences caused by effluents on ecosystems, it is important to examine ecotoxicology data. One of the most commonly used species for water quality testing is the fathead minnow, Pimephales promelas. Ecotoxicology can then be taken one step further to understand the effects of pollutants on a molecular level. Previous research had identified effluents as causes for abnormal minnow fin morphology. In order to collect additional data on development, tanks with fathead minnows were placed at the Charleston …

Gofish: A Versatile Nested Pcr Strategy For Environmental Dna Assays For Marine Vertebrates, Mark Y. Stoeckle, Mithun Das Mishu, Zachary Charlop-Powers

Publications and Research

Here we describe GoFish, a strategy for single-species environmental DNA (eDNA) presence/absence assays using nested PCR. The assays amplify a mitochondrial 12S rDNA segment with vertebrate metabarcoding primers, followed by nested PCR with M13-tailed, species-specific primers. Sanger sequencing confirms positives detected by gel electrophoresis. We first obtained 12S sequences from 77 fish specimens for 36 northwestern Atlantic taxa not well documented in GenBank. Using these and existing 12S records, we designed GoFish assays for 11 bony fish species common in the lower Hudson River estuary and tested seasonal abundance and habitat preference at two sites. Additional assays detected nine cartilaginous …

Red Snapper Distribution On Natural Habitats And Artificial Structures In The Northern Gulf Of Mexico, Mandy Karnauskas, John F. Walter Iii, Matthew D. Campbell, Adam G. Pollack, J. Marcus Drymon, Sean P. Powers

University Faculty and Staff Publications

In 2011, an intensive, multiple-gear, fishery-independent survey was carried out in the northern Gulf of Mexico (GOM) to collect comprehensive age and length information on Red Snapper Lutjanus campechanus. Based on this synoptic survey, we produced a spatial map of Red Snapper relative abundance that integrates both gear selectivity effects and ontogenetically varying habitat usage. Our methodology generated a spatial map of Red Snapper at a 10-km2 grid resolution that is consistent with existing knowledge of the species: Red Snapper occurred in relatively high abundances at depths of 50–90 m along the coasts of Texas and Louisiana and in smaller, …

Molecular Analysis Confirming The Introduction Of Nile Crocodiles, Crocodylus Niloticus Laurenti 1768 (Crocodylidae), In Southern Florida, With An Assessment Of Potential For Establishment, Spread, And Impacts., Michael R. Rochford, Kenneth L. Krysko, Frank J. Mazzotti, Matthew W. Shirley, Mark W. Parry, Joseph A. Wasilewski, Jeffrey S. Beauchamp, Christpher R. Gillette, Edward F. Metzger Iii, Michiko A. Squires, Louis A. Somma

Papers in Herpetology

The state of Florida, USA, has more introduced herpetofauna than any other governmental region on Earth. Four species of nonnative crocodilians have been introduced to Florida (all since 1960), one of which is established. Between 2000–2014 we field-collected three nonnative crocodilians in Miami-Dade County, Florida, and one in Hendry County, Florida. We used DNA barcoding and molecular phylogenetics to determine species identification and native range origin. Also, we described diet, movement, and growth for one crocodile. Our molecular analyses illustrated that two of the crocodiles we collected are most closely related to Nile Crocodiles (Crocodylus niloticus) from South Africa, suggesting …

Draft Genome Sequences For Seven Streptococcus Parauberis Isolates From Wild Fish In The Chesapeake Bay, Ashley Haines, Emily Nebergall, Elvira Besong, Kimaya Council, Onaysha Lambert, David Gauthier

Biological Sciences Faculty Publications

Streptococcus parauberis is a pathogen of cattle and fish, closely related Streptococcus uberis and Streptococcus iniae. We report the genomes of seven S. parauberis strains recovered from striped bass (Morone saxatilis) in the Chesapeake Bay. The availability of these genomes will allow comparative genomic analysis of Chesapeake Bay S. parauberis strains versus S. parauberis cultured from other animal hosts and geographic regions.

Investigating The Driving Mechanisms Behind Differences In Bleaching And Disease Susceptibility Between Two Scleractinian Corals, Pseudodiploria Strigosa And Diploria Labyrinthiformis, Zoe A. Pratte

FIU Electronic Theses and Dissertations

Disease and bleaching are two conditions which commonly lead to coral death. Among coral species, susceptibility to disease and bleaching is variable, and Pseudodiploria strigosa tends to be diseased more than Diploria labyrinthiformis, while D. labyrinthiformis bleaches more readily. The focus of this dissertation was to investigate and compare multiple components of these two coral species, and identify how they may relate to disease and bleaching resistance. Compenetnts examined included the surface mucopolysacharide layer (SML) thickness, gene expression, microbial associates, and a white plague aquarium study. The SML thickness decresased with increasing temperature regardless of coral species, indicating that SML …

Examination Of Polymorphism In The Serine Proteinase Inhibitor Gene In The Eastern Oyster, Crassostrea Virginica., Aine Lehane

Senior Honors Projects

Oysters are a keystone species; they are filter-feeders and reef-builders. Additionally, oysters are extremely important within the shellfish aquaculture industry; they are the second most widely produced species in world aquaculture production. Eastern oysters, Crassostrea virginica, are produced in aquaculture and are unfortunately susceptible to Dermo disease. Dermo is caused by a protozoan parasite, Perkinsus marinus, and infection is often fatal in oysters due to widespread tissue damage and blockage of blood vessels. Research in oyster disease is particularly needed because disease is one of the largest impediments faced by the aquaculture industry as entire oyster populations can …

Phylogenetic Analysis Of Algal Symbionts Associated With Four North American Amphibian Egg Masses, Eunsoo Kim, Yuan Lin, Ryan R. Kerney, Lili Blumenberg, Cory Bishop

Biology Faculty Publications

Egg masses of the yellow-spotted salamander Ambystoma maculatum form an association with the green alga “Oophila amblystomatis” (Lambert ex Wille), which, in addition to growing within individual egg capsules, has recently been reported to invade embryonic tissues and cells. The binomial O. amblystomatis refers to the algae that occur in A. maculatum egg capsules, but it is unknown whether this population of symbionts constitutes one or several different algal taxa. Moreover, it is unknown whether egg masses across the geographic range of A. maculatum, or other amphibians, associate with one or multiple algal taxa. To address these …

An Assessment Of Environmental Dna As A Tool To Detect Fish Species In Headwater Streams, Stephen F. Jane

Masters Theses 1911 - February 2014

Recent years have seen an explosion of interest in the use of freely available DNA present in aquatic systems, otherwise known as environmental DNA (eDNA), as a tool for monitoring aquatic organisms. However, much remains unknown about the behavior of eDNA over a range of environmental conditions. This is particularly true in high gradient headwater streams, which have received less attention than other types of water bodies. In the summer of 2011, a headwater stream system with well established species distributions was sampled using eDNA techniques. Though species were detected where known to be present, detections also occurred where traditional …

Frequency-Dependent Mate Selection In The Guppy (Poeciliidae: Poecilia Reticulata), Andre Porter, Jack Frankel

Department of Biology Faculty Publications

Heterogeneity within a population enhances its long-term survival. A fundamental method of maintaining population heterogeneity is the retention of rare or uncommon phenotypes by selective mating strategies. Employing two color morphs, red tuxedo and red, of the guppy (Poecilia reticulata, Poeciliidae), this study was designed to investigate whether P. reticulata females would preferentially seek out heterogeneous groupings of males exhibiting two color morphs. Adult female guppies were exposed simultaneously to two groups of males (n=10); one comprised of only the tuxedo color morph (n=5) and the other of both color morphs (n=5). For the latter group, the ratio of males …

A Genetic Survey Of English Sole Populations In The Salish Sea, Elizabeth S. Gutierrez, Gary A. Winans, Jon Baker, Amanda Cope

STAR Program Research Presentations

This summer I interned at the Northwest Fisheries Science Center in Seattle, WA and participated in NOAA’s Salish Sea Project. The Salish Sea Project’s goal is to identify genetically distinctive groups of species in the Salish Sea that may have unique evolutionary and/or adaptive backgrounds. These findings will allow NOAA to promote and monitor the natural production of species in the Salish Sea, to select representative populations for experimental work regarding pollution, ocean acidification and climate change, to contribute to managing the ecosystem for intra- and inter-species diversity, and to help make informed decisions about adaptive management and marine protected …

Inheritance Of Humeral Spotting In The Croaking Gourami (Osphronemidae: Trichopsis Vittatus), Jack Frankel, Lisa Alder-Golden, Andre Porter

Department of Biology Faculty Publications

The croaking gourami (Trichopsis vittatus) exhibits two phenotypes associated with humeral spotting. Fish possess a prominent, dark humeral patch or spot located behind the operculum or lack this spotting pattern. Segregation patterns observed from the progenies of eleven different crosses support the hypothesis that the inheritance of humeral spotting in T. vittatus is controlled by the action of a single autosomal locus, with complete dominance of the allele controlling the spotted phenotype.

Rna Interference In Marine And Freshwater Sponges: Actin Knockdown In Tethya Wilhelma And Ephydatia Muelleri By Ingested Dsrna Expressing Bacteria, Ajna S. Rivera, April L. Hill, Et. Al.

Biology Faculty Publications

Background: The marine sponge Tethya wilhelma and the freshwater sponge Ephydatia muelleri are emerging model organisms to study evolution, gene regulation, development, and physiology in non-bilaterian animal systems. Thus far, functional methods (i.e., loss or gain of function) for these organisms have not been available.

Results: We show that soaking developing freshwater sponges in double-stranded RNA and/or feeding marine and freshwater sponges bacteria expressing double-stranded RNA can lead to RNA interference and reduction of targeted transcript levels. These methods, first utilized in C. elegans, have been adapted for the development and feeding style of easily cultured marine and freshwater poriferans. …

The Effects Of Growth Hormone In The Inner Ear Of Zebrafish (Danio Rerio) During Hair Cell Regeneration, Chia-Hui Lin

Masters Theses & Specialist Projects

Although deafness is a universal problem, effective treatments have remained elusive. In order to develop potential treatments, an overall understanding of the cellular process of auditory hair cell regeneration, which occurs in fish but not mammals, must be established. A previous microarray analysis and qRT-PCR validation of noise-exposed zebrafish showed that growth hormone (GH) was significantly upregulated during the process of auditory hair cell regeneration. Thus, GH may play an important role during hair cell regeneration. However, cellular effects of exogenous GH in the zebrafish auditory hair cell regeneration have not been examined after noise exposure. To understand the effect …

Characterization Of 24 Microsatellite Loci In Delta Smelt, Hypomesus Transpacificus, And Their Cross-Species Amplification In Two Other Smelt Species Of The Osmeridae Family, Kathleen M. Fisch, Jessica Lynn Petersen, Melinda R. Baerwald, John K. Pedroia, Bernie May

Department of Animal Science: Faculty Publications

We characterized 24 polymorphic tetranucleotide microsatellite loci for delta smelt (Hypomesus transpacificus) endemic to the San Francisco Bay Estuary, California, USA. Screening of samples (n = 30) yielded two to 26 alleles per locus with observed levels of heterozygosity ranging from 0.17 to 1.0. Only one locus deviated from Hardy–Weinberg equilibrium, suggesting these individuals originate from a single panmictic population. Linkage disequilibrium was found in two pairs of loci after excluding the locus out of Hardy–Weinberg equilibrium. Twenty-two primer pairs cross-amplified in wakasagi smelt (Hypomesus nipponensis), and 15 primer pairs cross-amplified in longfin smelt ( …

Inheritance Of Shoulder Spotting In The Tetra, Hyphessobrycon Bentosi Characidae, Jack Frankel

Department of Biology Faculty Publications

The tetra (Hyphessobrycon bentosi) exhibits two phenotypes associated with shoulder spotting. Fish possess ei-ther a prominent black vertical spot located directly behind the operculum (H. b. bentosi, bentosi white tip tetra) or lack this spot (H. b. rosaceus, rosy tetra). Segregation patterns observed from the progenies of ten different crosses suggest that the inheritance of these phenotypes is controlled by two autosomal loci acting in a complementary fashion, with domi-nance at both loci required for the expression of the spotted phenotype.

Thirty-Seven Additional Microsatellite Loci In The Pacific Lion-Paw Scallop (Nodipecten Subnodosus) And Cross-Amplification In Other Pectinids, Jessica Lynn Petersen, Ana M. Ibarra, Bernie May

Department of Animal Science: Faculty Publications

We characterized 37 new microsatellite markers in the Pacific lion-paw scallop (Nodipecten subnodosus) and tested for cross-amplification in four other species. Genetic diversity was estimated using 24 individuals from the Lagoon Ojo de Liebre, B.C.S., Mexico. Allelic richness varied from 5 to 27 alleles per locus and the average expected heterozygosity was 0.76. Ten loci exhibited significant departure from Hardy–Weinberg equilibrium likely due to the presence of null alleles. Sixteen of these markers cross-amplified in closely related N. nodosus, while little or no amplification was observed in three Argopecten species.

Monogenic Control Of Sex-Limited Colouration In The Honey Gourami, Trichogaster Chuna, Jack Frankel

Department of Biology Faculty Publications

Of the numerous subtropical and tropical freshwater speciesof fish, labyrinth fish are among the most varied in bodymarkings and colouration patterns. Four taxonomic families(Belontiidae, Anabantidae, Helostomatidae, and Osphrone-midae) of the suborder Anabantoidei comprise the ‘tradi-tional’ labyrinth fishes, a group of about 80 African andSoutheast Asian species (Linke 1991). These Anabantoidsare popular with aquarists due to their interesting reproduc-tive behaviours, with males of most species brooding eggs intheir mouths or in floating bubble nests (Vevers 1980; Linke1991; Axelrod and Vorderwinkler 1995; Mills 2000). Theyhave also been the focus of genetic, environmental, and mor-phological studies (Sommer 1982; Gosline 1985; Klinkhardtet al. 1995; …

Optimal Data Partitioning And A Test Case For Ray-Finned Fishes (Actinopterygii) Based On Ten Nuclear Loci, Chenhong Li, Guoqing Lu, Guillermo Orti

Biology Faculty Publications

Data partitioning, the combined phylogenetic analysis of homogeneous blocks of data, is a common strategy used to accommodate heterogeneities in complex multilocus data sets. Variation in evolutionary rates and substitution patterns among sites are typically addressed by partitioning data by gene, codon position, or both. Excessive partitioning of the data, however, could lead to overparameterization; therefore, it seems critical to define the minimum numbers of partitions necessary to improve the overall fit of the model. We propose a new method, based on cluster analysis, to find an optimal partitioning strategy for multilocus protein-coding data sets. A heuristic exploration of alternative …