Sexual development in fish, practical applications for aquaculture.

PubMed

Cnaani, A; Levavi-Sivan, B

2009-01-01

Aquaculture is one of the fastest rising sectors of world food production. Hundreds of fish species are cultured, providing an affordable, high quality food source. Two aspects of sexual development are critically important for the continued improvement of cultured fish stocks: sexual dimorphism and control of reproduction. In this paper, we review the main methods used to control sex determination in fish and their application in some of the most widely cultured species. Specifically, we review the techniques available for the production of all-male, all-female, and sterile populations. Techniques for endocrinological control of reproduction are also discussed. 2009 S. Karger AG, Basel.

DNA barcoding of freshwater fishes and the development of a quantitative qPCR assay for the species-specific detection and quantification of fish larvae from plankton samples.

PubMed

Loh, W K W; Bond, P; Ashton, K J; Roberts, D T; Tibbetts, I R

2014-08-01

The barcoding of mitochondrial cytochrome c oxidase subunit 1 (coI) gene was amplified and sequenced from 16 species of freshwater fishes found in Lake Wivenhoe (south-eastern Queensland, Australia) to support monitoring of reservoir fish populations, ecosystem function and water health. In this study, 630-650 bp sequences of the coI barcoding gene from 100 specimens representing 15 genera, 13 families and two subclasses of fishes allowed 14 of the 16 species to be identified and differentiated. The mean ± s.e. Kimura 2 parameter divergence within and between species was 0.52 ± 0.10 and 23.8 ± 2.20% respectively, indicating that barcodes can be used to discriminate most of the fish species accurately. The two terapontids, Amniataba percoides and Leiopotherapon unicolor, however, shared coI DNA sequences and could not be differentiated using this gene. A barcoding database was established and a qPCR assay was developed using coI sequences to identify and quantify proportional abundances of fish species in ichthyoplankton samples from Lake Wivenhoe. These methods provide a viable alternative to the time-consuming process of manually enumerating and identifying ichthyoplankton samples. © 2014 The Fisheries Society of the British Isles.

Assessment of fish assemblages and minimum sampling effort required to determine botic integrity of large rivers in southern Idaho, 2002

USGS Publications Warehouse

Maret, Terry R.; Ott, D.S.

2004-01-01

width was determined to be sufficient for collecting an adequate number of fish to estimate species richness and evaluate biotic integrity. At most sites, about 250 fish were needed to effectively represent 95 percent of the species present. Fifty-three percent of the sites assessed, using an IBI developed specifically for large Idaho rivers, received scores of less than 50, indicating poor biotic integrity.

Development of species-specific rDNA probes for Giardia by multiple fluorescent in situ hybridization combined with immunocytochemical identification of cyst wall antigens.

PubMed

Erlandsen, Stanley L; Jarroll, Edward; Wallis, Peter; van Keulen, Harry

2005-08-01

In this study, we describe the development of fluorescent oligonucleotide probes to variable regions in the small subunit of 16S rRNA in three distinct Giardia species. Sense and antisense probes (17-22 mer) to variable regions 1, 3, and 8 were labeled with digoxygenin or selected fluorochomes (FluorX, Cy3, or Cy5). Optimal results were obtained with fluorochome-labeled oligonucleotides for detection of rRNA in Giardia cysts. Specificity of fluorescent in situ hybridization (FISH) was shown using RNase digestion and high stringency to diminish the hybridization signal, and oligonucleotide probes for rRNA in Giardia lamblia, Giardia muris, and Giardia ardeae were shown to specifically stain rRNA only within cysts or trophozoites of those species. The fluorescent oligonucleotide specific for rRNA in human isolates of Giardia was positive for ten different strains. A method for simultaneous FISH detection of cysts using fluorescent antibody (genotype marker) and two oligonucleotide probes (species marker) permitted visualization of G. lamblia and G. muris cysts in the same preparation. Testing of an environmental water sample revealed the presence of FISH-positive G. lamblia cysts with a specific rDNA probe for rRNA, while negative cysts were presumed to be of animal or bird origin.

Predicting invasiveness of species in trade: Climate match, trophic guild and fecundity influence establishment and impact of non-native freshwater fishes

USGS Publications Warehouse

Howeth, Jennifer G.; Gantz, Crysta A.; Angermeier, Paul; Frimpong, Emmanuel A.; Hoff, Michael H.; Keller, Reuben P.; Mandrak, Nicholas E.; Marchetti, Michael P.; Olden, Julian D.; Romagosa, Christina M.; Lodge, David M.

2016-01-01

AimImpacts of non-native species have motivated development of risk assessment tools for identifying introduced species likely to become invasive. Here, we develop trait-based models for the establishment and impact stages of freshwater fish invasion, and use them to screen non-native species common in international trade. We also determine which species in the aquarium, biological supply, live bait, live food and water garden trades are likely to become invasive. Results are compared to historical patterns of non-native fish establishment to assess the relative importance over time of pathways in causing invasions.LocationLaurentian Great Lakes region.MethodsTrait-based classification trees for the establishment and impact stages of invasion were developed from data on freshwater fish species that established or failed to establish in the Great Lakes. Fishes in trade were determined from import data from Canadian and United States regulatory agencies, assigned to specific trades and screened through the developed models.ResultsClimate match between a species’ native range and the Great Lakes region predicted establishment success with 75–81% accuracy. Trophic guild and fecundity predicted potential harmful impacts of established non-native fishes with 75–83% accuracy. Screening outcomes suggest the water garden trade poses the greatest risk of introducing new invasive species, followed by the live food and aquarium trades. Analysis of historical patterns of introduction pathways demonstrates the increasing importance of these trades relative to other pathways. Comparisons among trades reveal that model predictions parallel historical patterns; all fishes previously introduced from the water garden trade have established. The live bait, biological supply, aquarium and live food trades have also contributed established non-native fishes.Main conclusionsOur models predict invasion risk of potential fish invaders to the Great Lakes region and could help managers prioritize efforts among species and pathways to minimize such risk. Similar approaches could be applied to other taxonomic groups and geographic regions.

Species-specific mercury bioaccumulation in a diverse fish community.

PubMed

Donald, David B; Wissel, Björn; Anas, M U Mohamed

2015-12-01

Mercury bioaccumulation models developed for fish provide insight into the sources and transfer of Hg within ecosystems. Mercury concentrations were assessed for 16 fish species of the western reach of Lake Diefenbaker, Saskatchewan, Canada. For top predators (northern pike, Esox Lucius; walleye, Sander vitreum), Hg concentrations were positively correlated to δ(15)N, and δ(15)N to fish age, suggesting that throughout life these fish fed on organisms with increasingly higher trophic values and Hg concentrations. However, fish mass and/or age were the principal parameters related to Hg concentrations for most species. For 9 common species combined, individual variation in Hg concentration was explained in declining order of importance by fish mass, trophic position (δ(15)N), and fish age. Delta (15)N value was not the leading variable related to Hg concentration for the assemblage, probably because of the longevity of lower--trophic-level species (3 species ≥ 20 yr), substantial overlap in Hg concentration and δ(15)N values for large-bodied fish up to 3000 g, and complex relationships between Hg concentration and δ(15)N among species. These results suggest that the quantity of food (and Hg) consumed each year and converted to fish mass, the quantity of Hg bioaccumulated over years and decades, and trophic position were significant determinants of Hg concentration in Lake Diefenbaker fish. © 2015 SETAC.

Fillet proximate composition, lipid quality, yields, and organoleptic quality of Mediterranean-farmed marine fish: A review with emphasis on new species.

PubMed

Grigorakis, Kriton

2017-09-22

Species diversification in Mediterranean mariculture involves various important fish that contribute to the diet of many human populations. These include meagres (Sciaenidae), flatfishes, mullets, and various sparids. Their quality aspects (yields, fillet proximate composition, and lipid quality) are discussed in this review. Their filleting yield is mostly 40-45%. The viscerosomatic index ranges from 1.5% to 14%, depending on species. Low muscle fat contents of flatfishes and meagres differentiate them from the rest of the farmed species. Farmed fish contain high n-3 polyunsaturates fatty acids (PUFA; 12.3-36.3% vs. 5.48-37.2% in the wild) and have higher muscle fat and n-6 PUFA contents (mainly 18:2 n-6) than their wild counterparts. The aquaculture management, diet, and season can affect fillet composition and fatty acids, while season (i.e. food availability and maturation) largely affects lipid quality in wild fish. Data on the sensory quality of Mediterranean-farmed species are mainly limited to whether specific management differentiates the sensory quality; thus, further development of tools for sensory analysis is required. Observations on the quality features in farmed Mediterranean fish indicate that species diversification can also provide product diversification based on different commercial weights and fillet quality specifications.

Development of a probabilistic PCB-bioaccumulation model for six fish species in the Hudson River

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stackelberg, K. von; Menzie, C.

1995-12-31

In 1984 the US Environmental Protection Agency (USEPA) completed a Feasibility Study on the Hudson River that investigated remedial alternatives and issued a Record of Decision (ROD) later that year. In December 1989 USEPA decided to reassess the No Action decision for Hudson River sediments. This reassessment consists of three phases: Interim Characterization and Evaluation (Phase 1); Further Site Characterization and Analysis (Phase 2); and, Feasibility study (Phase 3). A Phase 1 report was completed in August, 1991. The team then completed a Final Work Plan for Phase 2 in September 1992. This work plan identified various PCB fate andmore » transport modeling activities to support the Hudson River PCB Reassessment Remedial Investigation and Feasibility Study (RI/FS). This talk provides a description of the development of a Probabilistic bioaccumulation models to describe the uptake of PCBs on a congener-specific basis in six fish species. The authors have developed a framework for relating body burdens of PCBs in fish to exposure concentrations in Hudson River water and sediments. This framework is used to understand historical and current relationships as well as to predict fish body burdens for future conditions under specific remediation and no action scenarios. The framework incorporates a probabilistic approach to predict distributions in PCB body burdens for selected fish species. These models can predict single population statistics such as the average expected values of PCBs under specific scenarios as well as the distribution of expected concentrations.« less

First record of three African trichodinids (Ciliophora: Peritrichida) in cultured Nile tilapia (Oreochromis niloticus) in Saudi Arabia with re-evaluation of their host specificity.

PubMed

Abdel-Baki, Abdel-Azeem Sh; Al Ghamdi, Ali; Al-Quraishy, Saleh

2017-04-01

Saudi Arabia has a developing aquaculture industry that farms primarily tilapia. Although trichodinids are presumably the most usually encountered protozoan parasites in these cultured fish, they have rarely been studied in this context, and there is no data on the species that might infect cultured tilapia in Saudi Arabia. The present study was therefore carried out as a general survey to investigate the occurrence and identify the species of trichodinids that can infect cultured tilapia (Oreochromis niloticus) in Saudi Arabia. A total of 500 tilapia fish were collected from fish farms in Riyadh city and examined in order to determine the species of trichodinids present in the positive specimens. Three species of trichodinids (Trichodina maritinkae, T. centrostrigeata and T. frenata) were isolated and described as new records in Saudi Arabia. These trichodinids were found simultaneously in the same fish with overall prevalence of 20% (100/500). The identification and characterization of these three species are documented based on Riyadh specimens, for the first time. Additionally, the present paper confirms the existence of T. frenata for the second time globally and establishes this trichodinid as a new parasite for O. niloticus. T. maritinkae is highly specific to clariids, and previously, it has not been reported from any fish species other than clariids. The present work also confirmed that T. centrostrigeata can also infest cichlid fish. The list of host records of these species is expanded and their host specificity re-evaluated based on the results of this study in addition to the previously published data. We conclude that there is a need for further study of the impacts of these Trichodina spp. on Saudi Arabian fishery sector.

An evaluation of the relations between flow regime components, stream characteristics, species traits and meta-demographic rates of warmwater stream fishes: Implications for aquatic resource management

USGS Publications Warehouse

Peterson, James T.; Shea, C.P.

2015-01-01

Fishery biologists are increasingly recognizing the importance of considering the dynamic nature of streams when developing streamflow policies. Such approaches require information on how flow regimes influence the physical environment and how those factors, in turn, affect species-specific demographic rates. A more cost-effective alternative could be the use of dynamic occupancy models to predict how species are likely to respond to changes in flow. To appraise the efficacy of this approach, we evaluated relative support for hypothesized effects of seasonal streamflow components, stream channel characteristics, and fish species traits on local extinction, colonization, and recruitment (meta-demographic rates) of stream fishes. We used 4 years of seasonal fish collection data from 23 streams to fit multistate, multiseason occupancy models for 42 fish species in the lower Flint River Basin, Georgia. Modelling results suggested that meta-demographic rates were influenced by streamflows, particularly short-term (10-day) flows. Flow effects on meta-demographic rates also varied with stream size, channel morphology, and fish species traits. Small-bodied species with generalized life-history characteristics were more resilient to flow variability than large-bodied species with specialized life-history characteristics. Using this approach, we simplified the modelling framework, thereby facilitating the development of dynamic, spatially explicit evaluations of the ecological consequences of water resource development activities over broad geographic areas. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments.

PubMed

Yuan, Zihao; Liu, Shikai; Zhou, Tao; Tian, Changxu; Bao, Lisui; Dunham, Rex; Liu, Zhanjiang

2018-02-13

Repetitive elements make up significant proportions of genomes. However, their roles in evolution remain largely unknown. To provide insights into the roles of repetitive elements in fish genomes, we conducted a comparative analysis of repetitive elements of 52 fish species in 22 orders in relation to their living aquatic environments. The proportions of repetitive elements in various genomes were found to be positively correlated with genome sizes, with a few exceptions. More importantly, there appeared to be specific enrichment between some repetitive element categories with species habitat. Specifically, class II transposons appear to be more abundant in freshwater bony fish than in marine bony fish when phylogenetic relationship is not considered. In contrast, marine bony fish harbor more tandem repeats than freshwater species. In addition, class I transposons appear to be more abundant in primitive species such as cartilaginous fish and lamprey than in bony fish. The enriched association of specific categories of repetitive elements with fish habitats suggests the importance of repetitive elements in genome evolution and their potential roles in fish adaptation to their living environments. However, due to the restriction of the limited sequenced species, further analysis needs to be done to alleviate the phylogenetic biases.

Otolith Length-Fish Length Relationships of Eleven US Arctic Fish Species and Their Application to Ice Seal Diet Studies

NASA Astrophysics Data System (ADS)

Walker, K. L.; Norcross, B.

2016-02-01

The Arctic ecosystem has moved into the spotlight of scientific research in recent years due to increased climate change and oil and gas exploration. Arctic fishes and Arctic marine mammals represent key parts of this ecosystem, with fish being a common part of ice seal diets in the Arctic. Determining sizes of fish consumed by ice seals is difficult because otoliths are often the only part left of the fish after digestion. Otolith length is known to be positively related to fish length. By developing species-specific otolith-body morphometric relationships for Arctic marine fishes, fish length can be determined for fish prey found in seal stomachs. Fish were collected during ice free months in the Beaufort and Chukchi seas 2009 - 2014, and the most prevalent species captured were chosen for analysis. Otoliths from eleven fish species from seven families were measured. All species had strong linear relationships between otolith length and fish total length. Nine species had coefficient of determination values over 0.75, indicating that most of the variability in the otolith to fish length relationship was explained by the linear regression. These relationships will be applied to otoliths found in stomachs of three species of ice seals (spotted Phoca largha, ringed Pusa hispida, and bearded Erignathus barbatus) and used to estimate fish total length at time of consumption. Fish lengths can in turn be used to calculate fish weight, enabling further investigation into ice seal energetic demands. This application will aid in understanding how ice seals interact with fish communities in the US Arctic and directly contribute to diet comparisons among and within ice seal species. A better understanding of predator-prey interactions in the US Arctic will aid in predicting how ice seal and fish species will adapt to a changing Arctic.

Disentangling the effects of a century of eutrophication and climate warming on freshwater lake fish assemblages

PubMed Central

Hansen, Gretchen J. A.; Bethke, Bethany J.; Cross, Timothy K.

2017-01-01

Eutrophication and climate warming are profoundly affecting fish in many freshwater lakes. Understanding the specific effects of these stressors is critical for development of effective adaptation and remediation strategies for conserving fish populations in a changing environment. Ecological niche models that incorporated the individual effects of nutrient concentration and climate were developed for 25 species of fish sampled in standard gillnet surveys from 1,577 Minnesota lakes. Lake phosphorus concentrations and climates were hindcasted to a pre-disturbance period of 1896–1925 using existing land use models and historical temperature data. Then historical fish assemblages were reconstructed using the ecological niche models. Substantial changes were noted when reconstructed fish assemblages were compared to those from the contemporary period (1981–2010). Disentangling the sometimes opposing, sometimes compounding, effects of eutrophication and climate warming was critical for understanding changes in fish assemblages. Reconstructed abundances of eutrophication-tolerant, warmwater taxa increased in prairie lakes that experienced significant eutrophication and climate warming. Eutrophication-intolerant, warmwater taxa abundance increased in forest lakes where primarily climate warming was the stressor. Coolwater fish declined in abundance in both ecoregions. Large changes in modeled abundance occurred when the effects of both climate and eutrophication operated in the same direction for some species. Conversely, the effects of climate warming and eutrophication operated in opposing directions for other species and dampened net changes in abundance. Quantifying the specific effects of climate and eutrophication will allow water resource managers to better understand how lakes have changed and provide expectations for sustainable fish assemblages in the future. PMID:28777816

Outlook for Development of High-throughput Cryopreservation for Small-bodied Biomedical Model Fishes★

PubMed Central

Tiersch, Terrence R.; Yang, Huiping; Hu, E.

2011-01-01

With the development of genomic research technologies, comparative genome studies among vertebrate species are becoming commonplace for human biomedical research. Fish offer unlimited versatility for biomedical research. Extensive studies are done using these fish models, yielding tens of thousands of specific strains and lines, and the number is increasing every day. Thus, high-throughput sperm cryopreservation is urgently needed to preserve these genetic resources. Although high-throughput processing has been widely applied for sperm cryopreservation in livestock for decades, application in biomedical model fishes is still in the concept-development stage because of the limited sample volumes and the biological characteristics of fish sperm. High-throughput processing in livestock was developed based on advances made in the laboratory and was scaled up for increased processing speed, capability for mass production, and uniformity and quality assurance. Cryopreserved germplasm combined with high-throughput processing constitutes an independent industry encompassing animal breeding, preservation of genetic diversity, and medical research. Currently, there is no specifically engineered system available for high-throughput of cryopreserved germplasm for aquatic species. This review is to discuss the concepts and needs for high-throughput technology for model fishes, propose approaches for technical development, and overview future directions of this approach. PMID:21440666

Quantitative approach for incorporating methylmercury risks and omega-3 fatty acid benefits in developing species-specific fish consumption advice.

PubMed

Ginsberg, Gary L; Toal, Brian F

2009-02-01

Despite general agreement about the toxicity of methylmercury (MeHg), fish consumption advice remains controversial. Concerns have been raised that negative messages will steer people away from fish and omega-3 fatty acid (FA) benefits. One approach is to provide advice for individual species that highlights beneficial fish while cautioning against riskier fish. Our goal in this study was to develop a method to quantitatively analyze the net risk/benefit of individual fish species based on their MeHg and omega-3 FA content. We identified dose-response relationships for MeHg and omega-3 FA effects on coronary heart disease (CHD) and neurodevelopment. We used the MeHg and omega-3 FA content of 16 commonly consumed species to calculate the net risk/benefit for each species. Estimated omega-3 FA benefits outweigh MeHg risks for some species (e.g., farmed salmon, herring, trout); however, the opposite was true for others (swordfish, shark). Other species were associated with a small net benefit (e.g., flounder, canned light tuna) or a small net risk (e.g., canned white tuna, halibut). These results were used to place fish into one of four meal frequency categories, with the advice tentative because of limitations in the underlying dose-response information. Separate advice appears warranted for the neurodevelopmental risk group versus the cardiovascular risk group because we found a greater net benefit from fish consumption for the cardiovascular risk group. This research illustrates a framework for risk/benefit analysis that can be used to develop categories of consumption advice ranging from "do not eat" to "unlimited," with the caveat that unlimited may need to be tempered for certain fish (e.g., farm-raised salmon) because of other contaminants and end points (e.g., cancer risk). Uncertainties exist in the underlying dose-response relationships, pointing in particular to the need for more research on the adverse effects of MeHg on cardiovascular end points.

Biology and Mucosal Immunity to Myxozoans

PubMed Central

Gómez, Daniela; Bartholomew, Jerri; Sunyer, J. Oriol

2014-01-01

Myxozoans are among the most abundant parasites in nature. Their life cycles involve two hosts: an invertebrate, usually an annelid, and a vertebrate, usually a fish. They affect fish species in their natural habitats but also constitute a menace for fish aquaculture. Using different strategies they are able to parasitize and cause damage in multiple organs, including mucosal tissues, which they use also as portals of entry. In fish, the main mucosal sites include the intestine, skin and gills. Recently the finding of a specific mucosal immunoglobulin in teleost (IgT), analogous to mammalian IgA, and the capacity of fish to develop a specific mucosal immune response against different pathogens, has highlighted the importance of studying immune responses at mucosal sites. In this review, we describe the major biological characteristics of myxozoan parasites and present the data available regarding immune responses for species that infect mucosal sites. As models for mucosal immunity we review the responses to Enteromyxum spp. and Ceratomyxa shasta, both of which parasitize the intestine. The immune response at the skin and gills is also described, as these mucosal tissues are used by myxozoans as attaching surfaces and portal of entry, and some species also parasitize these sites. Finally, the development of immunoprophylactic strategies is discussed. PMID:23994774

Specific IgE to fish extracts does not predict allergy to specific species within an adult fish allergic population

PubMed Central

2014-01-01

Background Fish is an important cause of food allergy. Studies on fish allergy are scarce and in most cases limited to serological evaluation. Our objective was to study patterns of self-reported allergy and tolerance to different commonly consumed fish species and its correlation to IgE sensitization to the same species. Methods Thirty-eight adult fish allergic patients completed a questionnaire regarding atopy, age of onset and symptoms to 13 commonly consumed fish species in the Netherlands (pangasius, cod, herring, eel, hake, pollock, mackerel, tilapia, salmon, sardine, tuna, plaice and swordfish). Specific IgE to these fish extracts were analyzed by ImmunoCAP. Results Median age of onset of fish allergy was 8.5 years. Severe reactions were reported by the majority of patients (n = 20 (53%) respiratory and of these 20 patients, 6 also had cardiovascular symptoms). After diagnosis, 66% of the patients had eliminated all fish from their diet. Allergy to all species ever tried was reported by 59%. In relation to species ever tried, cod (84%) and herring (79%) were the most frequently reported culprit species while hake (57%) and swordfish (55%) were the least frequent. A positive sIgE (value ≥ 0.35 kUA/L) to the culprit species ranged between 50% (swordfish) and 100% (hake). In tolerant patients, a negative sIgE (value < 0.35 kUA/L) ranged from 0% (hake, pollock and swordfish) to 75% (sardine). For cod, the agreement between sIgE test results and reported allergy or tolerance was 82% and 25%, respectively. Sensitization to cod parvalbumin (Gad c 1) was present in 77% of all patients. Conclusion Serological cross-reactivity between fish species is frequent, but in a significant proportion of patients, clinical relevance appears to be limited to only certain species. A well-taken history or food challenge is required for discrimination between allergy to the different fish species. PMID:25225608

Specific IgE to fish extracts does not predict allergy to specific species within an adult fish allergic population.

PubMed

Schulkes, Karlijn Jg; Klemans, Rob Jb; Knigge, Lidy; de Bruin-Weller, Marjolein; Bruijnzeel-Koomen, Carla Afm; Marknell deWitt, Asa; Lidholm, Jonas; Knulst, André C

2014-01-01

Fish is an important cause of food allergy. Studies on fish allergy are scarce and in most cases limited to serological evaluation. Our objective was to study patterns of self-reported allergy and tolerance to different commonly consumed fish species and its correlation to IgE sensitization to the same species. Thirty-eight adult fish allergic patients completed a questionnaire regarding atopy, age of onset and symptoms to 13 commonly consumed fish species in the Netherlands (pangasius, cod, herring, eel, hake, pollock, mackerel, tilapia, salmon, sardine, tuna, plaice and swordfish). Specific IgE to these fish extracts were analyzed by ImmunoCAP. Median age of onset of fish allergy was 8.5 years. Severe reactions were reported by the majority of patients (n = 20 (53%) respiratory and of these 20 patients, 6 also had cardiovascular symptoms). After diagnosis, 66% of the patients had eliminated all fish from their diet. Allergy to all species ever tried was reported by 59%. In relation to species ever tried, cod (84%) and herring (79%) were the most frequently reported culprit species while hake (57%) and swordfish (55%) were the least frequent. A positive sIgE (value ≥ 0.35 kUA/L) to the culprit species ranged between 50% (swordfish) and 100% (hake). In tolerant patients, a negative sIgE (value < 0.35 kUA/L) ranged from 0% (hake, pollock and swordfish) to 75% (sardine). For cod, the agreement between sIgE test results and reported allergy or tolerance was 82% and 25%, respectively. Sensitization to cod parvalbumin (Gad c 1) was present in 77% of all patients. Serological cross-reactivity between fish species is frequent, but in a significant proportion of patients, clinical relevance appears to be limited to only certain species. A well-taken history or food challenge is required for discrimination between allergy to the different fish species.

Sex differences in contaminant concentrations of fish: a synthesis

USGS Publications Warehouse

Madenjian, Charles P.; Rediske, Richard R.; Krabbenhoft, David P.; Stapanian, Martin A.; Chernyak, Sergei M.; O'Keefe, James P.

2016-01-01

Comparison of whole-fish polychlorinated biphenyl (PCB) and total mercury (Hg) concentrations in mature males with those in mature females may provide insights into sex differences in behavior, metabolism, and other physiological processes. In eight species of fish, we observed that males exceeded females in whole-fish PCB concentration by 17 to 43%. Based on results from hypothesis testing, we concluded that these sex differences were most likely primarily driven by a higher rate of energy expenditure, stemming from higher resting metabolic rate (or standard metabolic rate (SMR)) and higher swimming activity, in males compared with females. A higher rate of energy expenditure led to a higher rate of food consumption, which, in turn, resulted in a higher rate of PCB accumulation. For two fish species, the growth dilution effect also made a substantial contribution to the sex difference in PCB concentrations, although the higher energy expenditure rate for males was still the primary driver. Hg concentration data were available for five of the eight species. For four of these five species, the ratio of PCB concentration in males to PCB concentration in females was substantially greater than the ratio of Hg concentration in males to Hg concentration in females. In sea lamprey (Petromyzon marinus), a very primitive fish, the two ratios were nearly identical. The most plausible explanation for this pattern was that certain androgens, such as testosterone and 11-ketotestosterone, enhanced Hg-elimination rate in males. In contrast, long-term elimination of PCBs is negligible for both sexes. According to this explanation, males ingest Hg at a higher rate than females, but also eliminate Hg at a higher rate than females, in fish species other than sea lamprey. Male sea lamprey do not possess either of the above-specified androgens. These apparent sex differences in SMRs, activities, and Hg-elimination rates in teleost fishes may also apply, to some degree, to higher vertebrates including humans. Our synthesis findings will be useful in: (1) developing sex-specific bioenergetics models for fish, (2) developing sex-specific risk assessment models for exposure of humans and wildlife to contaminants, and (3) refining Hg mass balance models for fish and higher vertebrates.

Beyond the zebrafish: diverse fish species for modeling human disease

PubMed Central

Schartl, Manfred

2014-01-01

ABSTRACT In recent years, zebrafish, and to a lesser extent medaka, have become widely used small animal models for human diseases. These organisms have convincingly demonstrated the usefulness of fish for improving our understanding of the molecular and cellular mechanisms leading to pathological conditions, and for the development of new diagnostic and therapeutic tools. Despite the usefulness of zebrafish and medaka in the investigation of a wide spectrum of traits, there is evidence to suggest that other fish species could be better suited for more targeted questions. With the emergence of new, improved sequencing technologies that enable genomic resources to be generated with increasing efficiency and speed, the potential of non-mainstream fish species as disease models can now be explored. A key feature of these fish species is that the pathological condition that they model is often related to specific evolutionary adaptations. By exploring these adaptations, new disease-causing and disease-modifier genes might be identified; thus, diverse fish species could be exploited to better understand the complexity of disease processes. In addition, non-mainstream fish models could allow us to study the impact of environmental factors, as well as genetic variation, on complex disease phenotypes. This Review will discuss the opportunities that such fish models offer for current and future biomedical research. PMID:24271780

Species sensitivity distribution evaluation for selenium in fish eggs: considerations for development of a Canadian tissue-based guideline.

PubMed

DeForest, David K; Gilron, Guy; Armstrong, Sarah A; Robertson, Erin L

2012-01-01

A freshwater Se guideline was developed for consideration based on concentrations in fish eggs or ovaries, with a focus on Canadian species, following the Canadian Council of Ministers of the Environment protocol for developing guideline values. When sufficient toxicity data are available, the protocol recommends deriving guidelines as the 5th percentile of the species sensitivity distribution (SSD). When toxicity data are limited, the protocol recommends a lowest value approach, where the lowest toxicity threshold is divided by a safety factor (e.g., 10). On the basis of a comprehensive review of the current literature and an assessment of the data therein, there are sufficient egg and ovary Se data available for freshwater fish to develop an SSD. For most fish species, Se EC10 values (10% effect concentrations) could be derived, but for some species, only no-observed-effect concentrations and/or lowest-observed-effect concentrations could be identified. The 5th percentile egg and ovary Se concentrations from the SSD were consistently 20 µg/g dry weight (dw) for the best-fitting distributions. In contrast, the lowest value approach using a safety factor of 10 would result in a Se egg and ovary guideline of 2 µg/g dw, which is unrealistically conservative, as this falls within the range of egg and ovary Se concentrations in laboratory control fish and fish collected from reference sites. An egg and ovary Se guideline of 20 µg/g dw should be considered a conservative, broadly applicable guideline, as no species mean toxicity thresholds lower than this value have been identified to date. When concentrations exceed this guideline, site-specific studies with local fish species, conducted using a risk-based approach, may result in higher egg and ovary Se toxicity thresholds. Copyright © 2011 SETAC.

Deepwater Horizon crude oil impacts the developing hearts of large predatory pelagic fish

PubMed Central

Incardona, John P.; Gardner, Luke D.; Linbo, Tiffany L.; Brown, Tanya L.; Esbaugh, Andrew J.; Mager, Edward M.; Stieglitz, John D.; French, Barbara L.; Labenia, Jana S.; Laetz, Cathy A.; Tagal, Mark; Sloan, Catherine A.; Elizur, Abigail; Benetti, Daniel D.; Grosell, Martin; Block, Barbara A.; Scholz, Nathaniel L.

2014-01-01

The Deepwater Horizon disaster released more than 636 million L of crude oil into the northern Gulf of Mexico. The spill oiled upper surface water spawning habitats for many commercially and ecologically important pelagic fish species. Consequently, the developing spawn (embryos and larvae) of tunas, swordfish, and other large predators were potentially exposed to crude oil-derived polycyclic aromatic hydrocarbons (PAHs). Fish embryos are generally very sensitive to PAH-induced cardiotoxicity, and adverse changes in heart physiology and morphology can cause both acute and delayed mortality. Cardiac function is particularly important for fast-swimming pelagic predators with high aerobic demand. Offspring for these species develop rapidly at relatively high temperatures, and their vulnerability to crude oil toxicity is unknown. We assessed the impacts of field-collected Deepwater Horizon (MC252) oil samples on embryos of three pelagic fish: bluefin tuna, yellowfin tuna, and an amberjack. We show that environmentally realistic exposures (1–15 µg/L total PAH) cause specific dose-dependent defects in cardiac function in all three species, with circulatory disruption culminating in pericardial edema and other secondary malformations. Each species displayed an irregular atrial arrhythmia following oil exposure, indicating a highly conserved response to oil toxicity. A considerable portion of Gulf water samples collected during the spill had PAH concentrations exceeding toxicity thresholds observed here, indicating the potential for losses of pelagic fish larvae. Vulnerability assessments in other ocean habitats, including the Arctic, should focus on the developing heart of resident fish species as an exceptionally sensitive and consistent indicator of crude oil impacts. PMID:24706825

Species-specific patterns of hyperostosis in marine teleost fishes

USGS Publications Warehouse

Smith-Vaniz, William F.; Kaufman, L.S.; Glowacki, J.

1995-01-01

The occurrence of swollen or hyperostotic bones in skeletal preparations, preserved museum material or whole fresh specimens of marine teleost fishes was identified in 92 species belonging to 22 families. Patterns of hyperostotic skeletal growth were typically consistent and often species-specific in all individuals larger than a certain size. The taxonomic distribution of hyperostosis in diverse phylogenetic groups suggests that it has arisen independently many times. Selected bones from two species of the family Carangidae, horse-eye jack Caranx latus Agassiz and crevalle jackCaranx hippos (Linnaeus), were examined in detail by light and electron microscopy. Nonhyperostotic bone contained osteoid-producing osteoblasts, resorbing osteoclasts, occasional osteocytes, and a rich vascular network, all characteristics of cellular bone. Thus, these fishes have a spatial juxtaposition of cellular and acellular bone tissues in adjacent and often serially homologous bone sites. The functional significance of hyperostosis is unknown, but it is a predictable manifestation of bone growth and development for the many taxa in which it occurs.

A DNA Mini-Barcoding System for Authentication of Processed Fish Products.

PubMed

Shokralla, Shadi; Hellberg, Rosalee S; Handy, Sara M; King, Ian; Hajibabaei, Mehrdad

2015-10-30

Species substitution is a form of seafood fraud for the purpose of economic gain. DNA barcoding utilizes species-specific DNA sequence information for specimen identification. Previous work has established the usability of short DNA sequences-mini-barcodes-for identification of specimens harboring degraded DNA. This study aims at establishing a DNA mini-barcoding system for all fish species commonly used in processed fish products in North America. Six mini-barcode primer pairs targeting short (127-314 bp) fragments of the cytochrome c oxidase I (CO1) DNA barcode region were developed by examining over 8,000 DNA barcodes from species in the U.S. Food and Drug Administration (FDA) Seafood List. The mini-barcode primer pairs were then tested against 44 processed fish products representing a range of species and product types. Of the 44 products, 41 (93.2%) could be identified at the species or genus level. The greatest mini-barcoding success rate found with an individual primer pair was 88.6% compared to 20.5% success rate achieved by the full-length DNA barcode primers. Overall, this study presents a mini-barcoding system that can be used to identify a wide range of fish species in commercial products and may be utilized in high throughput DNA sequencing for authentication of heavily processed fish products.

Species-specific responses to landscape fragmentation: implications for management strategies

PubMed Central

Blanchet, Simon; Rey, Olivier; Etienne, Roselyne; Lek, Sovan; Loot, Géraldine

2010-01-01

Habitat fragmentation affects the integrity of many species, but little is known about species-specific sensitivity to fragmentation. Here, we compared the genetic structure of four freshwater fish species differing in their body size (Leuciscus cephalus; Leuciscus leuciscus; Gobio gobio and Phoxinus phoxinus) between a fragmented and a continuous landscape. We tested if, overall, fragmentation affected the genetic structure of these fish species, and if these species differed in their sensitivity to fragmentation. Fragmentation negatively affected the genetic structure of these species. Indeed, irrespective of the species identity, allelic richness and heterozygosity were lower, and population divergence was higher in the fragmented than in the continuous landscape. This response to fragmentation was highly species-specific, with the smallest fish species (P. phoxinus) being slightly affected by fragmentation. On the contrary, fish species of intermediate body size (L. leuciscus and G. gobio) were highly affected, whereas the largest fish species (L. cephalus) was intermediately affected by fragmentation. We discuss the relative role of dispersal ability and effective population size on the responses to fragmentation we report here. The weirs studied here are of considerable historical importance. We therefore conclude that restoration programmes will need to consider both this societal context and the biological characteristics of the species sharing this ecosystem. PMID:25567925

Hepatic retinoid levels in seven fish species (teleosts) from a tropical coastal lagoon receiving effluents from iron-ore mining and processing.

PubMed

Pereira, Adriana A; van Hattum, Bert; Brouwer, Abraham

2012-02-01

The present study was undertaken to investigate the possible effects of Fe and trace element exposure on hepatic levels of retinoids in seven fish species. Concentrations of retinoids were measured in fish collected from a coastal lagoon in Brazil that receives effluents from an iron-ore mining and processing plant. Fish from nearby coastal lagoons were also included to assess possible differences related to chemical exposure. Results indicated considerable differences in hepatic retinoid composition among the various species investigated. The most striking differences were in retinol and derivative-specific profiles and in didehydro retinol and derivative-specific profiles. The Perciformes species Geophagus brasiliensis, Tilapia rendalli, Mugil liza, and Cichla ocellaris and the Characiforme Hoplias malabaricus were characterized as retinol and derivative-specific, while the Siluriformes species Hoplosternum littorale and Rhamdia quelen were didehydro retinol and derivative-specific fish species. A negative association was observed between Al, Pb, As, and Cd and hepatic didehydro retinoid levels. Fish with higher levels of hepatic Fe, Cu, and Zn showed unexpectedly significant positive correlations with increased hepatic retinol levels. This finding, associated with the positive relationships between retinol and retinyl palmitate with lipid peroxidation, may suggest that vitamin A is mobilized from other tissues to increase hepatic antioxidant levels for protection against oxidative damage. These data show significant but dissimilar associations between trace element exposure and hepatic retinoid levels in fish species exposed to iron-ore mining and processing effluents, without apparent major impacts on fish health and condition. Copyright © 2011 SETAC.

Sex-specific gene expression in early life stage fathead minnows (Pimephales promelas) throughout development and after exposure to synthetic hormones

EPA Science Inventory

There is evidence that exposure to endocrine disrupting chemicals (EDCs) during early life stages can alter sex differentiation in fishes. Fathead minnows (Pimephales promelas) are commonly used as a model fish species in endocrine disruption studies. However, limited knowledge...

Characterization of Ras k 1 a novel major allergen in Indian mackerel and identification of parvalbumin as the major fish allergen in 33 Asia-Pacific fish species.

PubMed

Ruethers, T; Raith, M; Sharp, M F; Koeberl, M; Stephen, J N; Nugraha, R; Le, T T K; Quirce, S; Nguyen, H X M; Kamath, S D; Mehr, S S; Campbell, D E; Bridges, C R; Taki, A C; Swoboda, I; Lopata, A L

2018-04-01

Fish is a well-recognized cause of food allergy and anaphylaxis. The evolutionary and taxonomic diversity of the various consumed fish species pose a challenge in the identification and characterization of the major fish allergens critical for reliable diagnostics. Globally, fish is a rising cause of food allergy complicated by a large under-investigated variety of species as well as increasing global tourism and trade. This is the first comprehensive study on allergen profiles of heat-processed fish from Vietnam. The aim of this study was to identify the major heat-stable allergens from frequently exported Asia-Pacific freshwater and marine fish and to characterize the major allergen parvalbumin (PV) from one of the most consumed and exported fish species from Asia, the Indian mackerel (Rastrelliger kanagurta). Heated protein extracts from 33 fish species were separated by gel electrophoresis. PV isoforms were identified by immunoblotting utilizing 3 different PV-specific monoclonal and polyclonal antibodies and further characterized by mass spectrometry. IgE reactivity was investigated using sera from 21 patients with confirmed fish allergy. Heat-stable IgE-reactive PVs, with up to 5 isoforms per species, were identified in all 33 analysed fish species. In the Indian mackerel, 7 PV isoforms were identified by 2D-gel electrophoresis combined with mass spectrometric analyses. The amino acid sequence deduced from cDNA of the most expressed isoform showed a high identity (>90%) to PVs from 2 other mackerel species. Different PVs were identified as the major heat-stable allergens in all 33 analysed freshwater and marine fish species from Vietnam, many of which are exported world-wide and 21 species that have never been investigated before. The Indian mackerel PV represents a novel fish allergen, now officially registered as Ras k 1. Improved diagnostics for fish allergy against Asia-Pacific species should be developed with focus on PV. © 2017 John Wiley & Sons Ltd.

Sex-specific gonadal and gene expression changes throughout development in fathead minnow

EPA Science Inventory

Although fathead minnows (Pimephales promelas) are commonly used as a model fish in endocrine disruption studies, none have characterized sex-specific baseline expression of genes involved in sex differentiation during development in this species. Using a sex-linked DNA marker t...

Fish product mislabelling: failings of traceability in the production chain and implications for illegal, unreported and unregulated (IUU) fishing.

PubMed

Helyar, Sarah J; Lloyd, Hywel Ap D; de Bruyn, Mark; Leake, Jonathan; Bennett, Niall; Carvalho, Gary R

2014-01-01

Increasing consumer demand for seafood, combined with concern over the health of our oceans, has led to many initiatives aimed at tackling destructive fishing practices and promoting the sustainability of fisheries. An important global threat to sustainable fisheries is Illegal, Unreported and Unregulated (IUU) fishing, and there is now an increased emphasis on the use of trade measures to prevent IUU-sourced fish and fish products from entering the international market. Initiatives encompass new legislation in the European Union requiring the inclusion of species names on catch labels throughout the distribution chain. Such certification measures do not, however, guarantee accuracy of species designation. Using two DNA-based methods to compare species descriptions with molecular ID, we examined 386 samples of white fish, or products labelled as primarily containing white fish, from major UK supermarket chains. Species specific real-time PCR probes were used for cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) to provide a highly sensitive and species-specific test for the major species of white fish sold in the UK. Additionally, fish-specific primers were used to sequence the forensically validated barcoding gene, mitochondrial cytochrome oxidase I (COI). Overall levels of congruence between product label and genetic species identification were high, with 94.34% of samples correctly labelled, though a significant proportion in terms of potential volume, were mislabelled. Substitution was usually for a cheaper alternative and, in one case, extended to a tropical species. To our knowledge, this is the first published study encompassing a large-scale assessment of UK retailers, and if representative, indicates a potentially significant incidence of incorrect product designation.

Fish Allergens at a Glance: Variable Allergenicity of Parvalbumins, the Major Fish Allergens

PubMed Central

Kuehn, Annette; Swoboda, Ines; Arumugam, Karthik; Hilger, Christiane; Hentges, François

2014-01-01

Fish is a common trigger of severe, food-allergic reactions. Only a limited number of proteins induce specific IgE-mediated immune reactions. The major fish allergens are the parvalbumins. They are members of the calcium-binding EF-hand protein family characterized by a conserved protein structure. They represent highly cross-reactive allergens for patients with specific IgE to conserved epitopes. These patients might experience clinical reactions with various fish species. On the other hand, some individuals have IgE antibodies directed against unique, species-specific parvalbumin epitopes, and these patients show clinical symptoms only with certain fish species. Furthermore, different parvalbumin isoforms and isoallergens are present in the same fish and might display variable allergenicity. This was shown for salmon homologs, where only a single parvalbumin (beta-1) isoform was identified as allergen in specific patients. In addition to the parvalbumins, several other fish proteins, enolases, aldolases, and fish gelatin, seem to be important allergens. New clinical and molecular insights advanced the knowledge and understanding of fish allergy in the last years. These findings were useful for the advancement of the IgE-based diagnosis and also for the management of fish allergies consisting of advice and treatment of fish-allergic patients. PMID:24795722

Heavy metals in wild marine fish from South China Sea: levels, tissue- and species-specific accumulation and potential risk to humans.

PubMed

Liu, Jin-Ling; Xu, Xiang-Rong; Ding, Zhen-Hua; Peng, Jia-Xi; Jin, Ming-Hua; Wang, You-Shao; Hong, Yi-Guo; Yue, Wei-Zhong

2015-10-01

Heavy metal pollution in marine fish has become an important worldwide concern, not only because of the threat to fish in general, but also due to human health risks associated with fish consumption. To investigate the occurrence of heavy metals in marine fish species from the South China Sea, 14 fish species were collected along the coastline of Hainan China during the spring of 2012 and examined for species- and tissue-specific accumulation. The median concentrations of Cd, Cr, Cu, Zn, Pb and As in muscle tissue of the examined fish species were not detectable (ND), 2.02, 0.24, 2.64, 0.025, and 1.13 mg kg(-1) wet weight, respectively. Levels of Cu, Zn, Cd and Cr were found to be higher in the liver and gills than in muscle, while Pb was preferentially accumulated in the gills. Differing from other heavy metals, As did not exhibit tissue-specific accumulation. Inter-species differences of heavy metal accumulation were attributed to the different habitat and diet characteristics of marine fish. Human dietary exposure assessment suggested that the amounts of both Cr and As in marine wild fish collected from the sites around Hainan, China were not compliant with the safety standard of less than 79.2 g d(-1) for wild marine fish set by the Joint FAO/WHO Expert Committee on Food Additives. Further research to identify the explicit sources of Cr and As in marine fish from South China Sea should be established.

Mayfly and fish species identification and sex determination in bleak (Alburnus alburnus) by MALDI-TOF mass spectrometry.

PubMed

Maasz, G; Takács, P; Boda, P; Varbiro, G; Pirger, Z

2017-12-01

Besides food quality control of fish or cephalopods, the novel mass spectrometry (MS) approaches could be effective and beneficial methods for the investigation of biodiversity in ecological research. Our aims were to verify the applicability of MALDI-TOF MS in the rapid identification of closely related species, and to further develop it for sex determination in phenotypically similar fish focusing on the low mass range. For MALDI-TOF MS spectra analysis, ClinProTools software was applied, but our observed classification was also confirmed by Self Organizing Map. For verifying the wide applicability of the method, brains from invertebrate and vertebrate species were used in order to detect the species related markers from two mayflies and eight fish as well as sex-related markers within bleak. Seven Ephemera larvae and sixty-one fish species related markers were observed and nineteen sex-related markers were identified in bleak. Similar patterns were observed between the individuals within one species. In contrast, there were markedly diverse patterns between the different species and sexes visualized by SOMs. Two different Ephemera species and male or female fish were identified with 100% accuracy. The various fish species were classified into 8 species with a high level of accuracy (96.2%). Based on MS data, dendrogram was generated from different fish species by using ClinProTools software. This MS-based dendrogram shows relatively high correspondence with the phylogenetic relationships of both the studied species and orders. In summary, MALDI-TOF MS provides a cheap, reliable, sensitive and fast identification tool for researchers in the case of closely related species using mass spectra acquired in a low mass range to define specific molecular profiles. Moreover, we presented evidence for the first time for determination of sex within one fish species by using this method. We conclude that it is a powerful tool that can revolutionize ecological and environmental research. Copyright © 2017 Elsevier B.V. All rights reserved.

Antimicrobial Peptides from Fish

PubMed Central

Masso-Silva, Jorge A.; Diamond, Gill

2014-01-01

Antimicrobial peptides (AMPs) are found widely distributed through Nature, and participate in the innate host defense of each species. Fish are a great source of these peptides, as they express all of the major classes of AMPs, including defensins, cathelicidins, hepcidins, histone-derived peptides, and a fish-specific class of the cecropin family, called piscidins. As with other species, the fish peptides exhibit broad-spectrum antimicrobial activity, killing both fish and human pathogens. They are also immunomodulatory, and their genes are highly responsive to microbes and innate immuno-stimulatory molecules. Recent research has demonstrated that some of the unique properties of fish peptides, including their ability to act even in very high salt concentrations, make them good potential targets for development as therapeutic antimicrobials. Further, the stimulation of their gene expression by exogenous factors could be useful in preventing pathogenic microbes in aquaculture. PMID:24594555

Going with the flow: using species-discharge relationships to forecast losses in fish biodiversity.

PubMed

Xenopoulos, Marguerite A; Lodge, David M

2006-08-01

In response to the scarcity of tools to make quantitative forecasts of the loss of aquatic species from anthropogenic effects, we present a statistical model that relates fish species richness to river discharge. Fish richness increases logarithmically with discharge, an index of habitat space, similar to a species-area curve in terrestrial systems. We apply the species-discharge model as a forecasting tool to build scenarios of changes in riverine fish richness from climate change, water consumption, and other anthropogenic drivers that reduce river discharge. Using hypothetical reductions in discharges (of magnitudes that have been observed in other rivers), we predict that reductions of 20-90% in discharge would result in losses of 2-38% of the fish species in two biogeographical regions in the United States (Lower Ohio-Upper Mississippi and Southeastern). Additional data on the occurrence of specific species relative to specific discharge regimes suggests that fishes found exclusively in high discharge environments (e.g., Shovelnose sturgeon) would be most vulnerable to reductions in discharge. Lag times in species extinctions after discharge reduction provide a window of opportunity for conservation efforts. Applications of the species-discharge model can help prioritize such management efforts among species and rivers.

Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement

PubMed Central

Parris, Darren J.; Brooker, Rohan M.; Morgan, Michael A.; Dixson, Danielle L.

2016-01-01

The Pomacentridae (damselfish) and Apogonidae (cardinalfish) are among the most common fish families on coral reefs and in the aquarium trade. Members of both families undergo a pelagic larvae phase prior to settlement on the reef, where adults play key roles in benthic habitat structuring and trophic interactions. Fish-associated microbial communities (microbiomes) significantly influence fish health and ecology, yet little is known of how microbiomes change with life stage. We quantified the taxonomic (16S rRNA gene) composition of whole gut microbiomes from ten species of damselfish and two species of cardinalfish from Lizard Island, Australia, focusing specifically on comparisons between pelagic larvae prior to settlement on the reef versus post-settlement juvenile and adult individuals. On average, microbiome phylogenetic diversity increased from pre- to post-settlement, and was unrelated to the microbial composition in the surrounding water column. However, this trend varied among species, suggesting stochasticity in fish microbiome assembly. Pre-settlement fish were enriched with bacteria of the Endozoicomonaceae, Shewanellaceae, and Fusobacteriaceae, whereas settled fish harbored higher abundances of Vibrionaceae and Pasteurellaceae. Several individual operational taxonomic units, including ones related to Vibrio harveyi, Shewanella sp., and uncultured Endozoicomonas bacteria, were shared between both pre and post-settlement stages and may be of central importance in the intestinal niche across development. Richness of the core microbiome shared among pre-settlement fish was comparable to that of settled individuals, suggesting that changes in diversity with adulthood are due to the acquisition or loss of host-specific microbes. These results identify a key transition in microbiome structure across host life stage, suggesting changes in the functional contribution of microbiomes over development in two ecologically dominant reef fish families. PMID:27635360

Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement.

PubMed

Parris, Darren J; Brooker, Rohan M; Morgan, Michael A; Dixson, Danielle L; Stewart, Frank J

2016-01-01

The Pomacentridae (damselfish) and Apogonidae (cardinalfish) are among the most common fish families on coral reefs and in the aquarium trade. Members of both families undergo a pelagic larvae phase prior to settlement on the reef, where adults play key roles in benthic habitat structuring and trophic interactions. Fish-associated microbial communities (microbiomes) significantly influence fish health and ecology, yet little is known of how microbiomes change with life stage. We quantified the taxonomic (16S rRNA gene) composition of whole gut microbiomes from ten species of damselfish and two species of cardinalfish from Lizard Island, Australia, focusing specifically on comparisons between pelagic larvae prior to settlement on the reef versus post-settlement juvenile and adult individuals. On average, microbiome phylogenetic diversity increased from pre- to post-settlement, and was unrelated to the microbial composition in the surrounding water column. However, this trend varied among species, suggesting stochasticity in fish microbiome assembly. Pre-settlement fish were enriched with bacteria of the Endozoicomonaceae, Shewanellaceae, and Fusobacteriaceae, whereas settled fish harbored higher abundances of Vibrionaceae and Pasteurellaceae. Several individual operational taxonomic units, including ones related to Vibrio harveyi, Shewanella sp., and uncultured Endozoicomonas bacteria, were shared between both pre and post-settlement stages and may be of central importance in the intestinal niche across development. Richness of the core microbiome shared among pre-settlement fish was comparable to that of settled individuals, suggesting that changes in diversity with adulthood are due to the acquisition or loss of host-specific microbes. These results identify a key transition in microbiome structure across host life stage, suggesting changes in the functional contribution of microbiomes over development in two ecologically dominant reef fish families.

Development of Genetic Markers for Environmental DNA (eDNA) Monitoring of Sturgeon

DTIC Science & Technology

2014-09-01

sturgeon markers were tested for specificity against a battery of 32 non-target fish species common to the Mississippi and Illinois River watersheds...techniques. Such methods, including fishing , netting, seining, and electrofishing, can often be logistically complex and require considerable outlays of... fish and amphibian community composition (Minamoto et al. 2012, Thomsen et al. 2012) and biomass estimation (Takahara et al. 2012). Sturgeon are taxa

Infection experiments with Aphanomyces invadans in four species of estuarine fish

USGS Publications Warehouse

Johnson, R.A.; Zabrecky, J.; Kiryu, Y.; Shields, J.D.

2004-01-01

Along the eastern seaboard of the US, Atlantic menhaden, Brevoortia tyrannus, develop characteristic ulcerative lesions, a condition termed ulcerative mycosis. These lesions are identical to those seen across Asia in fish affected by epizootic ulcerative syndrome, a condition caused by the fungus-like oomycete Aphanomyces Invadans. Young-of-the-year menhaden inhabiting estuarine environments are the primary species affected in the USA and little is known about the factors involved in the initiation of the lesions, or why menhaden are predominantly infected. Atlantic menhaden, hogchoker, Trinectus maculatus, striped killifish, Fundulus majalis, and mummichog, Fundulus heteroclitus, were inoculated with A. invadans (80 zoospores per fish) to explore species differences in infection and lesion development. All four species developed lesions. Killifish developed frank lesions similar to those observed in menhaden but the gross lesions occurred later, approximately 5-10 days after those on menhaden. Hogchoker and mummichog did not develop gross skin ulcers; rather, their lesions appeared as reddened areas under the epidermis. Mummichogs also showed evidence of significant healing with a well-developed granuloma and significant myocyte regeneration. These experiments show that species barriers as well as ecological barriers can explain some of the factors involved in the development of lesions in, and specificity of the water mould for, menhaden.

Quantitative Approach for Incorporating Methylmercury Risks and Omega-3 Fatty Acid Benefits in Developing Species-Specific Fish Consumption Advice

PubMed Central

Ginsberg, Gary L.; Toal, Brian F.

2009-01-01

Background Despite general agreement about the toxicity of methylmercury (MeHg), fish consumption advice remains controversial. Concerns have been raised that negative messages will steer people away from fish and omega-3 fatty acid (FA) benefits. One approach is to provide advice for individual species that highlights beneficial fish while cautioning against riskier fish. Objectives Our goal in this study was to develop a method to quantitatively analyze the net risk/benefit of individual fish species based on their MeHg and omega-3 FA content. Methods We identified dose–response relationships for MeHg and omega-3 FA effects on coronary heart disease (CHD) and neurodevelopment. We used the MeHg and omega-3 FA content of 16 commonly consumed species to calculate the net risk/benefit for each species. Results Estimated omega-3 FA benefits outweigh MeHg risks for some species (e.g., farmed salmon, herring, trout); however, the opposite was true for others (swordfish, shark). Other species were associated with a small net benefit (e.g., flounder, canned light tuna) or a small net risk (e.g., canned white tuna, halibut). These results were used to place fish into one of four meal frequency categories, with the advice tentative because of limitations in the underlying dose–response information. Separate advice appears warranted for the neurodevelopmental risk group versus the cardiovascular risk group because we found a greater net benefit from fish consumption for the cardiovascular risk group. Conclusions This research illustrates a framework for risk/benefit analysis that can be used to develop categories of consumption advice ranging from “do not eat” to “unlimited,” with the caveat that unlimited may need to be tempered for certain fish (e.g., farm-raised salmon) because of other contaminants and end points (e.g., cancer risk). Uncertainties exist in the underlying dose–response relationships, pointing in particular to the need for more research on the adverse effects of MeHg on cardiovascular end points. PMID:19270798

Genetic assessment of ornamental fish species from North East India.

PubMed

Dhar, Bishal; Ghosh, Sankar Kumar

2015-01-25

Ornamental fishes are traded with multiple names from various parts around the world, including North East India. Most are collected from the wild, due to lack of species-specific culture or breeding, and therefore, such unmanaged collection of the wild and endemic species could lead to severe threats to biodiversity. Despite many regulatory policies, trade of threatened species, including the IUCN listed species have been largely uncontrolled, due to species identification problems arising from the utilization of multiple trade names. So, the development of species-specific DNA marker is indispensable where DNA Barcoding is proved to be helpful in species identification. Here, we investigated, through DNA Barcoding and morphological assessment, the identification of 128 ornamental fish specimens exported from NE India from different exporters. The generated sequences were subjected to similarity match in BOLD-IDS as well as BLASTN, and analysed using MEGA5.2 for species identification through Neighbour-Joining (NJ) clustering, and K2P distance based approach. The analysis revealed straightforward identification of 84 specimens into 35 species, while 44 specimens were difficult to distinguish based on CO1 barcode alone. However, these cases were resolved through morphology, NJ and distanced based method and found to be belonging to 16 species. Among the 51 identified species, 14 species represented multiple trade names; 17 species belonged to threatened category. Species-level identification through DNA Barcoding along with traditional morphotaxonomy reflects its efficacy in regulating ornamental fish trade and therefore, appeals for their conservation in nature. The use of trade names rather than the zoological name created the passage for trafficking of the threatened species and demands immediate attention for sustaining wildlife conservation. Copyright © 2014 Elsevier B.V. All rights reserved.

Effects of coalbed natural gas development on fish assemblages in tributary streams of the Powder and Tongue rivers

USGS Publications Warehouse

Davis, W.N.; Bramblett, R.G.; Zale, A.V.

2010-01-01

1. Extraction of coalbed natural gas (CBNG) often results in disposal of large quantities of CBNG product water, which may affect aquatic ecosystems. We evaluated the effects of CBNG development on fish assemblages in tributary streams of the Powder and Tongue rivers. We used treatment and control, impact versus reference sites comparisons, surveys of CBNG product-water streams and in situ fish survival approaches to determine if CBNG development affected fish assemblages.2. Several of our results suggested that CBNG development did not affect fish assemblages. Species richness and index of biotic integrity (IBI) scores were similar in streams with and streams without CBNG development, and overall biotic integrity was not related to the number or density of CBNG wells. Fish occurred in one stream that was composed largely or entirely of CBNG product water. Sentinel fish survived in cages at treatment sites where no or few fish were captured, suggesting that factors such as lack of stream connectivity rather than water quality limited fish abundance at these sites. Fish species richness did not differ significantly from 1994 to 2006 in comparisons of CBNG-developed and undeveloped streams. Biotic integrity declined from 1994 to 2006; however, declines occurred at both impact and reference sites, possibly because of long-term drought.3. Some evidence suggested that CBNG development negatively affected fish assemblages, or may do so over time. Specific conductivity was on average higher in treatment streams and was negatively related to biotic integrity. Four IBI species richness metrics were negatively correlated with the number or density of CBNG wells in the catchment above sampling sites. Bicarbonate, one of the primary ions in product water, was significantly higher in developed streams and may have limited abundance of longnose dace (Rhinichthys cataractae). Total dissolved solids, alkalinity, magnesium and sulphate were significantly higher in developed streams.4. Biological monitoring conducted before the development of CBNG, and continuing through the life of development and reclamation, together with data on the quantity, quality and fate of CBNG product water will allow robust assessment of potential effects of future CBNG development worldwide. ?? 2010 Blackwell Publishing Ltd.

50 CFR 270.3 - Submission of application.

Code of Federal Regulations, 2010 CFR

2010-10-01

... ADMINISTRATION, DEPARTMENT OF COMMERCE FISH AND SEAFOOD PROMOTION SPECIES-SPECIFIC SEAFOOD MARKETING COUNCILS... Marketing Council for one or more species of fish and fish products of that species. One signed original and... implement marketing and promotion plans under the Act. (The American Fisheries Society's “List of Common and...

Effects of lake trout refuges on lake whitefish and cisco in the Apostle Islands Region of Lake Superior

USGS Publications Warehouse

Zuccarino-Crowe , Chiara M.; Taylor, William W.; Hansen, Michael J.; Seider, Michael J.; Krueger, Charles C.

2016-01-01

Lake trout refuges in the Apostle Islands region of Lake Superior are analogous to the concept of marine protected areas. These refuges, established specifically for lake trout (Salvelinus namaycush) and closed to most forms of recreational and commercial fishing, were implicated as one of several management actions leading to successful rehabilitation of Lake Superior lake trout. To investigate the potential significance of Gull Island Shoal and Devils Island Shoal refuges for populations of not only lake trout but also other fish species, relative abundances of lake trout, lake whitefish (Coregonus clupeaformis), and cisco (Coregonus artedi) were compared between areas sampled inside versus outside of refuge boundaries. During 1982–2010, lake trout relative abundance was higher and increased faster inside the refuges, where lake trout fishing was prohibited, than outside the refuges. Over the same period, lake whitefish relative abundance increased faster inside than outside the refuges. Both evaluations provided clear evidence that refuges protected these species. In contrast, trends in relative abundance of cisco, a prey item of lake trout, did not differ significantly between areas inside and outside the refuges. This result did not suggest indirect or cascading refuge effects due to changes in predator levels. Overall, this study highlights the potential of species-specific refuges to benefit other fish species beyond those that were the refuges' original target. Improved understanding of refuge effects on multiple species of Great Lakes fishes can be valuable for developing rationales for refuge establishment and predicting associated fish community-level effects.

Functional diversity of non-lethal effects, chemical camouflage, and variation in fish avoidance in colonizing beetles.

PubMed

Resetarits, William J; Pintar, Matthew R

2016-12-01

Predators play an extremely important role in natural communities. In freshwater systems, fish can dominate sorting both at the colonization and post-colonization stage. Specifically, for many colonizing species, fish can have non-lethal, direct effects that exceed the lethal direct effects of predation. Functionally diverse fish species with a range of predatory capabilities have previously been observed to elicit functionally equivalent responses on oviposition in tree frogs. We tested this hypothesis of functional equivalence of non-lethal effects for four predatory fish species, using naturally colonizing populations of aquatic beetles. Among taxa other than mosquitoes, and with the exception of the chemically camouflaged pirate perch, Aphredoderus sayanus, we provide the first evidence of variation in colonization or oviposition responses to different fish species. Focusing on total abundance, Fundulus chrysotus, a gape-limited, surface-feeding fish, elicited unique responses among colonizing Hydrophilidae, with the exception of the smallest and most abundant taxa, Paracymus, while Dytiscidae responded similarly to all avoided fish. Neither family responded to A. sayanus. Analysis of species richness and multivariate characterization of the beetle assemblages for the four fish species and controls revealed additional variation among the three avoided species and confirmed that chemical camouflage in A. sayanus results in assemblages essentially identical to fishless controls. The origin of this variation in beetle responses to different fish is unknown, but may involve variation in cue sensitivity, different behavioral algorithms, or differential responses to species-specific fish cues. The identity of fish species occupying aquatic habitats is crucial to understanding community structure, as varying strengths of lethal and non-lethal effects, as well as their interaction, create complex landscapes of predator effects and challenge the notion of functional equivalence. © 2016 by the Ecological Society of America.

A 1.5 hour procedure for identification of Enterococcus Species directly from blood cultures.

PubMed

Morgan, Margie A; Marlowe, Elizabeth; Novak-Weekly, Susan; Miller, J M; Painter, T M; Salimnia, Hossein; Crystal, Benjamin

2011-02-10

Enterococci are a common cause of bacteremia with E. faecalis being the predominant species followed by E. faecium. Because resistance to ampicillin and vancomycin in E. faecalis is still uncommon compared to resistance in E. faecium, the development of rapid tests allowing differentiation between enterococcal species is important for appropriate therapy and resistance surveillance. The E. faecalis OE PNA FISH assay (AdvanDx, Woburn, MA) uses species-specific peptide nucleic acid (PNA) probes in a fluorescence in situ hybridization format and offers a time to results of 1.5 hours and the potential of providing important information for species-specific treatment. Multicenter studies were performed to assess the performance of the 1.5 hour E. faecalis/OE PNA FISH procedure compared to the original 2.5 hour assay procedure and to standard bacteriology methods for the identification of enterococci directly from a positive blood culture bottle.

A 1.5 Hour Procedure for Identification of Enterococcus Species Directly from Blood Cultures

PubMed Central

Morgan, Margie A.; Marlowe, Elizabeth; Novak-Weekly, Susan; Miller, J.M.; Painter, T.M.; Salimnia, Hossein; Crystal, Benjamin

2011-01-01

Enterococci are a common cause of bacteremia with E. faecalis being the predominant species followed by E. faecium. Because resistance to ampicillin and vancomycin in E. faecalis is still uncommon compared to resistance in E. faecium, the development of rapid tests allowing differentiation between enterococcal species is important for appropriate therapy and resistance surveillance. The E. faecalis OE PNA FISH assay (AdvanDx, Woburn, MA) uses species-specific peptide nucleic acid (PNA) probes in a fluorescence in situ hybridization format and offers a time to results of 1.5 hours and the potential of providing important information for species-specific treatment. Multicenter studies were performed to assess the performance of the 1.5 hour E. faecalis/OE PNA FISH procedure compared to the original 2.5 hour assay procedure and to standard bacteriology methods for the identification of enterococci directly from a positive blood culture bottle. PMID:21339730

Identifying Canadian Freshwater Fishes through DNA Barcodes

PubMed Central

Hubert, Nicolas; Hanner, Robert; Holm, Erling; Mandrak, Nicholas E.; Taylor, Eric; Burridge, Mary; Watkinson, Douglas; Dumont, Pierre; Curry, Allen; Bentzen, Paul; Zhang, Junbin; April, Julien; Bernatchez, Louis

2008-01-01

Background DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5′ region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons. Methodology/Principal Findings We bi-directionally sequenced the standard 652 bp “barcode” region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species. Conclusions/Significance The present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics. PMID:22423312

Vector specificity of Trypanosoma catostomi and its infectivity to freshwater fishes.

PubMed

Jones, S R; Woo, P T

1992-02-01

Trypanosoma catostomi was found in 36.2% of 558 white suckers (Catostomus commersoni) from Ontario, Canada. The abundance of Actinobdella inequiannulata was 35% (68 leeches/197 suckers examined for leeches). The susceptibility of 3 species of leeches (Hemiclepsis marginata, Desserobdella phalera, and A. inequiannulata) and 7 species of fishes (C. commersoni, Amia calva, Anguilla rostrata, Ictalurus nebulosus, Oncorhynchus mykiss, Perca flavescens, and Esox lucius) to infection with T. catostomi was examined. Metatrypanosomes were found in the crop and proboscis sheath of 13 of 21 A. inequiannulata and in the crop of 10 of 12 H. marginata and 1 of 21 D. phalera. Only flagellates from A. inequiannulata were infective to C. commersoni. Cultured T. catostomi infected C. commersoni and A. calva but not any other fish species. Laboratory-reared C. commersoni were more susceptible than wild-caught specimens. Cultured Trypanosoma phaleri did not infect its natural host, A. calva. Host specificity should be established experimentally before a specific diagnosis is made. Cultures may be useful in simulating factors that affect development in the vector.

Quantitative determination of rarity of freshwater fishes and implications for imperiled-species designations.

PubMed

Pritt, Jeremy J; Frimpong, Emmanuel A

2010-10-01

Conserving rare species and protecting biodiversity and ecosystem functioning depends on sound information on the nature of rarity. Rarity is multidimensional and has a variety of definitions, which presents the need for a quantitative classification scheme with which to categorize species as rare or common. We constructed such a classification for North American freshwater fishes to better describe rarity in fishes and provide researchers and managers with a tool to streamline conservation efforts. We used data on range extents, habitat specificities, and local population sizes of North American freshwater fishes and a variety of quantitative methods and statistical decision criteria, including quantile regression and a cost-function algorithm to determine thresholds for categorizing a species as rare or common. Species fell into eight groups that conform to an established framework for rarity. Fishes listed by the American Fisheries Society (AFS) as endangered, threatened, or vulnerable were most often rare because their local population sizes were low, ranges were small, and they had specific habitat needs, in that order, whereas unlisted species were most often considered common on the basis of these three factors. Species with large ranges generally had few specific habitat needs, whereas those with small ranges tended to have narrow habitat specificities. We identified 30 species not designated as imperiled by AFS that were rare along all dimensions of rarity and may warrant further study or protection, and we found three designated species that were common along all dimensions and may require a review of their imperilment status. Our approach could be applied to other taxa to aid conservation decisions and serve as a useful tool for future revisions of listings of fish species. © 2010 Society for Conservation Biology.

Host specificity of Argulus coregoni (Crustacea: Branchiura) increases at maturation.

PubMed

Mikheev, V N; Pasternak, A F; Valtonen, E T

2007-11-01

We tested the hypothesis that host specificity in ectoparasites does not depend exclusively on the features of the host but also on surrounding habitats, using 2 fish ectoparasites, Argulus coregoni and A. foliaceus (Crustacea: Branchiura), occurring sympatrically in Finnish lakes. Although these parasites are considered to be of low specificity, we found that the larger of the 2 species, A. coregoni developed a pronounced preference for salmonid hosts at the beginning of maturation (defined by the presence of copulating specimens). Argulus foliaceus infects a much wider range of fish hosts. We showed that specialization of A. coregoni on salmonids does not necessarily result from incompatibility with other fishes, but could instead reflect higher sensitivity of oxygen depletion compared with A. foliaceus. Adult A. coregoni may meet these demands by attaching to salmonids, the typical inhabitants of well-aerated waters. Young parasites of both species showed little host specificity and attached mainly to fishes with higher body reflectivity. In host choice experiments, A. coregoni of 4-5 mm length preferred salmonids (rainbow trout) to cyprinids (roach) irrespective of the type of fish host, on which it had been previously grown in the laboratory. We suggest that such an innate ontogenetic shift in host preference maintains the major part of the parasite population on its principal host, ensuring successful reproduction within suitable habitats.

Prevalence and proposal for cost-effective management of the ciguatera risk in the Noumea fish market, New Caledonia (South Pacific).

PubMed

Clua, Eric; Brena, Pierpaolo F; Lecasble, Côme; Ghnassia, Reine; Chauvet, Claude

2011-11-01

Ciguatera fish poisoning (CFP) is a common intoxication associated with the consumption of reef fish, which constitutes a critical issue for public health in many countries. The complexity of its epidemiology is responsible for the poor management of the risk in tropical fish markets. We used the example of the Noumea fish market in New Caledonia to develop a cost-effective methodology of assessing the CFP risk. We first used published reports and the knowledge of local experts to define a list of potentially poisonous local species, ranked by their ciguatoxic potential. Based on two 1-month surveys in the market, conducted in winters 2008 and 2009, we then calculated the consolidated ratio of biomass of potentially poisonous species vs. total biomass of fish sold on the market. The prevalence of high CFP-risk species in the market was 16.1% and 18.9% in 2008 and 2009, respectively. The most common high CFP risk species were groupers (serranids), king mackerels (scombrids), snappers (lutjanids), barracudas (sphyaraenids), emperors (lethrinids) and wrasses (labrids). The size (age) of the fish also plays a critical role in the potential ciguatoxic risk. According to proposals of average size thresholds provided by experts for high-risk species, we were also able to assess the additional risk induced by the sale of some large fish on the market. The data collected both from experts and from the market allowed us to develop a cost-effective proposal for improving the management of the CFP risk in this market. However, the successful implementation of any regulation aiming to ban some specific species and sizes from the market, with an acceptable economical impact, will require the improvement of the expertise in fish identification by public health officers and, ideally, the commitment of retailers. Copyright © 2011 Elsevier Ltd. All rights reserved.

A hierarchical community occurrence model for North Carolina stream fish

USGS Publications Warehouse

Midway, S.R.; Wagner, Tyler; Tracy, B.H.

2016-01-01

The southeastern USA is home to one of the richest—and most imperiled and threatened—freshwater fish assemblages in North America. For many of these rare and threatened species, conservation efforts are often limited by a lack of data. Drawing on a unique and extensive data set spanning over 20 years, we modeled occurrence probabilities of 126 stream fish species sampled throughout North Carolina, many of which occur more broadly in the southeastern USA. Specifically, we developed species-specific occurrence probabilities from hierarchical Bayesian multispecies models that were based on common land use and land cover covariates. We also used index of biotic integrity tolerance classifications as a second level in the model hierarchy; we identify this level as informative for our work, but it is flexible for future model applications. Based on the partial-pooling property of the models, we were able to generate occurrence probabilities for many imperiled and data-poor species in addition to highlighting a considerable amount of occurrence heterogeneity that supports species-specific investigations whenever possible. Our results provide critical species-level information on many threatened and imperiled species as well as information that may assist with re-evaluation of existing management strategies, such as the use of surrogate species. Finally, we highlight the use of a relatively simple hierarchical model that can easily be generalized for similar situations in which conventional models fail to provide reliable estimates for data-poor groups.

Are vegetated areas of mangroves attractive to juvenile and small fish? The case of Dongzhaigang Bay, Hainan Island, China

NASA Astrophysics Data System (ADS)

Wang, Mao; Huang, Zhenyuan; Shi, Fushan; Wang, Wenqing

2009-11-01

Well-developed aerial roots of mangroves make it difficult to study how fish utilize the mangrove forest as a habitat. In the present study, we compared the differences in fish assemblages in three major types of habitats of mangrove estuary (vegetated area, treeless mudflat, and creek) of a mangrove bay in Hainan Island, China, at different seasons during two consecutive years. Three types of gears, centipede net, gill net and cast net, were used in the different habitats of mangrove estuary and sampling efficiencies among gears were evaluated. Centipede nets were used in all the three types of habitats and cast nets and gill nets in treeless mudflats and creeks. Fish assemblages were dependent on gears used. Centipede net could efficiently catch fish occurring both inside and outside of vegetated areas efficiently. A total of 115 fish species in 51 families were collected. In terms of numbers of species per family, Gobiidae was the most diverse (17 species), followed by Mugilidae (5 species). Almost all of the fish were juvenile or small fish and few predators were recorded, implying low predation pressure in the bay. ANOVA analysis showed that significant seasonal and spatial variation existed in species richness, abundance, and biomass, which were less in the vegetated areas than those of treeless mudflats and creeks. The attraction of vegetated areas to fish was less than that of creeks and mudflats. Many species were specific to a particular habitat type, 4 species occurring exclusively in the creeks, 45 species occurring exclusively in the treeless mudflats, and 5 species occurring exclusively in the vegetated areas. The results indicated that mangrove estuaries were potentially attractive habitats for juvenile and small fish, but this attraction was accomplished by a connection of vegetated areas, treeless mudflats and creeks, not only by vegetated areas.

Comparative energetics of the 5 fish classes on the basis of dynamic energy budgets

NASA Astrophysics Data System (ADS)

Kooijman, Sebastiaan A. L. M.; Lika, Konstadia

2014-11-01

The eco-physiology of taxa in an evolutionary context can best be studied by a comparison of parameter values of the energy budget that accounts for the inter-relationships of all endpoints of energy allocation. To this end, the parameters of the standard Dynamic Energy Budget (DEB) model have been estimated for 64 fish species from all 5 fish classes. The values are compared with those of the whole collection of over 300 species from most large animal phyla. The goodness of fit was very high, but the data were rather incomplete, compared with the energy balance for full life cycles. Metabolic acceleration, where maximum specific assimilation and energy conductance increase with length between birth and metabolic metamorphosis, seems to be confined, among fish, to some species of ray-finned fish and seems to have evolved independently several times in this taxon. We introduce a new altriciality index, i.e. the ratio of the maturity levels at puberty and birth, and conclude that ray-finned fish are more altricial, and cartilaginous fish are more precocial than typical animals. Fish allocate more to reproduction than typical animals. Parameter estimates show that 66% of the fish species considered invest less in reproduction than the value that would maximize the reproduction rate of fully grown individuals. By comparison, 85% of all the animal species in the collection do so. Consistent with theoretical expectations, allocation to reproduction and maturity at birth increase with cubed (ultimate structural) length, and reserve capacity with length for non-ray-finned fish, with the consequence that reproduction rate decreases with length. Ray-finned fish, however, have a maturity at birth and a reserve capacity almost independent of length, and a reproduction rate that increases with cubed length. Reserve capacity tends to increase with ultimate length for non-accelerating ray-finned fish, but not for accelerating species. Reproduction rate decreases inter-specifically with length in non-ray-finned fish, as expected, but increases with cubed length in ray-finned fish. This pattern follows naturally from the patterns of size at birth and reserve capacity and can be seen as adaptation to the predation of prey of ray-finned fish on their tiny neonates. Both the von Bertalanffy growth rate and the specific allocation to reproduction in fully grown adults correlate positively with specific somatic maintenance among fish species. These observations support the recently proposed waste-to-hurry hypothesis. Determinatesness increases in the sequence: fish, amphibians, reptiles, mammals and birds.

Fish-allergic patients may be able to eat fish.

PubMed

Mourad, Ahmad A; Bahna, Sami L

2015-03-01

Reported fish allergy prevalence varies widely, with an estimated prevalence of 0.2% in the general population. Sensitization to fish can occur by ingestion, skin contact or inhalation. The manifestations can be IgE or non-IgE mediated. Several fish allergens have been identified, with parvalbumins being the major allergen in various species. Allergenicity varies among fish species and is affected by processing or preparation methods. Adverse reactions after eating fish are often claimed to be 'allergy' but could be a reaction to hidden food allergen, fish parasite, fish toxins or histamine in spoiled fish. Identifying such causes would allow free consumption of fish. Correct diagnosis of fish allergy, including the specific species, might provide the patient with safe alternatives. Patients have been generally advised for strict universal avoidance of fish. However, testing with various fish species or preparations might identify one or more forms that can be tolerated.

Effects of temperature on the development and survival of eggs of four coastal California fishes

USGS Publications Warehouse

Gadomski, D.M.; Caddell, S.M.

1996-01-01

Laboratory experiments were conducted to determine the effects of temperature on egg development and survival of four fish species found off southern California. Our objectives were to further understanding ofnatural spawning patterns and to aid in identifying and ageing field-collected specimens. An egg-staging procedure was devised and eggs were observed every two hours during development at a range of temperatures (8-28°Cl. Barred sand bass, Parolabrax nebulifer, eggs survived to hatching and produced viable embryos at the highest temperature range (l6-28°C), reflecting this species'summerspawning season. Fantail sole, Xystreurys liolepis, eggs also hatched at a higher temperature range (l6-24°C). This species spawns primarily from summer through fall. Eggs of the two species with winter-spring spawning peaks, white croaker, Genyonemuslineatus, and California halibut, Paralichthys californicus, had lower temperature-tolerance ranges (12- 2O"C). Developmental rate at a specific temperature did not significantly differ between species, whereas within tolerance limits, temperature strongly affected rate of development for all species. Time to hatching for all species was inversely related to temperature, and the relationship was approximately exponential. Species-specific differences in egg-stage sequence were observed; embryonic organogenesisin relation to germ-ring migration and blastopore closure was faster for barred sand bass and fantail sole than for white croaker and California halibut.

Fisheries conservation on the high seas: linking conservation physiology and fisheries ecology for the management of large pelagic fishes

PubMed Central

Horodysky, Andrij Z.; Cooke, Steven J.; Graves, John E.; Brill, Richard W.

2016-01-01

Populations of tunas, billfishes and pelagic sharks are fished at or over capacity in many regions of the world. They are captured by directed commercial and recreational fisheries (the latter of which often promote catch and release) or as incidental catch or bycatch in commercial fisheries. Population assessments of pelagic fishes typically incorporate catch-per-unit-effort time-series data from commercial and recreational fisheries; however, there have been notable changes in target species, areas fished and depth-specific gear deployments over the years that may have affected catchability. Some regional fisheries management organizations take into account the effects of time- and area-specific changes in the behaviours of fish and fishers, as well as fishing gear, to standardize catch-per-unit-effort indices and refine population estimates. However, estimates of changes in stock size over time may be very sensitive to underlying assumptions of the effects of oceanographic conditions and prey distribution on the horizontal and vertical movement patterns and distribution of pelagic fishes. Effective management and successful conservation of pelagic fishes requires a mechanistic understanding of their physiological and behavioural responses to environmental variability, potential for interaction with commercial and recreational fishing gear, and the capture process. The interdisciplinary field of conservation physiology can provide insights into pelagic fish demography and ecology (including environmental relationships and interspecific interactions) by uniting the complementary expertise and skills of fish physiologists and fisheries scientists. The iterative testing by one discipline of hypotheses generated by the other can span the fundamental–applied science continuum, leading to the development of robust insights supporting informed management. The resulting species-specific understanding of physiological abilities and tolerances can help to improve stock assessments, develop effective bycatch-reduction strategies, predict rates of post-release mortality, and forecast the population effects of environmental change. In this synthesis, we review several examples of these interdisciplinary collaborations that currently benefit pelagic fisheries management. PMID:27382467

Distribution characteristics of the fish assemblages to varying environmental conditions in artificial reefs of the Jeju Island, Korea.

PubMed

Noh, Junsung; Ryu, Jongseong; Lee, Dowon; Khim, Jong Seong

2017-05-15

Artificial reefs (ARs) have long been practiced to manage and enhance fisheries resources worldwide. Here, we aimed to identify relevant indicator species for the specific environmental conditions of ARs by comparing fish diversity against control sites (Conts). We used a combination of non-metric multidimensional scaling and indicator value analysis to identify the indicator species of the specific AR environments. More individuals and species of fish were present in ARs compared to Conts. Water temperature over the seasons was the most important environmental factor associated with the trophic group composition of fish. In particular, macrocarnivores and benthic invertivores/cleaners closely reflected habitat conditions in a consistent manner. Some dominant fish species were detected at all sites, while the indicator species were more predominant under certain environmental conditions. Altogether, ARs should be monitored at regular intervals to optimize management of their health by detecting the community representativeness via indicator species. Copyright © 2017 Elsevier Ltd. All rights reserved.

Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database.

PubMed

Pasquier, Jeremy; Cabau, Cédric; Nguyen, Thaovi; Jouanno, Elodie; Severac, Dany; Braasch, Ingo; Journot, Laurent; Pontarotti, Pierre; Klopp, Christophe; Postlethwait, John H; Guiguen, Yann; Bobe, Julien

2016-05-18

With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD event (TGD) that occurred at the root of the teleost lineage about 350 million years ago (Mya) and more recent WGD events in salmonids, carps, suckers and others. In plants and animals, WGD events are associated with adaptive radiations and evolutionary innovations. WGD-spurred innovation may be especially relevant in the case of teleost fish, which colonized a wide diversity of habitats on earth, including many extreme environments. Fish biodiversity, the use of fish models for human medicine and ecological studies, and the importance of fish in human nutrition, fuel an important need for the characterization of gene expression repertoires and corresponding evolutionary histories of ray-finned fish genes. To this aim, we performed transcriptome analyses and developed the PhyloFish database to provide (i) de novo assembled gene repertoires in 23 different ray-finned fish species including two holosteans (i.e. a group that diverged from teleosts before TGD) and 21 teleosts (including six salmonids), and (ii) gene expression levels in ten different tissues and organs (and embryos for many) in the same species. This resource was generated using a common deep RNA sequencing protocol to obtain the most exhaustive gene repertoire possible in each species that allows between-species comparisons to study the evolution of gene expression in different lineages. The PhyloFish database described here can be accessed and searched using RNAbrowse, a simple and efficient solution to give access to RNA-seq de novo assembled transcripts.

Species- and tissue-specific mercury bioaccumulation in five fish species from Laizhou Bay in the Bohai Sea of China

NASA Astrophysics Data System (ADS)

Liu, Jinhu; Cao, Liang; Huang, Wei; Dou, Shuozeng

2013-05-01

Mercury (Hg) concentrations in the tissues (muscle, stomach, liver, gills, skin, and gonads) of five fish species (mullet Liza ha em atocheil us, flathead fish Platycephalus indicus, sea bass Lateolabrax japonic u s, mackerel Scomberomorus niphonius and silver pomfret Pampus argenteus) collected from Laizhou Bay in the Bohai Sea of China were investigated. The results indicate that Hg bioaccumulation in the five fish was tissue-specific, with the highest levels in the muscle and liver, followed by the stomach and gonads. The lowest levels were found in the gills and skin. Fish at higher trophic levels (flathead fish and sea bass) exhibited higher Hg concentrations than consumers at lower trophic levels. Mercury bioaccumulation tended to be positively correlated with fish length in mullet, silver pomfret, mackerel, and flathead fish, but was negatively correlated with fish length in sea bass. The Hg concentrations in the muscles of all fish species in Laizhou Bay were within the permissible limits of food safety set by national and international criteria. However, the suggesting maximum consumption of sea bass is 263 g per week for human health.

Liquid chromatographic determination of oxytetracycline in edible fish fillets from six species of fish

USGS Publications Warehouse

Meinertz, J.R.; Stehly, G.R.; Gingerich, W.H.

1998-01-01

The approved use of oxytetracycline (OTC) in U.S. Aquaculture is limited to specific diseases in salmonids and channel catfish. OTC may also be effective in controlling diseases in other fish species important to public aquaculture, but before approved use of OTC can be augmented, an analytical method for determining OTC in fillet tissue from multiple species of fish will be required to support residue depletion studies. The objective of this study was to develop and validate a liquid chromatographic (LC) method that is accurate, precise, and sensitive for OTC in edible fillets from multiple species of fish. Homogenized fillet tissues from walleye, Atlantic salmon, striped bass, white sturgeon, rainbow trout, and channel catfish were fortified with OTC at nominal concentrations of 10, 20, 100, 1000, and 5000 ng/g. In tissues fortified with OTC at 100, 1000, and 5000 ng/g, mean recoveries ranged from 83 to 90%, and relative standard deviations (RSDs) ranged from 0.9 to 5.8%. In all other tissues, mean recoveries ranged from 59 to 98%, and RSDs ranged from 3.3 to 20%. Method quantitation limits ranged from 6 to 22 ng/g for the 6 species. The LC parameters produced easily integratable OTC peaks without coelution of endogenous compounds. The method is accurate, precise, and sensitive for OTC in fillet tissue from 6 species of fish from 5 phylogenetically diverse groups.

Evaluating analytical approaches for estimating pelagic fish biomass using simulated fish communities

USGS Publications Warehouse

Yule, Daniel L.; Adams, Jean V.; Warner, David M.; Hrabik, Thomas R.; Kocovsky, Patrick M.; Weidel, Brian C.; Rudstam, Lars G.; Sullivan, Patrick J.

2013-01-01

Pelagic fish assessments often combine large amounts of acoustic-based fish density data and limited midwater trawl information to estimate species-specific biomass density. We compared the accuracy of five apportionment methods for estimating pelagic fish biomass density using simulated communities with known fish numbers that mimic Lakes Superior, Michigan, and Ontario, representing a range of fish community complexities. Across all apportionment methods, the error in the estimated biomass generally declined with increasing effort, but methods that accounted for community composition changes with water column depth performed best. Correlations between trawl catch and the true species composition were highest when more fish were caught, highlighting the benefits of targeted trawling in locations of high fish density. Pelagic fish surveys should incorporate geographic and water column depth stratification in the survey design, use apportionment methods that account for species-specific depth differences, target midwater trawling effort in areas of high fish density, and include at least 15 midwater trawls. With relatively basic biological information, simulations of fish communities and sampling programs can optimize effort allocation and reduce error in biomass estimates.

Predictive Modeling and Mapping of Fish Distributions in Small Streams of the Canadian Rocky Mountain Foothills

NASA Astrophysics Data System (ADS)

McCleary, R. J.; Hassan, M. A.

2006-12-01

An automated procedure was developed to model spatial fish distributions within small streams in the Foothills of Alberta. Native fish populations and their habitats are susceptible to impacts arising from both industrial forestry and rapid development of petroleum resources in the region. Knowledge of fish distributions and the effects of industrial activities on their habitats is required to help conserve native fish populations. Resource selection function (RSF) models were used to explain presence/absence of fish in small streams. Target species were bull trout, rainbow trout and non-native brook trout. Using GIS, the drainage network was divided into reaches with uniform slope and drainage area and then polygons for each reach were created. Predictor variables described stream size, stream energy, climate and land-use. We identified a set of candidate models and selected the best model using a standard Akaike Information Criteria approach. The best models were validated with two external data sets. Drainage area and basin slope parameters were included in all best models. This finding emphasizes the importance of controlling for the energy dimension at the basin scale in investigations into the effects of land-use on aquatic resources in this transitional landscape between the mountains and plains. The best model for bull trout indicated a relation between the presence of artificial migration barriers in downstream areas and the extirpation of the species from headwater reaches. We produced reach-scale maps by species and summarized this information within all small catchments across the 12,000 km2 study area. These maps had included three categories based on predicted probability of capture for individual reaches. The high probability category had a 78 percent accuracy for correctly predicting both fish present and fish not-present reaches. Basin scale maps highlight specific watersheds likely to support both native bull trout and invasive brook trout, while reach-scale maps indicate specific reaches where interactions between these two species are likely to occur. With regional calibration, this automated modeling and mapping procedure could apply in headwater catchments throughout the Rocky Mountain Foothills and other areas where sporadic waterfalls or other natural migration barriers are not an important feature limiting fish distribution.

Multilocus sequence analysis reveals extensive genetic variety within Tenacibaculum spp. associated with ulcers in sea-farmed fish in Norway.

PubMed

Olsen, Anne Berit; Gulla, Snorre; Steinum, Terje; Colquhoun, Duncan J; Nilsen, Hanne K; Duchaud, Eric

2017-06-01

Skin ulcer development in sea-reared salmonids, commonly associated with Tenacibaculum spp., is a significant fish welfare- and economical problem in Norwegian aquaculture. A collection of 89 Tenacibaculum isolates was subjected to multilocus sequence analysis (MLSA). The isolates were retrieved from outbreaks of clinical disease in farms spread along the Norwegian coast line from seven different fish species over a period of 19 years. MLSA analysis reveals considerable genetic diversity, but allows identification of four main clades. One clade encompasses isolates belonging to the species T. dicentrarchi, whereas three clades encompass bacteria that likely represent novel, as yet undescribed species. The study identified T. maritimum in lumpsucker, T. ovolyticum in halibut, and has extended the host and geographic range for T. soleae, isolated from wrasse. The overall lack of clonality and host specificity, with some indication of geographical range restriction argue for local epidemics involving multiple strains. The diversity of Tenacibaculum isolates from fish displaying ulcerative disease may complicate vaccine development. Copyright © 2017 Elsevier B.V. All rights reserved.

Impacts of electromagnetic fields associated with marine and hydrokinetic surrogate technologies on fish movements and behaviors.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Claisse, Jeremy T.; Pondella, Daniel J.; Williams, Chelsea M.

Marine and hydrokinetic energy (MHK) and offshore wind devices are being developed and deployed in U.S. and international waters. Electric current flowing through subsea transmission cables associated with these devices will generate electromagnetic fields (EMF), which may interact with, and potentially impact, marine fishes. Some marine fishes can detect electric and/or magnetic fields and use them to navigate, orientate, and sense prey, mates and predators. Over the past five years there have been multiple comprehensive reviews and studies evaluating the potential vulnerability of marine fishes to EMF produced by MHK devices. Most documented effects involve sub-lethal behavioral responses of individualmore » fish when in close proximity to EMF (e.g., fish being repelled by or attracted to fields). These reviews reach conclusions that the current state of research on this topic is still in its infancy and evaluations of potential impacts are associated with great uncertainty. A variety of MHK technologies are likely to be considered for deployment offshore of the Hawaiian Islands, and there is a need to be able to better predict and assess potential associated environmental impacts. The goal of this study was to provide a complementary piece to these previous reviews (e.g., Normandeau et al. 2011) by focusing on marine fish species in the Hawaii region. We compiled the relevant available information, then prioritized fish species as candidates for various paths of future research. To address this, we first developed a list of Hawaii Region Focal Species, which included fishes that are more likely to be sensitive to EMF. We then compiled species-specific information available in the literature on their sensitivity to EMF, as well as life history, movement and habitat use information that could inform an analysis of their likelihood of encountering EMF from subsea cables associated with MHK devices. Studies have only documented EMF sensitivity in 11 of the marine fish species in this region. There was also relatively little detailed information on fish movement and habitat use patterns for most of the focal species. Our last objective was to develop recommendations for research needs to close the important knowledge gaps. We describe species-independent baseline research that primarily consists of in situ quantification of EMF generated by MHK devices and undersea cables that can occur as pilot and commercial scale MHK devices are deployed in Hawaii. Then we propose a simple approach for prioritizing Hawaii Region Focal Species (ranked relative to each other) as candidates in multiple related research paths. The prioritization approach incorporates EMF sensitivity information with the likelihood of interacting with EMF generated undersea transmission cables associated with MHK devices. Finally, we discuss the types of research needed to help fill gaps in the scientific knowledge base for this region. These involve studies to better define species-specific EMF sensitivity thresholds under various environmental conditions, studies of life history, movement and habitat use patterns to improve our understanding of the likelihood and frequency fishes may be in the vicinity of EMF generated by subsea transmission cables, and studies of the potential for related population, community or ecosystem impacts. Many of these studies can and should occur opportunistically as pilot and commercial scale MHK devices are deployed in Hawaii.« less

50 CFR 222.309 - Permits for listed species of sea turtles involving the Fish and Wildlife Service.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false Permits for listed species of sea turtles involving the Fish and Wildlife Service. 222.309 Section 222.309 Wildlife and Fisheries NATIONAL MARINE... species of sea turtles involving the Fish and Wildlife Service. (a) This section establishes specific...

50 CFR 222.309 - Permits for listed species of sea turtles involving the Fish and Wildlife Service.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 10 2013-10-01 2013-10-01 false Permits for listed species of sea turtles involving the Fish and Wildlife Service. 222.309 Section 222.309 Wildlife and Fisheries NATIONAL MARINE... species of sea turtles involving the Fish and Wildlife Service. (a) This section establishes specific...

50 CFR 222.309 - Permits for listed species of sea turtles involving the Fish and Wildlife Service.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 9 2011-10-01 2011-10-01 false Permits for listed species of sea turtles involving the Fish and Wildlife Service. 222.309 Section 222.309 Wildlife and Fisheries NATIONAL MARINE... species of sea turtles involving the Fish and Wildlife Service. (a) This section establishes specific...

50 CFR 222.309 - Permits for listed species of sea turtles involving the Fish and Wildlife Service.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 10 2012-10-01 2012-10-01 false Permits for listed species of sea turtles involving the Fish and Wildlife Service. 222.309 Section 222.309 Wildlife and Fisheries NATIONAL MARINE... species of sea turtles involving the Fish and Wildlife Service. (a) This section establishes specific...

50 CFR 222.309 - Permits for listed species of sea turtles involving the Fish and Wildlife Service.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 10 2014-10-01 2014-10-01 false Permits for listed species of sea turtles involving the Fish and Wildlife Service. 222.309 Section 222.309 Wildlife and Fisheries NATIONAL MARINE... species of sea turtles involving the Fish and Wildlife Service. (a) This section establishes specific...

DNA microarrays for identifying fishes.

PubMed

Kochzius, M; Nölte, M; Weber, H; Silkenbeumer, N; Hjörleifsdottir, S; Hreggvidsson, G O; Marteinsson, V; Kappel, K; Planes, S; Tinti, F; Magoulas, A; Garcia Vazquez, E; Turan, C; Hervet, C; Campo Falgueras, D; Antoniou, A; Landi, M; Blohm, D

2008-01-01

In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a "Fish Chip" for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products.

Identifying Fishes through DNA Barcodes and Microarrays.

PubMed

Kochzius, Marc; Seidel, Christian; Antoniou, Aglaia; Botla, Sandeep Kumar; Campo, Daniel; Cariani, Alessia; Vazquez, Eva Garcia; Hauschild, Janet; Hervet, Caroline; Hjörleifsdottir, Sigridur; Hreggvidsson, Gudmundur; Kappel, Kristina; Landi, Monica; Magoulas, Antonios; Marteinsson, Viggo; Nölte, Manfred; Planes, Serge; Tinti, Fausto; Turan, Cemal; Venugopal, Moleyur N; Weber, Hannes; Blohm, Dietmar

2010-09-07

International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

Quantifying tolerance indicator values for common stream fish species of the United States

USGS Publications Warehouse

Meador, M.R.; Carlisle, D.M.

2007-01-01

The classification of fish species tolerance to environmental disturbance is often used as a means to assess ecosystem conditions. Its use, however, may be problematic because the approach to tolerance classification is based on subjective judgment. We analyzed fish and physicochemical data from 773 stream sites collected as part of the U.S. Geological Survey's National Water-Quality Assessment Program to calculate tolerance indicator values for 10 physicochemical variables using weighted averaging. Tolerance indicator values (TIVs) for ammonia, chloride, dissolved oxygen, nitrite plus nitrate, pH, phosphorus, specific conductance, sulfate, suspended sediment, and water temperature were calculated for 105 common fish species of the United States. Tolerance indicator values for specific conductance and sulfate were correlated (rho = 0.87), and thus, fish species may be co-tolerant to these water-quality variables. We integrated TIVs for each species into an overall tolerance classification for comparisons with judgment-based tolerance classifications. Principal components analysis indicated that the distinction between tolerant and intolerant classifications was determined largely by tolerance to suspended sediment, specific conductance, chloride, and total phosphorus. Factors such as water temperature, dissolved oxygen, and pH may not be as important in distinguishing between tolerant and intolerant classifications, but may help to segregate species classified as moderate. Empirically derived tolerance classifications were 58.8% in agreement with judgment-derived tolerance classifications. Canonical discriminant analysis revealed that few TIVs, primarily chloride, could discriminate among judgment-derived tolerance classifications of tolerant, moderate, and intolerant. To our knowledge, this is the first empirically based understanding of fish species tolerance for stream fishes in the United States.

Facial Recognition in a Discus Fish (Cichlidae): Experimental Approach Using Digital Models

PubMed Central

Satoh, Shun; Tanaka, Hirokazu; Kohda, Masanori

2016-01-01

A number of mammals and birds are known to be capable of visually discriminating between familiar and unfamiliar individuals, depending on facial patterns in some species. Many fish also visually recognize other conspecifics individually, and previous studies report that facial color patterns can be an initial signal for individual recognition. For example, a cichlid fish and a damselfish will use individual-specific color patterns that develop only in the facial area. However, it remains to be determined whether the facial area is an especially favorable site for visual signals in fish, and if so why? The monogamous discus fish, Symphysopdon aequifasciatus (Cichlidae), is capable of visually distinguishing its pair-partner from other conspecifics. Discus fish have individual-specific coloration patterns on entire body including the facial area, frontal head, trunk and vertical fins. If the facial area is an inherently important site for the visual cues, this species will use facial patterns for individual recognition, but otherwise they will use patterns on other body parts as well. We used modified digital models to examine whether discus fish use only facial coloration for individual recognition. Digital models of four different combinations of familiar and unfamiliar fish faces and bodies were displayed in frontal and lateral views. Focal fish frequently performed partner-specific displays towards partner-face models, and did aggressive displays towards models of non-partner’s faces. We conclude that to identify individuals this fish does not depend on frontal color patterns but does on lateral facial color patterns, although they have unique color patterns on the other parts of body. We discuss the significance of facial coloration for individual recognition in fish compared with birds and mammals. PMID:27191162

Facial Recognition in a Discus Fish (Cichlidae): Experimental Approach Using Digital Models.

PubMed

Satoh, Shun; Tanaka, Hirokazu; Kohda, Masanori

2016-01-01

A number of mammals and birds are known to be capable of visually discriminating between familiar and unfamiliar individuals, depending on facial patterns in some species. Many fish also visually recognize other conspecifics individually, and previous studies report that facial color patterns can be an initial signal for individual recognition. For example, a cichlid fish and a damselfish will use individual-specific color patterns that develop only in the facial area. However, it remains to be determined whether the facial area is an especially favorable site for visual signals in fish, and if so why? The monogamous discus fish, Symphysopdon aequifasciatus (Cichlidae), is capable of visually distinguishing its pair-partner from other conspecifics. Discus fish have individual-specific coloration patterns on entire body including the facial area, frontal head, trunk and vertical fins. If the facial area is an inherently important site for the visual cues, this species will use facial patterns for individual recognition, but otherwise they will use patterns on other body parts as well. We used modified digital models to examine whether discus fish use only facial coloration for individual recognition. Digital models of four different combinations of familiar and unfamiliar fish faces and bodies were displayed in frontal and lateral views. Focal fish frequently performed partner-specific displays towards partner-face models, and did aggressive displays towards models of non-partner's faces. We conclude that to identify individuals this fish does not depend on frontal color patterns but does on lateral facial color patterns, although they have unique color patterns on the other parts of body. We discuss the significance of facial coloration for individual recognition in fish compared with birds and mammals.

Fish community changes in the St. Louis River estuary, Lake Superior, 1989-1996: Is it ruffe or population dynamics?

USGS Publications Warehouse

Bronte, Charles R.; Evrard, Lori M.; Brown, William P.; Mayo, Kathleen R.; Edwards, Andrew J.

1998-01-01

Ruffe (Gymnocephalus cernuus) have been implicated in density declines of native species through egg predation and competition for food in some European waters where they were introduced. Density estimates for ruffe and principal native fishes in the St. Louis River estuary (western Lake Superior) were developed for 1989 to 1996 to measure changes in the fish community in response to an unintentional introduction of ruffe. During the study, ruffe density increased and the densities of several native species decreased. The reductions of native stocks to the natural population dynamics of the same species from Chequamegon Bay, Lake Superior (an area with very few ruffe) were developed, where there was a 24-year record of density. Using these data, short- and long-term variations in catch and correlations among species within years were compared, and species-specific distributions were developed of observed trends in abundance of native fishes in Chequamegon Bay indexed by the slopes of densities across years. From these distributions and our observed trend-line slopes from the St. Louis River, probabilities of measuring negative change at the magnitude observed in the St. Louis River were estimated. Compared with trends in Chequamegon Bay, there was a high probability of obtaining the negative slopes measured for most species, which suggests natural population dynamics could explain, the declines rather than interactions with ruffe. Variable recruitment, which was not related to ruffe density, and associated density-dependent changes in mortality likely were responsible for density declines of native species.

Relations between introduced fish and environmental conditions at large geographic scales

USGS Publications Warehouse

Meador, M.R.; Brown, L.R.; Short, T.

2003-01-01

Data collected from 20 major river basins between 1993 and 1995 as part of the US Geological Survey's (USGS) National Water-Quality Assessment (NAWQA) Program were analyzed to assess patterns in introduced and native fish species richness and abundance relative to watershed characteristics and stream physicochemistry. Sites (N = 157) were divided into three regions-northeast, southeast, and west- to account for major longitudinal differences in precipitation/runoff and latitudinal limits of glaciation that affect zoogeographic patterns in fish communities. Common carp (Cyprinus carpio) and largemouth bass (Micropterus salmoides) were the most frequently collected introduced fish species across all river basins combined. Based on the percentage of introduced fish species, the fish communities most altered by the presence of introduced fish occurred in the western and northeastern parts of the US. Native fish species richness was not an indicator of introduced fish species richness for any of the three regions. However, in the west, introduced fish species richness was an indicator of total fish species richness and the abundance of introduced fish was negatively related to native fish species richness. Some relations between introduced fish species and environmental conditions were common between regions. Increased introduced fish species richness was related to increased population density in the northeast and southeast; increased total nitrogen in the northeast and west; and increased total phosphorous and water temperature in the southeast and west. These results suggest that introduced fish species tend to be associated with disturbance at large geographic scales, though specific relations may vary regionally. ?? 2003 Elsevier Science Ltd. All rights reserved.

Cryopreservation of Fish Sperm

NASA Astrophysics Data System (ADS)

Kurokura, Hisashi

Present status of research activities in cryopreservation of fish gamete in aquaculture field was introduced. More than 59 fish species have been reported in the research histories and nearly half of them were studied during recent 10 years. This means that the research activities are increasing, though commercial profit have not obtained yet. Fish species of which sperm can successfully cryopreserved is still limited comparing to numerous species in telost. One of the major obstacle for improvement of the technique is existence of wide specie specific variance in the freezing tolerance of fish sperm. The varianc can possibly be explaind thorugh the informations obtained by the studies in comparative spermatology, which is recently activated field in fish biology.

Molecular prey identification in Central European piscivores.

PubMed

Thalinger, Bettina; Oehm, Johannes; Mayr, Hannes; Obwexer, Armin; Zeisler, Christiane; Traugott, Michael

2016-01-01

Diet analysis is an important aspect when investigating the ecology of fish-eating animals and essential for assessing their functional role in food webs across aquatic and terrestrial ecosystems. The identification of fish remains in dietary samples, however, can be time-consuming and unsatisfying using conventional morphological analysis of prey remains. Here, we present a two-step multiplex PCR system, comprised of six assays, allowing for rapid, sensitive and specific detection of fish DNA in dietary samples. This approach encompasses 78 fish and lamprey species native to Central European freshwaters and enables the identification of 31 species, six genera, two families, two orders and two fish family clusters. All targeted taxa were successfully amplified from 25 template molecules, and each assay was specific when tested against a wide range of invertebrates and vertebrates inhabiting aquatic environments. The applicability of the multiplex PCR system was evaluated in a feeding trial, wherein it outperformed morphological prey analysis regarding species-specific prey identification in faeces of Eurasian otters. Additionally, a wide spectrum of fish species was detected in field-collected faecal samples and regurgitated pellets of Common Kingfishers and Great Cormorants, demonstrating the broad applicability of the approach. In conclusion, this multiplex PCR system provides an efficient, easy to use and cost-effective tool for assessing the trophic ecology of piscivores in Central Europe. Furthermore, the multiplex PCRs and the primers described therein will be applicable wherever DNA of the targeted fish species needs to be detected at high sensitivity and specificity. © 2015 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Levels of genetic diversity and taxonomic status of Epinephelus species in United Arab Emirates fish markets.

PubMed

Ketchum, Remi N; Dieng, Mame M; Vaughan, Grace O; Burt, John A; Idaghdour, Youssef

2016-04-30

Understanding the patterns of genetic diversity of fish species is essential for marine conservation and management. This is particularly important in the Arabian Gulf where marine life is subject to extreme environmental conditions that could impact genetic diversity. Here we assess genetic diversity of the most commercially important fish in the United Arab Emirates; groupers (Epinephelus spp.). Sequencing of 973 bp mitochondrial DNA from 140 tissue samples collected in four main fish markets revealed 58 haplotypes clustered within three groups. Data analysis revealed the presence of three distinct Epinephelus species being marketed as one species (hammour): Epinephelus coioides, Epinephelus areolatus and Epinephelus bleekeri. We report species-specific genetic markers and demonstrate that all three species exhibit relatively low levels of genetic variation, reflecting the effect of overfishing and environmental pressures. In light of the genetic evidence presented here, conservation and management of groupers in the UAE warrant the implementation of species-specific measures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Species‐ and habitat‐specific otolith chemistry patterns inform riverine fisheries management

USGS Publications Warehouse

Radigan, William; Carlson, Andrew K.; Kientz, Jeremy; Chipps, Steven R.; Fincel, Mark J.; Graeb, Brian D. S.

2018-01-01

Geology and hydrology are drivers of water chemistry and thus important considerations for fish otolith chemistry research. However, other factors such as species and habitat identity may have predictive ability, enabling selection of appropriate elemental signatures prior to costly, perhaps unnecessary water/age‐0 fish sampling. The goal of this study was to develop a predictive methodology for using species and habitat identity to design efficient otolith chemistry studies. Duplicate water samples and age‐0 fish were collected from 61 sites in 4 Missouri River reservoirs for walleye Sander vitreus and one impoundment (Lake Sharpe, South Dakota) for other fishes (bluegill Lepomis macrochirus, black crappie Pomoxis nigromaculatus, gizzard shad Dorosoma cepedianum, largemouth bass Micropterus salmoides, smallmouth bass M. dolomieu, white bass Morone chrysops, white crappie P. annularis, and yellow perch Perca flavescens). Water chemistry (barium:calcium [Ba:Ca], strontium:calcium [Sr:Ca]) was temporally stable, spatially variable, and highly correlated with otolith chemistry for all species except yellow perch. Classification accuracies based on bivariate Ba:Ca and Sr:Ca signatures were high (84% across species) yet varied between floodplain and main‐channel habitats in a species‐specific manner. Thus, to maximize the reliability of otolith chemistry, researchers can use species classifications presented herein to inform habitat selection (e.g., study reservoir‐oriented species such as white bass in main‐channel environments) and habitat‐based classifications to inform species selection (e.g., focus floodplain studies on littoral species such as largemouth bass). Overall, species and habitat identity are important considerations for efficient, effective otolith chemistry studies that inform and advance fisheries and aquatic resource management.

A quick and simple FISH protocol with hybridization-sensitive fluorescent linear oligodeoxynucleotide probes

PubMed Central

Wang, Dan Ohtan; Matsuno, Hitomi; Ikeda, Shuji; Nakamura, Akiko; Yanagisawa, Hiroyuki; Hayashi, Yasunori; Okamoto, Akimitsu

2012-01-01

Fluorescence in situ hybridization (FISH) is a powerful tool used in karyotyping, cytogenotyping, cancer diagnosis, species specification, and gene-expression analysis. Although widely used, conventional FISH protocols are cumbersome and time consuming. We have now developed a FISH method using exciton-controlled hybridization-sensitive fluorescent oligodeoxynucleotide (ECHO) probes. ECHO–FISH uses a 25-min protocol from fixation to mounting that includes no stringency washing steps. We use ECHO–FISH to detect both specific DNA and RNA sequences with multicolor probes. ECHO–FISH is highly reproducible, stringent, and compatible with other fluorescent cellular labeling techniques. The resolution allows detection of intranuclear speckles of poly(A) RNA in HeLa cells and dissociated hippocampal primary cultures, and mRNAs in the distal dendrites of hippocampal neurons. We also demonstrate detection of telomeric and centromeric DNA on metaphase mouse chromosomes. The simplicity of the ECHO–FISH method will likely accelerate cytogenetic and gene-expression analysis with high resolution. PMID:22101241

OCCURRENCE OF TWO LEECH SPECIES (ANNELIDA: HIRUDINEA) ON FISHES IN THE KENTUCKY RIVER

EPA Science Inventory

Little is known specifically on the feeding relationships between parasitic leeches and fish in North America. During an electrofishing survey conducted on the main stem of the Kentucky River in the summer of 2000, the presence of leeches was documented on six species of fish. ...

Immunity to betanodavirus infections of marine fish.

PubMed

Chen, Young-Mao; Wang, Ting-Yu; Chen, Tzong-Yueh

2014-04-01

Betanodaviruses cause viral nervous necrosis in numerous fish species, but some species are resistant to infection by these viruses. It is essential to fully characterize the immune responses that underlie this protective response. Complete characterization of the immune responses against nodaviruses may allow the development of methods that stimulate fish immunity and of an effective betanodavirus vaccine. Such strategies could include stimulation of specific immune system responses or blockage of factors that decrease the immune response. The innate immune system clearly provides a front-line defense, and this includes the production of interferons and other cytokines. Interferons that are released inside infected cells and that suppress viral replication may be the most ancient form of innate immunity. This review focuses on the immune responses of fish to betanodavirus infection. Copyright © 2013 Elsevier Ltd. All rights reserved.

Antibiotic Application and Emergence of Multiple Antibiotic Resistance (MAR) in Global Catfish Aquaculture.

PubMed

Chuah, Li-Oon; Effarizah, M E; Goni, Abatcha Mustapha; Rusul, Gulam

2016-06-01

Catfish is one of the most cultivated species worldwide. Antibiotics are usually used in catfish farming as therapeutic and prophylactic agents. In the USA, only oxytetracycline, a combination of sulfadimethoxine and ormetoprim, and florfenicol are approved by the Food Drug Administration for specific fish species (e.g., catfish and salmonids) and their specific diseases. Misuse of antibiotics as prophylactic agents in disease prevention, however, is common and contributes in the development of antibiotic resistance. Various studies had reported on antibiotic residues and/or resistance in farmed species, feral fish, water column, sediments, and, in a lesser content, among farm workers. Ninety percent of the world aquaculture production is carried out in developing countries, which lack regulations and enforcement on the use of antibiotics. Hence, efforts are needed to promote the development and enforcement of such a regulatory structure. Alternatives to antibiotics such as antibacterial vaccines, bacteriophages and their lysins, and probiotics have been applied to curtail the increasing emergence of antibiotic-resistant bacteria due to the imprudent application of antibiotics in aquaculture.

Defining critical habitats of threatened and endemic reef fishes with a multivariate approach.

PubMed

Purcell, Steven W; Clarke, K Robert; Rushworth, Kelvin; Dalton, Steven J

2014-12-01

Understanding critical habitats of threatened and endemic animals is essential for mitigating extinction risks, developing recovery plans, and siting reserves, but assessment methods are generally lacking. We evaluated critical habitats of 8 threatened or endemic fish species on coral and rocky reefs of subtropical eastern Australia, by measuring physical and substratum-type variables of habitats at fish sightings. We used nonmetric and metric multidimensional scaling (nMDS, mMDS), Analysis of similarities (ANOSIM), similarity percentages analysis (SIMPER), permutational analysis of multivariate dispersions (PERMDISP), and other multivariate tools to distinguish critical habitats. Niche breadth was widest for 2 endemic wrasses, and reef inclination was important for several species, often found in relatively deep microhabitats. Critical habitats of mainland reef species included small caves or habitat-forming hosts such as gorgonian corals and black coral trees. Hard corals appeared important for reef fishes at Lord Howe Island, and red algae for mainland reef fishes. A wide range of habitat variables are required to assess critical habitats owing to varied affinities of species to different habitat features. We advocate assessments of critical habitats matched to the spatial scale used by the animals and a combination of multivariate methods. Our multivariate approach furnishes a general template for assessing the critical habitats of species, understanding how these vary among species, and determining differences in the degree of habitat specificity. © 2014 Society for Conservation Biology.

Estimating the efficiency of fish cross-species cDNA microarray hybridization.

PubMed

Cohen, Raphael; Chalifa-Caspi, Vered; Williams, Timothy D; Auslander, Meirav; George, Stephen G; Chipman, James K; Tom, Moshe

2007-01-01

Using an available cross-species cDNA microarray is advantageous for examining multigene expression patterns in non-model organisms, saving the need for construction of species-specific arrays. The aim of the present study was to estimate relative efficiency of cross-species hybridizations across bony fishes, using bioinformatics tools. The methodology may serve also as a model for similar evaluations in other taxa. The theoretical evaluation was done by substituting comparative whole-transcriptome sequence similarity information into the thermodynamic hybridization equation. Complementary DNA sequence assemblages of nine fish species belonging to common families or suborders and distributed across the bony fish taxonomic branch were selected for transcriptome-wise comparisons. Actual cross-species hybridizations among fish of different taxonomic distances were used to validate and eventually to calibrate the theoretically computed relative efficiencies.

Method- and species-specific detection probabilities of fish occupancy in Arctic lakes: Implications for design and management

USGS Publications Warehouse

Haynes, Trevor B.; Rosenberger, Amanda E.; Lindberg, Mark S.; Whitman, Matthew; Schmutz, Joel A.

2013-01-01

Studies examining species occurrence often fail to account for false absences in field sampling. We investigate detection probabilities of five gear types for six fish species in a sample of lakes on the North Slope, Alaska. We used an occupancy modeling approach to provide estimates of detection probabilities for each method. Variation in gear- and species-specific detection probability was considerable. For example, detection probabilities for the fyke net ranged from 0.82 (SE = 0.05) for least cisco (Coregonus sardinella) to 0.04 (SE = 0.01) for slimy sculpin (Cottus cognatus). Detection probabilities were also affected by site-specific variables such as depth of the lake, year, day of sampling, and lake connection to a stream. With the exception of the dip net and shore minnow traps, each gear type provided the highest detection probability of at least one species. Results suggest that a multimethod approach may be most effective when attempting to sample the entire fish community of Arctic lakes. Detection probability estimates will be useful for designing optimal fish sampling and monitoring protocols in Arctic lakes.

Morphological and biochemical variations in the gills of 12 aquatic air-breathing anabantoid fish.

PubMed

Huang, Chun-Yen; Lin, Chung-Ping; Lin, Hui-Chen

2011-01-01

All fish species in the Anabantoidei suborder are aquatic air-breathing fish. These species have an accessory air-breathing organ, called the labyrinth organ, in the branchial cavity and can engulf air at the surface of the water to assist in gas exchange. It is therefore necessary to examine the extent of gill modification among anabantoid fish species and the potential trade-offs in their function. The experimental hypothesis that we aimed to test is whether anabantoid fishes have both morphological and functional variations in the gills among different species. We examined the gills of 12 species from three families and nine genera of Anabantoidei. Though the sizes of the fourth gill arch in three species of Trichogaster were reduced significantly, not all anabantoid species had morphological and functional variations in the gills. In these three species, the specific enzyme activity and relative protein abundance of Na(+)/K(+)-ATPase were significantly higher in the anterior gills as compared with the posterior gills and the labyrinth organ. The relative abundance of cytosolic carbonic anhydrase, an indicator of gas exchange, was found to be highest in the labyrinth organ. The phylogenetic distribution of the fourth gill's morphological differentiation suggests that these variations are lineage specific, which may imply a phylogenetic influence on gill morphology in anabantoid species.

[Distribution of coccidians (Sporozoa: Coccidiida) in various systematic groups of fishes].

PubMed

Belova, L M; Krylov, M V

2000-01-01

There are about 250 coccidian species associated with fishes. They belong to 8 genera (Calyptospora, Cryptosporidium, Crystallospora, Eimeria, Epieimeria, Goussia, Isospora, Octosporella) and 3 families (Calyptosporidae, Cryptosporidiidae, Eimeriidae). Two genera are represented by great number of species associated with fishes: Eimeria--157 and Goussia--69 species. Most diverse fauna of coccidians was found in fishes of the class Actinopterigii; fishes of the class Elasmobranchii have significantly less number of coccidians. These parasites have never been recorded on the class Holocephali. Coccidian have been recorded in 55 orders of fishes. Within the Actinopterigii, the richest coccidian fauna is recorded from Cypriniformes and Perciformes. Accumulated data on host associations proves that coccidian species have mainly a restricted hosts specificity.

Development of a new CARD-FISH protocol for quantification of Legionella pneumophila and its application in two hospital cooling towers.

PubMed

Kirschner, A K T; Rameder, A; Schrammel, B; Indra, A; Farnleitner, A H; Sommer, R

2012-06-01

Open cooling towers are frequent sources of infections with Legionella pneumophila. The gold standard for the detection of Leg. pneumophila is based on cultivation lasting up to 10 days and detecting only culturable cells. Alternative fluorescence in situ hybridization (FISH) protocols have been proposed, but they result in faint fluorescence signals and lack specificity because of cross-hybridization with other Legionella species. Our aim was thus to develop a new FISH protocol for rapid and specific detection of Leg. pneumophila in water samples. A novel catalysed reporter deposition FISH (CARD-FISH) protocol for the detection of Leg. pneumophila was developed, which significantly enhanced signal intensity as well as specificity of the probe through the use of a novel competitor probe. The developed protocol was compared with the culture method for monitoring the seasonal development of culturable and nonculturable Leg. pneumophila in two hospital cooling tower systems. Seasonal fluctuations of Leg. pneumophila concentrations detected via CARD-FISH were related to the development of the total bacterial community in both cooling towers, with temperature and biocide as the main factors controlling this development. Our results clearly showed that the majority of the Leg. pneumophila cells were in a nonculturable state. Thus, detection of Leg. pneumophila with culture methods may underestimate the total numbers of Leg. pneumophila present. Rapid, sensitive and specific detection and quantification of Leg. pneumophila in water systems is prerequisite for reliable risk estimation. The new protocol significantly improves current methodology and can be used to monitor and screen for Leg. pneumophila concentrations in cooling towers or other water systems. © 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.

Longitudinal zonation of Pacific Northwest (USA) fish assemblages and the species-discharge relationship

EPA Science Inventory

Fish ecologists often use species-discharge relationships (SDRs) to understand how species richness varies with aquatic habitat availability, but few SDR studies have considered whether the reported SDRs are scale-dependent, or attributed the SDR to a specific causal mechanism. ...

Fish species identification using PCR-RFLP analysis and lab-on-a-chip capillary electrophoresis: application to detect white fish species in food products and an interlaboratory study.

PubMed

Dooley, John J; Sage, Helen D; Clarke, Marie-Anne L; Brown, Helen M; Garrett, Stephen D

2005-05-04

Identification of 10 white fish species associated with U.K. food products was achieved using PCR-RFLP of the mitochondrial cytochrome b gene. Use of lab-on-a-chip capillary electrophoresis for end-point analysis enabled accurate sizing of DNA fragments and identification of fish species at a level of 5% (w/w) in a fish admixture. One restriction enzyme, DdeI, allowed discrimination of eight species. When combined with NlaIII and HaeIII, specific profiles for all 10 species were generated. The method was applied to a range of products and subjected to an interlaboratory study carried out by five U.K. food control laboratories. One hundred percent correct identification of single species samples and six of nine admixture samples was achieved by all laboratories. The results indicated that fish species identification could be carried out using a database of PCR-RFLP profiles without the need for reference materials.

DNA barcode-based molecular identification system for fish species.

PubMed

Kim, Sungmin; Eo, Hae-Seok; Koo, Hyeyoung; Choi, Jun-Kil; Kim, Won

2010-12-01

In this study, we applied DNA barcoding to identify species using short DNA sequence analysis. We examined the utility of DNA barcoding by identifying 53 Korean freshwater fish species, 233 other freshwater fish species, and 1339 saltwater fish species. We successfully developed a web-based molecular identification system for fish (MISF) using a profile hidden Markov model. MISF facilitates efficient and reliable species identification, overcoming the limitations of conventional taxonomic approaches. MISF is freely accessible at http://bioinfosys.snu.ac.kr:8080/MISF/misf.jsp .

Summer distribution and species richness of non-native fishes in the mainstem Willamette River, oregon, 1944-2006

EPA Science Inventory

We reviewed the results of seven extensive and two reach-specific fish surveys conducted on the mainstem Willamette River between 1944 and 2006 to document changes in the summer distribution and species richness of non-native fishes through time and the relative abundances of the...

Productivity of functional guilds of fishes in managed wetlands in coastal South Carolina

USGS Publications Warehouse

Robinson, Kelly F.; Jennings, Cecil A.

2014-01-01

In coastal South Carolina, many wetlands are impounded and managed as migratory waterfowl habitat. Impoundment effects on fish production and habitat quality largely are unknown. We used the size-frequency method to estimate summer production of fish guilds in three impoundments along the Combahee River, South Carolina. We predicted that guild-specific production would vary with impoundment salinity, which ranged from 3 to 21 practical salinity units. We expected that marine species that use the estuary as nursery habitat would have greatest production in the impoundment with the highest salinity regime, and that species that inhabit the upper reaches of the estuary would have greatest production in the impoundment with the lowest salinity regime. Finally, we expected that estuarine species would be highly productive in all study impoundments, because these species can reproduce within these structures. We found that guild-specific productivity varied both among years and among impoundments, generally following salinity gradients, though to a lesser extent than expected. Our guild-specific estimates of fish productivity fell on the low end of the range of previously published estuarine fish production estimates. Additionally, we observed large mortality events in the study impoundments each summer. The results of our study indicate that during the summer, the study impoundments provided poor-quality fish habitat to all guilds.

Theory and application of semiochemicals in nuisance fish control

USGS Publications Warehouse

Sorensen, Peter W.; Johnson, Nicholas

2016-01-01

Controlling unwanted, or nuisance, fishes is becoming an increasingly urgent issue with few obvious solutions. Because fish rely heavily on semiochemicals, or chemical compounds that convey information between and within species, to mediate aspects of their life histories, these compounds are increasingly being considered as an option to help control wild fish. Possible uses of semiochemicals include measuring their presence in water to estimate population size, adding them to traps to count or remove specific species of fish, adding them to waterways to manipulate large-scale movement patterns, and saturating the environment with synthesized semiochemicals to disrupt responses to the natural cue. These applications may be especially appropriate for pheromones, chemical signals that pass between members of same species and which also have extreme specificity and potency. Alarm cues, compounds released by injured fish, and cues released by potential predators also could function as repellents and be especially useful if paired with pheromonal attractants in “push-pull” configurations. Approximately half a dozen attractive pheromones now have been partially identified in fish, and those for the sea lamprey and the common carp have been tested in the field with modest success. Alarm and predator cues for sea lamprey also have been tested in the laboratory and field with some success. Success has been hampered by our incomplete understanding of chemical identity, a lack of synthesized compounds, the fact that laboratory bioassays do not always reflect natural environments, and the relative difficulty of conducting trials on wild fishes because of short field seasons and regulatory requirements. Nevertheless, workers continue efforts to identify pheromones because of the great potential elucidated by insect control and the fact that few tools are available to control nuisance fish. Approaches developed for nuisance fish also could be applied to valued fishes, which suffer from a lack of powerful management tools.

Theory and Application of Semiochemicals in Nuisance Fish Control.

PubMed

Sorensen, Peter W; Johnson, Nicholas S

2016-07-01

Controlling unwanted, or nuisance, fishes is becoming an increasingly urgent issue with few obvious solutions. Because fish rely heavily on semiochemicals, or chemical compounds that convey information between and within species, to mediate aspects of their life histories, these compounds are increasingly being considered as an option to help control wild fish. Possible uses of semiochemicals include measuring their presence in water to estimate population size, adding them to traps to count or remove specific species of fish, adding them to waterways to manipulate large-scale movement patterns, and saturating the environment with synthesized semiochemicals to disrupt responses to the natural cue. These applications may be especially appropriate for pheromones, chemical signals that pass between members of same species and which also have extreme specificity and potency. Alarm cues, compounds released by injured fish, and cues released by potential predators also could function as repellents and be especially useful if paired with pheromonal attractants in "push-pull" configurations. Approximately half a dozen attractive pheromones now have been partially identified in fish, and those for the sea lamprey and the common carp have been tested in the field with modest success. Alarm and predator cues for sea lamprey also have been tested in the laboratory and field with some success. Success has been hampered by our incomplete understanding of chemical identity, a lack of synthesized compounds, the fact that laboratory bioassays do not always reflect natural environments, and the relative difficulty of conducting trials on wild fishes because of short field seasons and regulatory requirements. Nevertheless, workers continue efforts to identify pheromones because of the great potential elucidated by insect control and the fact that few tools are available to control nuisance fish. Approaches developed for nuisance fish also could be applied to valued fishes, which suffer from a lack of powerful management tools.

Mangrove Habitat Use by Juvenile Reef Fish: Meta-Analysis Reveals that Tidal Regime Matters More than Biogeographic Region

PubMed Central

Igulu, Mathias M.; Nagelkerken, Ivan; Dorenbosch, Martijn; Grol, Monique G. G.; Harborne, Alastair R.; Kimirei, Ismael A.; Mumby, Peter J.; Olds, Andrew D.; Mgaya, Yunus D.

2014-01-01

Identification of critical life-stage habitats is key to successful conservation efforts. Juveniles of some species show great flexibility in habitat use while other species rely heavily on a restricted number of juvenile habitats for protection and food. Considering the rapid degradation of coastal marine habitats worldwide, it is important to evaluate which species are more susceptible to loss of juvenile nursery habitats and how this differs across large biogeographic regions. Here we used a meta-analysis approach to investigate habitat use by juvenile reef fish species in tropical coastal ecosystems across the globe. Densities of juvenile fish species were compared among mangrove, seagrass and coral reef habitats. In the Caribbean, the majority of species showed significantly higher juvenile densities in mangroves as compared to seagrass beds and coral reefs, while for the Indo-Pacific region seagrass beds harbored the highest overall densities. Further analysis indicated that differences in tidal amplitude, irrespective of biogeographic region, appeared to be the major driver for this phenomenon. In addition, juvenile reef fish use of mangroves increased with increasing water salinity. In the Caribbean, species of specific families (e.g. Lutjanidae, Haemulidae) showed a higher reliance on mangroves or seagrass beds as juvenile habitats than other species, whereas in the Indo-Pacific family-specific trends of juvenile habitat utilization were less apparent. The findings of this study highlight the importance of incorporating region-specific tidal inundation regimes into marine spatial conservation planning and ecosystem based management. Furthermore, the significant role of water salinity and tidal access as drivers of mangrove fish habitat use implies that changes in seawater level and rainfall due to climate change may have important effects on how juvenile reef fish use nearshore seascapes in the future. PMID:25551761

Mangrove habitat use by juvenile reef fish: meta-analysis reveals that tidal regime matters more than biogeographic region.

PubMed

Igulu, Mathias M; Nagelkerken, Ivan; Dorenbosch, Martijn; Grol, Monique G G; Harborne, Alastair R; Kimirei, Ismael A; Mumby, Peter J; Olds, Andrew D; Mgaya, Yunus D

2014-01-01

Identification of critical life-stage habitats is key to successful conservation efforts. Juveniles of some species show great flexibility in habitat use while other species rely heavily on a restricted number of juvenile habitats for protection and food. Considering the rapid degradation of coastal marine habitats worldwide, it is important to evaluate which species are more susceptible to loss of juvenile nursery habitats and how this differs across large biogeographic regions. Here we used a meta-analysis approach to investigate habitat use by juvenile reef fish species in tropical coastal ecosystems across the globe. Densities of juvenile fish species were compared among mangrove, seagrass and coral reef habitats. In the Caribbean, the majority of species showed significantly higher juvenile densities in mangroves as compared to seagrass beds and coral reefs, while for the Indo-Pacific region seagrass beds harbored the highest overall densities. Further analysis indicated that differences in tidal amplitude, irrespective of biogeographic region, appeared to be the major driver for this phenomenon. In addition, juvenile reef fish use of mangroves increased with increasing water salinity. In the Caribbean, species of specific families (e.g. Lutjanidae, Haemulidae) showed a higher reliance on mangroves or seagrass beds as juvenile habitats than other species, whereas in the Indo-Pacific family-specific trends of juvenile habitat utilization were less apparent. The findings of this study highlight the importance of incorporating region-specific tidal inundation regimes into marine spatial conservation planning and ecosystem based management. Furthermore, the significant role of water salinity and tidal access as drivers of mangrove fish habitat use implies that changes in seawater level and rainfall due to climate change may have important effects on how juvenile reef fish use nearshore seascapes in the future.

Study of the cross-reactivity of fish allergens based on a questionnaire and blood testing.

PubMed

Kobayashi, Yukihiro; Huge, Jiletu; Imamura, Shintaro; Hamada-Sato, Naoko

2016-07-01

Parvalbumin and collagen have been identified as cross-reactive allergens for fish allergies. Although doctors realize that various fish elicit allergies, the targets of food allergen labeling laws were only mackerels and salmons in Japan and mackerels in South Korea. This study aimed to reveal the causative species for fish allergy via questionnaires and blood tests. Questionnaire research was conducted in Japan via the internet concerning allergies for fish-allergic patients or their family members. Next, IgE reactivities and cross-reactivities of 26 fish species were analyzed using sera obtained from 16 Japanese patients who were allergic to fish parvalbumin or collagen by enzyme-linked immunosorbent assay (ELISA) and inhibition ELISA. Questionnaire research revealed that 88% patients cannot eat mackerel and salmon in addition to other fish. In addition, 85% respondents were not satisfied with the current food allergen labeling law. In ELISA analyses, we clarified that pooled serum obtained from patients with fish parvalbumin-specific allergies exhibited IgE reactivity to the extracts of most fish species, and pooled serum obtained from patients with fish collagen-specific allergies displayed IgE reactivity to the extracts of all types of fish. Inhibition ELISA experiments revealed cross-reactivities of parvalbumin or collagen to extracts from all fish tested. Most patients with fish allergies displayed allergic symptoms following the intake of various fish species. In addition, fish parvalbumin and collagen were causative factors of fish allergy and were highly cross-reactive fish panallergens. Therefore, current laws should be revised in Japan and South Korea. Copyright © 2016 Japanese Society of Allergology. Production and hosting by Elsevier B.V. All rights reserved.

Mitochondrial DNA identification of game and harvested freshwater fish species.

PubMed

Kyle, C J; Wilson, C C

2007-02-14

The use of DNA in forensics has grown rapidly for human applications along with the concomitant development of bioinformatics and demographic databases to help fully realize the potential of this molecular information. Similar techniques are also used routinely in many wildlife cases, such as species identification in food products, poaching and the illegal trade of endangered species. The use of molecular techniques in forensic cases related to wildlife and the development of associated databases has, however, mainly focused on large mammals with the exception of a few high-profile species. There is a need to develop similar databases for aquatic species for fisheries enforcement, given the large number of exploited and endangered fish species, the intensity of exploitation, and challenges in identifying species and their derived products. We sequenced a 500bp fragment of the mitochondrial cytochrome b gene from representative individuals from 26 harvested fish taxa from Ontario, Canada, focusing on species that support major commercial and recreational fisheries. Ontario provides a unique model system for the development of a fish species database, as the province contains an evolutionarily diverse array of freshwater fish families representing more than one third of all freshwater fish in Canada. Inter- and intraspecific sequence comparisons using phylogenetic analysis and a BLAST search algorithm provided rigorous statistical metrics for species identification. This methodology and these data will aid in fisheries enforcement, providing a tool to easily and accurately identify fish species in enforcement investigations that would have otherwise been difficult or impossible to pursue.

Electrocommunication behaviour during social interactions in two species of pulse-type weakly electric fishes (Mormyridae).

PubMed

Gebhardt, K; Böhme, M; von der Emde, G

2012-12-01

This study compares electrocommunication behaviour in groups of freely swimming weakly electric fishes of two species, Marcusenius altisambesi and Mormyrus rume. Animals emitted variable temporal sequences of stereotyped electric organ discharges (EOD) that served as communication signals. While the waveform of individual signals remained constant, the inter-discharge interval (IDI) patterns conveyed situation-specific information. Both species showed different types of group behaviour, e.g. they engaged in collective (group) foraging. The results show that in each species, during different behavioural conditions (resting, foraging and agonistic encounters), certain situation-specific IDI patterns occurred. In both species, neighbouring fishes swimming closely together interacted electrically by going in and out of synchronization episodes, i.e. periods of temporally correlated EOD production. These often resulted in echo responses between neighbours. During group foraging, fishes often signalled in a repetitive fixed order (fixed-order signalling). During foraging, EOD emission rates of M. altisambesi were higher and more regular than those of M. rume. The two species also differed in the quantity of group behaviours with M. altisambesi being more social than M. rume, which was reflected in the lack of specific agonistic IDI patterns, more fixed-order signalling and more communal resting behaviour in M. altisambesi. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Inferring Fish Escape Behaviour in Trawls Based on Catch Comparison Data: Model Development and Evaluation Based on Data from Skagerrak, Denmark

PubMed Central

Karlsen, Junita Diana

2014-01-01

During the fishing process, fish react to a trawl with a series of behaviours that often are species and size specific. Thus, a thorough understanding of fish behaviour in relation to fishing gear and a scientific understanding of the ability of different gear designs to utilize or stimulate various behavioural patterns during the catching process are essential for developing more efficient, selective, and environmentally friendly trawls. Although many behavioural studies using optical and acoustic observation systems have been conducted, harsh observation conditions on the fishing grounds often hamper the ability to directly observe fish behaviour in relation to fishing gear. As an alternative to optical and acoustic methods, we developed and applied a new mathematical model to catch data to extract detailed and quantitative information about species- and size-dependent escape behaviour in towed fishing gear such as trawls. We used catch comparison data collected with a twin trawl setup; the only difference between the two trawls was that a 12 m long upper section was replaced with 800 mm diamond meshes in one of them. We investigated the length-based escape behaviour of cod (Gadus morhua), haddock (Melanogrammus aeglefinus), saithe (Pollachius virens), witch flounder (Glyptocephalus cynoglossus), and lemon sole (Microstomus kitt) and quantified the extent to which behavioural responses set limits for the large mesh panel’s selective efficiency. Around 85% of saithe, 80% of haddock, 44% of witch flounder, 55% of lemon sole, and 55% of cod (below 68 cm) contacted the large mesh panel and escaped. We also demonstrated the need to account for potential selectivity in the trawl body, as it can bias the assessment of length-based escape behaviour. Our indirect assessment of fish behaviour was in agreement with the direct observations made for the same species in a similar section of the trawl body reported in the literature. PMID:24586403

Chemical composition, mineral content and amino acid and lipid profiles in bones from various fish species.

PubMed

Toppe, Jogeir; Albrektsen, Sissel; Hope, Britt; Aksnes, Anders

2007-03-01

The chemical composition, content of minerals and the profiles of amino acids and fatty acids were analyzed in fish bones from eight different species of fish. Fish bones varied significantly in chemical composition. The main difference was lipid content ranging from 23 g/kg in cod (Gadus morhua) to 509 g/kg in mackerel (Scomber scombrus). In general fatty fish species showed higher lipid levels in the bones compared to lean fish species. Similarly, lower levels of protein and ash were observed in bones from fatty fish species. Protein levels differed from 363 g/kg lipid free dry matter (dm) to 568 g/kg lipid free dm with a concomitant inverse difference in ash content. Ash to protein ratio differed from 0.78 to 1.71 with the lowest level in fish that naturally have highest swimming and physical activity. Saithe (Pollachius virens) and salmon (Salmo salar) were found to be significantly different in the levels of lipid, protein and ash, and ash/protein ratio in the bones. Only small differences were observed in the level of amino acids although species specific differences were observed. The levels of Ca and P in lipid free fish bones were about the same in all species analyzed. Fatty acid profile differed in relation to total lipid levels in the fish bones, but some minor differences between fish species were observed.

Selenium: Mercury Molar Ratios in Freshwater Fish in the Columbia River Basin: Potential Applications for Specific Fish Consumption Advisories.

PubMed

Cusack, Leanne K; Eagles-Smith, Collin; Harding, Anna K; Kile, Molly; Stone, Dave

2017-07-01

Fish provide a valuable source of beneficial nutrients and are an excellent source of low fat protein. However, fish are also the primary source of methylmercury exposure in humans. Selenium often co-occurs with mercury and there is some evidence that selenium can protect against mercury toxicity yet States issue fish consumption advisories based solely on the risks that methylmercury pose to human health. Recently, it has been suggested the selenium: mercury molar ratio be considered in risk management. In order for agencies to utilize the ratio to set consumption guidelines, it is important to evaluate the variability in selenium and mercury in different fish species. We examined 10 different freshwater fish species found within the Columbia River Basin in order to determine the inter- and intra-specific variability in the selenium: mercury molar ratios and the selenium health benefit values. We found significant variation in selenium: mercury molar ratios. The mean molar ratios for each species were all above 1:1, ranging from 3.42:1 in Walleye to 27.2:1 in Chinook salmon. There was a positive correlation between both mercury and selenium with length for each fish species apart from yellow perch and rainbow trout. All species had health benefit values greater than 2. We observed considerable variability in selenium: mercury molar ratios within fish species collected in the Columbia River Basin. Although incorporating selenium: mercury molar ratios into fish consumption holds the potential for refining advisories and assessing the risk of methylmercury exposure, the current understanding of how these ratios apply is insufficient, and further understanding of drivers of variability in the ratios is needed.

Selenium: Mercury molar ratios in freshwater fish in the Columbia River Basin: Potential applications for specific fish consumption advisories

USGS Publications Warehouse

Cusack, Leanne K.; Eagles-Smith, Collin A.; Harding, Anna K.; Kile, Molly; Stone, Dave

2017-01-01

Fish provide a valuable source of beneficial nutrients and are an excellent source of low fat protein. However, fish are also the primary source of methylmercury exposure in humans. Selenium often co-occurs with mercury and there is some evidence that selenium can protect against mercury toxicity yet States issue fish consumption advisories based solely on the risks that methylmercury pose to human health. Recently, it has been suggested the selenium: mercury molar ratio be considered in risk management. In order for agencies to utilize the ratio to set consumption guidelines, it is important to evaluate the variability in selenium and mercury in different fish species. We examined 10 different freshwater fish species found within the Columbia River Basin in order to determine the inter- and intra-specific variability in the selenium: mercury molar ratios and the selenium health benefit values. We found significant variation in selenium: mercury molar ratios. The mean molar ratios for each species were all above 1:1, ranging from 3.42:1 in Walleye to 27.2:1 in Chinook salmon. There was a positive correlation between both mercury and selenium with length for each fish species apart from yellow perch and rainbow trout. All species had health benefit values greater than 2. We observed considerable variability in selenium: mercury molar ratios within fish species collected in the Columbia River Basin. Although incorporating selenium: mercury molar ratios into fish consumption holds the potential for refining advisories and assessing the risk of methylmercury exposure, the current understanding of how these ratios apply is insufficient, and further understanding of drivers of variability in the ratios is needed.

Mercury in fish of the Madeira river (temporal and spatial assessment), Brazilian Amazon.

PubMed

Bastos, Wanderley R; Dórea, José G; Bernardi, José Vicente E; Lauthartte, Leidiane C; Mussy, Marilia H; Lacerda, Luiz D; Malm, Olaf

2015-07-01

The Madeira River is the largest tributary of the Amazon River Basin and one of the most impacted by artisanal gold-mining activities, deforestation for agricultural projects, and recent hydroelectric reservoirs. Total Hg (and methylmercury-MeHg) concentrations was determined in 3182 fish samples of 84 species from different trophic levels as a function of standard size. Species at the top of the trophic level (Piscivorous, Carnivorous) showed the highest mean total Hg concentrations (51-1242 µg/kg), Planctivorous and Omnivorous species showed intermediate total Hg concentrations (26-494 µg/kg), while Detritivorous and Herbivorous species showed the lowest range of mean total Hg concentrations (9-275 µg/kg). Significant correlations between fish size (standard length) and total Hg concentrations were seen for Planctivorous (r=0.474, p=0.0001), Piscivorous (r=0.459, p=0.0001), Detritivorous (r=0.227, p=0.0001), Carnivorous (r=0.212, p=0.0001), and Herbivorous (r=0.156, p=0.01), but not for the Omnivorous species (r=-0.064, p=0.0685). Moreover, fish trophic levels influenced the ratio of MeHg to total Hg (ranged from 70% to 92%). When adjusted for standard body length, significant increases in Hg concentrations in the last 10 years were species specific. Spatial differences, albeit significant for some species, were not consistent with time trends for environmental contamination from past alluvial gold mining activities. Fish-Hg bioaccumulation is species specific but fish feeding strategies are the predominant influence in the fish-Hg bioaccumulation pattern. Copyright © 2015 Elsevier Inc. All rights reserved.

Technical issues affecting the implementation of US Environmental Protection Agency's proposed fish tissue-based aquatic criterion for selenium.

PubMed

Lemly, A Dennis; Skorupa, Joseph P

2007-10-01

The US Environmental Protection Agency is developing a national water quality criterion for selenium that is based on concentrations of the element in fish tissue. Although this approach offers advantages over the current water-based regulations, it also presents new challenges with respect to implementation. A comprehensive protocol that answers the "what, where, and when" is essential with the new tissue-based approach in order to ensure proper acquisition of data that apply to the criterion. Dischargers will need to understand selenium transport, cycling, and bioaccumulation in order to effectively monitor for the criterion and, if necessary, develop site-specific standards. This paper discusses 11 key issues that affect the implementation of a tissue-based criterion, ranging from the selection of fish species to the importance of hydrological units in the sampling design. It also outlines a strategy that incorporates both water column and tissue-based approaches. A national generic safety-net water criterion could be combined with a fish tissue-based criterion for site-specific implementation. For the majority of waters nationwide, National Pollution Discharge Elimination System permitting and other activities associated with the Clean Water Act could continue without the increased expense of sampling and interpreting biological materials. Dischargers would do biotic sampling intermittently (not a routine monitoring burden) on fish tissue relative to the fish tissue criterion. Only when the fish tissue criterion is exceeded would a full site-specific analysis including development of intermedia translation factors be necessary.

Fish abundances in shoreline habitats and submerged aquatic vegetation in a tidal freshwater embayment of the Potomac River.

PubMed

Kraus, Richard T; Jones, R Christian

2012-05-01

Submerged aquatic vegetation (SAV) is considered an important habitat for juvenile and small forage fish species, but many long-term recruitment surveys do not effectively monitor fish communities in SAV. To better understand the impact of recent large increases of SAV on the fish community in tidal freshwater reaches of the Potomac River, we compared traditional seine sampling from shore with drop ring sampling of SAV beds (primarily Hydrilla) in a shallow water (depths, <1.5 m) embayment, Gunston Cove. To accomplish this, we developed species-specific catch efficiency values for the seine gear and calculated area-based density in both shoreline and SAV habitats in late summer of three different years (2007, 2008, and 2009). For the dominant species (Fundulus diaphanus, Lepomis macrochirus, Etheostoma olmstedi, Morone americana, Lepomis gibbosus, and Fundulus heteroclitus), density was nearly always higher in SAV, but overall, species richness was highest in shoreline habitats sampled with seines. Although historical monitoring of fish in Gunston Cove (and throughout Chesapeake Bay) is based upon seine sampling (and trawl sampling in deeper areas), the high densities of fish and larger areal extent of SAV indicated that complementary sampling of SAV habitats would produce more accurate trends in abundances of common species. Because drop ring samples cover much less area than seines and may miss rare species, a combination of methods that includes seine sampling is needed for biodiversity assessment. The resurgence of SAV in tidal freshwater signifies improving water quality, and methods we evaluated here support improved inferences about population trends and fish community structure as indicators of ecosystem condition.

Influence of Green Tides in Coastal Nursery Grounds on the Habitat Selection and Individual Performance of Juvenile Fish

PubMed Central

Murillo, Laurence; Randon, Marine; Lebot, Clément

2017-01-01

Coastal ecosystems, which provide numerous essential ecological functions for fish, are threatened by the proliferation of green macroalgae that significantly modify habitat conditions in intertidal areas. Understanding the influence of green tides on the nursery function of these ecosystems is essential to determine their potential effects on fish recruitment success. In this study, the influence of green tides on juvenile fish was examined in an intertidal sandy beach area, the Bay of Saint-Brieuc (Northwestern France), during two annual cycles of green tides with varying levels of intensity. The responses of three nursery-dependent fish species, the pelagic Sprattus sprattus (L.), the demersal Dicentrarchus labrax (L.) and the benthic Pleuronectes platessa L., were analysed to determine the effects of green tides according to species-specific habitat niche and behaviour. The responses to this perturbation were investigated based on habitat selection and a comparison of individual performance between a control and an impacted site. Several indices on different integrative scales were examined to evaluate these responses (antioxidant defence capacity, muscle total lipid, morphometric condition and growth). Based on these analyses, green tides affect juvenile fish differently according to macroalgal density and species-specific tolerance, which is linked to their capacity to move and to their distribution in the water column. A decreasing gradient of sensitivity was observed from benthic to demersal and pelagic fish species. At low densities of green macroalgae, the three species stayed at the impacted site and the growth of plaice was reduced. At medium macroalgal densities, plaice disappeared from the impacted site and the growth of sea bass and the muscle total lipid content of sprat were reduced. Finally, when high macroalgal densities were reached, none of the studied species were captured at the impacted site. Hence, sites affected by green tides are less favourable nursery grounds for all the studied species, with species-specific effects related to macroalgal density. PMID:28125605

Influence of Green Tides in Coastal Nursery Grounds on the Habitat Selection and Individual Performance of Juvenile Fish.

PubMed

Le Luherne, Emilie; Le Pape, Olivier; Murillo, Laurence; Randon, Marine; Lebot, Clément; Réveillac, Elodie

2017-01-01

Coastal ecosystems, which provide numerous essential ecological functions for fish, are threatened by the proliferation of green macroalgae that significantly modify habitat conditions in intertidal areas. Understanding the influence of green tides on the nursery function of these ecosystems is essential to determine their potential effects on fish recruitment success. In this study, the influence of green tides on juvenile fish was examined in an intertidal sandy beach area, the Bay of Saint-Brieuc (Northwestern France), during two annual cycles of green tides with varying levels of intensity. The responses of three nursery-dependent fish species, the pelagic Sprattus sprattus (L.), the demersal Dicentrarchus labrax (L.) and the benthic Pleuronectes platessa L., were analysed to determine the effects of green tides according to species-specific habitat niche and behaviour. The responses to this perturbation were investigated based on habitat selection and a comparison of individual performance between a control and an impacted site. Several indices on different integrative scales were examined to evaluate these responses (antioxidant defence capacity, muscle total lipid, morphometric condition and growth). Based on these analyses, green tides affect juvenile fish differently according to macroalgal density and species-specific tolerance, which is linked to their capacity to move and to their distribution in the water column. A decreasing gradient of sensitivity was observed from benthic to demersal and pelagic fish species. At low densities of green macroalgae, the three species stayed at the impacted site and the growth of plaice was reduced. At medium macroalgal densities, plaice disappeared from the impacted site and the growth of sea bass and the muscle total lipid content of sprat were reduced. Finally, when high macroalgal densities were reached, none of the studied species were captured at the impacted site. Hence, sites affected by green tides are less favourable nursery grounds for all the studied species, with species-specific effects related to macroalgal density.

Context-Specific Trophic and Functional Ecology of Fishes of Small Stream Ecosystems in the Ouachita National Forest

Treesearch

William J. Matthews; A. Maria Miller-Lemke; Melvin L. Warren; Donna Cobb; Jeffery G. Stewart; Betty Crump; Frances P. Gelwick

2004-01-01

Abstract - Fish play diverse and important roles in stream ecosystems, but details about ecosystem effects are poorly known for many freshwater fish species. A requisite first step to understanding functional roles of individual species is information on their trophic ecology in the context of particular environmental settings. Stomach contents were...

Consumption of freshwater fish by recreational and native freshwater anglers in the upper St-Maurice (Quebec, Canada) and estimation of the intake of methylmercury in humans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Loranger, S.; Houde, L.; Schetagne, R.

1995-12-31

Hydro-Quebec is planning to build two hydroelectric reservoirs in the upper Saint-Maurice River, which would flood about 80% of the surrounding area. The methylmercury (MeHg) content in freshwater fish will therefore tend to increase during the first few years. This development will have a direct impact on the amount of MeHg that the actual users of this river section are exposed to. The objective of this study is to assess the consumption of local fish of these target groups using a Monte-Carlo approach. This study is part of a larger research project aimed at assessing human exposure and the healthmore » risks related to MeHg contamination in local fish. The fish consumption rate for recreational freshwater anglers was calculated using the duration of the average annual fishing trip, the average number of catches per species, the average fish weight per species exceeding a specific length of fish usually caught, and the edible portion of fish consumed. This rate was calculated for the native communities based on the total number of meals per year per species, the average fish weight per species, and the edible portion. Based on these calculations, average intake for sport fishermen is estimated at 6.9 g/day (sd = 6.4). This value is 5 to 25 times lower on average than for other North American native communities. However, it must be pointed out that the food habits of the native population were very similar to those of non-native populations; less than 30% of the food comes from traditional sources.« less

Upstream dispersal of an invasive crayfish aided by a fish passage facility

USGS Publications Warehouse

Welsh, Stuart A.; Loughman, Zachary J.

2015-01-01

Fish passage facilities for reservoir dams have been used to restore habitat connectivity within riverine networks by allowing upstream passage for native species. These facilities may also support the spread of invasive species, an unintended consequence and potential downside of upstream passage structures. We documented dam passage of the invasive virile crayfish, Orconectes virilis (Hagen, 1870), at fish ladders designed for upstream passage of American eels, Anguilla rostrata (Lesueur, 1817), in the Shenandoah River drainage, USA. Ladder use and upstream passage of 11 virile crayfish occurred from 2007–2014 during periods of low river discharge (<30 m3s–1) and within a wide range of water temperatures from 9.0–28.6 °C. Virile crayfish that used the eel ladders were large adults with a mean carapace length and width of 48.0 mm and 24.1 mm, respectively. Our data demonstrated the use of species-specific fish ladders by a non-target non-native species, which has conservation and management implications for the spread of aquatic invasive species and upstream passage facilities. Specifically, managers should consider implementing long-term monitoring of fish passage facilities with emphasis on detection of invasive species, as well as methods to reduce or eliminate passage of invasive species. 

Biological and communication skills needed for introduced fish biologists

USGS Publications Warehouse

Bonar, Scott A.

2016-01-01

What skills and knowledge will a new graduate seeking employment need to work with introduced fishes? Clearly, success in introduced species management—similar to other disciplines in fisheries—requires a mixture of scientific and communication skills. However, specific abilities especially important to a biologist who manages introduced fishes should be highlighted. Unlike most other management strategies, stocking an introduced species can result in unintended and irreversible impacts, so particular care must be employed when stocking is considered. Furthermore, fish populations in areas outside of the introduced species management area might also be affected, usually negatively, if the introduced fish escapes. Therefore, rock-solid knowledge of basic aquatic ecology, including risk management; fish taxonomy (so the wrong fish species is not mistakenly stocked!); familiarity with human values of both the time and the place (which requires communication skills); and a strong understanding of human history are all important.

Estimating the impact of oyster restoration scenarios on transient fish production

USGS Publications Warehouse

McCoy, Elizabeth; Borrett, Stuart R.; LaPeyre, Megan K.; Peterson, Bradley J.

2017-01-01

Oyster reef restoration projects are increasing in number both to enhance oyster density and to retain valuable ecosystem services provided by oyster reefs. Although some oyster restoration projects have demonstrated success by increasing density and biomass of transient fish, it still remains a challenge to quantify the effects of oyster restoration on transient fish communities. We developed a bioenergetics model to assess the impact of selected oyster reef restoration scenarios on associated transient fish species. We used the model to analyze the impact of changes in (1) oyster population carrying capacity; (2) oyster population growth rate; and (3) diet preference of transient fish on oyster reef development and associated transient fish species. Our model results indicate that resident fish biomass is directly affected by oyster restoration and oyster biomass, and oyster restoration can have cascading impacts on transient fish biomass. Furthermore, the results highlight the importance of a favorable oyster population growth rate during early restoration years, as it can lead to rapid increases in mean oyster biomass and biomass of transient fish species. The model also revealed that a transient fish's diet solely dependent on oyster reef-derived prey could limit the biomass of transient fish species, emphasizing the importance of habitat connectivity in estuarine areas to enhance transient fish species biomass. Simple bioenergetics models can be developed to understand the dynamics of a system and make qualitative predictions of management and restoration scenarios.

Climate extremes drive changes in functional community structure.

PubMed

Boucek, Ross E; Rehage, Jennifer S

2014-06-01

The response of communities to climate extremes can be quite variable. Much of this variation has been attributed to differences in community-specific functional trait diversity, as well as community composition. Yet, few if any studies have explicitly tested the response of the functional trait structure of communities following climate extremes (CEs). Recently in South Florida, two independent, but sequential potential CEs took place, a 2010 cold front, followed by a 2011 drought, both of which had profound impacts on a subtropical estuarine fish community. These CEs provided an opportunity to test whether the structure of South Florida fish communities following each extreme was a result of species-specific differences in functional traits. From historical temperature (1927-2012) and freshwater inflows records into the estuary (1955-2012), we determined that the cold front was a statistically extreme disturbance, while the drought was not, but rather a decadal rare disturbance. The two disturbances predictably affected different parts of functional community structure and thus different component species. The cold front virtually eliminated tropical species, including large-bodied snook, mojarra species, nonnative cichlids, and striped mullet, while having little affect on temperate fishes. Likewise, the drought severely impacted freshwater fishes including Florida gar, bowfin, and two centrarchids, with little effect on euryhaline species. Our findings illustrate the ability of this approach to predict and detect both the filtering effects of different types of disturbances and the implications of the resulting changes in community structure. Further, we highlight the value of this approach to developing predictive frameworks for better understanding community responses to global change. © 2014 John Wiley & Sons Ltd.

DNA barcoding of marine ornamental fishes from India.

PubMed

Bamaniya, Dhaval C; Pavan-Kumar, A; Gireesh-Babu, P; Sharma, Niti; Reang, Dhalongsaih; Krishna, Gopal; Lakra, W S

2016-09-01

India has rich marine ornamental fish diversity with 400 fish species distributed in Gulf of Munnar/Palk Bay, Gulf of Kutch, and in reefs around Andaman & Nicobar and Lakshadweep Islands. Marine ornamental fish identification at the field level is very difficult because of their high diversity and profound changes in appearance during their developmental stages and camouflage. To facilitate ornamental fish trading with ease and in compliance with the biodiversity act, DNA barcoding technique could be used to accurately identify species. In this study, DNA barcodes were generated for 31 species of commercially important marine ornamental fishes from India. The average genetic distance (K2P model) within species, genus, and family was 0.446, 13.08, and 20.09%, respectively. Intraspecific variation has increased several folds (15-20 times) after including conspecific sequences from different geographical locations. The presence of allopatric lineages/cryptic species was observed in the Indo-pacific region. The NJ tree constructed based on K2P values showed distinct clusters shared by congeneric species specific to populations.

Interspecific and intraspecific variation in selenium:mercury molar ratios in saltwater fish from the Aleutians: Potential protection on mercury toxicity by selenium

PubMed Central

Burger, Joanna; Gochfeld, Michael; Jeitner, Christian; Donio, Mark; Pittfield, Taryn

2014-01-01

A number of factors affect the consumption risk from mercury in fish, including mercury levels, seasonal patterns of mercury concentrations, human consumption patterns, and sensitive populations (e.g. pregnant women, fetuses, young children, and yet unknown genetic factors). Recently the protective effects of selenium on methylmercury toxicity have been publicized, particularly for saltwater fish. We examine levels of mercury and selenium in several species of fish and seabirds from the Aleutians (Alaska), determine selenium:mercury molar ratios, and examine species-specific and individual variation in the ratios as a means of exploring the use of the ratio in risk assessment and risk management. Variation among species was similar for mercury and selenium. There was significant inter-specific and intraspecific variation in selenium:mercury molar ratios for fish, and for birds. The mean selenium:mercury molar ratios for all fish and bird species were above 1, meaning there was an excess of selenium relative to mercury. It has been suggested that an excess of selenium confers some protective advantage for salt water fish, although the degree of excess necessary is unclear. The selenium:mercury molar ratio was significantly correlated negatively with total length for most fish species, but not for dolly varden. Some individuals of Pacific cod, yellow irish lord, rock greenling, Pacific halibut, dolly varden, and to a lesser extent, flathead sole, had selenium:mercury ratios below 1. No bird muscle had an excess of mercury (ratio below 1), and only glaucous-winged gull and pigeon guillemot had ratios between 1 and 5. There was a great deal of variation in selenium:mercury molar ratios within fish species, and within bird species, making it difficult and impractical to use these ratios in risk assessment or management, for fish advisories, or for consumers, particularly given the difficulty of interpreting the ratios. PMID:22664537

The Astonishing Diversity of Ig Classes and B Cell Repertoires in Teleost Fish

PubMed Central

Fillatreau, Simon; Six, Adrien; Magadan, Susanna; Castro, Rosario; Sunyer, J. Oriol; Boudinot, Pierre

2013-01-01

With lymphoid tissue anatomy different than mammals, and diverse adaptations to all aquatic environments, fish constitute a fascinating group of vertebrate to study the biology of B cell repertoires in a comparative perspective. Fish B lymphocytes express immunoglobulin (Ig) on their surface and secrete antigen-specific antibodies in response to immune challenges. Three antibody classes have been identified in fish, namely IgM, IgD, and IgT, while IgG, IgA, and IgE are absent. IgM and IgD have been found in all fish species analyzed, and thus seem to be primordial antibody classes. IgM and IgD are normally co-expressed from the same mRNA through alternative splicing, as in mammals. Tetrameric IgM is the main antibody class found in serum. Some species of fish also have IgT, which seems to exist only in fish and is specialized in mucosal immunity. IgM/IgD and IgT are expressed by two different sub-populations of B cells. The tools available to investigate B cell responses at the cellular level in fish are limited, but the progress of fish genomics has started to unravel a rich diversity of IgH and immunoglobulin light chain locus organization, which might be related to the succession of genome remodelings that occurred during fish evolution. Moreover, the development of deep sequencing techniques has allowed the investigation of the global features of the expressed fish B cell repertoires in zebrafish and rainbow trout, in steady state or after infection. This review provides a description of the organization of fish Ig loci, with a particular emphasis on their heterogeneity between species, and presents recent data on the structure of the expressed Ig repertoire in healthy and infected fish. PMID:23408183

Oral vaccination of fish: Lessons from humans and veterinary species.

PubMed

Embregts, Carmen W E; Forlenza, Maria

2016-11-01

The limited number of oral vaccines currently approved for use in humans and veterinary species clearly illustrates that development of efficacious and safe oral vaccines has been a challenge not only for fish immunologists. The insufficient efficacy of oral vaccines is partly due to antigen breakdown in the harsh gastric environment, but also to the high tolerogenic gut environment and to inadequate vaccine design. In this review we discuss current approaches used to develop oral vaccines for mass vaccination of farmed fish species. Furthermore, using various examples from the human and veterinary vaccine development, we propose additional approaches to fish vaccine design also considering recent advances in fish mucosal immunology and novel molecular tools. Finally, we discuss the pros and cons of using the zebrafish as a pre-screening animal model to potentially speed up vaccine design and testing for aquaculture fish species. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Morphological and molecular characterization of a marine fish trypanosome from South Africa, including its development in a leech vector.

PubMed

Hayes, Polly M; Lawton, Scott P; Smit, Nico J; Gibson, Wendy C; Davies, Angela J

2014-01-24

Trypanosomes are ubiquitous blood parasites of marine and freshwater fishes, typically transmitted by aquatic leeches. Phylogenetic studies have been dominated by examples derived from freshwater fishes, with few marine representatives. Furthermore, life cycle studies on marine fish trypanosomes have focused on those of the northern hemisphere. In this investigation, we have examined the life cycle and molecular taxonomy of a marine fish trypanosome from South Africa. To locate trypanosome stages, leeches were removed from fishes captured on the west and south coasts of South Africa, and fish blood films and leech squashes were Giemsa-stained and screened; leeches were also examined histologically. To determine whether trypanosome stages in fishes and leeches were of the same genotype, DNA was extracted from Giemsa-stained fish blood films and leech squashes, and from fish whole blood. Fragments of the 18S rRNA gene were amplified by PCR using trypanosome-specific primers and sequenced. Resulting sequence data were compared with each other and with published trypanosome 18S rDNA sequences, and used for phylogenetic analysis. Trypanosomes were detected in blood films from fishes of the families Clinidae, Blenniidae and Gobiidae. The flagellates ranged in size and staining properties within the films and across fish hosts. In squashes and histological sections of adult and juvenile leeches, identified as Zeylanicobdella arugamensis, trypanosome developmental stages were predominantly slender epimastigotes. Sequence data showed that trypanosomes derived from fishes were identical, irrespective of whether they were small or large forms; sequences derived largely from leech epimastigotes were also identical to those obtained from fish trypanosomes. Fish and leech trypanosome sequences fell into a marine fish aquatic clade, and aligned most closely with two trypanosome sequences from marine fishes off Norway. Combined morphological and molecular methods indicate that the trypanosomes examined here represent a single pleomorphic species, rather than the three species described originally. This species is identified as Trypanosoma nudigobii Fantham, 1919 with the leech Z. arugamensis as its vector, and T. capigobii Fantham, 1919 and T. blenniclini Fantham, 1930 are regarded as junior synonyms of the species. Phylogenetic analysis establishes its affinity with marine fish trypanosomes off Norway.

Diversity and composition of estuarine and lagoonal fish assemblages of Socotra Island, Yemen.

PubMed

Lavergne, E; Zajonz, U; Krupp, F; Naseeb, F; Aideed, M S

2016-05-01

Estuarine and lagoonal surveys of Socotra Island and selected sites on the Hadhramout coast of Yemen were conducted with the objective of documenting and analysing fish diversity and assemblage structure. A total of 74 species in 35 families were recorded, among which 65 species in 32 families were from Socotra and 20 species in 17 families were from mainland Yemen. Twenty-one species represent new faunal records for Socotra. Including historic records re-examined in this study, the total fish species richness of estuaries and lagoons of Socotra Island reaches 76, which is relatively high compared to species inventories of well-researched coastal estuaries in southern Africa. Five species dominate the occurrence and abundance frequencies: Terapon jarbua, Hyporhamphus sindensis, Aphanius dispar, Ambassis gymnocephala and Chelon macrolepis. Rarefaction and extrapolation analyses suggest that the actual number of fish species inhabiting some of those estuaries might be higher than the one observed. Thus, additional sampling at specific sites should be conducted to record other less conspicuous species. Ordination and multivariate analyses identified four main distinct assemblage clusters. Two groups are geographically well structured and represent northern Socotra and mainland Yemen, respectively. The other two assemblage groups tend to be determined to a greater extent by the synchrony between physical (e.g. estuary opening periods) and biological (e.g. spawning and recruitment periods) variables than by geographical location. Finally, the single intertidal lagoon of Socotra represents by itself a specific fish assemblage. The high proportion of economically important fish species (38) recorded underscores the paramount importance of these coastal water bodies as nursery sites, and for sustaining vital provisioning ecosystem services. © 2016 The Fisheries Society of the British Isles.

Development of DNA-based Identification methods to track the species composition of fish larvae within nearshore areas of the Great Lakes

EPA Science Inventory

The ability to track the identity and abundance of larval fish, which are ubiquitous during spawning season, may lead to a greater understanding of fish species distributions in Great Lakes nearshore areas including early-detection of invasive fish species before they become esta...

Spatial Scaling of Environmental Variables Improves Species-Habitat Models of Fishes in a Small, Sand-Bed Lowland River

PubMed Central

Radinger, Johannes; Wolter, Christian; Kail, Jochem

2015-01-01

Habitat suitability and the distinct mobility of species depict fundamental keys for explaining and understanding the distribution of river fishes. In recent years, comprehensive data on river hydromorphology has been mapped at spatial scales down to 100 m, potentially serving high resolution species-habitat models, e.g., for fish. However, the relative importance of specific hydromorphological and in-stream habitat variables and their spatial scales of influence is poorly understood. Applying boosted regression trees, we developed species-habitat models for 13 fish species in a sand-bed lowland river based on river morphological and in-stream habitat data. First, we calculated mean values for the predictor variables in five distance classes (from the sampling site up to 4000 m up- and downstream) to identify the spatial scale that best predicts the presence of fish species. Second, we compared the suitability of measured variables and assessment scores related to natural reference conditions. Third, we identified variables which best explained the presence of fish species. The mean model quality (AUC = 0.78, area under the receiver operating characteristic curve) significantly increased when information on the habitat conditions up- and downstream of a sampling site (maximum AUC at 2500 m distance class, +0.049) and topological variables (e.g., stream order) were included (AUC = +0.014). Both measured and assessed variables were similarly well suited to predict species’ presence. Stream order variables and measured cross section features (e.g., width, depth, velocity) were best-suited predictors. In addition, measured channel-bed characteristics (e.g., substrate types) and assessed longitudinal channel features (e.g., naturalness of river planform) were also good predictors. These findings demonstrate (i) the applicability of high resolution river morphological and instream-habitat data (measured and assessed variables) to predict fish presence, (ii) the importance of considering habitat at spatial scales larger than the sampling site, and (iii) that the importance of (river morphological) habitat characteristics differs depending on the spatial scale. PMID:26569119

Selective breeding in fish and conservation of genetic resources for aquaculture.

PubMed

Lind, C E; Ponzoni, R W; Nguyen, N H; Khaw, H L

2012-08-01

To satisfy increasing demands for fish as food, progress must occur towards greater aquaculture productivity whilst retaining the wild and farmed genetic resources that underpin global fish production. We review the main selection methods that have been developed for genetic improvement in aquaculture, and discuss their virtues and shortcomings. Examples of the application of mass, cohort, within family, and combined between-family and within-family selection are given. In addition, we review the manner in which fish genetic resources can be lost at the intra-specific, species and ecosystem levels and discuss options to best prevent this. We illustrate that fundamental principles of genetic management are common in the implementation of both selective breeding and conservation programmes, and should be emphasized in capacity development efforts. We highlight the value of applied genetics approaches for increasing aquaculture productivity and the conservation of fish genetic resources. © 2012 Blackwell Verlag GmbH.

Mercury in Fish of the American and Bear River Watershed Reservoirs: Tissue Analysis and Strategies for Minimizing Exposure at Lake Clementine and Rollins Reservoir, California

NASA Astrophysics Data System (ADS)

Keeble-Toll, A. K.; Monohan, C.; Brown, D. L.; Pearson, G.

2016-12-01

The primary pathway of human exposure to mercury is the consumption of contaminated fish. Identification of patterns of fish tissue mercury levels are a key mechanism for understanding risk drivers and human exposure potential. Site-specific fish tissue data aid the Office of Environmental Health Hazard Assessment (OEHHA) in the development of consumption advisories. This research consists of Year 1 of a three year project to collect fish data from six reservoirs downstream of historic hydraulic mines in the Cosumnes, American, Bear, Yuba watershed region. Angler survey data informed sampling to ensure that commonly caught and consumed species were harvested from Lake Clementine and Rollins Reservoir and was used to evaluate posted fish consumption advice as a mechanism for protecting human health. A total of 72 samples from four species groups were collected in 2015. Geometric mean THg (ppm, wet weight) were highest for black bass at both Lake Clementine (n = 8, THg = 0.40) and Rollins Reservoir (n = 26, THg = 0.54), with a significant positive relationship between fish total length and THg at both water bodies (Lake Clementine: rho = 0.85, p<0.05; Rollins Reservoir: rho = 0.85, p<0.01). Sunfish data for both reservoirs were lower in THg than black bass (Rollins Reservoir: n = 24, THg= 0.16; Lake Clementine: n = 29; THg = 0.12), with a significant positive relationship between fish total length and THg at Lake Clementine (rho = 0.83, p<0.01) but not Rollins Reservoir. These data allow OEHHA to develop site-specific fish consumption advice at both locations and can be used as baseline data to determine if future actions to address inorganic mercury (Hg) sources at legacy gold mines results in reduced human exposure risk at downstream water bodies.

Not Simply a Matter of Fish Intake.

PubMed

Scherr, Carlos; Figueiredo, Valeria N; Moura, Filipe A; Sposito, Andrei C

2015-01-01

Recent findings have highlighted enhanced fish consumption as a potential measure to increase intake of healthy fatty acids, particularly omega-3. The generalizability of this recommendation, however, may fall short of differences in fish species and cooking techniques. Hence, we investigated how these 2 variables affect the lipid content in fish flesh. Nine species of freshwater, deep sea or shore fish were grilled, steamed or fried with or without the addition of soybean oil, olive oil or butter. The lipid composition was analysed and a significant difference was observed in cholesterol, saturated fatty acids, polyunsaturated fatty acids, omega-3 fatty acids and omega-6 fatty acids contents between species (p<0.05). The use of soybean or olive oil was associated with a significant change in flesh concentration of polyunsaturated, omega-3 and omega-6 fatty acids (p<0.05). This study calls attention to the specific lipid content that must be expected from different fish species and cooking techniques.

50 CFR 660.370 - Specifications and management measures.

Code of Federal Regulations, 2010 CFR

2010-10-01

... rebuild overfished species; to enhance the quality of the recreational fishing experience. (iii) Season... overfished species; to avoid waste; to enhance the quality of the recreational fishing experience. (3) All..., rex, rock, and sand soles, Pacific sanddab, and starry flounder) north and south of latitudinal...

Development of DNA-based Identification methods to track the ...

EPA Pesticide Factsheets

The ability to track the identity and abundance of larval fish, which are ubiquitous during spawning season, may lead to a greater understanding of fish species distributions in Great Lakes nearshore areas including early-detection of invasive fish species before they become established. However, larval fish are notoriously hard to identify using traditional morphological techniques. While DNA-based identification methods could increase the ability of aquatic resource managers to determine larval fish composition, use of these methods in aquatic surveys is still uncommon and presents many challenges. In response to this need, we have been working with the U. S. Fish and Wildlife Service to develop field and laboratory methods to facilitate the identification of larval fish using DNA-meta-barcoding. In 2012, we initiated a pilot-project to develop a workflow for conducting DNA-based identification, and compared the species composition at sites within the St. Louis River Estuary of Lake Superior using traditional identification versus DNA meta-barcoding. In 2013, we extended this research to conduct DNA-identification of fish larvae collected from multiple nearshore areas of the Great Lakes by the USFWS. The species composition of larval fish generally mirrored that of fish species known from the same areas, but was influenced by the timing and intensity of sampling. Results indicate that DNA-based identification needs only very low levels of biomass to detect pre

Development of molecular techniques for detection of lymphocystis disease virus in different marine fish species.

PubMed

Cano, I; Ferro, P; Alonso, M C; Bergmann, S M; Römer-Oberdörfer, A; Garcia-Rosado, E; Castro, D; Borrego, J J

2007-01-01

The development and evaluation of a protocol based on polymerase chain reaction (PCR) and nucleic acid hybridization techniques for the specific detection of lymphocystis disease virus (LCDV) in several marine fish species. The pair of primers for PCR, OBL3 and OBL4, was designed based on published nucleotide sequence (LCDV-1) and amplifies a fragment within the major capsid protein. The sensitivity was evaluated using DNA from purified viral particles, as well as from cells inoculated with several viral concentrations. The PCR combined with slot blot was the most sensitive methodology, detecting 2.5 ng of viral DNA. Using this methodology LCDV was detected at 5 days postinoculation from SAF-1 cells initially inoculated with 10(-5) TCID(50) ml(-1). The combination of PCR with membrane hybridization has also been proved to be adequate to detect LCDV from apparently healthy carriers by means of caudal fin sample analysis. This asymptomatic infection was also demonstrated by classical virological methods (cell culture and immunoblot). The protocol described in this study allows the specific detection of LCDV, both in cell cultures and in fin homogenates from asymptomatic fish. The detection of asymptomatic carriers by a rapid molecular method using caudal fin sampling, which does not imply animal killing, could be an important tool to control epizootics caused by LCDV, as fish could be analysed before their introduction and/or mobilization in farm facilities.

A pharmaco-epidemiological study of antibacterial treatments and bacterial diseases in Norwegian aquaculture from 2011 to 2016.

PubMed

Lillehaug, Atle; Børnes, Christine; Grave, Kari

2018-05-07

The sales and prescription of antibacterials for use in Norwegian fish-farming according to diagnosis, fish species and production stage from 2011 to 2016 are analysed. The study is based on antibacterial sales data from wholesalers, pharmacies and feed mills and on prescription data obtained from a register of all prescriptions of antibacterials used in farmed fish. The results show that the fish-farming industry uses very small volumes of antibacterials. In 2016, a total of 212 kg were sold; the only antibacterial substances sold were florfenicol and oxolinic acid. The total amount corresponded to 0.16 mg kg-1 fish slaughtered, or to approximately 0.14% of the fish produced that year. The majority of prescriptions were for non-specific bacterial infections; as most common diseases are under control by vaccination. Most prescriptions for salmonid fish were during early production stages. However, due to higher biomasses of fish, the highest quantities of antibacterials were prescribed during the seawater production phase of Atlantic salmon Salmo salar. An increasing proportion of the prescriptions was for other species, including cleaner fish used for salmon lice control; in 2016 most prescriptions were for this fish category. Due to the negligible use of antibacterials in Norwegian aquaculture, in particular for on-growers, the risk of development of antimicrobial resistance and its transmission to humans through consumption of fish is considered negligible.

77 FR 56027 - 2012-2013 Refuge-Specific Hunting and Sport Fishing Regulations

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-11

... that pertain to migratory game bird hunting, upland game hunting, big game hunting, and sport fishing... fishing regulations when we open wildlife refuges to migratory game bird hunting, upland game hunting, big game hunting, or sport fishing. These regulations list the wildlife species that you may hunt or fish...

Species detection using HyBeacon(®) probe technology: Working towards rapid onsite testing in non-human forensic and food authentication applications.

PubMed

Dawnay, Nick; Hughes, Rebecca; Court, Denise Syndercombe; Duxbury, Nicola

2016-01-01

Identifying individual species or determining species' composition in an unknown sample is important for a variety of forensic applications. Food authentication, monitoring illegal trade in endangered species, forensic entomology, sexual assault case work and counter terrorism are just some of the fields that can require the detection of the biological species present. Traditional laboratory based approaches employ a wide variety of tools and technologies and exploit a number of different species specific traits including morphology, molecular differences and immuno-chemical analyses. A large number of these approaches require laboratory based apparatus and results can take a number of days to be returned to investigating authorities. Having a presumptive test for rapid identification could lead to savings in terms of cost and time and allow sample prioritisation if confirmatory testing in a laboratory is required later. This model study describes the development of an assay using a single HyBeacon(®) probe and melt curve analyses allowing rapid screening and authentication of food products labelled as Atlantic cod (Gadus morhua). Exploiting melt curve detection of species specific SNP sites on the COI gene the test allows detection of a target species (Atlantic cod) and closely related species which may be used as substitutes. The assay has been designed for use with the Field Portable ParaDNA system, a molecular detection platform for non-expert users. The entire process from sampling to result takes approximately 75min. Validation studies were performed on both single source genomic DNA, mixed genomic DNA and commercial samples. Data suggests the assay has a lower limit of detection of 31 pg DNA. The specificity of the assay to Atlantic cod was measured by testing highly processed food samples including frozen, defrosted and cooked fish fillets as well as fish fingers, battered fish fillet and fish pie. Ninety-six (92.7%) of all Atlantic cod food products, tested, provided a correct single species result with the remaining samples erroneously identified as containing non-target species. The data shows that the assay was quick to design and characterise and is also capable of yielding results that would be beneficial in a variety of fields, not least the authentication of food. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

FishVis, A regional decision support tool for identifying vulnerabilities of riverine habitat and fishes to climate change in the Great Lakes Region

USGS Publications Warehouse

Stewart, Jana S.; Covert, S. Alex; Estes, Nick J.; Westenbroek, Stephen M.; Krueger, Damon; Wieferich, Daniel J.; Slattery, Michael T.; Lyons, John D.; McKenna, James E.; Infante, Dana M.; Bruce, Jennifer L.

2016-10-13

Climate change is expected to alter the distributions and community composition of stream fishes in the Great Lakes region in the 21st century, in part as a result of altered hydrological systems (stream temperature, streamflow, and habitat). Resource managers need information and tools to understand where fish species and stream habitats are expected to change under future conditions. Fish sample collections and environmental variables from multiple sources across the United States Great Lakes Basin were integrated and used to develop empirical models to predict fish species occurrence under present-day climate conditions. Random Forests models were used to predict the probability of occurrence of 13 lotic fish species within each stream reach in the study area. Downscaled climate data from general circulation models were integrated with the fish species occurrence models to project fish species occurrence under future climate conditions. The 13 fish species represented three ecological guilds associated with water temperature (cold, cool, and warm), and the species were distributed in streams across the Great Lakes region. Vulnerability (loss of species) and opportunity (gain of species) scores were calculated for all stream reaches by evaluating changes in fish species occurrence from present-day to future climate conditions. The 13 fish species included 4 cold-water species, 5 cool-water species, and 4 warm-water species. Presently, the 4 cold-water species occupy from 15 percent (55,000 kilometers [km]) to 35 percent (130,000 km) of the total stream length (369,215 km) across the study area; the 5 cool-water species, from 9 percent (33,000 km) to 58 percent (215,000 km); and the 4 warm-water species, from 9 percent (33,000 km) to 38 percent (141,000 km).Fish models linked to projections from 13 downscaled climate models projected that in the mid to late 21st century (2046–65 and 2081–2100, respectively) habitats suitable for all 4 cold-water species and 4 of 5 cool-water species under present-day conditions will decline as much as 86 percent and as little as 33 percent, and habitats suitable for all 4 warm-water species will increase as much as 33 percent and as little as 7 percent. This report documents the approach and data used to predict and project fish species occurrence under present-day and future climate conditions for 13 lotic fish species in the United States Great Lakes Basin. A Web-based decision support mapping application termed “FishVis” was developed to provide a means to integrate, visualize, query, and download the results of these projected climate-driven responses and help inform conservation planning efforts within the region.

Key issues concerning environmental enrichment for laboratory-held fish species.

PubMed

Williams, T D; Readman, G D; Owen, S F

2009-04-01

An improved knowledge and understanding of the fundamental biological requirements is needed for many of the species of fish held in captivity and, without this knowledge it is difficult to determine the optimal conditions for laboratory culture. The aim of this paper is to review the key issues concerning environmental enrichment for laboratory-held fish species and identify where improvements are required. It provides background information on environmental enrichment, describes enrichment techniques currently used in aquatic ecotoxicology studies, identifies potential restrictions in their use and discusses why more detailed and species-specific guidance is needed.

Essential coastal habitats for fish in the Baltic Sea

NASA Astrophysics Data System (ADS)

Kraufvelin, Patrik; Pekcan-Hekim, Zeynep; Bergström, Ulf; Florin, Ann-Britt; Lehikoinen, Annukka; Mattila, Johanna; Arula, Timo; Briekmane, Laura; Brown, Elliot John; Celmer, Zuzanna; Dainys, Justas; Jokinen, Henri; Kääriä, Petra; Kallasvuo, Meri; Lappalainen, Antti; Lozys, Linas; Möller, Peter; Orio, Alessandro; Rohtla, Mehis; Saks, Lauri; Snickars, Martin; Støttrup, Josianne; Sundblad, Göran; Taal, Imre; Ustups, Didzis; Verliin, Aare; Vetemaa, Markus; Winkler, Helmut; Wozniczka, Adam; Olsson, Jens

2018-05-01

Many coastal and offshore fish species are highly dependent on specific habitat types for population maintenance. In the Baltic Sea, shallow productive habitats in the coastal zone such as wetlands, vegetated flads/lagoons and sheltered bays as well as more exposed rocky and sandy areas are utilized by fish across many life history stages including spawning, juvenile development, feeding and migration. Although there is general consensus about the critical importance of these essential fish habitats (EFH) for fish production along the coast, direct quantitative evidence for their specific roles in population growth and maintenance is still scarce. Nevertheless, for some coastal species, indirect evidence exists, and in many cases, sufficient data are also available to carry out further quantitative analyses. As coastal EFH in the Baltic Sea are often found in areas that are highly utilized and valued by humans, they are subjected to many different pressures. While cumulative pressures, such as eutrophication, coastal construction and development, climate change, invasive species and fisheries, impact fish in coastal areas, the conservation coverage for EFH in these areas remains poor. This is mainly due to the fact that historically, fisheries management and nature conservation are not integrated neither in research nor in management in Baltic Sea countries. Setting joint objectives for fisheries management and nature conservation would hence be pivotal for improved protection of EFH in the Baltic Sea. To properly inform management, improvements in the development of monitoring strategies and mapping methodology for EFH are also needed. Stronger international cooperation between Baltic Sea states will facilitate improved management outcomes across ecologically arbitrary boundaries. This is especially important for successful implementation of international agreements and legislative directives such as the Baltic Sea Action Plan, the Marine Strategy Framework Directive, the Habitats Directive, and the Maritime Spatial Planning Directive, but also for improving the communication of information related to coastal EFH among researchers, stakeholders, managers and decision makers. In this paper, efforts are made to characterize coastal EFH in the Baltic Sea, their importance and the threats/pressures they face, as well as their current conservation status, while highlighting knowledge gaps and outlining perspectives for future work in an ecosystem-based management framework.

Physiological basis of climate change impacts on North American inland fishes

USGS Publications Warehouse

Whitney, James E.; Al-Chokhachy, Robert K.; Bunnell, David B.; Caldwell, Colleen A.; Cooke, Steven J.; Eliason, Erika J.; Rogers, Mark W.; Lynch, Abigail J.; Paukert, Craig P.

2016-01-01

Global climate change is altering freshwater ecosystems and affecting fish populations and communities. Underpinning changes in fish distribution and assemblage-level responses to climate change are individual-level physiological constraints. In this review, we synthesize the mechanistic effects of climate change on neuroendocrine, cardiorespiratory, immune, osmoregulatory, and reproductive systems of freshwater and diadromous fishes. Observed climate change effects on physiological systems are varied and numerous, including exceedance of critical thermal tolerances, decreased cardiorespiratory performance, compromised immune function, and altered patterns of individual reproductive investment. However, effects vary widely among and within species because of species, population, and even sex-specific differences in sensitivity and resilience and because of habitat-specific variation in the magnitude of climate-related environmental change. Research on the interactive effects of climate change with other environmental stressors across a broader range of fish diversity is needed to further our understanding of climate change effects on fish physiology.

Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

USGS Publications Warehouse

Brenkman, Samuel J.; Connolly, Patrick J.

2008-01-01

Rivers and streams that drain from Olympic, Mount Rainier, and North Cascades National Parks are among the most protected corridors in the lower 48 States, and represent some of the largest tracts of contiguous, undisturbed habitat throughout the range of several key fish species of the Pacific Northwest. These watersheds are of high regional importance as freshwater habitat sanctuaries for native fish, where habitat conditions are characterized as having little to no disturbance from development, channelization, impervious surfaces, roads, diversions, or hydroelectric projects. Fishery resources are of high ecological and cultural importance in Pacific Northwest National Parks, and significantly contribute to economically important recreational, commercial, and tribal fisheries. This protocol describes procedures to monitor trends in fish assemblages, fish abundance, and water temperature in eight rivers and five wadeable streams in Olympic National Park during summer months, and is based on 4 years of field testing. Fish assemblages link freshwater, marine, and terrestrial ecosystems. They also serve as focal resources of national parks and are excellent indicators of ecological conditions of rivers and streams. Despite the vital importance of native anadromous and resident fish populations, there is no existing monitoring program for fish assemblages in the North Coast and Cascades Network. Specific monitoring objectives of this protocol are to determine seasonal and annual trends in: (1) fish species composition, (2) timing of migration of adult fish, (3) relative abundance, (4) age and size structure, (5) extent of non-native and hatchery fish, and (6) water temperature. To detect seasonal and annual trends in fish assemblages in reference sites, we rely on repeated and consistent annual sampling at each monitoring site. The general rationale for the repeated sampling of reference sites is to ensure that we account for the high interannual variability in fish movements and abundances in rivers. One underlying assumption is that the monitoring program is designed in perpetuity, and consequently our capability to detect trends substantially increases with time. The protocol describes sampling designs, methods, training procedures, safety considerations, data management, data analysis, and reporting. The allocation of sampling effort represents a balance between ecological considerations, a sound monitoring approach, and practical limitations caused by logistical constraints and a limited annual budget of $55,000. The widespread declines of native fish species in western North America highlights the importance and urgency of understanding trends in fish assemblages from undisturbed habitats. Seasonal and annual trends in fish assemblages will provide insights at the individual, population, and assemblage level. This protocol will allow managers to detect increases and decreases in abundance of priority management species, and occurrence of non-native, hatchery, and federally listed fish. The detection of trends in fish assemblages will allow for specific management actions that may include: implementation of more appropriate fishing regulations, evaluation of existing hatchery releases, control of non-native fish species, and prioritization of habitat restoration projects. Dissemination and communication of scientific findings on North Coast and Cascades Network fish assemblages will be a core product of this protocol, which will have much relevance to decision makers, park visitors, researchers, and educators.

Multiple hypotheses testing of fish incidence patterns in an urbanized ecosystem

USGS Publications Warehouse

Chizinski, C.J.; Higgins, C.L.; Shavlik, C.E.; Pope, K.L.

2006-01-01

Ecological and evolutionary theories have focused traditionally on natural processes with little attempt to incorporate anthropogenic influences despite the fact that humans are such an integral part of virtually all ecosystems. A series of alternate models that incorporated anthropogenic factors and traditional ecological mechanisms of invasion to account for fish incidence patterns in urban lakes was tested. The models were based on fish biology, human intervention, and habitat characteristics. However, the only models to account for empirical patterns were those that included fish invasiveness, which incorporated species-specific information about overall tolerance and fecundity. This suggests that species-specific characteristics are more important in general distributional patterns than human-mediated dispersal. Better information of illegal stocking activities is needed to improve human-mediated models, and more insight into basic life history of ubiquitous species is needed to truly understand underlying mechanisms of biotic homogenization. ?? Springer 2005.

Factors influencing tropical island freshwater fishes:Species, status, and management implications in puerto rico [Factores que influencian a los peces tropicales de agua dulce: Especies, estado actual e implicaciones para el manejo en Puerto Rico

USGS Publications Warehouse

Wesley, Neal J.; Lilyestrom, Craig G.; Kwak, T.J.

2009-01-01

Anthropogenic effects including river regulation, watershed development, contamination, and fish introductions have substantially affected the majority of freshwater habitats in Europe and North America. This pattern of resource development and degradation is widespread in the tropics, and often little is known about the resources before they are lost. This article describes the freshwater resources of Puerto Rico and identifies factors that threaten conservation of native fishes. The fishes found in freshwater habitats of Puerto Rico represent a moderately diverse assemblage composed of 14 orders, 29 families, and 82 species. There are fewer than 10 species of native peripherally-freshwater fish that require a link to marine systems. Introductions of nonindigenous species have greatly expanded fish diversity in freshwater systems, and native estuarine and marine species (18 families) also commonly enter lowland rivers and brackish lagoons. Environmental alterations, including land use and development, stream channelization, pollution, and the impoundment of rivers, combined with nonnative species introductions threaten the health and sustainability of aquatic resources in Puerto Rico. Six principal areas for attention that are important influences on the current and future status of the freshwater fish resources of Puerto Rico are identified and discussed.

Fishery-independent data reveal negative effect of human population density on Caribbean predatory fish communities.

PubMed

Stallings, Christopher D

2009-01-01

Understanding the current status of predatory fish communities, and the effects fishing has on them, is vitally important information for management. However, data are often insufficient at region-wide scales to assess the effects of extraction in coral reef ecosystems of developing nations. Here, I overcome this difficulty by using a publicly accessible, fisheries-independent database to provide a broad scale, comprehensive analysis of human impacts on predatory reef fish communities across the greater Caribbean region. Specifically, this study analyzed presence and diversity of predatory reef fishes over a gradient of human population density. Across the region, as human population density increases, presence of large-bodied fishes declines, and fish communities become dominated by a few smaller-bodied species. Complete disappearance of several large-bodied fishes indicates ecological and local extinctions have occurred in some densely populated areas. These findings fill a fundamentally important gap in our knowledge of the ecosystem effects of artisanal fisheries in developing nations, and provide support for multiple approaches to data collection where they are commonly unavailable.

Fishery-Independent Data Reveal Negative Effect of Human Population Density on Caribbean Predatory Fish Communities

PubMed Central

Stallings, Christopher D.

2009-01-01

Background Understanding the current status of predatory fish communities, and the effects fishing has on them, is vitally important information for management. However, data are often insufficient at region-wide scales to assess the effects of extraction in coral reef ecosystems of developing nations. Methodology/Principal Findings Here, I overcome this difficulty by using a publicly accessible, fisheries-independent database to provide a broad scale, comprehensive analysis of human impacts on predatory reef fish communities across the greater Caribbean region. Specifically, this study analyzed presence and diversity of predatory reef fishes over a gradient of human population density. Across the region, as human population density increases, presence of large-bodied fishes declines, and fish communities become dominated by a few smaller-bodied species. Conclusions/Significance Complete disappearance of several large-bodied fishes indicates ecological and local extinctions have occurred in some densely populated areas. These findings fill a fundamentally important gap in our knowledge of the ecosystem effects of artisanal fisheries in developing nations, and provide support for multiple approaches to data collection where they are commonly unavailable. PMID:19421312

Species-specific identification of Dekkera/Brettanomyces yeasts by fluorescently labeled DNA probes targeting the 26S rRNA.

PubMed

Röder, Christoph; König, Helmut; Fröhlich, Jürgen

2007-09-01

Sequencing of the complete 26S rRNA genes of all Dekkera/Brettanomyces species colonizing different beverages revealed the potential for a specific primer and probe design to support diagnostic PCR approaches and FISH. By analysis of the complete 26S rRNA genes of all five currently known Dekkera/Brettanomyces species (Dekkera bruxellensis, D. anomala, Brettanomyces custersianus, B. nanus and B. naardenensis), several regions with high nucleotide sequence variability yet distinct from the D1/D2 domains were identified. FISH species-specific probes targeting the 26S rRNA gene's most variable regions were designed. Accessibility of probe targets for hybridization was facilitated by the construction of partially complementary 'side'-labeled probes, based on secondary structure models of the rRNA sequences. The specificity and routine applicability of the FISH-based method for yeast identification were tested by analyzing different wine isolates. Investigation of the prevalence of Dekkera/Brettanomyces yeasts in the German viticultural regions Wonnegau, Nierstein and Bingen (Rhinehesse, Rhineland-Palatinate) resulted in the isolation of 37 D. bruxellensis strains from 291 wine samples.

Using silver and bighead carp cell lines for the identification of a unique metabolite fingerprint from thiram-specific chemical exposure

USGS Publications Warehouse

Putnam, Joel G.; Nelson, Justine; Leis, Eric M; Erickson, Richard A.; Hubert, Terrance D.; Amberg, Jon J.

2017-01-01

Conservation biology often requires the control of invasive species. One method is the development and use of biocides. Identifying new chemicals as part of the biocide registration approval process can require screening millions of compounds. Traditionally, screening new chemicals has been done in vivo using test organisms. Using in vitro (e.g., cell lines) and in silico (e.g., computer models) methods decrease test organism requirements and increase screening speed and efficiency. These methods, however, would be greatly improved by better understanding how individual fish species metabolize selected compounds.We combined cell assays and metabolomics to create a powerful tool to facilitate the identification of new control chemicals. Specifically, we exposed cell lines established from bighead carp and silver carp larvae to thiram (7 concentrations) then completed metabolite profiling to assess the dose-response of the bighead carp and silver carp metabolome to thiram. Forty one of the 700 metabolomic markers identified in bighead carp exhibited a dose-response to thiram exposure compared to silver carp in which 205 of 1590 metabolomic markers exhibited a dose-response. Additionally, we identified 11 statistically significant metabolomic markers based upon volcano plot analysis common between both species. This smaller subset of metabolites formed a thiram-specific metabolomic fingerprint which allowed for the creation of a toxicant specific, rather than a species-specific, metabolomic fingerprint. Metabolomic fingerprints may be used in biocide development and improve our understanding of ecologically significant events, such as mass fish kills.

Experimental evaluation of diversity-productivity relationships in a coral reef fish assemblage.

PubMed

Messmer, Vanessa; Blowes, Shane A; Jones, Geoffrey P; Munday, Philip L

2014-09-01

The global decline in biodiversity is causing increasing concern about the effects of biodiversity loss on ecosystem services such as productivity. Biodiversity has been hypothesised to be important in maintaining productivity of biological assemblages because niche complementarity and facilitation among the constituent species can result in more efficient use of resources. However, these conclusions are primarily based on studies with plant communities, and the relationship between diversity and productivity at higher trophic levels is largely unknown, especially in the marine environment. Here, we used a manipulative field experiment to test the effects of species richness and species identity on biomass accumulation in coral reef fish assemblages at Lizard Island. Small patch reefs were stocked with a total of 30 juveniles belonging to three planktivorous damselfish (genus Pomacentrus) according to three different levels of fish species richness (one, two and three species) and seven different combinations of fish species. Species richness had no effect on the relative growth in this assemblage after 18 days, but relative growth differed among individual fish species and the different combinations of species. Patterns of increase in biomass were best explained by species-specific differences and variable effects of intra- and interspecific competition on growth. These results suggest that niche complementarity and facilitation are not the most influential drivers of total productivity within this guild of planktivorous fishes. Total productivity may be resilient to declining reef fish biodiversity, but this will depend on which species are lost and on the life-history traits of remaining species.

Diversity "down under": monogeneans in the Antipodes (Australia) with a prediction of monogenean biodiversity worldwide.

PubMed

Whittington, I D

1998-10-01

There are approximately 25,000 species of fishes known in the world. The Monogenea are believed to be among the most host-specific of parasites and if each species of fish is host to a different species of monogenean, there could be almost 25,000 monogenean species on Earth. Currently, I estimate that between 3000 and 4000 of these are described. Australia has a rich marine fish fauna with approximately 3500 species of teleosts. If the same formula of one monogenean species per host fish species is applied, Australia marine fishes could host potentially 3500 species of monogeneans. The first monogenean species described from Australia was Encotyllabe pagrosomi MacCallum, 1917 and approximately 300 more species have since been described from the continent. Even in a region of Australia such as Heron Island on the Great Barrier Reef that has been a focus of sustained research on these parasites, only about 85 species are described from 40 of the most common, easily-caught species of fish. Reasons are discussed for the relatively small numbers of monogenean species described so far from Australia. Endemicity is difficult to judge, but only one is certain: Concinnocotyla australensis (Polystomatidae) from Neoceratodus forsteri (Dipnoi). Despite reductions in research funding, the value of parasite taxonomy must not be underestimated, particularly in regions of the world that have a rich diversity of potential hosts.

Toxicity of Clostridium botulinum type E neurotoxin to Great Lakes fish: implications for avian botulism.

PubMed

Yule, Adam M; Barker, Ian K; Austin, John W; Moccia, Richard D

2006-07-01

Since 1999, large-scale mortalities of fish-eating birds have been observed on the Great Lakes, and more specifically on Lake Erie. Type E botulism has been established as the primary cause of death. The mechanism of type E botulism exposure in fish-eating birds is unclear. Given that these birds are thought to eat live fish exclusively, it seems likely that their prey play a key role in the process, but the role of fish as potential transport vectors of botulinum neurotoxin type E (BoNT/E) to birds has not been adequately investigated. Between June 2003 and April 2004 a methodological model for exposing fish to Clostridium botulinum was developed and used to compare the sensitivity of rainbow trout (Oncorhynchus mykiss), round goby (Neogobius melanostomas), walleye (Stizostedion vitreum), and yellow perch (Perca flavescens) to four doses (0, 800, 1,500, and 4,000 Mouse Lethal Doses) of Clostridium botulinum type E neurotoxin. Each fish species expressed unique changes in both behavior and skin pigmentation prior to death. Yellow perch survived significantly longer (P < 0.05) than the three other species at all toxin treatments. Results of this study suggest that live fish can represent a significant vector for transfer of BoNT/E to birds.

Testing for synchrony in recruitment among four Lake Michigan fish species

USGS Publications Warehouse

Bunnell, David B.; Höök, Tomas O.; Troy, Cary D.; Liu, Wentao; Madenjian, Charles P.; Adams, Jean V.

2017-01-01

In the Great Lakes region, multiple fish species display intra-specific spatial synchrony in 28 recruitment success, with inter-annual climate variation hypothesized as the most likely driver. 29 In Lake Michigan, we evaluated whether climatic or other physical variables could also induce 30 spatial synchrony across multiple species, including bloater (Coregonus hoyi), rainbow smelt 31 (Osmerus mordax), yellow perch (Perca flavescens), and alewife (Alosa pseudoharengus). The 32 residuals from stock-recruitment relationships revealed yellow perch recruitment to be correlated 33 with recruitment of both rainbow smelt (r = 0.37) and alewife (r = 0.36). Across all four species, 34 higher than expected recruitment occurred in 5 years between 1978 and 1987 and then switched 35 to lower than expected recruitment in 5 years between 1996 and 2004. Generalized additive 36 models revealed warmer spring and summer water temperatures and lower wind speeds 37 corresponded to higher than expected recruitment for the nearshore-spawning species, and 38 overall variance explained ranged from 14% (yellow perch) to 61% (alewife). For all species 39 but rainbow smelt, higher recruitment also occurred in extremely high or low years of the North 40 Atlantic Oscillation index. Future development of indices that describe the physical Great Lakes 41 environment could improve understanding of how climate can synchronize fish populations 42 within and across species.

Monoclonal antibodies specific to sailfish serum albumin: development of an assay for the identification of fish species in the field.

PubMed

Rossi, E A; Shepard, S R; Poyer, J C; Hartmann, J X

1992-06-01

Balb/c mice were immunized with albumin purified from sailfish (Istiophorus albicans) serum. Hybridomas were produced and screened by ELISA for reactivity with the purified albumins of sailfish, blue marlin (Makaira nigricans) and white marlin (Tetrapturus albidus). Monoclonal antibodies (MAbs) from 16 different clones exhibited activity against sailfish albumin. Thirteen of the MAbs showed cross-reactivity with the marlin species. Three MAbs exhibited distinct specificity for sailfish albumin. One of these species specific MAbs (M2D1) was conjugated to horseradish peroxidase (HRP) in order to construct an ELISA for identification of sailfish from serum. The ELISA for sailfish correctly identified eight sailfish from 26 billfish serum samples. The MAb-peroxidase conjugate was highly specific toward sailfish in that no reaction against heterologous species was detected.

Identification of enolases and aldolases as important fish allergens in cod, salmon and tuna: component resolved diagnosis using parvalbumin and the new allergens.

PubMed

Kuehn, A; Hilger, C; Lehners-Weber, C; Codreanu-Morel, F; Morisset, M; Metz-Favre, C; Pauli, G; de Blay, F; Revets, D; Muller, C P; Vogel, L; Vieths, S; Hentges, F

2013-07-01

The majority of fish-allergic patients are sensitized to parvalbumin, known to be the cause of important IgE cross-reactivity among fish species. Little is known about the importance of fish allergens other than parvalbumin. The aim of this study was to characterize hitherto undefined fish allergens in three commonly consumed fish species, cod, salmon and tuna, and to evaluate their importance for in vitro IgE-diagnosis in addition to parvalbumin and fish gelatin. Sixty-two patients were diagnosed by clinical history, skin prick tests and specific IgE to fish extracts. Two new fish allergens from cod, salmon and tuna were identified by microsequencing. These proteins were characterized by immunoblot, ELISA and mediator release assay. Purified parvalbumin, enolase, aldolase and fish gelatin were used for quantification of specific IgE in ELISA. Parvalbumin and two other allergens of 50 and 40 kDa were detected in IgE-immunoblots of cod, salmon and tuna extracts by most patient sera. The 50 and 40 kDa proteins were identified as beta-enolase and fructose-bisphosphate aldolase A respectively. Both purified enzymes showed allergenic activity in the mediator release assay. Indeed, 72.6% of the patients were sensitized to parvalbumin, 20% of these had specific IgE to salmon parvalbumin only. IgE to enolases were found in 62.9% (0.5-95.0 kUA /L), to aldolases in 50.0% (0.4-26.0 kUA /L) and to fish gelatin in 19.3% (0.4-20.0 kUA /L) of the patients. Inter-species cross-reactivity, even though limited, was found for enolases and aldolases by IgE-inhibition ELISA. Fish enolase and aldolase have been identified as important new fish allergens. In fish allergy diagnosis, IgE to enolase and aldolase are especially relevant when IgE to parvalbumin are absent. © 2013 John Wiley & Sons Ltd.

Comparative molecular cytogenetic analyses of a major tandemly repeated DNA family and retrotransposon sequences in cultivated jute Corchorus species (Malvaceae).

PubMed

Begum, Rabeya; Zakrzewski, Falk; Menzel, Gerhard; Weber, Beatrice; Alam, Sheikh Shamimul; Schmidt, Thomas

2013-07-01

The cultivated jute species Corchorus olitorius and Corchorus capsularis are important fibre crops. The analysis of repetitive DNA sequences, comprising a major part of plant genomes, has not been carried out in jute but is useful to investigate the long-range organization of chromosomes. The aim of this study was the identification of repetitive DNA sequences to facilitate comparative molecular and cytogenetic studies of two jute cultivars and to develop a fluorescent in situ hybridization (FISH) karyotype for chromosome identification. A plasmid library was generated from C. olitorius and C. capsularis with genomic restriction fragments of 100-500 bp, which was complemented by targeted cloning of satellite DNA by PCR. The diversity of the repetitive DNA families was analysed comparatively. The genomic abundance and chromosomal localization of different repeat classes were investigated by Southern analysis and FISH, respectively. The cytosine methylation of satellite arrays was studied by immunolabelling. Major satellite repeats and retrotransposons have been identified from C. olitorius and C. capsularis. The satellite family CoSat I forms two undermethylated species-specific subfamilies, while the long terminal repeat (LTR) retrotransposons CoRetro I and CoRetro II show similarity to the Metaviridea of plant retroelements. FISH karyotypes were developed by multicolour FISH using these repetitive DNA sequences in combination with 5S and 18S-5·8S-25S rRNA genes which enable the unequivocal chromosome discrimination in both jute species. The analysis of the structure and diversity of the repeated DNA is crucial for genome sequence annotation. The reference karyotypes will be useful for breeding of jute and provide the basis for karyotyping homeologous chromosomes of wild jute species to reveal the genetic and evolutionary relationship between cultivated and wild Corchorus species.

DNA barcoding reveals high levels of genetic diversity in the fishes of the Itapecuru Basin in Maranhão, Brazil.

PubMed

Nascimento, M H S; Almeida, M S; Veira, M N S; Limeira Filho, D; Lima, R C; Barros, M C; Fraga, E C

2016-08-29

DNA barcoding is a useful complementary tool for use in traditional taxonomic studies due to its ability to detect cryptic species, and may be particularly efficient in the identification of fish species. The fish fauna of the Itapecuru River represents an important fishery resource in the Brazilian State of Maranhão, although it is currently suffering increasing degradation as a result of anthropogenic impacts. Therefore, DNA barcoding was used in the present study to identify fish species and establish a database of the rich freshwater fish fauna of Maranhão. A total of 440 specimens were analyzed, corresponding to 64 species belonging to 59 genera, 31 families, and 10 orders. Overall, 92.19% of these species could be identified by DNA barcoding, and were characterized by low levels (average 0.80%) of intra-specific divergence. However, five species (Anableps anableps, Gymnotus carapo, Sciades couma, Pseudauchenipterus nodosus, and Leporinus piau) presented values of mean genetic divergence above 3%, indicating the existence of cryptic diversity in these fishes. The DNA barcoding approach permitted the analysis of a large number of specimens and facilitated the discrimination and identification of closely related fish species in the Itapecuru Basin.

Determination of toxins involved in ciguatera fish poisoning in the Pacific by LC/MS.

PubMed

Yogi, Kentaro; Sakugawa, Satsuki; Oshiro, Naomasa; Ikehara, Tsuyoshi; Sugiyama, Kiminori; Yasumoto, Takeshi

2014-01-01

Ciguatera fish poisoning is the most extensive and difficult to control of the seafood poisonings. To facilitate monitoring of fish toxicity, toxin profiles were investigated by an LC/MS/MS method using 14 reference toxins on eight representative species of fish collected in four different areas of the Pacific. Snappers and groupers from Okinawa contained ciguatoxin-1B (CTX1B) and two deoxy congeners at variable but species-specific ratios, while red snapper, Lutjanus bohar, from Minamitorishima, and amberjack, Seriola dumerili, from Hawaii, contained both CTX1B-type and CTX3C-type toxins. Spotted knifejaw, Oplegnathus punctatus, from Okinawan waters, contained mainly CTX4A and CTX4B, but the same species caught at Miyazaki was contaminated primarily with the CTX3C-type toxins. Otherwise, the toxin profiles were consistently species-specific in fish collected from various locations around Okinawa over 20 years. The LC/MS/MS and mouse bioassay results agreed well, indicating the LC/MS/MS method is a promising alternative to the mouse bioassay. Pure CTX1B and CTX3C were prepared for use in future LC/MS/MS analysis.

Metazoan parasites of fishes from the Celestun coastal lagoon, Yucatan, Mexico.

PubMed

Sosa-Medina, Trinidad; Vidal-Martínez, Víctor M; Aguirre-Macedo, M Leopoldina

2015-08-31

The aims of this study were to produce a checklist of the metazoan parasites of fishes from the Celestun coastal lagoon and to determine the degree of faunal similarity among the fishes based on the metazoan parasites they share. A checklist was prepared including all available records (1996-2014) of parasites of marine, brackish water and freshwater fishes of the area. All of these data were included in a presence/absence database and used to determine similarity via Jaccard's index. The results indicate the presence of 62 metazoan parasite species infecting 22 fish species. The number of metazoan parasite species found in the fishes from the Celestún lagoon is apparently the highest reported worldwide for a tropical coastal lagoon. The parasites included 12 species of adult digeneans, 27 digeneans in the metacercarial stage, 6 monogeneans, 3 metacestodes, 9 nematodes, 2 acanthocephalans, 2 crustaceans and 1 annelid. Forty parasite species were autogenic and 23 were allogenic and 1 unknown. The overall similarity among all of the species of fish with respect to the metazoan parasites they share was low (0.08 ± 0.12), with few similarity values above 0.4 being obtained. This low similarity was due primarily to the presence of suites of parasites exclusive to specific species of fish. The autogenic component of the parasite fauna (40 species) dominated the allogenic component (21 species). The most likely explanation for the large number of fish parasites found at Celestún is the good environmental condition of the lagoon, which allows the completion of parasite life cycles and free circulation of euryhaline fishes from the marine environment bringing marine parasites into the lagoon.

Stable isotope signatures and trophic-step fractionation factors of fish tissues collected as non-lethal surrogates of dorsal muscle.

PubMed

Busst, Georgina M A; Bašić, Tea; Britton, J Robert

2015-08-30

Dorsal white muscle is the standard tissue analysed in fish trophic studies using stable isotope analyses. As muscle is usually collected destructively, fin tissues and scales are often used as non-lethal surrogates; we examined the utility of scales and fin tissue as muscle surrogates. The muscle, fin and scale δ(15) N and δ(13) C values from 10 cyprinid fish species determined with an elemental analyser coupled with an isotope ratio mass spectrometer were compared. The fish comprised (1) samples from the wild, and (2) samples from tank aquaria, using six species held for 120 days and fed a single food resource. Relationships between muscle, fin and scale isotope ratios were examined for each species and for the entire dataset, with the efficacy of four methods of predicting muscle isotope ratios from fin and scale values being tested. The fractionation factors between the three tissues of the laboratory fishes and their food resource were then calculated and applied to Bayesian mixing models to assess their effect on fish diet predictions. The isotopic data of the three tissues per species were distinct, but were significantly related, enabling estimations of muscle values from the two surrogates. Species-specific equations provided the least erroneous corrections of scale and fin isotope ratios (errors < 0.6‰). The fractionation factors for δ(15) N values were in the range obtained for other species, but were often higher for δ(13) C values. Their application to data from two fish populations in the mixing models resulted in significant alterations in diet predictions. Scales and fin tissue are strong surrogates of dorsal muscle in food web studies as they can provide estimates of muscle values within an acceptable level of error when species-specific methods are used. Their derived fractionation factors can also be applied to models predicting fish diet composition from δ(15) N and δ(13) C values. Copyright © 2015 John Wiley & Sons, Ltd.

Case studies of spinal deformities in ornamental koi, Cyprinus carpio L.

PubMed

Chin, H N; Loh, R; Hong, Y C; Gibson-Kueh, S

2017-01-01

This is a study of vertebral deformities in ornamental koi based on computed radiography and skeletons cleaned by dermestid beetles (Dermestes maculatus). All koi developed gradual onset of swimming abnormalities as adults. Extensive intervertebral osteophyte formation correlated with age of fish and was associated with hindquarter paresis in one koi. Vertebral compression and fusion were the most common spinal deformities occurring at multiple sites, similar to findings in other farmed fish. Site-specific spinal deformities were thought to develop due to differences in swimming behaviour and rates of vertebral growth. One koi had offspring with spinal deformities. Spinal deformities are significant problems in both European and Australian food fish hatcheries. The heritability of vertebral deformities in farmed fish is reportedly low unless there is concurrent poor husbandry or nutritional deficiencies. The specific aetiologies for vertebral deformities in koi in this study could not be ascertained. Current knowledge on spinal deformities in the better studied European food fish species suggests multifactorial aetiologies. Future research should include prospective longitudinal studies of larger numbers of koi from hatch and consideration of all potential risk factors such as husbandry, nutrition, temperature, photoperiod and genetics. © 2016 John Wiley & Sons Ltd.

Ethnic differences in risk from mercury among Savannah River fishermen.

PubMed

Burger, J; Gaines, K F; Gochfeld, M

2001-06-01

Fishing plays an important role in people's lives and contaminant levels in fish are a public health concern. Many states have issued consumption advisories; South Carolina and Georgia have issued them for the Savannah River based on mercury and radionuclide levels. This study examined ethnic differences in risk from mercury exposure among people consuming fish from the Savannah River, based on site-specific consumption patterns and analysis of mercury in fish. Among fish, there were significant interspecies differences in mercury levels, and there were ethnic differences in consumption patterns. Two methods of examining risk are presented: (1) Hazard Index (HI), and (2) estimates of how much and how often people of different body mass can consume different species of fish. Blacks consumed more fish and had higher HIs than Whites. Even at the median consumption, the HI for Blacks exceeded 1.0 for bass and bowfin, and, at the 75th percentile of consumption, the HI exceeded 1.0 for almost all species. At the White male median consumption, noHI exceeded 1, but for the 95th percentile consumer, the HI exceeded 1.0 almost regardless of which species were eaten. Although females consumed about two thirds the quantity of males, HIs exceeded 1 for most Black females and for White females at or above the 75th percentile of consumption. Thus, close to half of the Black fishermen were eating enough Savannah River fish to exceed HI = 1. Caution must be used in evaluating an HI because the RfDs were developed to protect the most vulnerable individuals. The percentage of each fish species tested that exceeded the maximum permitted limits of mercury in fish was also examined. Over 80% of bowfin, 38% of bass, and 21% of pickerel sampled exceeded 0.5 ppm. The risk methodology is applicable anywhere that comparable data can be obtained. The risk estimates are representative for fishermen along the Savannah River, and are not necessarily for the general populations.

Can Mixed-Species Groups Reduce Individual Parasite Load? A Field Test with Two Closely Related Poeciliid Fishes (Poecilia reticulata and Poecilia picta)

PubMed Central

Dargent, Felipe; Torres-Dowdall, Julián; Scott, Marilyn E.; Ramnarine, Indar; Fussmann, Gregor F.

2013-01-01

Predation and parasitism are two of the most important sources of mortality in nature. By forming groups, individuals can gain protection against predators but may increase their risk of being infected with contagious parasites. Animals might resolve this conflict by forming mixed-species groups thereby reducing the costs associated with parasites through a relative decrease in available hosts. We tested this hypothesis in a system with two closely related poeciliid fishes (Poecilia reticulata and Poecilia picta) and their host-specific monogenean ectoparasites (Gyrodactylus spp.) in Trinidad. Fish from three different rivers were sampled from single and mixed-species groups, measured and scanned for Gyrodactylus. The presence and abundance of Gyrodactylus were lower when fish of both species were part of mixed-species groups relative to single-species groups. This is consistent with the hypothesis that mixed-species groups provide a level of protection against contagious parasites. We discuss the importance of potentially confounding factors such as salinity and individual fish size. PMID:23437237

Status and opportunities for genomics research with rainbow trout

USGS Publications Warehouse

Thorgaard, G.H.; Bailey, G.S.; Williams, D.; Buhler, D.R.; Kaattari, S.L.; Ristow, S.S.; Hansen, J.D.; Winton, J.R.; Bartholomew, J.L.; Nagler, J.J.; Walsh, P.J.; Vijayan, M.M.; Devlin, R.H.; Hardy, R.W.; Overturf, K.E.; Young, W.P.; Robison, B.D.; Rexroad, C.; Palti, Y.

2002-01-01

The rainbow trout (Oncorhynchus mykiss) is one of the most widely studied of model fish species. Extensive basic biological information has been collected for this species, which because of their large size relative to other model fish species are particularly suitable for studies requiring ample quantities of specific cells and tissue types. Rainbow trout have been widely utilized for research in carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. They are distinctive in having evolved from a relatively recent tetraploid event, resulting in a high incidence of duplicated genes. Natural populations are available and have been well characterized for chromosomal, protein, molecular and quantitative genetic variation. Their ease of culture, and experimental and aquacultural significance has led to the development of clonal lines and the widespread application of transgenic technology to this species. Numerous microsatellites have been isolated and two relatively detailed genetic maps have been developed. Extensive sequencing of expressed sequence tags has begun and four BAC libraries have been developed. The development and analysis of additional genomic sequence data will provide distinctive opportunities to address problems in areas such as evolution of the immune system and duplicate genes. ?? 2002 Elsevier Science Inc. All rights reserved.

Genetic evidence for gonochoristic reproduction in gynogenetic silver crucian carp (Carassius auratus gibelio bloch) as revealed by RAPD assays.

PubMed

Zhou, L; Wang, Y; Gui, J F

2000-11-01

Sex evolution has been a debating focus in evolutionary genetics. In lower vertebrates of reptiles, amphibians, and fish, a species or a bioform reproduces either sexually or asexually but never both. A few species were found to consist of all females in fish. These all-female species can propagate by asexual reproduction modes, such as gynogenesis and hybridogenesis. However, the coexistence of sexuality and asexuality in a single species was recently noted only in a cyprinid fish silver crucian carp, Carassius auratus gibelio. This fish had been demonstrated to be capable of gynogenesis stimulated by sperm from other related species. Surprisingly, natural populations of this fish consist of a minor but significant portion (approx. 20%) of males. As different clones with specific phenotypic and genetic characteristics have been found, and RAPD markers specific to each clone have recently been identified, this fish offers many advantages for analyzing whether or not genetic recombination occurs between different clones. In this study, artificial propagation was performed in clone F and clone D. Ovulated eggs from clone F were divided into two parts and respectively inseminated with sperm from a clone D male and from a red common carp (Cyprinus carpio) male. The control clone D individuals were selected from gynogenetic offspring of clone D activated by sperm of red common carp. The phenotype and sex ratio in the experimental groups were also observed. Using RAPD molecular markers, which allow for reliable discrimination and genetic analysis of different clones, we have revealed direct molecular evidence for gonochoristic reproduction in the gynogenetic silver crucian carp and confirmed a previous hypothesis that the silver crucian carp might reproduce both gynogenetically and gonochoristically. Therefore, we conclude that the silver crucian carp possesses two reproductive modes, i.e., gynogenetic and gonochoristic reproduction. The response mechanism of two reproductive development modes may be the first discovery in vertebrates. Additionally, we discuss the evolutionary implication between gynogenetic and gonochoristic reproduction modes and the contribution of the minor proportion of males to genetic flexibility in the gynogenetic silver crucian carp.

Embryonic and larval development in the Midas cichlid fish species flock (Amphilophus spp.): a new evo-devo model for the investigation of adaptive novelties and species differences.

PubMed

Kratochwil, Claudius F; Sefton, Maggie M; Meyer, Axel

2015-02-26

Central American crater lake cichlid fish of the Midas species complex (Amphilophus spp.) are a model system for sympatric speciation and fast ecological diversification and specialization. Midas cichlids have been intensively analyzed from an ecological and morphological perspective. Genomic resources such as transcriptomic and genomic data sets, and a high-quality draft genome are available now. Many ecologically relevant species-specific traits and differences such as pigmentation and cranial morphology arise during development. Detailed descriptions of the early development of the Midas cichlid in particular, will help to investigate the ontogeny of species differences and adaptations. We describe the embryonic and larval development of the crater lake cichlid, Amphilophus xiloaensis, until seven days after fertilization. Similar to previous studies on teleost development, we describe six periods of embryogenesis - the zygote, cleavage, blastula, gastrula, segmentation, and post-hatching period. Furthermore, we define homologous stages to well-described teleost models such as medaka and zebrafish, as well as other cichlid species such as the Nile tilapia and the South American cichlid Cichlasoma dimerus. Key morphological differences between the embryos of Midas cichlids and other teleosts are highlighted and discussed, including the presence of adhesive glands and different early chromatophore patterns, as well as variation in developmental timing. The developmental staging of the Midas cichlid will aid researchers in the comparative investigation of teleost ontogenies. It will facilitate comparative developmental biological studies of Neotropical and African cichlid fish in particular. In the past, the species flocks of the African Great Lakes have received the most attention from researchers, but some lineages of the 300-400 species of Central American lakes are fascinating model systems for adaptive radiation and rapid phenotypic evolution. The availability of genetic resources, their status as a model system for evolutionary research, and the possibility to perform functional experiments including transgenesis makes the Midas cichlid complex a very attractive model for evolutionary-developmental research.

Specific cross-reactivity of antibodies raised against two major stress proteins, stress 70 and chaperonin 60, in diverse species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanders, B.M.; Martin, L.S.; Nakagawa, P.A.

1994-08-01

Immunoblot analysis using several antibodies raised against two major families of stress proteins, stress 70 and chaperonin 60 (cpn60), which are highly conserved in mammals, was carried out in diverse species often used in environmental research, including molluscs, annelids, crustaceans, echinoderms, and fish. The study revealed surprisingly different patterns of antibody cross-reactivity among species. The monoclonal anti-stress 70 antibody (mAb) C92 was the least cross-reactive for all species tested. The mAbs anti-stress 70 N27, BRM-22, and 3a3 were more broadly cross-reactive, but their binding specifities to stress 70 isoforms in the diverse species tested did not correlate with one anothermore » or follow taxonomic lines. The polyclonal anti-stress 70 antibody reacted to proteins in the 70 to 74 kDa range in all fish examined and in most invertebrates. When a polyclonal antibody (pAb) raised against cpn60 from a moth was used as a probe, specific binding was observed with proteins in the 60 to 64 kDa range in all fish examined and in most invertebrates. However, the size and number of isoforms that reacted with the pAb were species specific. These data suggest that these two major stress protein families are less highly conserved in invertebrates and fish than in mammals. Therefore, to minimize misinterpretation when using antibodies in heterologous assays with species in which the stress response has not been well characterized, it is important to determine which isoforms of stress 70 react with a particular antibody and to take into account the differential regulation of each member of this multigene family.« less

Not all fish are equal: functional biodiversity of cartilaginous fishes (Elasmobranchii and Holocephali) in Chile.

PubMed

Bustamante, C; Vargas-Caro, C; Bennett, M B

2014-11-01

A review of the primary literature on the cartilaginous fishes (sharks, skates, rays and chimaeras), together with new information suggests that 106 species occur in Chilean waters, comprising 58 sharks, 30 skates, 13 rays and five chimaeras. The presence of 93 species was confirmed, although 30 species were encountered rarely, through validated catch records and sightings made in artisanal and commercial fisheries and on specific research cruises. Overall, only 63 species appear to have a range distribution that normally includes Chilean waters. Actual reliable records of occurrence are lacking for 13 species. Chile has a cartilaginous fish fauna that is relatively impoverished compared with the global species inventory, but conservative compared with countries in South America with warm-temperate waters. The region of highest species richness occurs in the mid-Chilean latitudes of c. 30-40° S. This region represents a transition zone with a mix of species related to both the warm-temperate Peruvian province to the north and cold-temperate Magellan province to the south. This study provides clarification of species occurrence and the functional biodiversity of Chile's cartilaginous fish fauna. © 2014 The Fisheries Society of the British Isles.

Development of a Sandwich Hybridization Assay to Rapidly Detect and Quantify Harmful Algal Bloom (hab) Species Linked with Coastal Fish Kills and Public Health Concerns

NASA Astrophysics Data System (ADS)

Greenfield, D.; Jones, W. J.; Mortensen, R.; Doll, C.; Reed, M.

2016-02-01

Molecular probe technologies have enabled more rapid and specific phytoplankton identification and enumeration compared to traditional technologies, such as microscopy. The method considered for this study is sandwich hybridization assay (SHA), a fast, efficient, and economic approach to detecting and quantifying plankton species. SHA employs two DNA probes, capture and signal, to detect ribosomal RNA (rRNA) sequences. The reaction entails an anti-digoxygenin horse-radish peroxidase (HRP) conjugate to which a HRP substrate is applied. The result is a colorimetric reaction, and the resultant absorbance can be used to estimate organism abundances. This project focuses on two raphidophyte HAB species that have been responsible for declining water quality and fish kills globally, but are particularly problematic in states along the southeastern (US) coast, Fibrocapsa japonica and Chattonella subsalsa. These species produce recurrent, dense blooms annually, and are directly linked with fish kills. Work presented here also includes the domoic acid (DA) producing diatom Pseudo-nitzschia pseudodelicatissima because DA has been associated with pigmy and dwarf sperm whale strandings in the southeastern US, and blooms of this genus are frequently reported in regional waters. Here we present findings from field samplings and multiple blooms (2014-2015) of all three species that occurred in South Carolina (US) and regional waters. We also provide updates on the development, validation, and quantification of SHA applications for each of these HAB species.

Morphological and molecular characterization of a marine fish trypanosome from South Africa, including its development in a leech vector

PubMed Central

2014-01-01

Background Trypanosomes are ubiquitous blood parasites of marine and freshwater fishes, typically transmitted by aquatic leeches. Phylogenetic studies have been dominated by examples derived from freshwater fishes, with few marine representatives. Furthermore, life cycle studies on marine fish trypanosomes have focused on those of the northern hemisphere. In this investigation, we have examined the life cycle and molecular taxonomy of a marine fish trypanosome from South Africa. Methods To locate trypanosome stages, leeches were removed from fishes captured on the west and south coasts of South Africa, and fish blood films and leech squashes were Giemsa-stained and screened; leeches were also examined histologically. To determine whether trypanosome stages in fishes and leeches were of the same genotype, DNA was extracted from Giemsa-stained fish blood films and leech squashes, and from fish whole blood. Fragments of the 18S rRNA gene were amplified by PCR using trypanosome-specific primers and sequenced. Resulting sequence data were compared with each other and with published trypanosome 18S rDNA sequences, and used for phylogenetic analysis. Results Trypanosomes were detected in blood films from fishes of the families Clinidae, Blenniidae and Gobiidae. The flagellates ranged in size and staining properties within the films and across fish hosts. In squashes and histological sections of adult and juvenile leeches, identified as Zeylanicobdella arugamensis, trypanosome developmental stages were predominantly slender epimastigotes. Sequence data showed that trypanosomes derived from fishes were identical, irrespective of whether they were small or large forms; sequences derived largely from leech epimastigotes were also identical to those obtained from fish trypanosomes. Fish and leech trypanosome sequences fell into a marine fish aquatic clade, and aligned most closely with two trypanosome sequences from marine fishes off Norway. Conclusions Combined morphological and molecular methods indicate that the trypanosomes examined here represent a single pleomorphic species, rather than the three species described originally. This species is identified as Trypanosoma nudigobii Fantham, 1919 with the leech Z. arugamensis as its vector, and T. capigobii Fantham, 1919 and T. blenniclini Fantham, 1930 are regarded as junior synonyms of the species. Phylogenetic analysis establishes its affinity with marine fish trypanosomes off Norway. PMID:24460725

Reef Fishes in Biodiversity Hotspots Are at Greatest Risk from Loss of Coral Species

PubMed Central

Holbrook, Sally J.; Schmitt, Russell J.; Messmer, Vanessa; Brooks, Andrew J.; Srinivasan, Maya; Munday, Philip L.; Jones, Geoffrey P.

2015-01-01

Coral reef ecosystems are under a variety of threats from global change and anthropogenic disturbances that are reducing the number and type of coral species on reefs. Coral reefs support upwards of one third of all marine species of fish, so the loss of coral habitat may have substantial consequences to local fish diversity. We posit that the effects of habitat degradation will be most severe in coral regions with highest biodiversity of fishes due to greater specialization by fishes for particular coral habitats. Our novel approach to this important but untested hypothesis was to conduct the same field experiment at three geographic locations across the Indo-Pacific biodiversity gradient (Papua New Guinea; Great Barrier Reef, Australia; French Polynesia). Specifically, we experimentally explored whether the response of local fish communities to identical changes in diversity of habitat-providing corals was independent of the size of the regional species pool of fishes. We found that the proportional reduction (sensitivity) in fish biodiversity to loss of coral diversity was greater for regions with larger background species pools, reflecting variation in the degree of habitat specialization of fishes across the Indo-Pacific diversity gradient. This result implies that habitat-associated fish in diversity hotspots are at greater risk of local extinction to a given loss of habitat diversity compared to regions with lower species richness. This mechanism, related to the positive relationship between habitat specialization and regional biodiversity, and the elevated extinction risk this poses for biodiversity hotspots, may apply to species in other types of ecosystems. PMID:25970588

Reef fishes in biodiversity hotspots are at greatest risk from loss of coral species.

PubMed

Holbrook, Sally J; Schmitt, Russell J; Messmer, Vanessa; Brooks, Andrew J; Srinivasan, Maya; Munday, Philip L; Jones, Geoffrey P

2015-01-01

Coral reef ecosystems are under a variety of threats from global change and anthropogenic disturbances that are reducing the number and type of coral species on reefs. Coral reefs support upwards of one third of all marine species of fish, so the loss of coral habitat may have substantial consequences to local fish diversity. We posit that the effects of habitat degradation will be most severe in coral regions with highest biodiversity of fishes due to greater specialization by fishes for particular coral habitats. Our novel approach to this important but untested hypothesis was to conduct the same field experiment at three geographic locations across the Indo-Pacific biodiversity gradient (Papua New Guinea; Great Barrier Reef, Australia; French Polynesia). Specifically, we experimentally explored whether the response of local fish communities to identical changes in diversity of habitat-providing corals was independent of the size of the regional species pool of fishes. We found that the proportional reduction (sensitivity) in fish biodiversity to loss of coral diversity was greater for regions with larger background species pools, reflecting variation in the degree of habitat specialization of fishes across the Indo-Pacific diversity gradient. This result implies that habitat-associated fish in diversity hotspots are at greater risk of local extinction to a given loss of habitat diversity compared to regions with lower species richness. This mechanism, related to the positive relationship between habitat specialization and regional biodiversity, and the elevated extinction risk this poses for biodiversity hotspots, may apply to species in other types of ecosystems.

Fish Karyome: A karyological information network database of Indian Fishes.

PubMed

Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra

2012-01-01

'Fish Karyome', a database on karyological information of Indian fishes have been developed that serves as central source for karyotype data about Indian fishes compiled from the published literature. Fish Karyome has been intended to serve as a liaison tool for the researchers and contains karyological information about 171 out of 2438 finfish species reported in India and is publically available via World Wide Web. The database provides information on chromosome number, morphology, sex chromosomes, karyotype formula and cytogenetic markers etc. Additionally, it also provides the phenotypic information that includes species name, its classification, and locality of sample collection, common name, local name, sex, geographical distribution, and IUCN Red list status. Besides, fish and karyotype images, references for 171 finfish species have been included in the database. Fish Karyome has been developed using SQL Server 2008, a relational database management system, Microsoft's ASP.NET-2008 and Macromedia's FLASH Technology under Windows 7 operating environment. The system also enables users to input new information and images into the database, search and view the information and images of interest using various search options. Fish Karyome has wide range of applications in species characterization and identification, sex determination, chromosomal mapping, karyo-evolution and systematics of fishes.

Internal exposure dynamics drive the Adverse Outcome Pathways of synthetic glucocorticoids in fish

NASA Astrophysics Data System (ADS)

Margiotta-Casaluci, Luigi; Owen, Stewart F.; Huerta, Belinda; Rodríguez-Mozaz, Sara; Kugathas, Subramanian; Barceló, Damià; Rand-Weaver, Mariann; Sumpter, John P.

2016-02-01

The Adverse Outcome Pathway (AOP) framework represents a valuable conceptual tool to systematically integrate existing toxicological knowledge from a mechanistic perspective to facilitate predictions of chemical-induced effects across species. However, its application for decision-making requires the transition from qualitative to quantitative AOP (qAOP). Here we used a fish model and the synthetic glucocorticoid beclomethasone dipropionate (BDP) to investigate the role of chemical-specific properties, pharmacokinetics, and internal exposure dynamics in the development of qAOPs. We generated a qAOP network based on drug plasma concentrations and focused on immunodepression, skin androgenisation, disruption of gluconeogenesis and reproductive performance. We showed that internal exposure dynamics and chemical-specific properties influence the development of qAOPs and their predictive power. Comparing the effects of two different glucocorticoids, we highlight how relatively similar in vitro hazard-based indicators can lead to different in vivo risk. This discrepancy can be predicted by their different uptake potential, pharmacokinetic (PK) and pharmacodynamic (PD) profiles. We recommend that the development phase of qAOPs should include the application of species-species uptake and physiologically-based PK/PD models. This integration will significantly enhance the predictive power, enabling a more accurate assessment of the risk and the reliable transferability of qAOPs across chemicals.

INTERACTIVE HABITAT SUITABILITY MODELS FOR STREAM FISHES IN THE MID-ATLANTIC HIGHLANDS

EPA Science Inventory

Models that predict the presence of stream fish species based on habitat characteristics can be useful in watershed management. We developed such models for each of fourteen Mid-Atlantic Highlands stream fish species/groups.

Guidelines for use of fishes in research

USGS Publications Warehouse

Use of Fishes in Research Committee (joint committee of the American Fisheries Society, the American Institute of Fishery Research Biologists

2014-01-01

The 2004 and 2014 Guidelines were developed to provide a structure that advances appropriate attention toward valid experimental designs and procedures with aquatic animals while ensuring humane treatment of the experimental subjects. At a practical level, the Guidelines are intended to provide general recommendations on field and laboratory endeavors, such as sampling, holding, and handling fishes; to offer information on administrative matters, including regulations and permits; and to address typical ethical concerns, such as perceptions of pain or discomfort experienced by experimental subjects. These Guidelines must be recognized as guidelines. They are not intended to provide detailed instructions but rather to alert investigators to a broad array of topics and concerns to consider prior to initiating study. At a comprehensive level, the principles upon which these Guidelines are based are broadly applicable, and many of the described practices and approaches can be adapted to situations involving other aquatic animal species and conditions. Understanding the differences between fishes and other vertebrates, especially mammals, is critically important to conducting scientifically sound research with fishes. Disparities in life histories and mortality rates in fishes versus other vertebrates are critical in designing sustainable sampling levels in fish populations. The UFR Committee points out that (1) compared to mammalian populations, adult populations of many fish species persist despite very high natural mortality rates in juvenile stages by virtue of the fact that most species lay thousands or tens of thousands of eggs; (2) because of these mortality patterns, research on fishes, especially field research or research on early life stages, can involve, and often requires, much larger numbers of research subjects than does research on mammals; and (3) the animal handling and husbandry requirements for fishes are fundamentally different from those for mammals and other vertebrates, in general. Policies, regulations, and recommendations developed for research on mammals, birds, reptiles, or even amphibians are frequently inappropriate for research with fishes. The Guidelines also address some of the ethical concerns that motivate guidelines used for research with other vertebrates, while being mindful of the unique physiology and general nature of fishes. The Guidelines were developed for general use by investigators within the United States; therefore, the roles, responsibilities, and informational needs of Institutional Animal Care and Use Committees (IACUCs) were given specific attention. All United States institutions that use vertebrate animals for research, teaching, research training, and biological testing are required to create an IACUC to oversee and evaluate all aspects of the institution’s animal care and use program. Investigators from other nations who read this document may disregard specific references to U.S. state and federal laws and regulations, as their institutional infrastructure and processes may differ from those of an internal committee such as IACUCs. The principles described herein, however, are applicable to research on fishes regardless of geographic location. Investigators in other nations may benefit by modifying any of the specific provisions pertaining to the United States, thereby adopting guidelines consistent with the laws and regulations of their own government. The UFR Committee urges that the Guidelines be endorsed and adopted (adapted, where necessary) by those state and federal authorities with regulatory responsibilities for fishes, offices with federal oversight (e.g., National Institutes of Health, Office of Laboratory Animal Welfare; http://grants.nih.gov/grants/olaw/olaw.htm) as well as by universities and other institutions and authorities using fishes and aquatic animals within their research and teaching programs.

Weight dependence of arsenic concentration in the Arabian Sea tuna fish

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ashraf, M.; Jaffar, M.

1988-02-01

The objective of the present investigation was to estimate the arsenic concentration in the edible muscle of Thunnus thynnus and Thunnus toggel (hereafter called tuna and longtail tune) as they have great commercial value. These fish are widely available along the coastal line of Pakistan and are consumed abundantly in large bulk. Thus, it was felt justifiable on the basis of safety of human health that data, in the first instance, be obtained on arsenic concentration in tuna as a function of weight to check whether the metal distribution was species-specific or it depended on individual mode of development. Themore » data, the first of the kind so far presented on the Arabian Sea tuna, would thus provide the required baseline quantitative information needed in future studies on the physiological processes regulating the distribution and uptake of arsenic by these and other species of fish common to the region.« less

Diets and niche overlap among nine co-occurring demersal fishes in the southern continental shelf of East/Japan Sea, Korea

NASA Astrophysics Data System (ADS)

Myun Park, Joo; Nam Kwak, Seok; Huh, Sung-Hoi; Han, In-Seong

2017-09-01

Dietary niches and food resource partitioning can support the coexistence of many fishes in benthic marine systems, which can lead to the greater abundances of those species that can potentially support their fisheries. Diets and niche overlap among nine demersal fish species were investigated in the southern continental shelf of East/Japan Sea, Korea. Specimens were collected monthly from January to November 2007 on soft bottoms between 40 and 100 m depth using a bottom trawl. A total of 20 prey taxa were found in 1904 stomachs of the nine species. Comparison of the stomach contents among the nine species showed that inter-specific dietary compositions differed significantly. Although all fish species consumed similar types of prey items, their contributions to the diet of different species varied. Among prey taxa, carid shrimps contributed greatly to the diets of Amblychaeturichthys hexanema, Amblychaeturichthys sciistius, Coelorinchus multispinulosus, Lepidotrigla guentheri, and Liparis tanakae, whereas polychaetes and teleosts contributed to the diets of Callionymus lunatus and Lophius litulon, respectively. On the other hand, carid shrimps and teleosts together contributed to the diets of Pseudorhombus pentophthalmus. Non-metric multivariate analysis of the mass contributions of dietary categories for food resources emphasized visually that the dietary compositions of the nine species differed. Although C. multispinulosus, L. guentheri, L. litulon, and L. tanakae showed similar dietary compositions between small and large size classes, ontogenetic diet changes of the remaining six species were evident. Feeding relationships among the nine demersal species were complicated, but inter- and intra-specific differences in dietary composition among the species reduced potential competition for food resources within the fish community in the southern continental shelf of East/Japan Sea, Korea.

Nutrients and Chemical Pollutants in Fish and Shellfish. Balancing Health Benefits and Risks of Regular Fish Consumption.

PubMed

Domingo, José L

2016-01-01

Dietary patterns and lifestyle factors are clearly associated with at least five of the ten leading causes of death, including coronary heart disease, certain types of cancer, stroke, non-insulin insulin-dependent diabetes mellitus, and atherosclerosis. Concerning specifically fish and seafood consumption, its beneficial health effects in humans are clearly supported by an important number of studies performed in the last 30 years. These studies have repeatedly linked fish consumption, especially those species whose contents in omega-3 fatty acids are high, with healthier hearts in the aging population. The nutritional benefits of fish and seafood are also due to the content of high-quality protein, vitamins, as well as other essential nutrients. However, a number of studies, particularly investigations performed in recent years, have shown that the unavoidable presence of environmental contaminants in fish and shellfish can also mean a certain risk for the health of some consumers. While prestigious international associations as the American Heart Association have recommended eating fish at least two times (two servings a week), based on our own experimental results, as well as in results from other laboratories, we cannot be in total agreement with that recommendation. Although a regular consumption of most fish and shellfish species should not mean adverse health effects for the consumers, the specific fish and shellfish species consumed, the frequency of consumption, as well as the meal size, are essential issues for adequately balancing the health benefits and risks of regular fish consumption.

Diversity among macroalgae-consuming fishes on coral reefs: a transcontinental comparison.

PubMed

Vergés, Adriana; Bennett, Scott; Bellwood, David R

2012-01-01

Despite high diversity and abundance of nominally herbivorous fishes on coral reefs, recent studies indicate that only a small subset of taxa are capable of removing dominant macroalgae once these become established. This limited functional redundancy highlights the potential vulnerability of coral reefs to disturbance and stresses the need to assess the functional role of individual species of herbivores. However, our knowledge of species-specific patterns in macroalgal consumption is limited geographically, and there is a need to determine the extent to which patterns observed in specific reefs can be generalised at larger spatial scales. In this study, video cameras were used to quantify rates of macroalgae consumption by fishes in two coral reefs located at a similar latitude in opposite sides of Australia: the Keppel Islands in the Great Barrier Reef (eastern coast) and Ningaloo Reef (western coast). The community of nominally herbivorous fish was also characterised in both systems to determine whether potential differences in the species observed feeding on macroalgae were related to spatial dissimilarities in herbivore community composition. The total number of species observed biting on the dominant brown alga Sargassum myriocystum differed dramatically among the two systems, with 23 species feeding in Ningaloo, compared with just 8 in the Keppel Islands. Strong differences were also found in the species composition and total biomass of nominally herbivorous fish, which was an order of magnitude higher in Ningaloo. However, despite such marked differences in the diversity, biomass, and community composition of resident herbivorous fishes, Sargassum consumption was dominated by only four species in both systems, with Naso unicornis and Kyphosus vaigiensis consistently emerging as dominant feeders of macroalgae.

Fish community-based measures of estuarine ecological quality and pressure-impact relationships

NASA Astrophysics Data System (ADS)

Fonseca, Vanessa F.; Vasconcelos, Rita P.; Gamito, Rita; Pasquaud, Stéphanie; Gonçalves, Catarina I.; Costa, José L.; Costa, Maria J.; Cabral, Henrique N.

2013-12-01

Community-based responses of fish fauna to anthropogenic pressures have been extensively used to assess the ecological quality of estuarine ecosystems. Several methodologies have been developed recently combining metrics reflecting community structure and function. A fish community facing significant environmental disturbances will be characterized by a simplified structure, with lower diversity and complexity. However, estuaries are naturally dynamic ecosystems exposed to numerous human pressures, making it difficult to distinguish between natural and anthropogenic-induced changes to the biological community. In the present work, the variability of several fish metrics was assessed in relation to different pressures in estuarine sites. The response of a multimetric index (Estuarine Fish Assessment Index) was also analysed. Overall, fish metrics and the multimetric index signalled anthropogenic stress, particularly environmental chemical pollution. The fish assemblage associated with this type of pressure was characterized by lower species diversity, lower number of functional guilds, lower abundance of marine migrants and of piscivorous individuals, and higher abundance of estuarine resident species. A decreased ecological quality status, based on the EFAI, was also determined for sites associated with this pressure group. Ultimately, the definition of each pressure groups favoured a stressor-specific analysis, evidencing pressure patterns and accounting for multiple factors in a highly dynamic environment.

Steroids in teleost fishes: A functional point of view.

PubMed

Tokarz, Janina; Möller, Gabriele; Hrabě de Angelis, Martin; Adamski, Jerzy

2015-11-01

Steroid hormones are involved in the regulation of a variety of processes like embryonic development, sex differentiation, metabolism, immune responses, circadian rhythms, stress response, and reproduction in vertebrates. Teleost fishes and humans show a remarkable conservation in many developmental and physiological aspects, including the endocrine system in general and the steroid hormone related processes in particular. This review provides an overview of the current knowledge about steroid hormone biosynthesis and the steroid hormone receptors in teleost fishes and compares the findings to the human system. The impact of the duplicated genome in teleost fishes on steroid hormone biosynthesis and perception is addressed. Additionally, important processes in fish physiology regulated by steroid hormones, which are most dissimilar to humans, are described. We also give a short overview on the influence of anthropogenic endocrine disrupting compounds on steroid hormone signaling and the resulting adverse physiological effects for teleost fishes. By this approach, we show that the steroidogenesis, hormone receptors, and function of the steroid hormones are reasonably well understood when summarizing the available data of all teleost species analyzed to date. However, on the level of a single species or a certain fish-specific aspect of physiology, further research is needed. Copyright © 2015 Elsevier Inc. All rights reserved.

Characterization, specificity and sensibility of produced anti-Rhamdia quelen vitellogenin in Brazilian fish species.

PubMed

Moura Costa, Daniele Dietrich; Bozza, Dandie Antunes; Rizzo, Luiz Eduardo; Garcia, Juan; Costa, Michele Dietrich Moura; de Oliveira Ribeiro, Ciro Alberto

2016-12-01

Endocrine-disrupting chemicals (EDCs) are widespread used and can interfere on hormone regulation with adverse consequences for both biota and human. Vitellogenin (vtg) is a yolk precursor protein synthesized by the liver in response to estrogen. In order to characterize the vtg of tropical fish Rhamdia quelen and establish a molecular biomarker, adult male individuals were exposed to 17-β-estradiol (E 2 ) for vtg induction and anti-R. quelen vtg polyclonal antibodies production. Vitellogenic female fish were used as positive control group. E 2 -induced vtg was characterized as a glycolipophosphoprotein of high molecular mass with peptide mass fingerprint very similar in E 2 -exposed male and vitellogenic female fish. A polyclonal serum containing anti-R. quelen vtg antibodies was produced and showed high specificity and sensibility to detect the vtg of three fish species: R. quelen, Piaractus mesopotamicus and Prochilodus lineatus. Wildlife and laboratory studies reported that EDCs released into the environment may alter the levels of plasma vtg in male fish, making this protein a valuable biomarker of xenoestrogens exposure. Then, we propose the use of anti-R. quelen vtg as a tool for biomonitoring studies and water quality assessment in Brazil and South American countries where the three fish species occur.

Responses of coral reef fishes to past climate changes are related to life-history traits.

PubMed

Ottimofiore, Eduardo; Albouy, Camille; Leprieur, Fabien; Descombes, Patrice; Kulbicki, Michel; Mouillot, David; Parravicini, Valeriano; Pellissier, Loïc

2017-03-01

Coral reefs and their associated fauna are largely impacted by ongoing climate change. Unravelling species responses to past climatic variations might provide clues on the consequence of ongoing changes. Here, we tested the relationship between changes in sea surface temperature and sea levels during the Quaternary and present-day distributions of coral reef fish species. We investigated whether species-specific responses are associated with life-history traits. We collected a database of coral reef fish distribution together with life-history traits for the Indo-Pacific Ocean. We ran species distribution models (SDMs) on 3,725 tropical reef fish species using contemporary environmental factors together with a variable describing isolation from stable coral reef areas during the Quaternary. We quantified the variance explained independently by isolation from stable areas in the SDMs and related it to a set of species traits including body size and mobility. The variance purely explained by isolation from stable coral reef areas on the distribution of extant coral reef fish species largely varied across species. We observed a triangular relationship between the contribution of isolation from stable areas in the SDMs and body size. Species, whose distribution is more associated with historical changes, occurred predominantly in the Indo-Australian archipelago, where the mean size of fish assemblages is the lowest. Our results suggest that the legacy of habitat changes of the Quaternary is still detectable in the extant distribution of many fish species, especially those with small body size and the most sedentary. Because they were the least able to colonize distant habitats in the past, fish species with smaller body size might have the most pronounced lags in tracking ongoing climate change.

Life cycle ecophysiology of small pelagic fish and climate-driven changes in populations

NASA Astrophysics Data System (ADS)

Peck, Myron A.; Reglero, Patricia; Takahashi, Motomitsu; Catalán, Ignacio A.

2013-09-01

Due to their population characteristics and trophodynamic role, small pelagic fishes are excellent bio-indicators of climate-driven changes in marine systems world-wide. We argue that making robust projections of future changes in the productivity and distribution of small pelagics will require a cause-and-effect understanding of historical changes based upon physiological principles. Here, we reviewed the ecophysiology of small pelagic (clupeiform) fishes including a matrix of abiotic and biotic extrinsic factors (e.g., temperature, salinity, light, and prey characteristics) and stage-specific vital rates: (1) adult spawning, (2) survival and development of eggs and yolk sac larvae, and (3) feeding and growth of larvae, post-larvae and juveniles. Emphasis was placed on species inhabiting Northwest Pacific and Northeast Atlantic (European) waters for which summary papers are particularly scarce compared to anchovy and sardine in upwelling systems. Our review revealed that thermal niches (optimal and sub-optimal ranges in temperatures) were species- and stage-specific but that temperature effects only partly explained observed changes in the distribution and/or productivity of populations in the Northwest Pacific and Northeast Atlantic; changes in temperature may be necessary but not sufficient to induce population-level shifts. Prey availability during the late larval and early juvenile period was a common, density-dependent mechanism linked to fluctuations in populations but recruitment mechanisms were system-specific suggesting that generalizations of climate drivers across systems should be avoided. We identified gaps in knowledge regarding basic elements of the growth physiology of each life stage that will require additional field and laboratory study. Avenues of research are recommended that will aid the development of models that provide more robust, physiological-based projections of the population dynamics of these and other small pelagic fish. In our opinion, the continued development of biophysical models that close the life cycle (depict all life stages) offers the best chance of revealing processes causing historical fluctuations on the productivity and distribution of small pelagic fishes and to project future climate-driven impacts. Correctly representing physiological-based mechanisms will increase confidence in the outcomes of models simulating the potential impacts of bottom-up processes, a first step towards evaluating the mixture of factors and processes (e.g. intra-guild dynamics, predation, fisheries exploitation) which interact with climate to affect populations of small pelagic fishes. Understand the impacts of reduced growth rates during the juvenile stage on the process of maturation and spawning condition of small pelagic fishes. Examine the effects of changes in prey quality on the duration and magnitude of spawning by small pelagic fishes to capture how climate-driven changes in zooplankton species composition might act as a “bottom-up” regulator of fish productivity. Identify the drivers for spawning location and timing to better understand how spawning dynamics may be influenced by climate change (e.g. changes in water salinity or turbidity resulting from changes in river discharges or wind-driven turbulence, respectively).

A new species of Dactylogyrus (Monogenea: Dactylogyridae) parasitic on an endangered freshwater fish, Rhodeus atremius atremius, endemic to Japan.

PubMed

Nitta, Masato; Nagasawa, Kazuya

2016-10-01

A new dactylogyrid monogenean Dactylogyrus bicorniculus sp. nov. is described from the gills of the kazetoge bitterling, Rhodeus atremius atremius (Jordan and Thompson, 1914), an endemic species in Japan, from Saga Prefecture, northern Kyūshū. D. bicorniculus sp. nov. resembles Dactylogyrus bicornis Malevitskaja, 1941 and Dactylogyrus lophogonus Zhang and Ji, 1980 because they have two common features, a large V-shaped ventral bar and well-developed second marginal hooks. However, the new species is distinguished from these congeners by a shorter penis and an accessory piece. A phylogenetic analysis of 28S rDNA shows that D. bicorniculus sp. nov. is a basal species with the T-shaped ventral bar in the genus. The new species has strict host-specificity to R. a. atremius, one of the endangered freshwater fishes in Japan, and may face the danger of co-extinction with its host. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Coral reef grazer-benthos dynamics complicated by invasive algae in a small marine reserve

PubMed Central

Stamoulis, Kostantinos A.; Friedlander, Alan M.; Meyer, Carl G.; Fernandez-Silva, Iria; Toonen, Robert J.

2017-01-01

Blooms of alien invasive marine algae have become common, greatly altering the health and stability of nearshore marine ecosystems. Concurrently, herbivorous fishes have been severely overfished in many locations worldwide, contributing to increases in macroalgal cover. We used a multi-pronged, interdisciplinary approach to test if higher biomass of herbivorous fishes inside a no-take marine reserve makes this area more resistant to invasive algal overgrowth. Over a two year time period, we (1) compared fish biomass and algal cover between two fished and one unfished patch reef in Hawai’i, (2) used acoustic telemetry to determine fidelity of herbivorous fishes to the unfished reef, and (3) used metabarcoding and next-generation sequencing to determine diet composition of herbivorous fishes. Herbivore fish biomass was significantly higher in the marine reserve compared to adjacent fished reefs, whereas invasive algal cover differed by species. Herbivorous fish movements were largely confined to the unfished patch reef where they were captured. Diet analysis indicated that the consumption of invasive algae varied among fish species, with a high prevalence of comparatively rare native algal species. Together these findings demonstrate that the contribution of herbivores to coral reef resilience, via resistance to invasive algae invasion, is complex and species-specific. PMID:28276458

Resource partitioning within major bottom fish species in a highly productive upwelling ecosystem

NASA Astrophysics Data System (ADS)

Abdellaoui, Souad; El Halouani, Hassan; Tai, Imane; Masski, Hicham

2017-09-01

The Saharan Bank (21-26°N) is a wide subtropical continental shelf and a highly productive upwelling ecosystem. The bottom communities are dominated by octopus and sparid fish, which are the main targets of bottom-trawl fishing fleets. To investigate resource partitioning within the bottom fish community, adult fish from 14 of the most abundant species were investigated for stomach content analysis. Samples were collected during two periods: October 2003 and May 2007. The diet of the analysed species showed more variation between periods than between size classes, suggesting that temporal or spatial variability in prey availability appears to play a significant role in their diet. Multivariate analysis and subsequent clustering led to a grouping of the species within five trophic guilds. Two species were fish feeders, and the others mainly fed on benthic invertebrates, where epibenthic crustaceans, lamellibranchs and fish were the most important groups in defining trophic guilds. We found that the studied species had a high rate of overlapping spatial distributions and overlapping trophic niches. In this highly productive upwelling ecosystem, where food resources may not be a limiting factor, inter-specific competition did not appear to be an important factor in structuring bottom fish communities. For the species that showed differences in the proportions of prey categories in comparison with other ecosystems, the rise of the proportion of epibenthic crustaceans in their diet was a common feature; a possible consequence of the benthic productivity of this highly productive upwelling ecosystem.

Monitoring fish distributions along electrofishing segments

USGS Publications Warehouse

Miranda, Leandro E.

2014-01-01

Electrofishing is widely used to monitor fish species composition and relative abundance in streams and lakes. According to standard protocols, multiple segments are selected in a body of water to monitor population relative abundance as the ratio of total catch to total sampling effort. The standard protocol provides an assessment of fish distribution at a macrohabitat scale among segments, but not within segments. An ancillary protocol was developed for assessing fish distribution at a finer scale within electrofishing segments. The ancillary protocol was used to estimate spacing, dispersion, and association of two species along shore segments in two local reservoirs. The added information provided by the ancillary protocol may be useful for assessing fish distribution relative to fish of the same species, to fish of different species, and to environmental or habitat characteristics.

The Neuroendocrine Regulation of Food Intake in Fish: A Review of Current Knowledge

PubMed Central

Volkoff, Helene

2016-01-01

Fish are the most diversified group of vertebrates and, although progress has been made in the past years, only relatively few fish species have been examined to date, with regards to the endocrine regulation of feeding in fish. In fish, as in mammals, feeding behavior is ultimately regulated by central effectors within feeding centers of the brain, which receive and process information from endocrine signals from both brain and peripheral tissues. Although basic endocrine mechanisms regulating feeding appear to be conserved among vertebrates, major physiological differences between fish and mammals and the diversity of fish, in particular in regard to feeding habits, digestive tract anatomy and physiology, suggest the existence of fish- and species-specific regulating mechanisms. This review provides an overview of hormones known to regulate food intake in fish, emphasizing on major hormones and the main fish groups studied to date. PMID:27965528

Detection probabilities of electrofishing, hoop nets, and benthic trawls for fishes in two western North American rivers

USGS Publications Warehouse

Smith, Christopher D.; Quist, Michael C.; Hardy, Ryan S.

2015-01-01

Research comparing different sampling techniques helps improve the efficiency and efficacy of sampling efforts. We compared the effectiveness of three sampling techniques (small-mesh hoop nets, benthic trawls, boat-mounted electrofishing) for 30 species in the Green (WY, USA) and Kootenai (ID, USA) rivers by estimating conditional detection probabilities (probability of detecting a species given its presence at a site). Electrofishing had the highest detection probabilities (generally greater than 0.60) for most species (88%), but hoop nets also had high detectability for several taxa (e.g., adult burbot Lota lota, juvenile northern pikeminnow Ptychocheilus oregonensis). Benthic trawls had low detection probabilities (<0.05) for most taxa (84%). Gear-specific effects were present for most species indicating large differences in gear effectiveness among techniques. In addition to gear effects, habitat characteristics also influenced detectability of fishes. Most species-specific habitat relationships were idiosyncratic and reflected the ecology of the species. Overall findings of our study indicate that boat-mounted electrofishing and hoop nets are the most effective techniques for sampling fish assemblages in large, coldwater rivers.

The Application of Traits-Based Assessment Approaches to Estimate the Effects of Hydroelectric Turbine Passage on Fish Populations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cada, Glenn F; Schweizer, Peter E

One of the most important environmental issues facing the hydropower industry is the adverse impact of hydroelectric projects on downstream fish passage. Fish that migrate long distances as part of their life cycle include not only important diadromous species (such as salmon, shads, and eels) but also strictly freshwater species. The hydropower reservoirs that downstream-moving fish encounter differ greatly from free-flowing rivers. Many of the environmental changes that occur in a reservoir (altered water temperature and transparency, decreased flow velocities, increased predation) can reduce survival. Upon reaching the dam, downstream-migrating fish may suffer increased mortality as they pass through themore » turbines, spillways and other bypasses, or turbulent tailraces. Downstream from the dam, insufficient environmental flow releases may slow downstream fish passage rates or decrease survival. There is a need to refine our understanding of the relative importance of causative factors that contribute to turbine passage mortality (e.g., strike, pressure changes, turbulence) so that turbine design efforts can focus on mitigating the most damaging components. Further, present knowledge of the effectiveness of turbine improvements is based on studies of only a few species (mainly salmon and American shad). These data may not be representative of turbine passage effects for the hundreds of other fish species that are susceptible to downstream passage at hydroelectric projects. For example, there are over 900 species of fish in the United States. In Brazil there are an estimated 3,000 freshwater fish species, of which 30% are believed to be migratory (Viana et al. 2011). Worldwide, there are some 14,000 freshwater fish species (Magurran 2009), of which significant numbers are susceptible to hydropower impacts. By comparison, in a compilation of fish entrainment and turbine survival studies from over 100 hydroelectric projects in the United States, Winchell et al. (2000) found useful turbine passage survival data for only 30 species. Tests of advanced hydropower turbines have been limited to seven species - Chinook and coho salmon, rainbow trout, alewife, eel, smallmouth bass, and white sturgeon. We are investigating possible approaches for extending experimental results from the few tested fish species to predict turbine passage survival of other, untested species (Cada and Richmond 2011). In this report, we define the causes of injury and mortality to fish tested in laboratory and field studies, based on fish body shape and size, internal and external morphology, and physiology. We have begun to group the large numbers of unstudied species into a small number of categories, e.g., based on phylogenetic relationships or ecological similarities (guilds), so that subsequent studies of a few representative species (potentially including species-specific Biological Index Testing) would yield useful information about the overall fish community. This initial effort focused on modifying approaches that are used in the environmental toxicology field to estimate the toxicity of substances to untested species. Such techniques as the development of species sensitivity distributions (SSDs) and Interspecies Correlation Estimation (ICE) models rely on a considerable amount of data to establish the species-toxicity relationships that can be extended to other organisms. There are far fewer studies of turbine passage stresses from which to derive the turbine passage equivalent of LC{sub 50} values. Whereas the SSD and ICE approaches are useful analogues to predicting turbine passage injury and mortality, too few data are available to support their application without some form of modification or simplification. In this report we explore the potential application of a newer, related technique, the Traits-Based Assessment (TBA), to the prediction of downstream passage mortality at hydropower projects.« less

The development of a preliminary rock reef fish multimetric index for assessing thermal and urban impacts in a tropical bay.

PubMed

Teixeira-Neves, Tatiana Pires; Neves, Leonardo Mitrano; Araújo, Francisco Gerson

2016-08-15

We developed a multimetric index for assessing ecological conditions in rocky reefs areas to evaluate thermal and urban influences on fish community. Eight metrics were selected to assess thermal influence: (1) total number of species; (2) number of water column species; (3) number of transient species; (4) density of individuals with low resilience; (5) density of omnivores; (6) density of carnivores; (7) number of cryptic species; (8) density of herbivores. For urban influence, six metrics were selected: (1) total density; (2) ratio between the number of rare species and the total number of species; (3) density of individuals with heavy fishing pressure; (4) number of resident species; (5) number of cryptic species; (6) density of herbivores. This preliminary index succeed in discriminating control/impacted sites and proved to be an important tool to assess impacts that alter fish community and have potential to be used in tropical rock reef coastal areas. Copyright © 2016 Elsevier Ltd. All rights reserved.

Development of a fluorescence in situ hybridization (FISH) method for rapid detection of Ulva prolifera

NASA Astrophysics Data System (ADS)

Zhang, Qing-Chun; Liu, Qing; Kang, Zhen-Jun; Yu, Ren-Cheng; Yan, Tian; Zhou, Ming-Jiang

2015-09-01

Large-scale green tides have occurred consecutively since 2007 in the Yellow Sea (YS), China. The dominant causative species of the green tides has been identified as Ulva prolifera. The origin of green tides in the YS has been traced back to the Subei Shoal based on the results of remote-sensing, numerical simulations and field investigations. However, it is difficult to study the early development of green tides in the Subei Shoal because of the mixture of multiple green algae and the morphological diversity of U. prolifera when under variable environmental conditions. In this study, a rapid and accurate fluorescence in situ hybridization (FISH) method was developed to detect U. prolifera from the community of green algae targeting the 5S rDNA spacer region of U. prolifera. Two specific probes, 5S-1 and 5S-2, were designed based on the sequences of the 5S rDNA spacer regions of U. prolifera, Ulva linza and Ulva flexuosa. Specificity of the FISH method was tested using the six species of green algae commonly occurring in the Subei Shoal, including U. prolifera, U. linza, U. flexuosa, Ulva compressa, Ulva pertusa and Blidingia sp. The results showed that only U. prolifera could be labeled with both probes. Probe 5S-1, which showed a much higher labeling efficiency on U. prolifera, was ultimately selected as the probe for the FISH detection. The sample preparation method was optimized, particularly for the mature green algae, by the addition of cellulase and proteinase K in the pre-hybridization solution. Labeling efficiency with the probe 5S-1 reached 96% on average under the optimized conditions. The successful development of the FISH method has been applied to qualitative and quantitative analysis of field samples collected from the YS, and the results indicate a potential use in future green algae studies.

Global patterns of marine mammal, seabird, and sea turtle bycatch reveal taxa-specific and cumulative megafauna hotspots

PubMed Central

Lewison, Rebecca L.; Crowder, Larry B.; Wallace, Bryan P.; Moore, Jeffrey E.; Cox, Tara; Zydelis, Ramunas; McDonald, Sara; DiMatteo, Andrew; Dunn, Daniel C.; Kot, Connie Y.; Bjorkland, Rhema; Kelez, Shaleyla; Soykan, Candan; Stewart, Kelly R.; Sims, Michelle; Boustany, Andre; Read, Andrew J.; Halpin, Patrick; Nichols, W. J.; Safina, Carl

2014-01-01

Recent research on ocean health has found large predator abundance to be a key element of ocean condition. Fisheries can impact large predator abundance directly through targeted capture and indirectly through incidental capture of nontarget species or bycatch. However, measures of the global nature of bycatch are lacking for air-breathing megafauna. We fill this knowledge gap and present a synoptic global assessment of the distribution and intensity of bycatch of seabirds, marine mammals, and sea turtles based on empirical data from the three most commonly used types of fishing gears worldwide. We identify taxa-specific hotspots of bycatch intensity and find evidence of cumulative impacts across fishing fleets and gears. This global map of bycatch illustrates where data are particularly scarce—in coastal and small-scale fisheries and ocean regions that support developed industrial fisheries and millions of small-scale fishers—and identifies fishing areas where, given the evidence of cumulative hotspots across gear and taxa, traditional species or gear-specific bycatch management and mitigation efforts may be necessary but not sufficient. Given the global distribution of bycatch and the mitigation success achieved by some fleets, the reduction of air-breathing megafauna bycatch is both an urgent and achievable conservation priority. PMID:24639512

Global patterns of marine mammal, seabird, and sea turtle bycatch reveal taxa-specific and cumulative megafauna hotspots.

PubMed

Lewison, Rebecca L; Crowder, Larry B; Wallace, Bryan P; Moore, Jeffrey E; Cox, Tara; Zydelis, Ramunas; McDonald, Sara; DiMatteo, Andrew; Dunn, Daniel C; Kot, Connie Y; Bjorkland, Rhema; Kelez, Shaleyla; Soykan, Candan; Stewart, Kelly R; Sims, Michelle; Boustany, Andre; Read, Andrew J; Halpin, Patrick; Nichols, W J; Safina, Carl

2014-04-08

Recent research on ocean health has found large predator abundance to be a key element of ocean condition. Fisheries can impact large predator abundance directly through targeted capture and indirectly through incidental capture of nontarget species or bycatch. However, measures of the global nature of bycatch are lacking for air-breathing megafauna. We fill this knowledge gap and present a synoptic global assessment of the distribution and intensity of bycatch of seabirds, marine mammals, and sea turtles based on empirical data from the three most commonly used types of fishing gears worldwide. We identify taxa-specific hotspots of bycatch intensity and find evidence of cumulative impacts across fishing fleets and gears. This global map of bycatch illustrates where data are particularly scarce--in coastal and small-scale fisheries and ocean regions that support developed industrial fisheries and millions of small-scale fishers--and identifies fishing areas where, given the evidence of cumulative hotspots across gear and taxa, traditional species or gear-specific bycatch management and mitigation efforts may be necessary but not sufficient. Given the global distribution of bycatch and the mitigation success achieved by some fleets, the reduction of air-breathing megafauna bycatch is both an urgent and achievable conservation priority.

X. couchianus and X. hellerii genome models provide genomic variation insight among Xiphophorus species.

PubMed

Shen, Yingjia; Chalopin, Domitille; Garcia, Tzintzuni; Boswell, Mikki; Boswell, William; Shiryev, Sergey A; Agarwala, Richa; Volff, Jean-Nicolas; Postlethwait, John H; Schartl, Manfred; Minx, Patrick; Warren, Wesley C; Walter, Ronald B

2016-01-07

Xiphophorus fishes are represented by 26 live-bearing species of tropical fish that express many attributes (e.g., viviparity, genetic and phenotypic variation, ecological adaptation, varied sexual developmental mechanisms, ability to produce fertile interspecies hybrids) that have made attractive research models for over 85 years. Use of various interspecies hybrids to investigate the genetics underlying spontaneous and induced tumorigenesis has resulted in the development and maintenance of pedigreed Xiphophorus lines specifically bred for research. The recent availability of the X. maculatus reference genome assembly now provides unprecedented opportunities for novel and exciting comparative research studies among Xiphophorus species. We present sequencing, assembly and annotation of two new genomes representing Xiphophorus couchianus and Xiphophorus hellerii. The final X. couchianus and X. hellerii assemblies have total sizes of 708 Mb and 734 Mb and correspond to 98 % and 102 % of the X. maculatus Jp 163 A genome size, respectively. The rates of single nucleotide change range from 1 per 52 bp to 1 per 69 bp among the three genomes and the impact of putatively damaging variants are presented. In addition, a survey of transposable elements allowed us to deduce an ancestral TE landscape, uncovered potential active TEs and document a recent burst of TEs during evolution of this genus. Two new Xiphophorus genomes and their corresponding transcriptomes were efficiently assembled, the former using a novel guided assembly approach. Three assembled genome sequences within this single vertebrate order of new world live-bearing fishes will accelerate our understanding of relationship between environmental adaptation and genome evolution. In addition, these genome resources provide capability to determine allele specific gene regulation among interspecies hybrids produced by crossing any of the three species that are known to produce progeny predisposed to tumor development.

Simple processes drive unpredictable differences in estuarine fish assemblages: Baselines for understanding site-specific ecological and anthropogenic impacts

NASA Astrophysics Data System (ADS)

Sheaves, Marcus

2016-03-01

Predicting patterns of abundance and composition of biotic assemblages is essential to our understanding of key ecological processes, and our ability to monitor, evaluate and manage assemblages and ecosystems. Fish assemblages often vary from estuary to estuary in apparently unpredictable ways, making it challenging to develop a general understanding of the processes that determine assemblage composition. This makes it problematic to transfer understanding from one estuary situation to another and therefore difficult to assemble effective management plans or to assess the impacts of natural and anthropogenic disturbance. Although system-to-system variability is a common property of ecological systems, rather than being random it is the product of complex interactions of multiple causes and effects at a variety of spatial and temporal scales. I investigate the drivers of differences in estuary fish assemblages, to develop a simple model explaining the diversity and complexity of observed estuary-to-estuary differences, and explore its implications for management and conservation. The model attributes apparently unpredictable differences in fish assemblage composition from estuary to estuary to the interaction of species-specific, life history-specific and scale-specific processes. In explaining innate faunal differences among estuaries without the need to invoke complex ecological or anthropogenic drivers, the model provides a baseline against which the effects of additional natural and anthropogenic factors can be evaluated.

Comparative Transcriptomics in East African Cichlids Reveals Sex- and Species-Specific Expression and New Candidates for Sex Differentiation in Fishes

PubMed Central

Böhne, Astrid; Sengstag, Thierry; Salzburger, Walter

2014-01-01

Males and females of the same species differ largely in gene expression, which accounts for most of the morphological and physiological differences and sex-specific phenotypes. Here, we analyzed sex-specific gene expression in the brain and the gonads of cichlid fishes from Lake Tanganyika belonging to four different lineages, so-called tribes (Eretmodini, Ectodini, Haplochromini, and Lamprologini), using the outgroup Nile tilapia (Oreochromis niloticus) as reference. The comparison between male and female brains revealed few differences between the sexes, consistent in all investigated species. The gonads, on the other hand, showed a large fraction of differentially expressed transcripts with the majority of them showing the same direction of expression in all four species. All here-studied cichlids, especially the three investigated mouth-breeding species, showed a trend toward more male- than female-biased transcripts. Transcripts, which were female-biased in expression in all four species, were overrepresented on linkage group (LG)1 in the reference genome and common male-biased transcripts showed accumulation on LG23, the presumable sex chromosomes of the Nile tilapia. Sex-specific transcripts contained candidate genes for sex determination and differentiation in fishes, especially members of the transforming growth factor-β-superfamily and the Wnt-pathway and also prominent members of the sox-, dm-domain-, and high mobility group-box families. We further confirmed our previous finding on species/lineage-specific gene expression shifts in the sex steroid pathway, including synthesizing enzymes as the aromatase cyp19a1 and estrogen and androgen receptors. PMID:25364805

Gear and seasonal bias associated with abundance and size structure estimates for lentic freshwater fishes

USGS Publications Warehouse

Fischer, Jesse R.; Quist, Michael C.

2014-01-01

All freshwater fish sampling methods are biased toward particular species, sizes, and sexes and are further influenced by season, habitat, and fish behavior changes over time. However, little is known about gear-specific biases for many common fish species because few multiple-gear comparison studies exist that have incorporated seasonal dynamics. We sampled six lakes and impoundments representing a diversity of trophic and physical conditions in Iowa, USA, using multiple gear types (i.e., standard modified fyke net, mini-modified fyke net, sinking experimental gill net, bag seine, benthic trawl, boat-mounted electrofisher used diurnally and nocturnally) to determine the influence of sampling methodology and season on fisheries assessments. Specifically, we describe the influence of season on catch per unit effort, proportional size distribution, and the number of samples required to obtain 125 stock-length individuals for 12 species of recreational and ecological importance. Mean catch per unit effort generally peaked in the spring and fall as a result of increased sampling effectiveness in shallow areas and seasonal changes in habitat use (e.g., movement offshore during summer). Mean proportional size distribution decreased from spring to fall for white bass Morone chrysops, largemouth bass Micropterus salmoides, bluegill Lepomis macrochirus, and black crappie Pomoxis nigromaculatus, suggesting selectivity for large and presumably sexually mature individuals in the spring and summer. Overall, the mean number of samples required to sample 125 stock-length individuals was minimized in the fall with sinking experimental gill nets, a boat-mounted electrofisher used at night, and standard modified nets for 11 of the 12 species evaluated. Our results provide fisheries scientists with relative comparisons between several recommended standard sampling methods and illustrate the effects of seasonal variation on estimates of population indices that will be critical to the future development of standardized sampling methods for freshwater fish in lentic ecosystems.

Comparative Analysis of State Fish Consumption Advisories Targeting Sensitive Populations

PubMed Central

Scherer, Alison C.; Tsuchiya, Ami; Younglove, Lisa R.; Burbacher, Thomas M.; Faustman, Elaine M.

2008-01-01

Objective Fish consumption advisories are issued to warn the public of possible toxicological threats from consuming certain fish species. Although developing fetuses and children are particularly susceptible to toxicants in fish, fish also contain valuable nutrients. Hence, formulating advice for sensitive populations poses challenges. We conducted a comparative analysis of advisory Web sites issued by states to assess health messages that sensitive populations might access. Data sources We evaluated state advisories accessed via the National Listing of Fish Advisories issued by the U.S. Environmental Protection Agency. Data extraction We created criteria to evaluate advisory attributes such as risk and benefit message clarity. Data synthesis All 48 state advisories issued at the time of this analysis targeted children, 90% (43) targeted pregnant women, and 58% (28) targeted women of childbearing age. Only six advisories addressed single contaminants, while the remainder based advice on 2–12 contaminants. Results revealed that advisories associated a dozen contaminants with specific adverse health effects. Beneficial health effects of any kind were specifically associated only with omega-3 fatty acids found in fish. Conclusions These findings highlight the complexity of assessing and communicating information about multiple contaminant exposure from fish consumption. Communication regarding potential health benefits conferred by specific fish nutrients was minimal and focused primarily on omega-3 fatty acids. This overview suggests some lessons learned and highlights a lack of both clarity and consistency in providing the breadth of information that sensitive populations such as pregnant women need to make public health decisions about fish consumption during pregnancy. PMID:19079708

Estimation and modeling of electrofishing capture efficiency for fishes in wadeable warmwater streams

USGS Publications Warehouse

Price, A.; Peterson, James T.

2010-01-01

Stream fish managers often use fish sample data to inform management decisions affecting fish populations. Fish sample data, however, can be biased by the same factors affecting fish populations. To minimize the effect of sample biases on decision making, biologists need information on the effectiveness of fish sampling methods. We evaluated single-pass backpack electrofishing and seining combined with electrofishing by following a dual-gear, mark–recapture approach in 61 blocknetted sample units within first- to third-order streams. We also estimated fish movement out of unblocked units during sampling. Capture efficiency and fish abundances were modeled for 50 fish species by use of conditional multinomial capture–recapture models. The best-approximating models indicated that capture efficiencies were generally low and differed among species groups based on family or genus. Efficiencies of single-pass electrofishing and seining combined with electrofishing were greatest for Catostomidae and lowest for Ictaluridae. Fish body length and stream habitat characteristics (mean cross-sectional area, wood density, mean current velocity, and turbidity) also were related to capture efficiency of both methods, but the effects differed among species groups. We estimated that, on average, 23% of fish left the unblocked sample units, but net movement varied among species. Our results suggest that (1) common warmwater stream fish sampling methods have low capture efficiency and (2) failure to adjust for incomplete capture may bias estimates of fish abundance. We suggest that managers minimize bias from incomplete capture by adjusting data for site- and species-specific capture efficiency and by choosing sampling gear that provide estimates with minimal bias and variance. Furthermore, if block nets are not used, we recommend that managers adjust the data based on unconditional capture efficiency.

Development of a fish assemblage tolerance index for the National Rivers and Streams Assessment

EPA Science Inventory

Whittier et al (Trans. Amer. Fish. Soc. 136:254-271) developed an assemblage tolerance index (ATI) for stream fishes in the western US based on quantitative tolerance values developed for individual fish and amphibian species. The ATI is conceptually similar to the Hilsenhoff Bi...

Identifying a breeding habitat of a critically endangered fish, Acheilognathus typus, in a natural river in Japan

NASA Astrophysics Data System (ADS)

Sakata, Masayuki K.; Maki, Nobutaka; Sugiyama, Hideki; Minamoto, Toshifumi

2017-12-01

Freshwater biodiversity has been severely threatened in recent years, and to conserve endangered species, their distribution and breeding habitats need to be clarified. However, identifying breeding sites in a large area is generally difficult. Here, by combining the emerging environmental DNA (eDNA) analysis with subsequent traditional collection surveys, we successfully identified a breeding habitat for the critically endangered freshwater fish Acheilognathus typus in the mainstream of Omono River in Akita Prefecture, Japan, which is one of the original habitats of this species. Based on DNA cytochrome B sequences of A. typus and closely related species, we developed species-specific primers and a probe that were used in real-time PCR for detecting A. typus eDNA. After verifying the specificity and applicability of the primers and probe on water samples from known artificial habitats, eDNA analysis was applied to water samples collected at 99 sites along Omono River. Two of the samples were positive for A. typus eDNA, and thus, small fixed nets and bottle traps were set out to capture adult fish and verify egg deposition in bivalves (the preferred breeding substrate for A. typus) in the corresponding regions. Mature female and male individuals and bivalves containing laid eggs were collected at one of the eDNA-positive sites. This was the first record of adult A. typus in Omono River in 11 years. This study highlights the value of eDNA analysis to guide conventional monitoring surveys and shows that combining both methods can provide important information on breeding sites that is essential for species' conservation.

Identifying a breeding habitat of a critically endangered fish, Acheilognathus typus, in a natural river in Japan.

PubMed

Sakata, Masayuki K; Maki, Nobutaka; Sugiyama, Hideki; Minamoto, Toshifumi

2017-11-14

Freshwater biodiversity has been severely threatened in recent years, and to conserve endangered species, their distribution and breeding habitats need to be clarified. However, identifying breeding sites in a large area is generally difficult. Here, by combining the emerging environmental DNA (eDNA) analysis with subsequent traditional collection surveys, we successfully identified a breeding habitat for the critically endangered freshwater fish Acheilognathus typus in the mainstream of Omono River in Akita Prefecture, Japan, which is one of the original habitats of this species. Based on DNA cytochrome B sequences of A. typus and closely related species, we developed species-specific primers and a probe that were used in real-time PCR for detecting A. typus eDNA. After verifying the specificity and applicability of the primers and probe on water samples from known artificial habitats, eDNA analysis was applied to water samples collected at 99 sites along Omono River. Two of the samples were positive for A. typus eDNA, and thus, small fixed nets and bottle traps were set out to capture adult fish and verify egg deposition in bivalves (the preferred breeding substrate for A. typus) in the corresponding regions. Mature female and male individuals and bivalves containing laid eggs were collected at one of the eDNA-positive sites. This was the first record of adult A. typus in Omono River in 11 years. This study highlights the value of eDNA analysis to guide conventional monitoring surveys and shows that combining both methods can provide important information on breeding sites that is essential for species' conservation.

Trophic characteristics of a mangrove fish community in Southwest Thailand: Important mangrove contribution and intraspecies feeding variability

NASA Astrophysics Data System (ADS)

Zagars, Matiss; Ikejima, Kou; Kasai, Akihide; Arai, Nobuaki; Tongnunui, Prasert

2013-03-01

Mangrove production has been found to make a major contribution to the nutrition of a fish community in the Sikao Creek mangrove estuary, Southwest Thailand. Gut content analysis and carbon and nitrogen stable isotope analysis were used to assess fish feeding behavior and trophic reliance on different primary producers (mangrove leaves, phytoplankton, microphytobenthos) focusing on 19 dominant fish species, and 4 potential fish food items. Cluster analysis identified 5 trophic groups and the IsoSource model indicated the importance of primary food sources in trophically supporting different fish species. Most analyzed fish species had carbon isotopic signatures that were more depleted than those reported in previous studies, and the IsoSource model indicated that mangrove leaves were an important primary food source. This may be a specific characteristic of our study site, which is not well connected to other productive coastal habitats that provide alternative primary food sources. Thus we suggest that food chains in trophically isolated mangrove estuaries of southwest Thailand are more dependent on mangrove tree production. We also assessed the relationship of individuality in fish feeding habits and variability of δ13C values and showed that several mangrove fish species have significant intraspecies variability in feeding habits, possibly due to high intraspecific competition.

A Transcriptome Derived Female-Specific Marker from the Invasive Western Mosquitofish (Gambusia affinis)

PubMed Central

Lamatsch, Dunja K.; Adolfsson, Sofia; Senior, Alistair M.; Christiansen, Guntram; Pichler, Maria; Ozaki, Yuichi; Smeds, Linnea; Schartl, Manfred; Nakagawa, Shinichi

2015-01-01

Sex-specific markers are a prerequisite for understanding reproductive biology, genetic factors involved in sex differences, mechanisms of sex determination, and ultimately the evolution of sex chromosomes. The Western mosquitofish, Gambusia affinis, may be considered a model species for sex-chromosome evolution, as it displays female heterogamety (ZW/ZZ), and is also ecologically interesting as a worldwide invasive species. Here, de novo RNA-sequencing on the gonads of sexually mature G. affinis was used to identify contigs that were highly transcribed in females but not in males (i.e., transcripts with ovary-specific expression). Subsequently, 129 primer pairs spanning 79 contigs were tested by PCR to identify sex-specific transcripts. Of those primer pairs, one female-specific DNA marker was identified, Sanger sequenced and subsequently validated in 115 fish. Sequence analyses revealed a high similarity between the identified sex-specific marker and the 3´ UTR of the aminomethyl transferase (amt) gene of the closely related platyfish (Xiphophorus maculatus). This is the first time that RNA-seq has been used to successfully characterize a sex-specific marker in a fish species in the absence of a genome map. Additionally, the identified sex-specific marker represents one of only a handful of such markers in fishes. PMID:25707007

Diastereoisomer- and species-specific distribution of hexabromocyclododecane (HBCD) in fish and marine invertebrates.

PubMed

Son, Min-Hui; Kim, Jongchul; Shin, Eun-Su; Seo, Sung-Hee; Chang, Yoon-Seok

2015-12-30

The levels and distributional characteristics of hexabromocyclododecane (HBCD) diastereoisomers have been largely reported for various fish and select shellfish. In this study, we reclassified a number and variety of marine invertebrates, including shellfish, to further contribute to the comprehensive understanding of the effects and assessment of human exposure to HBCD. Overall, 30 marine invertebrate species (n=188) were investigated and the following order of ∑2HBCD (α- and γ-HBCD) was observed: fish>chordata>cephalopoda>echinodermata>bivalve>crustacea. The marine invertebrates that were reclassified into nektonic and benthic organisms showed similar concentration of ∑2HBCD. The feeding habits and modes of the marine organisms were considered to compare the degree of bioaccumulation and diastereoisomer-specific distribution of HBCD due to the effects of the environment in and around pollution sources, as well as the organisms' metabolic capacities. To the best of our knowledge, this is the first study to examine the species-specific distribution patterns of HBCD for both fish and marine invertebrates. We expect to significantly expand the understanding of the environmental fate of HBCD for marine organisms. Copyright © 2015 Elsevier B.V. All rights reserved.

Myxosporean hyperparasites of gill monogeneans are basal to the Multivalvulida

PubMed Central

2011-01-01

Background Myxosporeans are known from aquatic annelids but parasitism of platyhelminths by myxosporeans has not been widely reported. Hyperparasitism of gill monogeneans by Myxidium giardi has been reported from the European eel and Myxidium-like hyperparasites have also been observed during studies of gill monogeneans from Malaysia and Japan. The present study aimed to collect new hyperparasite material from Malaysia for morphological and molecular descriptions. In addition, PCR screening of host fish was undertaken to determine whether they are also hosts for the myxosporean. Results Heavy myxosporean infections were observed in monogeneans from two out of 14 fish and were detected from a further five fish using specific PCRs and pooled monogenean DNA. Positive DNA isolates were sequenced and were from a single species of myxosporean. Myxospore morphology was consistent with Myxidium with histozoic development in the parenchymal tissues of the monogenean. Simultaneous infections in the fish could not be confirmed microscopically; however, identical myxosporean DNA could be amplified from kidney, spleen and intestinal tract tissues using the specific PCR. Small subunit (SSU) rDNA for the myxosporean was amplified and was found to be most similar (92%) to that of another hyperparasitic myxosporean from a gill monogenean from Japan and to numerous multivalvulidan myxosporeans from the genus Kudoa (89-91%). Phylogenetic analyses placed the hyperparasite sequence basally to clades containing Kudoa, Unicapsula and Sphaerospora. Conclusions The myxosporean infecting the gill monogenean, Diplectanocotyla gracilis, from the Indo-Pacific tarpon, Megalops cyprinoides, is described as a new species, Myxidium incomptavermi, based on a histozoic development in the monogenean host and its phylogenetic placement. We have demonstrated for the first time that a myxosporean hyperparasite of gill monogeneans is detectable in the fish host. However, myxospores could not be isolated from the fish and confirmation was by PCR alone. The relationship between the myxosporean infection in gill monogeneans and the presence of parasitic DNA in fish is not yet fully understood. Nonetheless, myxospores with a Myxidium-like morphology, two of which we have shown to be phylogenetically related, have now been reported to develop in three different gill monogeneans, indicating that myxosporeans are true parasites of monogeneans. PMID:22115202

Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii).

PubMed

Bar, Ido; Cummins, Scott; Elizur, Abigail

2016-03-10

Controlling and managing the breeding of bluefin tuna (Thunnus spp.) in captivity is an imperative step towards obtaining a sustainable supply of these fish in aquaculture production systems. Germ cell transplantation (GCT) is an innovative technology for the production of inter-species surrogates, by transplanting undifferentiated germ cells derived from a donor species into larvae of a host species. The transplanted surrogates will then grow and mature to produce donor-derived seed, thus providing a simpler alternative to maintaining large-bodied broodstock such as the bluefin tuna. Implementation of GCT for new species requires the development of molecular tools to follow the fate of the transplanted germ cells. These tools are based on key reproductive and germ cell-specific genes. RNA-Sequencing (RNA-Seq) provides a rapid, cost-effective method for high throughput gene identification in non-model species. This study utilized RNA-Seq to identify key genes expressed in the gonads of Southern bluefin tuna (Thunnus maccoyii, SBT) and their specific expression patterns in male and female gonad cells. Key genes involved in the reproductive molecular pathway and specifically, germ cell development in gonads, were identified using analysis of RNA-Seq transcriptomes of male and female SBT gonad cells. Expression profiles of transcripts from ovary and testis cells were compared, as well as testis germ cell-enriched fraction prepared with Percoll gradient, as used in GCT studies. Ovary cells demonstrated over-expression of genes related to stem cell maintenance, while in testis cells, transcripts encoding for reproduction-associated receptors, sex steroids and hormone synthesis and signaling genes were over-expressed. Within the testis cells, the Percoll-enriched fraction showed over-expression of genes that are related to post-meiosis germ cell populations. Gonad development and germ cell related genes were identified from SBT gonads and their expression patterns in ovary and testis cells were determined. These expression patterns correlate with the reproductive developmental stage of the sampled fish. The majority of the genes described in this study were sequenced for the first time in T. maccoyii. The wealth of SBT gonadal and germ cell-related gene sequences made publicly available by this study provides an extensive resource for further GCT and reproductive molecular biology studies of this commercially valuable fish.

Fish population studies using parasites from the Southeastern Pacific Ocean: considering host population changes and species body size as sources of variability of parasite communities.

PubMed

George-Nascimento, Mario; Oliva, Marcelo

2015-01-01

Research using parasites in fish population studies in the South Eastern Pacific (SEP) is summarized. There are 27 such studies (snapshots mainly) in single host species sampled at different geographic localities and at somewhat similar times. They have been devoted mainly to economically important species, though others on coastal and intertidal fish or on less- or non-commercial species provide insights on scales of temporal and spatial variation of parasite infracommunities. Later, we assess whether the probability of harbouring parasites depends on the host species body size. Our results indicate that a stronger tool for fish population studies may be developed under regular (long term) scrutiny of parasite communities, especially of small fish host species, due to their larger variability in richness, abundance and total biomass, than in large fish species. Finally, it might also be necessary to consider the effects of fishing on parasite communities as well as the natural oscillations (coupled or not) of host and parasite populations.

Using field data to assess the tolerance of freshwater fish to elevated ionic concentrations

EPA Science Inventory

We used field data of fish occurrences and specific conductivity to assess the tolerance of freshwater fish to elevated ions. The concentration at which a species was expected to no longer be observed [the extirpation concentration (XC95)] was identified from the 95th percentile ...

Analysis of stable isotopes in fish to identify habitat use and switching

EPA Science Inventory

In our isotopic studies of fish in Oregon Coast Range streams we have found stable isotopes of carbon, oxygen and sulfur to be surprisingly useful in identifying and discriminating specific habitat or tributary use by a variety of fish species. Stable isotopes of carbon can be u...

Stable isotopes in fish as indicators of habitat use

EPA Science Inventory

In our isotopic studies of fish in Oregon Coast Range streams we have found stable isotopes of carbon, oxygen and sulfur to be surprisingly useful in identifying and discriminating specific habitat or tributary use by a variety of fish species. Stable isotopes of carbon can be u...

Indicators of AEI applied to the Delaware Estuary.

PubMed

Barnthouse, Lawrence W; Heimbuch, Douglas G; Anthony, Vaughn C; Hilborn, Ray W; Myers, Ransom A

2002-05-18

We evaluated the impacts of entrainment and impingement at the Salem Generating Station on fish populations and communities in the Delaware Estuary. In the absence of an agreed-upon regulatory definition of "adverse environmental impact" (AEI), we developed three independent benchmarks of AEI based on observed or predicted changes that could threaten the sustainability of a population or the integrity of a community. Our benchmarks of AEI included: (1) disruption of the balanced indigenous community of fish in the vicinity of Salem (the "BIC" analysis); (2) a continued downward trend in the abundance of one or more susceptible fish species (the "Trends" analysis); and (3) occurrence of entrainment/impingement mortality sufficient, in combination with fishing mortality, to jeopardize the future sustainability of one or more populations (the "Stock Jeopardy" analysis). The BIC analysis utilized nearly 30 years of species presence/absence data collected in the immediate vicinity of Salem. The Trends analysis examined three independent data sets that document trends in the abundance of juvenile fish throughout the estuary over the past 20 years. The Stock Jeopardy analysis used two different assessment models to quantify potential long-term impacts of entrainment and impingement on susceptible fish populations. For one of these models, the compensatory capacities of the modeled species were quantified through meta-analysis of spawner-recruit data available for several hundred fish stocks. All three analyses indicated that the fish populations and communities of the Delaware Estuary are healthy and show no evidence of an adverse impact due to Salem. Although the specific models and analyses used at Salem are not applicable to every facility, we believe that a weight of evidence approach that evaluates multiple benchmarks of AEI using both retrospective and predictive methods is the best approach for assessing entrainment and impingement impacts at existing facilities.

Fishing down nutrients on coral reefs.

PubMed

Allgeier, Jacob E; Valdivia, Abel; Cox, Courtney; Layman, Craig A

2016-08-16

Fishing is widely considered a leading cause of biodiversity loss in marine environments, but the potential effect on ecosystem processes, such as nutrient fluxes, is less explored. Here, we test how fishing on Caribbean coral reefs influences biodiversity and ecosystem functions provided by the fish community, that is, fish-mediated nutrient capacity. Specifically, we modelled five processes of nutrient storage (in biomass) and supply (via excretion) of nutrients, as well as a measure of their multifunctionality, onto 143 species of coral reef fishes across 110 coral reef fish communities. These communities span a gradient from extreme fishing pressure to protected areas with little to no fishing. We find that in fished sites fish-mediated nutrient capacity is reduced almost 50%, despite no substantial changes in the number of species. Instead, changes in community size and trophic structure were the primary cause of shifts in ecosystem function. These findings suggest that a broader perspective that incorporates predictable impacts of fishing pressure on ecosystem function is imperative for effective coral reef conservation and management.

Evaluation of an integrated cell culture RT-PCR assay to detect and quantify infectious lymphocystis disease virus.

PubMed

Valverde, Estefania J; Borrego, Juan J; Castro, Dolores

2016-12-01

The lymphocystis disease virus (LCDV), a member of the Iridoviridae family, infects a wide range of fish species including gilthead seabream (Sparus aurata L.), the most important species cultured in the Mediterranean. LCDV is difficult to propagate in cell culture and does not produce clear and consistent cytopathic effects (CPE), especially in samples collected from subclinically infected fish. An integrated cell culture reverse transcription-polymerase chain reaction (ICC-RT-PCR) assay, followed by dot-blot hybridization of the RT-PCR products, was developed to improve the detection of infectious LCDV. The sensitivity of the ICC-RT-PCR assay, which can be performed in 7 d, was at least 100-fold higher than viral diagnosis obtained by CPE development. The developed assay thus allows the determination of infectious titres in samples with low viral loads, including those from asymptomatic carrier fish, in which no CPE was recorded after a 14-d incubation period. The ICC-RT-PCR assay enables rapid, specific and sensitive detection and quantification of infectious LCDV, and may be a valuable tool in the study of aspects of LCDV infection including transmission or epizootiology. Copyright © 2016 Elsevier B.V. All rights reserved.

Spatial and temporal variation of the gill rakers of gizzard shad and silver carp in three Midwestern rivers

USGS Publications Warehouse

Walleser, Liza R.; Sandheinrich, Mark B.; Howard, David R.; Gaikowski, Mark P.; Amberg, Jon J.

2014-01-01

Improved management of invasive Silver Carp Hypophthalmichthys molitrix in the upper Mississippi River basin may be possible by better understanding the feeding abilities of this population. Food collection for filter-feeding fishes, such as Silver Carp, is influenced by the species-specific structure of their gill rakers. To investigate structural variation in gill rakers of Silver Carp, the morphology of gill rakers was quantified and compared with that of a native filter-feeding fish species which may compete with Silver Carp for food resources, Gizzard Shad Dorosoma cepedianum. Intra- and interspecies variation of gill rakers was examined in both species collected from three locations among four months. Interspecies analysis indicated the size of pores in gill rakers of Silver Carp were much larger than the interraker spacings of Gizzard Shad (95% CI ranged from 80.69 to 185.75 μm versus 16.72 to 47.36 μm, respectively). Intraspecies variation of gill rakers from Silver Carp was related to the overall size of fish and occurred only among sites where dissimilar sizes of fish were collected. This suggested the size of particles filtered by Silver Carp may be dependent upon ontogenic development rather than phenotypic plasticity in response to spatial or temporal factors. Intraspecies variation of gill rakers from Gizzard Shad occurred among site and monthly sampling data; however, variation was only attributable to overall size of fish for monthly sampling data. This suggested ontogeny may influence the filter-feeding ability of this species within a habitat. However, variation noted among sites, which was not attributable to size of fish, may indicate gill rakers are phenotypically plastic among Gizzard Shad populations of various river systems of the upper Mississippi River basin.

Effect of heat treatment on the n-3/n-6 ratio and content of polyunsaturated fatty acids in fish tissues.

PubMed

Schneedorferová, Ivana; Tomčala, Aleš; Valterová, Irena

2015-06-01

The aim of this study was to compare the effect of different heat treatments (pan-frying, oven-baking, and grilling) on the contents of polyunsaturated fatty acids (PUFAs) in fish tissue. Four fish species were examined: pike, carp, cod, and herring. High performance liquid chromatography, coupled with electrospray ionization and mass spectrometric detection (HPLC/ESI/MS), was employed for determination of intact lipid molecules containing n-3 and n-6 PUFAs. Although mostly non-polar lipids (triacylglycerols, TGs) were present in the fish tissue, the PUFAs were present preferentially in the phospholipid fraction. Omnivorous fish species (carp, herring) contained more TGs than did predatory ones (pike, cod). Higher amounts of PUFAs were detected in the marine species than in the freshwater ones. The impact of heat treatments on the lipid composition in the fish tissue seems to be species-specific, as indicated by multivariate data analysis. Herring tissue is most heat-stable, and the mildest heat treatment for PUFA preservation was oven-baking. Copyright © 2014 Elsevier Ltd. All rights reserved.

Bioaccumulation of Heavy Metals in Some Tissues of Fish in Lake Geriyo, Adamawa State, Nigeria.

PubMed

Bawuro, A A; Voegborlo, R B; Adimado, A A

2018-01-01

Bioaccumulation of heavy metals (Zn, Pb, Cd, and Cu) was determined in the liver, gills, and flesh from benthic and pelagic fish species collected from Lake Geriyo covering two seasons. The levels of the heavy metals varied significantly among fish species and organs. Flesh possessed the lowest concentration of all the metals. Liver was the target organ for Zn, Cu, and Pb accumulations. Cd however exhibited higher concentration in the gills. Fish species showed interspecific variation of metals. These differences were discussed for the contribution of potential factors that affected metals uptake like age, geographical distribution, and species-specific factors. The concentration of metals in fish flesh was accepted by the international legislation limits for Cu, Zn, and Cd; however, Pb transcend in Clarias and Tilapia during wet season and Heterotis in both seasons, hence unsafe for human consumption and a threat to public health. These levels might be due to anthropogenic inputs as there is no industrial activity around the lake.

DNA Barcoding of Freshwater Fishes of Indo-Myanmar Biodiversity Hotspot.

PubMed

Barman, Anindya Sundar; Singh, Mamta; Singh, Soibam Khogen; Saha, Himadri; Singh, Yumlembam Jackie; Laishram, Martina; Pandey, Pramod Kumar

2018-06-05

To develop an effective conservation and management strategy, it is required to assess the biodiversity status of an ecosystem, especially when we deal with Indo-Myanmar biodiversity hotspot. Importance of this reaches to an entirely different level as the hotspot represents the area of high endemism which is under continuous threat. Therefore, the need of the present study was conceptualized, dealing with molecular assessment of the fish fauna of Indo-Myanmar region, which covers the Indian states namely, Manipur, Meghalaya, Mizoram, and Nagaland. A total of 363 specimens, representing 109 species were collected and barcoded from the different rivers and their tributaries of the region. The analyses performed in the present study, i.e. Kimura 2-Parameter genetic divergence, Neighbor-Joining, Automated Barcode Gap Discovery and Bayesian Poisson Tree Processes suggest that DNA barcoding is an efficient and reliable tool for species identification. Most of the species were clearly delineated. However, presence of intra-specific and inter-specific genetic distance overlap in few species, revealed the existence of putative cryptic species. A reliable DNA barcode reference library, established in our study provides an adequate knowledge base to the groups of non-taxonomists, researchers, biodiversity managers and policy makers in sketching effective conservation measures for this ecosystem.

Reef flattening effects on total richness and species responses in the Caribbean.

PubMed

Newman, Steven P; Meesters, Erik H; Dryden, Charlie S; Williams, Stacey M; Sanchez, Cristina; Mumby, Peter J; Polunin, Nicholas V C

2015-11-01

There has been ongoing flattening of Caribbean coral reefs with the loss of habitat having severe implications for these systems. Complexity and its structural components are important to fish species richness and community composition, but little is known about its role for other taxa or species-specific responses. This study reveals the importance of reef habitat complexity and structural components to different taxa of macrofauna, total species richness, and individual coral and fish species in the Caribbean. Species presence and richness of different taxa were visually quantified in one hundred 25-m(2) plots in three marine reserves in the Caribbean. Sampling was evenly distributed across five levels of visually estimated reef complexity, with five structural components also recorded: the number of corals, number of large corals, slope angle, maximum sponge and maximum octocoral height. Taking advantage of natural heterogeneity in structural complexity within a particular coral reef habitat (Orbicella reefs) and discrete environmental envelope, thus minimizing other sources of variability, the relative importance of reef complexity and structural components was quantified for different taxa and individual fish and coral species on Caribbean coral reefs using boosted regression trees (BRTs). Boosted regression tree models performed very well when explaining variability in total (82·3%), coral (80·6%) and fish species richness (77·3%), for which the greatest declines in richness occurred below intermediate reef complexity levels. Complexity accounted for very little of the variability in octocorals, sponges, arthropods, annelids or anemones. BRTs revealed species-specific variability and importance for reef complexity and structural components. Coral and fish species occupancy generally declined at low complexity levels, with the exception of two coral species (Pseudodiploria strigosa and Porites divaricata) and four fish species (Halichoeres bivittatus, H. maculipinna, Malacoctenus triangulatus and Stegastes partitus) more common at lower reef complexity levels. A significant interaction between country and reef complexity revealed a non-additive decline in species richness in areas of low complexity and the reserve in Puerto Rico. Flattening of Caribbean coral reefs will result in substantial species losses, with few winners. Individual structural components have considerable value to different species, and their loss may have profound impacts on population responses of coral and fish due to identity effects of key species, which underpin population richness and resilience and may affect essential ecosystem processes and services. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

Use of DNA barcoding to reveal species composition of convenience seafood.

PubMed

Huxley-Jones, Elizabeth; Shaw, Jennifer L A; Fletcher, Carly; Parnell, Juliette; Watts, Phillip C

2012-04-01

Increased education of consumers can be an effective tool for conservation of commercially harvested marine species when product labeling is accurate and allows an informed choice. However, generic labeling (e.g., as white fish or surimi) and mislabeling of seafood prevents this and may erode consumer confidence in seafood product labels in general. We used DNA barcoding to identify the species composition of two types of convenience seafood (i.e., products processed for ease of consumption): fish fingers (long pieces of fish covered with bread crumbs or batter, n = 241) and seafood sticks (long pieces of cooked fish, n = 30). In products labeled as either white fish or surimi, four teleost species were present. Less than 1.5% of fish fingers with species-specific information were mislabeled. Results of other studies show substantially more mislabeling (e.g., >25%) of teleost products, which likely reflects the lower economic gains associated with mislabeling of convenience seafood compared with whole fillets. In addition to species identification, seafood product labels should be required to contain information about, for example, harvesting practices, and our data indicate that consumers can have reasonable confidence in the accuracy of the labels of convenience seafood and thus select brands on the basis of information about current fisheries practice. ©2012 Society for Conservation Biology.

Ethnotaxonomical considerations and usage of ichthyofauna in a fishing community in Ceará State, Northeast Brazil.

PubMed

Pinto, Márcia Freire; Mourão, José da Silva; Alves, Rômulo Romeu Nóbrega

2013-03-08

Artisanal fishery is one of the most important economic activities for human populations living in coastal areas. The traditional knowledge that fishermen have of fishes is of utmost importance for the establishment of conservation strategies for many species. This study aimed to analyse the knowledge of and utilization of fishes by the artisanal fishermen in a fishing community on the coast of Ceará State (Northeast Brazil). In 2011, a number of semi-structured interviews were performed with fishermen with more than 20 years of fishery experience. The interviews were about fisheries (collecting spots, artefacts, etc.) and fish use. The fishes cited by the fishermen were identified scientifically and ethnotaxonomically. Considered masters of fishery, they cited 162 vernacular names of fishes, which corresponded to 290 different species, also including other animals such as dolphins, porpoises, whales and manatees. The criteria for the classification of the fishes were well known and utilised by the fishermen, and they were based on morphology, behaviour, habitat and the importance of commercial and fishing activities. Four hierarchical categories were identified in their classification system: kingdom, life-form, generic and specific. The fish nomenclature created by the fishermen was mostly composed of generic and monotypic names. The main uses of fish were for food and commercial purposes. The results stress the richness and complexity of the knowledge of the artisanal fishermen of Redonda Beach, and they provide support for the possibility of future studies and for the development of management plans and the management of wildlife resources.

Ethnotaxonomical considerations and usage of ichthyofauna in a fishing community in Ceará State, Northeast Brazil

PubMed Central

2013-01-01

Background Artisanal fishery is one of the most important economic activities for human populations living in coastal areas. The traditional knowledge that fishermen have of fishes is of utmost importance for the establishment of conservation strategies for many species. This study aimed to analyse the knowledge of and utilization of fishes by the artisanal fishermen in a fishing community on the coast of Ceará State (Northeast Brazil). Methods In 2011, a number of semi-structured interviews were performed with fishermen with more than 20 years of fishery experience. The interviews were about fisheries (collecting spots, artefacts, etc.) and fish use. The fishes cited by the fishermen were identified scientifically and ethnotaxonomically. Results Considered masters of fishery, they cited 162 vernacular names of fishes, which corresponded to 290 different species, also including other animals such as dolphins, porpoises, whales and manatees. The criteria for the classification of the fishes were well known and utilised by the fishermen, and they were based on morphology, behaviour, habitat and the importance of commercial and fishing activities. Four hierarchical categories were identified in their classification system: kingdom, life-form, generic and specific. The fish nomenclature created by the fishermen was mostly composed of generic and monotypic names. The main uses of fish were for food and commercial purposes. Conclusions The results stress the richness and complexity of the knowledge of the artisanal fishermen of Redonda Beach, and they provide support for the possibility of future studies and for the development of management plans and the management of wildlife resources. PMID:23497491

Development of a spatially distributed model of fish population density for habitat assessment of rivers

NASA Astrophysics Data System (ADS)

Sui, Pengzhe; Iwasaki, Akito; Ryo, Masahiro; Saavedra, Oliver; Yoshimura, Chihiro

2013-04-01

Flow conditions play an important role in sustaining biodiversity of river ecosystem. However, their relations to freshwater fishes, especially to fish population density, have not been clearly described. This study, therefore, aimed to propose a new methodology to quantitatively link habitat conditions, including flow conditions and other physical conditions, to population density of fish species. We developed a basin-scale fish distribution model by integrating the concept of habitat suitability assessment with a distributed hydrological model (DHM) in order to estimate fish population density with particular attention to flow conditions. Generalized linear model (GLM) was employed to evaluate the relationship between population density of fish species and major environmental factors. The target basin was Sagami River in central Japan, where the river reach was divided into 10 sections by estuary, confluences of tributaries, and river-crossing structures (dams, weirs). The DHM was employed to simulate river discharge from 1998 to 2005, which was used to calculate 10 flow indices including mean discharge, 25th and 75th percentile discharge, duration of low and high flows, number of floods. In addition, 5 water quality parameters and 13 other physical conditions (such as basin area, river width, mean diameter of riverbed material, and number of river-crossing structures upstream and downstream) of each river section were considered as environmental variables. In case of Sagami River, 10 habitat variables among them were then selected based on their correlations to avoid multicollinearity. Finally, the best GLM was developed for each species based on Akaike's information criterion. As results, population densities of 16 fish species in Sagami River were modelled, and correlation coefficients between observed and calculated population densities for 10 species were more than 0.70. The key habitat factors for population density varied among fish species. Minimum discharge (MID) was found to be positively correlated to 9 among 16 fish species. For duration of high and low flows (DHF and DLF), longer DHF/DLF was corresponded to lower population density for 7/6 fish species, respectively, such as Rhinogobius kurodai and Plecoglossus altivelis altivelis. Among physical habitat conditions, sinuosity index (SI, the ratio between actual river section length and straight line length) seems to be the most important parameter for fish population density in Sagami River basin, since it affects 12 out of 16 fish species, followed by mean longitudinal slope (S) and number of downstream dams (NLD). Above results demonstrated the applicability of fish distribution model to provide quantitative information on flow conditions required to maintain fish population, which enabled us to evaluate and project ecological consequences of water resource management policy, such as flood management and water withdrawal.

Evolutionary analyses of hedgehog and Hoxd-10 genes in fish species closely related to the zebrafish

PubMed Central

Zardoya, Rafael; Abouheif, Ehab; Meyer, Axel

1996-01-01

The study of development has relied primarily on the isolation of mutations in genes with specific functions in development and on the comparison of their expression patterns in normal and mutant phenotypes. Comparative evolutionary analyses can complement these approaches. Phylogenetic analyses of Sonic hedgehog (Shh) and Hoxd-10 genes from 18 cyprinid fish species closely related to the zebrafish provide novel insights into the functional constraints acting on Shh. Our results confirm and extend those gained from expression and crystalline structure analyses of this gene. Unexpectedly, exon 1 of Shh is found to be almost invariant even in third codon positions among these morphologically divergent species suggesting that this exon encodes for a functionally important domain of the hedgehog protein. This is surprising because the main functional domain of Shh had been thought to be that encoded by exon 2. Comparisons of Shh and Hoxd-10 gene sequences and of resulting gene trees document higher evolutionary constraints on the former than on the latter. This might be indicative of more general evolutionary patterns in networks of developmental regulatory genes interacting in a hierarchical fashion. The presence of four members of the hedgehog gene family in cyprinid fishes was documented and their homologies to known hedgehog genes in other vertebrates were established. PMID:8917540

Evolutionary analyses of hedgehog and Hoxd-10 genes in fish species closely related to the zebrafish.

PubMed

Zardoya, R; Abouheif, E; Meyer, A

1996-11-12

The study of development has relied primarily on the isolation of mutations in genes with specific functions in development and on the comparison of their expression patterns in normal and mutant phenotypes. Comparative evolutionary analyses can complement these approaches. Phylogenetic analyses of Sonic hedgehog (Shh) and Hoxd-10 genes from 18 cyprinid fish species closely related to the zebrafish provide novel insights into the functional constraints acting on Shh. Our results confirm and extend those gained from expression and crystalline structure analyses of this gene. Unexpectedly, exon 1 of Shh is found to be almost invariant even in third codon positions among these morphologically divergent species suggesting that this exon encodes for a functionally important domain of the hedgehog protein. This is surprising because the main functional domain of Shh had been thought to be that encoded by exon 2. Comparisons of Shh and Hoxd-10 gene sequences and of resulting gene trees document higher evolutionary constraints on the former than on the latter. This might be indicative of more general evolutionary patterns in networks of developmental regulatory genes interacting in a hierarchical fashion. The presence of four members of the hedgehog gene family in cyprinid fishes was documented and their homologies to known hedgehog genes in other vertebrates were established.

The Transcription Factor Atonal homolog 8 Regulates Gata4 and Friend of Gata-2 during Vertebrate Development

PubMed Central

Rawnsley, David R.; Xiao, Jiping; Lee, John S.; Liu, Xi; Mericko-Ishizuka, Patricia; Kumar, Vinayak; He, Jie; Basu, Arindam; Lu, MinMin; Lynn, Francis C.; Pack, Michael; Gasa, Rosa; Kahn, Mark L.

2013-01-01

GATA and Friend of GATA (FOG) form a transcriptional complex that plays a key role in cardiovascular development in both fish and mammals. In the present study we demonstrate that the basic helix-loop-helix transcription factor Atonal homolog 8 (Atoh8) is required for development of the heart in fish but not in mice. Genetic studies reveal that Atoh8 interacts specifically with Gata4 and Fog1 during development of the heart and swim bladder in the fish. Biochemical studies reveal that ATOH8, GATA4, and FOG2 associate in a single complex in vitro. In contrast to fish, ATOH8-deficient mice exhibit normal cardiac development and loss of ATOH8 does not alter cardiac development in Gata4+/− mice. This species difference in the role of ATOH8 is explained in part by LacZ and GFP reporter alleles that reveal restriction of Atoh8 expression to atrial but not ventricular myocardium in the mouse. Our findings identify ATOH8 as a novel regulator of GATA-FOG function that is required for cardiac development in the fish but not the mouse. Whether ATOH8 modulates GATA-FOG function at other sites or in more subtle ways in mammals is not yet known. PMID:23836893

Response diversity, nonnative species, and disassembly rules buffer freshwater ecosystem processes from anthropogenic change.

PubMed

Moore, Jonathan W; Olden, Julian D

2017-05-01

Integrating knowledge of environmental degradation, biodiversity change, and ecosystem processes across large spatial scales remains a key challenge to illuminating the resilience of earth's systems. There is now a growing realization that the manner in which communities will respond to anthropogenic impacts will ultimately control the ecosystem consequences. Here, we examine the response of freshwater fishes and their nutrient excretion - a key ecosystem process that can control aquatic productivity - to human land development across the contiguous United States. By linking a continental-scale dataset of 533 fish species from 8100 stream locations with species functional traits, nutrient excretion, and land remote sensing, we present four key findings. First, we provide the first geographic footprint of nutrient excretion by freshwater fishes across the United States and reveal distinct local- and continental-scale heterogeneity in community excretion rates. Second, fish species exhibited substantial response diversity in their sensitivity to land development; for native species, the more tolerant species were also the species contributing greater ecosystem function in terms of nutrient excretion. Third, by modeling increased land-use change and resultant shifts in fish community composition, land development is estimated to decrease fish nutrient excretion in the majority (63%) of ecoregions. Fourth, the loss of nutrient excretion would be 28% greater if biodiversity loss was random or 84% greater if there were no nonnative species. Thus, ecosystem processes are sensitive to increased anthropogenic degradation but biotic communities provide multiple pathways for resistance and this resistance varies across space. © 2016 John Wiley & Sons Ltd.

Early social learning triggers neurogenomic expression changes in a swordtail fish.

PubMed

Cui, Rongfeng; Delclos, Pablo J; Schumer, Molly; Rosenthal, Gil G

2017-05-17

Mate choice can play a pivotal role in the nature and extent of reproductive isolation between species. Mating preferences are often dependent on an individual's social experience with adult phenotypes throughout development. We show that olfactory preference in a swordtail fish ( Xiphophorus malinche ) is affected by previous experience with adult olfactory signals. We compare transcriptome-wide gene expression levels of pooled sensory and brain tissues between three treatment groups that differ by social experience: females with no adult exposure, females exposed to conspecifics and females exposed to heterospecifics. We identify potential functionally relevant genes and biological pathways differentially expressed not only between control and exposure groups, but also between groups exposed to conspecifics and heterospecifics. Based on our results, we speculate that vomeronasal receptor type 2 paralogs may detect species-specific pheromone components and thus play an important role in reproductive isolation between species. © 2017 The Author(s).

Habitat geology studies on and near Georges Bank, off New England

USGS Publications Warehouse

Valentine, P.C.

2001-01-01

Marine habitat geology is the study of the distribution of geologic materials that form the seabed, the geologic processes (such as sediment movement and deposition) that affect the seabed, and the interplay of geologic factors and species behavior that gives rise to biological habitats in general and to specific habitats deemed essential to the success of a particular species (essential fish habitats, EFH's). Georges Bank was once the premier East Coast fishing ground for groundfish and scallops. The decline of groundfish species due to overfishing contributed to the increasingly restrictive management of fish stocks and a need to identify and protect EFH's.

Mate choice and body pattern variations in the Crown Butterfly fish Chaetodon paucifasciatus (Chaetodontidae)

PubMed Central

Levy, Keren; Lerner, Amit; Shashar, Nadav

2014-01-01

ABSTRACT Mate choice is an important ecological behavior in fish, and is often based on visual cues of body patterns. The Crown Butterfly fish Chaetodon paucifasciatus (Chaetodontidae) is a monogamist, territorial species; it swims in close proximity to its partner throughout most of its life. This species is characterized by a pattern of 6–8 vertical black stripes on a white background, on both sides of its body. Our aim was to define spatial features (variations) in body patterns by evaluating the level of dissimilarity between both sides of each individual fish, and the level of dissimilarity between patterns of different individuals. In addition, we tested whether the fish are attracted to or reject specific features of the body patterns. Features were defined and counted using photographs of body patterns. Attraction to or rejection of specific features were tested behaviorally using a dual-choice experiment of video animations of individuals swimming over a coral-reef background. We found that the patterns of each fish and sides of the body were no less dissimilar, compared intraspecificly to other fish, and that each side pattern was unique and distinguishable. Variations in the patterns occurred mostly in the last three posterior stripes. Individuals were mainly attracted to conspecifics with multiple crossing patterns (two or more consecutive crossings), and rejected patterns with holes. Our results suggest that in this species the unique body pattern of each fish is used for conspecific identification of mates and intruders. PMID:25432516

Fishery management problems and possibilities on large southeastern reservoirs

USGS Publications Warehouse

Parsons, John W.

1958-01-01

In recognition of these problems, the development and application of sound management procedures may be accomplished by controlling species composition and availability of fish through water level control, timber clearing, application of selective toxicants, commercial fishing, introduction of new fish species, and the management of tailwaters and tributaries. Extended research and interagency cooperation are necessary to properly develop and apply sound management. Promotion of angling and regulation of the fishery may best be realized by providing adequate fishing facilities, elimination of certain restricted areas, and in some cases revision of laws and regulations. Biologists must not only meet the present demands for improved sport fishing but must also balance fish yield by increasing the use of food fish by sport and commercial operations.

Interspecific variation in hypoxia tolerance, swimming performance and plasticity in cyprinids that prefer different habitats.

PubMed

Fu, Shi-Jian; Fu, Cheng; Yan, Guan-Jie; Cao, Zhen-Dong; Zhang, An-Jie; Pang, Xu

2014-02-15

This study quantified and compared hypoxia tolerance and swim performance among cyprinid fish species from rapid-, slow- and intermediate-flow habitats (four species per habitat) in China. In addition, we explored the effects of short-term acclimation on swim performance, maximum metabolic rate (M(O2,max)) and gill remodelling to detect habitat-associated patterns of plastic response to hypoxia. Indices of hypoxia tolerance included oxygen threshold for loss of equilibrium (LOE50) and aquatic surface respiration (ASR50), and critical oxygen tension for routine metabolic rate (Pcrit). Critical swimming speed (Ucrit) and M(O2,max) were measured under normoxic and hypoxic conditions after 48 h acclimation to normoxia and hypoxia, and gill remodelling was estimated after 48 h of hypoxia exposure. Both traditional ANCOVA and phylogenetically independent contrast (PDANOVA) analyses showed that fish species from rapid-flow habitats exhibited lower LOE50 compared with fish from intermediate- and slow-flow habitats. Habitat-specific differences in Pcrit and Ucrit were detected using PDANOVA but not traditional ANCOVA analyses, with fish species from rapid-flow habitats exhibiting lower Pcrit but higher Ucrit values compared with fish from intermediate- and slow-flow habitats. Fish species from rapid-flow habitats were also characterized by less plasticity in swim performance and gill morphology in response to hypoxia acclimation compared with species from slow-flow habitats, but a greater drop in swim performance in response to acute hypoxia exposure. The study detected a habitat-specific difference in hypoxia tolerance, swimming performance and its plasticity among fish from habitats with different flow conditions, possibly because of the long-term adaptation to the habitat caused by selection stress. The PDANOVA analyses were more powerful than traditional statistical analyses according to the habitat effects in both hypoxia tolerance and swimming performance in this study.

Rapid and Sensitive Detection of Lymphocystis Disease Virus Genotype VII by Loop-Mediated Isothermal Amplification.

PubMed

Valverde, Estefanía J; Cano, Irene; Castro, Dolores; Paley, Richard K; Borrego, Juan J

2017-03-01

Lymphocystis disease virus (LCDV) infections have been described in gilthead seabream (Sparus aurata L.) and Senegalese sole (Solea senegalensis, Kaup), two of the most important marine fish species in the Mediterranean aquaculture. In this study, a rapid, specific, and sensitive detection method for LCDV genotype VII based on loop-mediated isothermal amplification (LAMP) was developed. The LAMP assay, performed using an apparatus with real-time amplification monitoring, was able to specifically detect LCDV genotype VII from clinically positive samples in less than 12 min. In addition, the assay allowed the detection of LCDV in all asymptomatic carrier fish analysed, identified by qPCR, showing an analytical sensitivity of ten copies of viral DNA per reaction. The LCDV LAMP assay has proven to be a promising diagnostic method that can be used easily in fish farms to detect the presence and spread of this iridovirus.

Air-breathing fishes in aquaculture. What can we learn from physiology?

PubMed

Lefevre, S; Wang, T; Jensen, A; Cong, N V; Huong, D T T; Phuong, N T; Bayley, M

2014-03-01

During the past decade, the culture of air-breathing fish species has increased dramatically and is now a significant global source of protein for human consumption. This development has generated a need for specific information on how to maximize growth and minimize the environmental effect of culture systems. Here, the existing data on metabolism in air-breathing fishes are reviewed, with the aim of shedding new light on the oxygen requirements of air-breathing fishes in aquaculture, reaching the conclusion that aquatic oxygenation is much more important than previously assumed. In addition, the possible effects on growth of the recurrent exposure to deep hypoxia and associated elevated concentrations of carbon dioxide, ammonia and nitrite, that occurs in the culture ponds used for air-breathing fishes, are discussed. Where data on air-breathing fishes are simply lacking, data for a few water-breathing species will be reviewed, to put the physiological effects into a growth perspective. It is argued that an understanding of air-breathing fishes' respiratory physiology, including metabolic rate, partitioning of oxygen uptake from air and water in facultative air breathers, the critical oxygen tension, can provide important input for the optimization of culture practices. Given the growing importance of air breathers in aquaculture production, there is an urgent need for further data on these issues. © 2014 The Fisheries Society of the British Isles.

Distribution and habitat association of benthic fish on the Condor seamount (NE Atlantic, Azores) from in situ observations

NASA Astrophysics Data System (ADS)

Porteiro, Filipe M.; Gomes-Pereira, José N.; Pham, Christopher K.; Tempera, Fernando; Santos, Ricardo S.

2013-12-01

Distribution of fish assemblages and habitat associations of demersal fishes on the Condor seamount were investigated by analyzing in situ video imagery acquired by the Remotely-Operated Vehicles ROV SP300 and Luso 6000. A total of 51 fish taxa from 32 families were inventoried. Zooplanktivores (10 species) were the most abundant group followed by carnivores (23 species) and benthivores (18 species). Non-metric multidimensional scaling (MDS) analyses were performed on dive segments to visualize the spatial relationships between species and habitat type, substrate type or depth, with depth being the most significant parameter influencing fish distribution. Four major fish groups were identified from their vertical distribution alone: summit species (generally to <300 m depth); broad ranging species (ca. from 200 to 800 m); intermediate ranging slope species (ca. from 400 m to 800-850 m); and deeper species (800-850-1100 m). The fish fauna observed at the summit is more abundant (15.2 fish/100 m2) and habitat-specialized than the fish observed along the seamount slope. Down the seamount slope, the summit fish assemblage is gradually replaced as depth increases, with an overall reduction in abundance. On the summit, three species (Callanthias ruber, Anthias anthias and Lappanella fasciata) had higher affinity to coral habitats compared to non-coral habitats. A coherent specialized fish assemblage associated to coral habitats could not be identified, because most species were observed also in non-coral areas. On the seamount's slope (300-1100 m), no relationship between fish and coral habitats could be identified, although these might occur at larger scales. This study shows that in situ video imagery complements traditional fishing surveys, by providing information on unknown or rarely seen species, being fundamental for the development of more comprehensive ecosystem-based management towards a sustainable use of the marine environment.

Multiplex PCR method for use in real-time PCR for identification of fish fillets from grouper (Epinephelus and Mycteroperca species) and common substitute species.

PubMed

Trotta, Michele; Schönhuth, Susana; Pepe, Tiziana; Cortesi, M Luisa; Puyet, Antonio; Bautista, José M

2005-03-23

Mitochondrial 16S rRNA sequences from morphological validated grouper (Epinephelus aeneus, E. caninus, E. costae, and E. marginatus; Mycteroperca fusca and M. rubra), Nile perch (Lates niloticus), and wreck fish (Polyprion americanus) were used to develop an analytical system for group diagnosis based on two alternative Polymerase Chain Reaction (PCR) approaches. The first includes conventional multiplex PCR in which electrophoretic migration of different sizes of bands allowed identification of the fish species. The second approach, involving real-time PCR, produced a single amplicon from each species that showed different Tm values allowing the fish groups to be directly identified. Real-time PCR allows the quick differential diagnosis of the three groups of species and high-throughput screening of multiple samples. Neither PCR system cross-reacted with DNA samples from 41 common marketed fish species, thus conforming to standards for species validation. The use of these two PCR-based methods makes it now possible to discriminate grouper from substitute fish species.

Using extirpation to evaluate ionic tolerance of freshwater fish.

PubMed

Griffith, Michael B; Zheng, Lei; Cormier, Susan M

2018-03-01

Field data of fish occurrences and specific conductivity were used to estimate the tolerance of freshwater fish to elevated ion concentrations and to compare the differences between species- and genus-level analyses for individual effects. We derived extirpation concentrations at the 95th percentile (XC95) of a weighted cumulative frequency distribution for fish species inhabiting streams of the central and southern Appalachians by customizing methods used previously with macroinvertebrate genera. Weighting factors were calculated based on the number of sites in basins where each species occurred, reducing overweighting observations of species restricted to fewer basins. Comparing the species- and genus-level fish XC95 values, XC95s for fish genera were near the XC95s for the most salt-tolerant species in the genus. Therefore, a genus-level effect threshold is not reliably predictive of species-level extirpation, unless the genus is monospecific in the assessed assemblage. Of the 101 fish species XC95 values, 5% were <509 and 10% were <565 µS/cm. The lowest XC95 for a species was 322 µS/cm, which is >300 µS/cm, the exposure estimated to extirpate 5% of macroinvertebrate genera in the central Appalachians. Above 509 µS/cm, 41 of the 101 species are expected to decline in occurrence. Environ Toxicol Chem 2018;37:871-883. Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America. Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.

Implications of movement for species distribution models - Rethinking environmental data tools.

PubMed

Bruneel, Stijn; Gobeyn, Sacha; Verhelst, Pieterjan; Reubens, Jan; Moens, Tom; Goethals, Peter

2018-07-01

Movement is considered an essential process in shaping the distributions of species. Nevertheless, most species distribution models (SDMs) still focus solely on environment-species relationships to predict the occurrence of species. Furthermore, the currently used indirect estimates of movement allow to assess habitat accessibility, but do not provide an accurate description of movement. Better proxies of movement are needed to assess the dispersal potential of individual species and to gain a more practical insight in the interconnectivity of communities. Telemetry techniques are rapidly evolving and highly capable to provide explicit descriptions of movement, but their usefulness for SDMs will mainly depend on the ability of these models to deal with hitherto unconsidered ecological processes. More specifically, the integration of movement is likely to affect the environmental data requirements as the connection between environmental and biological data is crucial to provide reliable results. Mobility implies the occupancy of a continuum of space, hence an adequate representation of both geographical and environmental space is paramount to study mobile species distributions. In this context, environmental models, remote sensing techniques and animal-borne environmental sensors are discussed as potential techniques to obtain suitable environmental data. In order to provide an in-depth review of the aforementioned methods, we have chosen to use the modelling of fish distributions as a case study. The high mobility of fish and the often highly variable nature of the aquatic environment generally complicate model development, making it an adequate subject for research. Furthermore, insight into the distribution of fish is of great interest for fish stock assessments and water management worldwide, underlining its practical relevance. Copyright © 2018 Elsevier B.V. All rights reserved.

New locality record for Haplorchoides mehrai and possible interactions with Opisthorchis viverrini metacercariae in cyprinid fishes in Northeast Thailand.

PubMed

Manpratum, Yupin; Kaewkes, Wanlop; Echaubard, Pierre; Sripa, Banchob; Kaewkes, Sasithorn

2017-02-01

Metacercariae of Opisthorchis viverrini, a carcinogenic liver fluke, and Haplorchoides sp., a trematode maturing in catfish, are commonly found in cyprinid fish, the second intermediate hosts of both flukes. However, the specific identity of Haplorchoides sp. in Thailand and a precise assessment of the effects of co-infections with O. viverrini have never been clarified. Therefore, we aimed to identify the species of Haplorchoides and to investigate possible interactions of the two trematode species in cyprinid fishes. Based on the morphology and morphometry of the cercaria, metacercaria, and adult stages, the Haplorchoides species found was identified as Haplorchoides mehrai Pande and Shukla 1976. Thailand is formally recorded as a new locality for H. mehrai, where naturally infected hosts include the snail Melanoides tuberculata (first intermediate host), the cyprinid fishes Hampala dispar, Cyclocheilichthys apogon, Puntius leiacanthus, Labiobarbus burmanicus, and Cirrhina jullieni (second intermediate hosts), and a catfish, Mystus nemurus (definitive host). The co-infection rates of O. viverrini and H. mehrai were significantly associated with fish species and fish body region (P < 0.001), with an overall significantly higher average intensity of H. mehrai (126.26 metacercariae/fish) than that of O. viverrini (18.02 metacercariae/fish). Further work is required to demonstrate the extent and mechanisms of possible interactions between these trematode species in the fish host. These data may provide a better understanding of O. viverrini transmission dynamics, and help design integrated control interventions.

Bipartite networks improve understanding of effects of waterbody size and angling method on angler–fish interactions

USGS Publications Warehouse

Chizinski, Christopher J.; Martin, Dustin R.; Shizuka, Daizaburo; Pope, Kevin L.

2018-01-01

Networks used to study interactions could provide insights to fisheries. We compiled data from 27 297 interviews of anglers across waterbodies that ranged in size from 1 to 12 113 ha. Catch rates of fish species among anglers grouped by species targeted generally differed between angling methods (bank or boat). We constructed angler–catch bipartite networks (angling method specific) between anglers and fish and measured several network metrics. There was considerable variation in networks among waterbodies, with multiple metrics influenced by waterbody size. Number of species-targeting angler groups and number of fish species caught increased with increasing waterbody size. Mean number of links for species-targeting angler groups and fish species caught also increased with waterbody size. Connectance (realized proportion of possible links) of angler–catch interaction networks decreased slower for boat anglers than for bank anglers with increasing waterbody size. Network specialization (deviation of number of interactions from expected) was not significantly related to waterbody size or angling methods. Application of bipartite networks in fishery science requires careful interpretation of outputs, especially considering the numerous confounding factors prevalent in recreational fisheries.

Impacts of golden alga Prymnesium parvum on fish populations in reservoirs of the upper Colorado River and Brazos River basins, Texas

USGS Publications Warehouse

VanLandeghem, Matthew M.; Farooqi, Mukhtar; Farquhar, B.; Patino, Reynaldo

2013-01-01

Several reservoirs in the upper Colorado River and Brazos River basins in Texas have experienced toxic blooms of golden alga Prymnesium parvum and associated fish kills since 2001. There is a paucity of information, however, regarding the population-level effects of such kills in large reservoirs, species-specific resistance to or recovery from kills, or potential differences in the patterns of impacts among basins. We used multiple before-after, control-impact analysis to determine whether repeated golden alga blooms have led to declines in the relative abundance and size structure of fish populations. Sustained declines were noted for 9 of 12 fish species surveyed in the upper Colorado River, whereas only one of eight species was impacted by golden alga in the Brazos River. In the upper Colorado River, White Bass Morone chrysops, White Crappie Pomoxis annularis, Largemouth Bass Micropterus salmoides, Bluegill Lepomis macrochirus, River Carpsucker Carpiodes carpio, Freshwater Drum Aplodinotus grunniens, Channel Catfish Ictalurus punctatus, Flathead Catfish Pylodictis olivaris, and Blue Catfish I. furcatus exhibited sustained declines in relative abundance, size structure, or both; Gizzard Shad Dorosoma cepedianum, Longnose Gar Lepisosteus osseus, and Common Carp Cyprinus carpio did not exhibit those declines. In the Brazos River, only the relative abundance of Blue Catfish was impacted. Overall, toxic golden alga blooms can negatively impact fish populations over the long-term, but the patterns of impact can vary considerably among river basins and species. In the Brazos River, populations of most fish species appear to be healthy, suggesting a positive angling outlook for this basin. In the upper Colorado River, fish populations have been severely impacted, and angling opportunities have been reduced. Basin-specific management plans aimed at improving water quality and quantity will likely reduce bloom intensity and allow recovery of fish populations to the abundances and size structures present before golden alga. Received August 26, 2011; accepted November 25, 2012

Species-specific preferences of German recreational anglers for freshwater fishing experiences, with emphasis on the intrinsic utilities of fish stocking and wild fishes.

PubMed

Arlinghaus, R; Beardmore, B; Riepe, C; Meyerhoff, J; Pagel, T

2014-12-01

To answer the question, whether anglers have an intrinsic preference for stocking or a preference for catch outcomes (e.g. catch rates) believed to be maintained by stocking, a discrete choice experiment was conducted among a sample of anglers (n = 1335) in Lower Saxony, Germany. After controlling for catch aspects of the fishing experience, no significant influence of two stocking attributes (stocking frequency and composition of the catch in terms of wild v. hatchery fishes) on the utility gained from fishing was found for any of the freshwater species that were studied. It was concluded that the previously documented large appreciation of fish stocking by anglers may be indicative of an underlying preference for sufficiently high catches rather than reflect an intrinsic preference for stocking or the catching of wild fishes per se. © 2014 The Fisheries Society of the British Isles.

LC-MS/MS Identification of Species-Specific Muscle Peptides in Processed Animal Proteins.

PubMed

Marchis, Daniela; Altomare, Alessandra; Gili, Marilena; Ostorero, Federica; Khadjavi, Amina; Corona, Cristiano; Ru, Giuseppe; Cappelletti, Benedetta; Gianelli, Silvia; Amadeo, Francesca; Rumio, Cristiano; Carini, Marina; Aldini, Giancarlo; Casalone, Cristina

2017-12-06

An innovative analytical strategy has been applied to identify signature peptides able to distinguish among processed animal proteins (PAPs) derived from bovine, pig, fish, and milk products. Proteomics was first used to elucidate the proteome of each source. Starting from the identified proteins and using a funnel based approach, a set of abundant and well characterized peptides with suitable physical-chemical properties (signature peptides) and specific for each source was selected. An on-target LC-ESI-MS/MS method (MRM mode) was set up using standard peptides and was then applied to selectively identify the PAP source and also to distinguish proteins from bovine carcass and milk proteins. We believe that the method described meets the request of the European Commission which has developed a strategy for gradually lifting the "total ban" toward "species to species ban", therefore requiring official methods for species-specific discrimination in feed.

SE Asian freshwater fish population and networks: the impacts of climatic and environmental change on a vital resource

NASA Astrophysics Data System (ADS)

Santos, Rita; Parsons, Daniel; Cowx, Ian

2016-04-01

The Mekong River is the 10th largest freshwater river in the world, with the second highest biodiversity wealth, behind the much larger Amazon basin. The fisheries activity in the Lower Mekong countries counts for 2.7 million tons of fish per year, with an estimated value worth up to US 7 billion. For the 60 million people living in the basin, fish represent their primary source of economic income and protein intake, with an average per capita consumption estimated at 45.4 Kg. The proposed hydropower development in the basin is threatening its sustainability and resilience. Such developments affect fish migration patterns, hydrograph flood duration and magnitudes and sediment flux. Climate change is also likely to impact the basin, exacerbating the issues created by development. As a monsoonal system, the Mekong River's pronounced annual flood pulse cycle is important in creating variable habitat for fish productivity. Moreover, the annual flood also triggers fish migration and provides vital nutrients carried by the sediment flux. This paper examines the interactions between both dam development and climate change scenarios on fish habitat and habitat connectivity, with the aim of predicting how these will affect fish species composition and fisheries catch. The project will also employ Environmental DNA (eDNA) to quantify and understand the species composition of this complex and large freshwater system. By applying molecular analysis, it is possible to trace species abundance and migration patterns of fish and evaluate the ecological networks establish between an inland system. The aim of this work is to estimate, using process-informed models, the impacts of the proposed dam development and climate change scenarios on the hydrological and hydraulic conditions of habitat availability for fish. Furthermore, it will evaluate the connectivity along the Mekong and its tributaries, and the importance of maintaining these migration pathways, used by a great diversity of fish species. It will also present the preliminary findings on eDNA analysis for species composition and the ecological networks established along the river and particularly on the fish hotspot place for biodiversity, the Tonle Sap system in Cambodia. Keywords: Mekong River, climate change, fish production, dams, eDNA analysis, numerical modelling.

Acute toxicity value extrapolation with fish and aquatic invertebrates

USGS Publications Warehouse

Buckler, Denny R.; Mayer, Foster L.; Ellersieck, Mark R.; Asfaw, Amha

2005-01-01

Assessment of risk posed by an environmental contaminant to an aquatic community requires estimation of both its magnitude of occurrence (exposure) and its ability to cause harm (effects). Our ability to estimate effects is often hindered by limited toxicological information. As a result, resource managers and environmental regulators are often faced with the need to extrapolate across taxonomic groups in order to protect the more sensitive members of the aquatic community. The goals of this effort were to 1) compile and organize an extensive body of acute toxicity data, 2) characterize the distribution of toxicant sensitivity across taxa and species, and 3) evaluate the utility of toxicity extrapolation methods based upon sensitivity relations among species and chemicals. Although the analysis encompassed a wide range of toxicants and species, pesticides and freshwater fish and invertebrates were emphasized as a reflection of available data. Although it is obviously desirable to have high-quality acute toxicity values for as many species as possible, the results of this effort allow for better use of available information for predicting the sensitivity of untested species to environmental contaminants. A software program entitled “Ecological Risk Analysis” (ERA) was developed that predicts toxicity values for sensitive members of the aquatic community using species sensitivity distributions. Of several methods evaluated, the ERA program used with minimum data sets comprising acute toxicity values for rainbow trout, bluegill, daphnia, and mysids provided the most satisfactory predictions with the least amount of data. However, if predictions must be made using data for a single species, the most satisfactory results were obtained with extrapolation factors developed for rainbow trout (0.412), bluegill (0.331), or scud (0.041). Although many specific exceptions occur, our results also support the conventional wisdom that invertebrates are generally more sensitive to contaminants than fish are.

Effects of pharmaceuticals present in aquatic environment on Phase I metabolism in fish.

PubMed

Burkina, Viktoriia; Zlabek, Vladimir; Zamaratskaia, Galia

2015-09-01

The fate of pharmaceuticals in aquatic environments is an issue of concern. Current evidence indicates that the risks to fish greatly depend on the nature and concentrations of the pharmaceuticals and might be species-specific. Assessment of risks associated with the presence of pharmaceuticals in water is hindered by an incomplete understanding of the metabolism of these pharmaceuticals in aquatic species. In mammals and fish, pharmaceuticals are primarily metabolized by cytochrome P450 enzymes (CYP450). Thus, CYP450 activity is a crucial factor determining the detoxification abilities of organisms. Massive numbers of toxicological studies have investigated the interactions of human pharmaceuticals with detoxification systems in various fish species. In this paper, we review the effects of pharmaceuticals found in aquatic environments on fish hepatic CYP450. Moreover, we discuss the roles of nuclear receptors in cellular regulation and the effects of various groups of chemicals on fish, presented in the recent literature. Copyright © 2015 Elsevier B.V. All rights reserved.

Patterns of fish assemblage structure and habitat use among main- and side-channel environments in the lower Kootenai River, Idaho

USGS Publications Warehouse

Watkins, Carson J.; Stevens, Bryan S.; Quist, Michael C.; Shepard, Bradley B.; Ireland, Susan C.

2015-01-01

The lower Kootenai River, Idaho, was sampled during the summers of 2012 and 2013 to evaluate its fish assemblage structure at seven sites within main- and side-channel habitats where large-scale habitat rehabilitation was undertaken. Understanding the current patterns of fish assemblage structure and their relationships with habitat is important for evaluating the effects of past and future rehabilitation projects on the river. Species-specific habitat associations were modeled, and the variables that best explained the occurrence and relative abundance of fish were identified in order to guide future habitat rehabilitation so that it benefits native species. The results indicated that the side-channel habitats supported higher species richness than the main-channel habitats and that nonnative fishes were closely associated with newly rehabilitated habitats. This research provides valuable insight on the current fish assemblages in the Kootenai River and the assemblage-level responses that may occur as a result of future rehabilitation activities.

Manipulations of the reproductive system of fishes by means of exogenous chemicals

USGS Publications Warehouse

Patino, R.

1997-01-01

Environmental control of reproductive activity of captive fish is feasible (or potentially feasible) but, with few exceptions, is currently impractical for most species. Therefore, chemical methods of manipulating reproductive activity continue to be widely used in fish production operations worldwide. However, the control of fish reproduction in captivity cannot be exercised without regard to adequate environmental conditions, which can differ markedly for different species. This review provides a synopsis of relevant aspects of fish reproductive physiology and addresses current and promising future chemical methods of sex control, gonadal recrudescence, and spawning. Most research on the control of reproduction in fishes has focused on female physiology because ovarian development and maturation are easily disturbed by environmental stressors. Control of sex ratios by steroid treatment has become a well-established technique for several fish species, but the technique continues to be problematic in some cases. Final gonadal growth and spawning usually can be achieved by implant treatment with gonadotropin-releasing hormone analogs (GnRHa), which in some species have to be applied in combination with dopamine antagonists to enhance responsiveness to GnRHa. However, efforts to accelerate gonadal recrudescence and maturational competence by chemical means have yielded mixed results, reflecting a relative lack of understanding of the basic physiological and biochemic mechanisms controlling these processes. The potential benefits of using reproductive pheromone, to manipulate gonadal development and spawning has been demonstrated in a few species, but further research is needed to determine whether this technique is applicable to fish culture. Because a reliable supply of young fish is critical for the expansion and diversification of fish culture operations, the use of chemicals in combination with adequate environmental conditions to contain gametogenesis and spawning in fishes will continue to be an important tool for the fish culture.

Two gonad-infecting species of Philometra (Nematoda: Philometridae) from marine fishes off the northern coast of Australia

PubMed Central

Moravec, František; Barton, Diane P.

2015-01-01

Two different gonad-infecting species of Philometra Costa, 1845 were collected from the ovary of marine perciform fishes, the blackspotted croaker Protonibea diacanthus (Sciaenidae) and the John’s snapper Lutjanus johnii (Lutjanidae), from off the northern coast of Australia. Nematodes (males and females) from P. diacanthus represent a new taxon, Philometra protonibeae n. sp., which is mainly characterized by the body length of the males (3.37–3. 90 mm), broad, equally long spicules (length 126–141 μm) and the shape and structure of the gubernaculum with a dorsally lamellate distal tip. The nematodes (only females) from L. johnii may represent an undescribed species, but, because of the absence of conspecific males, they could not be specifically identified. Philometra protonibeae is the fifth nominal gonad-infecting species of this genus recorded from marine fishes in Australian waters and the seventh species of these parasites described from fishes of the family Sciaenidae. PMID:25654578

Comparative molecular cytogenetic analyses of a major tandemly repeated DNA family and retrotransposon sequences in cultivated jute Corchorus species (Malvaceae)

PubMed Central

Begum, Rabeya; Zakrzewski, Falk; Menzel, Gerhard; Weber, Beatrice; Alam, Sheikh Shamimul; Schmidt, Thomas

2013-01-01

Background and Aims The cultivated jute species Corchorus olitorius and Corchorus capsularis are important fibre crops. The analysis of repetitive DNA sequences, comprising a major part of plant genomes, has not been carried out in jute but is useful to investigate the long-range organization of chromosomes. The aim of this study was the identification of repetitive DNA sequences to facilitate comparative molecular and cytogenetic studies of two jute cultivars and to develop a fluorescent in situ hybridization (FISH) karyotype for chromosome identification. Methods A plasmid library was generated from C. olitorius and C. capsularis with genomic restriction fragments of 100–500 bp, which was complemented by targeted cloning of satellite DNA by PCR. The diversity of the repetitive DNA families was analysed comparatively. The genomic abundance and chromosomal localization of different repeat classes were investigated by Southern analysis and FISH, respectively. The cytosine methylation of satellite arrays was studied by immunolabelling. Key Results Major satellite repeats and retrotransposons have been identified from C. olitorius and C. capsularis. The satellite family CoSat I forms two undermethylated species-specific subfamilies, while the long terminal repeat (LTR) retrotransposons CoRetro I and CoRetro II show similarity to the Metaviridea of plant retroelements. FISH karyotypes were developed by multicolour FISH using these repetitive DNA sequences in combination with 5S and 18S–5·8S–25S rRNA genes which enable the unequivocal chromosome discrimination in both jute species. Conclusions The analysis of the structure and diversity of the repeated DNA is crucial for genome sequence annotation. The reference karyotypes will be useful for breeding of jute and provide the basis for karyotyping homeologous chromosomes of wild jute species to reveal the genetic and evolutionary relationship between cultivated and wild Corchorus species. PMID:23666888

Can species traits predict the susceptibility of riverine fish to water resource development? An Australian case study.

PubMed

Rolls, Robert J; Sternberg, David

2015-06-01

Water resource developments alter riverine environments by disrupting longitudinal connectivity, transforming lotic habitats, and modifying in-stream hydraulic conditions. Effective management of anthropogenic disturbances therefore requires an understanding of the range of potential ecosystem effects and the inherent traits symptomatic of elevated vulnerability to disturbance. Using 42 riverine fish native to South Eastern Australia as a case study, we quantified six morphological, behavioral, and life-history traits to classify species into groups reflecting potential differences in their response to ecosystem changes as a result of water resource development. Classification analysis identified five strategies based on fish life-history dispersal requirements, climbing potential, and habitat preference. These strategies in turn highlight the potential species at risk from the separate impacts of water resource development and inform management decisions to mitigate those risks. Swimming ability did not contribute to distinguishing species into functional groups, likely due to methodological inconsistencies in quantifying swimming performance that may ultimately hinder the ability of fish passage facilities to function within the physical capabilities of species at risk of habitat fragmentation. This study improves our ability to predict the performance of groups of species at risk from the multiple environmental changes imposed by humans and goes beyond broad-scale dispersal requirements as a predictor of individual species response.

Environmental factors structuring fish composition and assemblages in a small macrotidal estuary (eastern English Channel)

NASA Astrophysics Data System (ADS)

Selleslagh, Jonathan; Amara, Rachid

2008-09-01

The fish assemblage structure was analyzed along an estuarine gradient of a small macrotidal estuary (the Canche, France). Fishes were collected every two months between May 2006 and July 2007 from 12 sampling stations using a 1.5-m beam trawl with a 5 mm mesh size in the cod end. To complement this information, sampling was also performed using 15-m fyke nets (8 mm mesh size in the cod end). For each sample, abiotic (temperature, salinity, pH, oxygen, turbidity, river flow, wind speed and depth) and biotic (macro crustacean species abundances) were recorded. Throughout the study, 28 fish species belonging to 20 families were collected. Fish catches were dominated by juveniles, especially Young-Of-the-Year (YOY) for the majority of the species. According to the Index of Relative Importance (IRI), common goby Pomatoschistus microps, flounder Platichtys flesus, sprat Sprattus sprattus, sea-bass Dicentrarchus labrax and plaice Pleuronectes platessa were the most abundant species, together accounting for 99.2% of the total IRI. Estuarine residents (ER = 66.2%) and marine juvenile migrants species (MJ = 31.4%) were the most important ecological guilds. The structure of the fish assemblage and its relationship to environmental variables was examined using multivariate techniques. Cluster and non-metric multidimensional scaling (nMDS) analysis defined six distinct groups in the Canche estuary, which are discriminated by specific species (SIMPER). Spatio-temporal variations in fish assemblage structure reflect the density peaks of the most abundant species. Spearman rank correlations and canonical correspondence analysis (CCA) showed that among the ten environmental variables examined, temperature, salinity and Crangon crangon (a potential predator for YOY fish or prey for older ones) are the three most important factors influencing fish species richness and abundances. Our observations reinforce the idea that certain fish species may have different life history styles in different geographic areas. The present study highlights the necessity of a better knowledge of the connectivity between estuaries and adjacent marine areas. The Canche constitutes an important ecosystem for fishes and as it is subject to little anthropogenic disturbance; its ichthyofauna can be viewed as a reference or normal assemblage for small temperate macrotidal estuaries.

Ammonia and urea handling by early life stages of fishes.

PubMed

Zimmer, Alex M; Wright, Patricia A; Wood, Chris M

2017-11-01

Nitrogen metabolism in fishes has been a focus of comparative physiologists for nearly a century. In this Review, we focus specifically on early life stages of fishes, which have received considerable attention in more recent work. Nitrogen metabolism and excretion in early life differs fundamentally from that of juvenile and adult fishes because of (1) the presence of a chorion capsule in embryos that imposes a limitation on effective ammonia excretion, (2) an amino acid-based metabolism that generates a substantial ammonia load, and (3) the lack of a functional gill, which is the primary site of nitrogen excretion in juvenile and adult fishes. Recent findings have shed considerable light on the mechanisms by which these constraints are overcome in early life. Perhaps most importantly, the discovery of Rhesus (Rh) glycoproteins as ammonia transporters and their expression in ion-transporting cells on the skin of larval fishes has transformed our understanding of ammonia excretion by fishes in general. The emergence of larval zebrafish as a model species, together with genetic knockdown techniques, has similarly advanced our understanding of ammonia and urea metabolism and excretion by larval fishes. It has also now been demonstrated that ammonia excretion is one of the primary functions of the developing gill in rainbow trout larvae, leading to new hypotheses regarding the physiological demands driving gill development in larval fishes. Here, we highlight and discuss the dramatic changes in nitrogen handling that occur over early life development in fishes. © 2017. Published by The Company of Biologists Ltd.

Spatial and seasonal variations of fish assemblages in mangrove creek systems in Zanzibar (Tanzania)

NASA Astrophysics Data System (ADS)

Mwandya, Augustine W.; Gullström, Martin; Andersson, Mathias H.; Öhman, Marcus C.; Mgaya, Yunus D.; Bryceson, Ian

2010-11-01

Spatial and seasonal variations of fish assemblage composition were studied in three non-estuarine mangrove creeks of Zanzibar (Tanzania). Fish were collected monthly for one year at three sites (lower, intermediate and upper reaches) in each creek using a seine net (each haul covering 170 m 2). Density, species number and diversity of fish were all higher at sites with dense cover of macrophytes (seagrass and macroalgae) than over unvegetated sandy sites. In general, fish assemblages mainly comprised juveniles of a few abundant taxa, e.g. Mugil cephalus, Mugilidae spp. and Leiognathus equulus at sites with mud substratum and Gerres oyena, Lethrinus harak and Sillago sihama at sites dominated by macrophytes. Multivariate analyses revealed significant separations in fish assemblage composition within the two creeks where the bottom substratum differed among sites. Overall, season seemed to have little effect on density, species number, diversity index ( H') and assemblage structure of fish. Water condition variables were also relatively stable across the season, although a short-term fluctuation primarily induced by decreased salinity, occurred during the heavy rains in April and May. Fish assemblage structure was not significantly affected by any of the abiotic factors tested. However, significant regressions were found between the other fish variables and environmental variables, but since these associations were mostly species-specific and generally inconsistent, we suggest that the overall distribution patterns of fish were mainly an effect of particular substrate preferences of fish species rather than contemporary water conditions.

[Fish community structure and its seasonal change in subtidal sandy beach habitat off southern Gouqi Island].

PubMed

Wang, Zhen-Hua; Wang, Kai; Zhao, Jing; Zhang, Shou-Yu

2011-05-01

To understand the characteristics of fish community structure in sandy beach habitats of island reef water areas, and to evaluate the potential capacity of these habitats in local fish stock maintenance, fishes were monthly collected with multi-mesh trammel nets in 2009 from the subtidal sandy beach habitat off southern Gouqi Island, taking the adjacent rocky reef habitat as the control. alpha and beta species diversity indices, index of relative importance (IRI), relative catch rate, and dominance curve for abundance and biomass (ABC curve) were adopted to compare the fish species composition, diversity, and community pattern between the two habitats, and multivariate statistical analyses such as non-metric multidimensional scaling (nMDS) and cluster were conducted to discuss the fish assemblage patterns. A total of 63 fish species belonging to 11 orders, 38 families, and 56 genera were collected, of which, 46 fish species were appeared in the two habitats. Due to the appearance of more warm water species in sandy bottom, the fishes in subtidal sandy beach habitat showed much higher richness, and the abundance catch rate (ACR) from May to July was higher than that in rocky reef habitat. In most rest months, the ACR in subtidal sandy beach habitat also showed the similar trend. However, the species richness and diversity in spring and summer were significantly lower in subtidal sandy beach habitat than in rocky reef habitat, because of the high species dominance and low evenness in the sandy beach habitat. Japanese tonguefish (Paraplagusia japonica) was the indicator species in the sandy beach habitat, and dominated in early spring, later summer, autumn, and winter when the fishing pressure was not strong. In sandy bottom, a unique community structure was formed and kept in dynamic, due to the nursery use of sandy beach by Japanese anchovy (Engraulis japonicus) from May to July, the gathering of gray mullet (Mugil cephalus) in most months for feeding, and the large quantity appearance of plotosid catfish (Plotosus anguillaris) in early Autumn, which was quite different from the community structure pattern dominated by reef fishes in rocky-algae habitat. The subtidal sandy bottom off Gouqi Island was serving as both nursery and feeding grounds for many fish species, being a suitable habitat for flatfishes. It was concluded that the sandy beaches around Gouqi Island could be a very important habitat for economic fish species, especially as a nursery ground for juvenile fishes, contributing to the fish stock maintenance in specific area.

Identifying bio-physical, social and political challenges to catchment governance for sustainable freshwater fisheries in West Africa: Systems overview through scenario development in the SUSFISH project.

NASA Astrophysics Data System (ADS)

Sendzimir, Jan; Slezak, Gabriele; Melcher, Andreas

2015-04-01

Chronic and episodic water scarcity prompted construction of 1400 reservoirs in Burkina Faso since 1950, greatly expanding fisheries production. These fisheries provided an increasingly important protein source for a population that has risen 600% since 1920, but production has plateaued, and dramatic declines in adult fish size suggest these fisheries are not sustainable. The SUSFISH project joined Austrian and Burkinabe scientists to increase local capacities to manage fisheries sustainably. SUSFISH has successfully increased capacity to monitor fish populations, identify endangered species, and use specific fish and macroinvertebrate species as bio-indicators of water and habitat quality as well as anthropogenic pressures. But projects to support sustainable development in Africa have a long history of failure if only based on transfer of technology and theory based on bio-physical sciences. This paper describes the processes and products of knowledge elicitation, scenario development and systems analysis to identify barriers and bridges to long-term sustainable fisheries development that arise from bio-physical, social, political and cultural causes, and, especially, interactions between them. Lessons learned and important on-going research questions are identified for both the natural and social sciences as they apply to managing catchments at multiple scales of governance, from local to national.

The effects of substratum material and surface orientation on the developing epibenthic community on a designed artificial reef.

PubMed

Ushiama, Shinjiro; Smith, James A; Suthers, Iain M; Lowry, Michael; Johnston, Emma L

2016-10-01

Artificial reefs provide shelter and can be an important source of food for fish depending on the epibenthic community on the structure. The growth and diversity of this community is influenced by the substratum material and the surface orientation of the reef. Settlement plates of four materials (Perspex, sandstone, wood and steel) were deployed in three orientations (upwards, downwards and vertical) at a depth of 33 m on a designed artificial reef (DAR) off the coast of Sydney, Australia. After three months, the steel surfaces had lower invertebrate species richness, total abundance and diversity compared to other surfaces. Steel was not an ideal material for the initial recruitment and growth of epibenthic invertebrates. A longer duration would be required to develop a mature epibenthic community. Surface orientation had species-specific impacts. Surface material and orientation are important factors for developing epibenthic assemblages, and are thus likely to affect the broader artificial reef assemblage, including fish.

An O-"fish"-ial Research Project

ERIC Educational Resources Information Center

Newman, James; Krustchinsky, Rick; Vanek, Karen; Nguyen, Kim-Thoa

2009-01-01

In this "O-"fish"-ial" research project, third-grade students use multiple resources to research several fish species, write a research paper and develop a PowerPoint presentation to communicate their findings. In addition, students actually examine these species up close with samples from the local market, and then conclude the project with a…

Spatio-Temporal Dynamics of Exploited Groundfish Species Assemblages Faced to Environmental and Fishing Forcings: Insights from the Mauritanian Exclusive Economic Zone

PubMed Central

Kidé, Saïkou Oumar; Manté, Claude; Dubroca, Laurent; Demarcq, Hervé; Mérigot, Bastien

2015-01-01

Environmental changes and human activities can have strong impacts on biodiversity and ecosystem functioning. This study investigates how, from a quantitative point of view, simultaneously both environmental and anthropogenic factors affect species composition and abundance of exploited groundfish assemblages (i.e. target and non-target species) at large spatio-temporal scales. We aim to investigate (1) the spatial and annual stability of groundfish assemblages, (2) relationships between these assemblages and structuring factors in order to better explain the dynamic of the assemblages’ structure. The Mauritanian Exclusive Economic Zone (MEEZ) is of particular interest as it embeds a productive ecosystem due to upwelling, producing abundant and diverse resources which constitute an attractive socio-economic development. We applied the multi-variate and multi-table STATICO method on a data set consisting of 854 hauls collected during 14-years (1997–2010) from scientific trawl surveys (species abundance), logbooks of industrial fishery (fishing effort), sea surface temperature and chlorophyll a concentration as environmental variables. Our results showed that abiotic factors drove four main persistent fish assemblages. Overall, chlorophyll a concentration and sea surface temperature mainly influenced the structure of assemblages of coastal soft bottoms and those of the offshore near rocky bottoms where upwellings held. While highest levels of fishing effort were located in the northern permanent upwelling zone, effects of this variable on species composition and abundances of assemblages were relatively low, even if not negligible in some years and areas. The temporal trajectories between environmental and fishing conditions and assemblages did not match for all the entire time series analyzed in the MEEZ, but interestingly for some specific years and areas. The quantitative approach used in this work may provide to stakeholders, scientists and fishers a useful assessment for the spatio-temporal dynamics of exploited assemblages under stable or changing conditions in fishing and environment. PMID:26505198

Myxozoan pathogens in cultured Malaysian fishes. II. Myxozoan infections of redtail catfish Hemibagrus nemurus in freshwater cage cultures.

PubMed

Molnár, K; Székely, C; Mohamed, K; Shaharom-Harrison, F

2006-03-02

Cage-cultured Asian redtail catfish Hemibagrus nemurus (Valenciennes, 1840), a popular food fish in Southeast Asia, proved to be infected by 3 myxozoan species. All the 3 species belonged to the genus Henneguya: 2 were identified as H. mystusia Sarkar, 1985 and H. hemibagri Tchang et Ma, 1993, while the other was described as H. basifilamentalis sp. n. All plasmodia were found in the gills and were characterised by a specific site selection. H. mystusia formed plasmodia in the multi-layered epithelium between the gill lamellae and in the non-lamellar edge of the gill filaments, while H. hemibagri developed in the capillary network of the lamellae. H. basifilamentalis sp. n. had large oval plasmodia located deep among the filaments just above the gill arch.

Population and habitat viability assessments for Golden-cheeked Warblers and Black-capped Vireos: Usefulness to Partners in Flight Conservation Planning

USGS Publications Warehouse

Beardmore, C.J.; Hatfield, J.S.; Bonney, Rick; Pashley, David N.; Cooper, Robert; Niles, Larry

2000-01-01

Golden-cheeked Warblers and Black-capped Vireos are Neotropical migratory birds that are federally listed as endangered. Recovery plans for both species advise the use of viability modeling as a tool for setting specific recovery and management targets. Population and Habitat Viability Assessment workshops were conducted to develop population targets and conservation recommendations for these species. Results of the workshops were based on modeling demographic and environmental factors, as well as discussions of management issues, management options, and public outreach strategies. The approach is intended to be iterative, and to be tracked by research and monitoring efforts. This paper discusses the consensus-building workshop process and how the approach could be useful to Partners in Flight. Population and Habitat Viability Assessments (PHVA) were used to develop population targets and conservation recommendations for Golden-cheeked Warblers (Dendroica chrysoparia) and Black-capped Vireos (Vireo atricapillus). This paper explains what PHVAs are, discusses how they are conducted, describes the general results that are produced, and suggests how Partners in Flight (PIF) might use a similar process for bird conservation planning. Detailed results of the assessments are not discussed here; however they can be found elsewhere (U. S. Fish and Wildlife Service 1996a, U. S. Fish and Wildlife Service 1996b). PHVAs were considered for Golden-cheeked Warblers and Black-capped Vireos because they are controversial, endangered species, and the species? recovery plans list PHVAs as tools to develop recovery recommendations. The U. S. Fish and Wildlife Service (USFWS) realized that the data needed to perform PHVAs for these species is limited, but that various conservation efforts, such as the Balcones Canyonlands Conservation Plan and other endeavors, were proceeding without benefit of the biological summarization and guidance that a PHVA could provide.

Sequential Cross-Species Chromosome Painting among River Buffalo, Cattle, Sheep and Goat: A Useful Tool for Chromosome Abnormalities Diagnosis within the Family Bovidae

PubMed Central

Pauciullo, Alfredo; Perucatti, Angela; Cosenza, Gianfranco; Iannuzzi, Alessandra; Incarnato, Domenico; Genualdo, Viviana; Di Berardino, Dino; Iannuzzi, Leopoldo

2014-01-01

The main goal of this study was to develop a comparative multi-colour Zoo-FISH on domestic ruminants metaphases using a combination of whole chromosome and sub-chromosomal painting probes obtained from the river buffalo species (Bubalus bubalis, 2n = 50,XY). A total of 13 DNA probes were obtained through chromosome microdissection and DOP-PCR amplification, labelled with two fluorochromes and sequentially hybridized on river buffalo, cattle (Bos taurus, 2n = 60,XY), sheep (Ovis aries, 2n = 54,XY) and goat (Capra hircus, 2n = 60,XY) metaphases. The same set of paintings were then hybridized on bovine secondary oocytes to test their potential use for aneuploidy detection during in vitro maturation. FISH showed excellent specificity on metaphases and interphase nuclei of all the investigated species. Eight pairs of chromosomes were simultaneously identified in buffalo, whereas the same set of probes covered 13 out 30 chromosome pairs in the bovine and goat karyotypes and 40% of the sheep karyotype (11 out of 27 chromosome pairs). This result allowed development of the first comparative M-FISH karyotype within the domestic ruminants. The molecular resolution of complex karyotypes by FISH is particularly useful for the small chromosomes, whose similarity in the banding patterns makes their identification very difficult. The M-FISH karyotype also represents a practical tool for structural and numerical chromosome abnormalities diagnosis. In this regard, the successful hybridization on bovine secondary oocytes confirmed the potential use of this set of probes for the simultaneous identification on the same germ cell of 12 chromosome aneuploidies. This is a fundamental result for monitoring the reproductive health of the domestic animals in relation to management errors and/or environmental hazards. PMID:25330006

Comparative analysis of Edwardsiella tarda isolates from fish in the eastern United States suggests the existence of two genetically distinct species, Edwardsiella tarda and Edwardsiella pseudotarda sp. nov

USDA-ARS?s Scientific Manuscript database

Edwardsiella tarda, a Gram-negative member of the family Enterobacteriaceae, is often implicated in significant losses in aquaculture facilities worldwide. Here, we assessed the intra-specific variability of a collection of E. tarda isolates from 4 different fish species in the eastern United State...

Approximate sample sizes required to estimate length distributions

USGS Publications Warehouse

Miranda, L.E.

2007-01-01

The sample sizes required to estimate fish length were determined by bootstrapping from reference length distributions. Depending on population characteristics and species-specific maximum lengths, 1-cm length-frequency histograms required 375-1,200 fish to estimate within 10% with 80% confidence, 2.5-cm histograms required 150-425 fish, proportional stock density required 75-140 fish, and mean length required 75-160 fish. In general, smaller species, smaller populations, populations with higher mortality, and simpler length statistics required fewer samples. Indices that require low sample sizes may be suitable for monitoring population status, and when large changes in length are evident, additional sampling effort may be allocated to more precisely define length status with more informative estimators. ?? Copyright by the American Fisheries Society 2007.

Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System.

PubMed

Civade, Raphaël; Dejean, Tony; Valentini, Alice; Roset, Nicolas; Raymond, Jean-Claude; Bonin, Aurélie; Taberlet, Pierre; Pont, Didier

2016-01-01

In the last few years, the study of environmental DNA (eDNA) has drawn attention for many reasons, including its advantages for monitoring and conservation purposes. So far, in aquatic environments, most of eDNA research has focused on the detection of single species using species-specific markers. Recently, species inventories based on the analysis of a single generalist marker targeting a larger taxonomic group (eDNA metabarcoding) have proven useful for bony fish and amphibian biodiversity surveys. This approach involves in situ filtering of large volumes of water followed by amplification and sequencing of a short discriminative fragment from the 12S rDNA mitochondrial gene. In this study, we went one step further by investigating the spatial representativeness (i.e. ecological reliability and signal variability in space) of eDNA metabarcoding for large-scale fish biodiversity assessment in a freshwater system including lentic and lotic environments. We tested the ability of this approach to characterize large-scale organization of fish communities along a longitudinal gradient, from a lake to the outflowing river. First, our results confirm that eDNA metabarcoding is more efficient than a single traditional sampling campaign to detect species presence, especially in rivers. Second, the species list obtained using this approach is comparable to the one obtained when cumulating all traditional sampling sessions since 1995 and 1988 for the lake and the river, respectively. In conclusion, eDNA metabarcoding gives a faithful description of local fish biodiversity in the study system, more specifically within a range of a few kilometers along the river in our study conditions, i.e. longer than a traditional fish sampling site.

Functional diversity measures revealed impacts of non-native species and habitat degradation on species-poor freshwater fish assemblages.

PubMed

Colin, Nicole; Villéger, Sébastien; Wilkes, Martin; de Sostoa, Adolfo; Maceda-Veiga, Alberto

2018-06-01

Trait-based ecology has been developed for decades to infer ecosystem responses to stressors based on the functional structure of communities, yet its value in species-poor systems is largely unknown. Here, we used an extensive dataset in a Spanish region highly prone to non-native fish invasions (15 catchments, N=389 sites) to assess for the first time how species-poor communities respond to large-scale environmental gradients using a taxonomic and functional trait-based approach in riverine fish. We examined total species richness and three functional trait-based indices available when many sites have ≤3 species (specialization, FSpe; originality, FOri and entropy, FEnt). We assessed the responses of these taxonomic and functional indices along gradients of altitude, water pollution, physical habitat degradation and non-native fish biomass. Whilst species richness was relatively sensitive to spatial effects, functional diversity indices were responsive across natural and anthropogenic gradients. All four diversity measures declined with altitude but this decline was modulated by physical habitat degradation (richness, FSpe and FEnt) and the non-native:total fish biomass ratio (FSpe and FOri) in ways that varied between indices. Furthermore, FSpe and FOri were significantly correlated with Total Nitrogen. Non-native fish were a major component of the taxonomic and functional structure of fish communities, raising concerns about potential misdiagnosis between invaded and environmentally-degraded river reaches. Such misdiagnosis was evident in a regional fish index widely used in official monitoring programs. We recommend the application of FSpe and FOri to extensive datasets from monitoring programs in order to generate valuable cross-system information about the impacts of non-native species and habitat degradation, even in species-poor systems. Scoring non-native species apart from habitat degradation in the indices used to determine ecosystem health is essential to develop better management strategies. Copyright © 2018 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cada, Glenn F; Bevelhimer, Mark S

The development of hydrokinetic (HK) energy projects is under consideration at over 150 sites in large rivers in the United States, including the Mississippi, Ohio, Tennessee, and Atchafalaya Rivers. These waterbodies support numerous fish species that might interact with the HK projects in a variety of ways, e.g., by attraction to or avoidance of project structures. Although many fish species inhabit these rivers (about 172 species in the Mississippi River alone), not all of them will encounter the HK projects. Some species prefer low-velocity, backwater habitats rather than the high-velocity, main channel areas that would be the best sites formore » HK. Other, riverbank-oriented species are weak swimmers or too small to inhabit the main channel for significant periods of time. Some larger, main channel fish species are not known to be attracted to structures. Based on a consideration of habitat preferences, size/swim speed, and behavior, fish species that are most likely to be attracted to HK structures in the main channel include carps, suckers, catfish, white bass, striped bass, smallmouth bass, spotted bass, and sauger. Proper siting of the project in order to avoid sensitive fish populations, backwater and fish nursery habitat areas, and fish migration corridors will likely minimize concerns about fish attraction to or avoidance of HK structures.« less

Characterization of the Cultivable Gut Microflora in Wild-Caught 
Mediterranean Fish Species.

PubMed

Jammal, Ahmad; Bariche, Michel; Zu Dohna, Heinrich; Kambris, Zakaria

2017-05-01

Microflora of the gastrointestinal tract plays important roles in food digestion, nutrient absorption and in host defense against ingested pathogens. Several studies have focused on the microflora of farmed fishes, but the gut flora of wild fishes remains poorly characterized. The aim of this work was to provide an overview of the bacteria colonizing the gut of wild-caught fishes and to determine whether some bacterial species can be pathogenic. We isolated cultivable bacteria from fifteen wild-caught Mediterranean fish species corresponding to different habitat, diet and origin. Bacterial species identity was determined by 16s rRNA gene sequencing for the 61 isolates. The potential pathogenicity of isolated bacteria was investigated using fruit fly (Drosophila melanogaster) and zebrafish (Danio rerio) as model organisms. Two bacterial strains (Serratia sp. and Aeromonas salmonicida) were lethal when microinjected to Drosophila, while zebrafish did not develop any disease when exposed to any of 34 isolated bacterial strains. However, it was interesting to note that two bacterial strains (Shewanella and Arthrobacter) isolated from marine fishes were able to colonize the guts of freshwater zebrafish. The results of this study give an overview of the bacterial species found in the guts of wild fishes living off Beirut seashore. It shows that some parameters believed to be limiting factors to host-gut colonization by bacteria can be overcome by some species. This pilot study could be extended by sampling a larger number of fish species with several specimens per fish species, and by identifying uncultivable bacteria that reside in the fish guts. Our results may have implications for the utilization of certain bacterial species in fish farming or their use as bio-indicators for water and/or food quality.

Production and characterization of monoclonal antibodies specific to pangasius catfish, basa, and tra.

PubMed

Gajewski, K G; Chen, Y-T; Hsieh, Y-H P

2009-04-01

Four IgG (subclass IgG1) class monoclonal antibodies (MAbs) strongly reactive to Asian farm-raised Pangasius catfish, tra (Pangasius hypophthalmus) and basa (Pangasius bocourti), have been developed. These MAbs were raised by immunizing an animal with thermal-stable crude sarcoplasmic protein extract of cooked tra. The MAbs were selected by screening hybridoma clones against more than 70 common fish and meat protein extracts. Two MAbs, T7E10 and T1G11, were found to be specific to the Asian Pangasius catfish, tra, and basa, with no cross-reactions with any of the common fish and meat species or with the food additive proteins (bovine serum albumin, soy proteins, milk proteins, egg proteins, and gelatin) tested. MAb T7E10 recognized 2 antigenic proteins (molecular weight approximately 36 and 75 kDa) in raw and cooked tra and basa extracts, while T1G11 bound to several proteins (molecular weight between 13 and 18 kDa) in tra and basa extracts. Two other MAbs, F7B8 and F1G11, recognized a common protein (36 KDa) and cross-reacted with all the fish extracts tested and with several mammalian species. These MAbs can be employed individually or in combination in various formats of immunoassays for rapid identification of Pangasius catfish, either raw or cooked. They can also be used to study the biological, biochemical, and physiological aspects of thermal-stable antigenic proteins. This is the first study identifying these thermal-stable antigenic proteins present in Pangasius catfish as species-specific biomarkers.

Cold physiology: postprandial blood flow dynamics and metabolism in the Antarctic fish Pagothenia borchgrevinki.

PubMed

Sandblom, Erik; Davison, William; Axelsson, Michael

2012-01-01

Previous studies on metabolic responses to feeding (i.e. the specific dynamic action, SDA) in Antarctic fishes living at temperatures below zero have reported long-lasting increases and small peak responses. We therefore hypothesized that the postprandial hyperemia also would be limited in the Antarctic fish Pagothenia borchgrevinki. The proportion of cardiac output directed to the splanchnic circulation in unfed fish was 18%, which is similar to temperate fish species. Contrary to our prediction, however, gastrointestinal blood flow had increased by 88% at twenty four hours after feeding due to a significant increase in cardiac output and a significant decrease in gastrointestinal vascular resistance. While gastric evacuation time appeared to be longer than in comparable temperate species, digestion had clearly commenced twenty four hours after feeding as judged by a reduction in mass of the administered feed. Even so, oxygen consumption did not increase suggesting an unusually slowly developing SDA. Adrenaline and angiotensin II was injected into unfed fish to investigate neuro-humoral control mechanisms of gastrointestinal blood flow. Both agonists increased gastrointestinal vascular resistance and arterial blood pressure, while systemic vascular resistance was largely unaffected. The hypertension was mainly due to increased cardiac output revealing that the heart and the gastrointestinal vasculature, but not the somatic vasculature, are important targets for these agonists. It is suggested that the apparently reduced SDA in P. borchgrevinki is due to a depressant effect of the low temperature on protein assimilation processes occurring outside of the gastrointestinal tract, while the gastrointestinal blood flow responses to feeding and vasoactive substances resemble those previously observed in temperate species.

[Taxonomic and functional diversity of the bycatch fishes community of trawl fishing from Northern Gulf of California, Mexico].

PubMed

Herrera-Valdivia, Eloísa; López-Martínez, Juana; Castillo Vargasmachuca, Sergio; García-Juárez, Rosa

2016-06-01

The Northern Gulf of California (NGC) is a mega diverse area of high endemism with major economic interest because of the multi-specific fisheries developed, mainly shrimp. There is a lack of recent studies on bycatch fish assemblages, so during the fishing seasons from 2009-2010 and 2010-2011, on board 13 shrimp boats, 14 commercial fishing trips were performed from 5 m - 90 m in depth with a total of 119 catches. The 119 catches were analyzed to assess fish community structure using taxonomic diversity indices to detect changes in the community following the taxonomic distinctness average Δ+ and the diversity index Δ* (TAXDEST of the PRIMER v6 program). To confirm the structure of functional groups, we considered similarities of ecologic and morphologic traits among species. The results showed that the indices Δ+ and Δ* were within the expected average and confidence intervals at 95%, finding significant differences between the indices. The analyses showed a well-structured community because of the great variety of forms and functions of the species within the community. In the community of the functional groups, reproduction was the ecological attribute that contributed the most to their structure. The community structure was represented by intermediate trophic levels (3-3.9), preferably primary and secondary carnivores within the trophic categories of predators of benthic ichthyo-fauna that belong to demersal species of soft bottoms and mostly fusiform body. To conclude, the NGC showed high functional redundancy according to the estimated functional groups, thus the ecosystem was considered stable and with great diversity. This type of studies should be followed using fishing and environmental effort due to the great biological and ecologic importance in the area.

Checklist of the marine and estuarine fishes of Madang District, Papua New Guinea, western Pacific Ocean, with 820 new records.

PubMed

Fricke, Ronald; Allen, Gerald R; Andréfouët, Serge; Chen, Wei-Jen; Hamel, Mélanie A; Laboute, Pierre; Mana, Ralph; Hui, Tan Heok; Uyeno, Daisuke

2014-06-08

A checklist of the marine and estuarine fishes of Madang District is presented, combining both previous and new records. After the recent PAPUA NIUGINI 2012 expedition, a total of 1337 species in 129 families have been recorded from the region. One species and one family is not native (Cichlidae: Oreochromis mossambicus), but has been introduced. The native fish fauna of Madang therefore consists of 1336 species in 128 families. The largest families are the Gobiidae, Labridae, Pomacentridae, Apogonidae, Serranidae, Blenniidae, Chaetodontidae, Syngnathidae and Muraenidae, Scorpaenidae and Lutjanidae, Myctophidae, Acanthuridae, Scaridae, Holocentridae, Carangidae, Pomacanthidae and Tetraodontidae, and Caesionidae. A total of 820 fish species (61.4 % of the total marine and estuarine fish fauna) are recorded from Madang for the first time. The fish fauna of Madang includes a total of 187 species of transitional waters and 1326 species in marine habitats. A total of 156 species of the marine or estuarine species also occurs in freshwater. Zoogeographically, 1271 species have a wide distribution range, most frequently a broad Indo-West Pacific distribution. Among the remaining species, only 8 are endemic to Madang District. Anthropogenic threats to the fish fauna and habitats of Madang District include extensive fishing in Madang Lagoon, sometimes with destructive fishing practices; the discharge of untreated sewage of human settlements, mining and industrial developments into the lagoon and nearby oceanic habitats; and destruction of mangrove habitats by extensive construction work on the shores. These anthropogenic threats may call for conservation and monitoring measures in the near future.

Linking removal targets to the ecological effects of invaders: a predictive model and field test.

PubMed

Green, Stephanie J; Dulvy, Nicholas K; Brooks, Annabelle M L; Akins, John L; Cooper, Andrew B; Miller, Skylar; Côté, Isabelle M

Species invasions have a range of negative effects on recipient ecosystems, and many occur at a scale and magnitude that preclude complete eradication. When complete extirpation is unlikely with available management resources, an effective strategy may be to suppress invasive populations below levels predicted to cause undesirable ecological change. We illustrated this approach by developing and testing targets for the control of invasive Indo-Pacific lionfish (Pterois volitans and P. miles) on Western Atlantic coral reefs. We first developed a size-structured simulation model of predation by lionfish on native fish communities, which we used to predict threshold densities of lionfish beyond which native fish biomass should decline. We then tested our predictions by experimentally manipulating lionfish densities above or below reef-specific thresholds, and monitoring the consequences for native fish populations on 24 Bahamian patch reefs over 18 months. We found that reducing lionfish below predicted threshold densities effectively protected native fish community biomass from predation-induced declines. Reductions in density of 25–92%, depending on the reef, were required to suppress lionfish below levels predicted to overconsume prey. On reefs where lionfish were kept below threshold densities, native prey fish biomass increased by 50–70%. Gains in small (<6 cm) size classes of native fishes translated into lagged increases in larger size classes over time. The biomass of larger individuals (>15 cm total length), including ecologically important grazers and economically important fisheries species, had increased by 10–65% by the end of the experiment. Crucially, similar gains in prey fish biomass were realized on reefs subjected to partial and full removal of lionfish, but partial removals took 30% less time to implement. By contrast, the biomass of small native fishes declined by >50% on all reefs with lionfish densities exceeding reef-specific thresholds. Large inter-reef variation in the biomass of prey fishes at the outset of the study, which influences the threshold density of lionfish, means that we could not identify a single rule of thumb for guiding control efforts. However, our model provides a method for setting reef-specific targets for population control using local monitoring data. Our work is the first to demonstrate that for ongoing invasions, suppressing invaders below densities that cause environmental harm can have a similar effect, in terms of protecting the native ecosystem on a local scale, to achieving complete eradication.

Morphologic, Pathologic, and Genetic Investigations of Bolbophorus Species Affecting Cultured Channel Catfish in the Mississippi Delta.

PubMed

Levy, M G; Flowers, J R; Poore, M F; Mullen, J E; Khoo, L H; Pote, L M; Paperna, I; Dzikowski, R; Litaker, R W

2006-12-01

Trematodes belonging to the genus Bolbophorus have recently been reported as the cause of substantial morbidity and mortality in cultured channel catfish Ictalurus punctatus in Mississippi and Louisiana. Previous investigators identified only a single species, B. confusus. In this investigation, genetic techniques were used to identify all stages of the parasite in all of its hosts. The 18s rRNA genes from specimens collected in Mississippi were sequenced and compared; this analysis revealed that there are two distinct species, B. damnificus (previously identified as B. confusus) and another, undescribed species. (Phylogenetic analysis indicated that a third species, B. levantinus, is also closely related to the Mississippi species.) Species-specific polymerase chain reaction assays capable of identifying and differentiating between these two parasites were developed. Both species were found to infect the first intermediate host (the ram's horn snail Planorbella trivolvis) in commercial channel catfish ponds, but only B. damnificus was recovered from the fish themselves. The new, unidentified Bolbophorus species was determined to be highly pathogenic to a number of fish species. The contribution of B. damnificus to disease in cultured channel catfish remains undetermined. Future investigations of these parasites must now take into account the presence of two distinct species.

Morphologic, Pathologic, and Genetic Investigations of Bolbophorus Species Affecting Cultured Channel Catfish in the Mississippi Delta.

PubMed

Levy, M G; Flowers, J R; Poore, M F; Mullen, J E; Khoo, L H; Pote, L M; Paperna, I; Dzikowski, R; Litaker, R W

2002-12-01

Trematodes belonging to the genus Bolbophorus have recently been reported as the cause of substantial morbidity and mortality in cultured channel catfish Ictalurus punctatus in Mississippi and Louisiana. Previous investigators identified only a single species, B. confusus. In this investigation, genetic techniques were used to identify all stages of the parasite in all of its hosts. The 18s rRNA genes from specimens collected in Mississippi were sequenced and compared; this analysis revealed that there are two distinct species, B. damnificus (previously identified as B. confusus) and another, undescribed species. (Phylogenetic analysis indicated that a third species, B. levantinus, is also closely related to the Mississippi species.) Species-specific polymerase chain reaction assays capable of identifying and differentiating between these two parasites were developed. Both species were found to infect the first intermediate host (the ram's horn snail Planorbella trivolvis) in commercial channel catfish ponds, but only B. damnificus was recovered from the fish themselves. The new, unidentified Bolbophorus species was determined to be highly pathogenic to a number of fish species. The contribution of B. damnificus to disease in cultured channel catfish remains undetermined. Future investigations of these parasites must now take into account the presence of two distinct species.

Identifying selectively important amino acid positions associated with alternative habitat environments in fish mitochondrial genomes.

PubMed

Xia, Jun Hong; Li, Hong Lian; Zhang, Yong; Meng, Zi Ning; Lin, Hao Ran

2018-05-01

Fish species inhabitating seawater (SW) or freshwater (FW) habitats have to develop genetic adaptations to alternative environment factors, especially salinity. Functional consequences of the protein variations associated with habitat environments in fish mitochondrial genomes have not yet received much attention. We analyzed 829 complete fish mitochondrial genomes and compared the amino acid differences of 13 mitochondrial protein families between FW and SW fish groups. We identified 47 specificity determining sites (SDS) that associated with FW or SW environments from 12 mitochondrial protein families. Thirty-two (68%) of the SDS sites are hydrophobic, 13 (28%) are neutral, and the remaining sites are acidic or basic. Seven of those SDS from ND1, ND2 and ND5 were scored as probably damaging to the protein structures. Furthermore, phylogenetic tree based Bayes Empirical Bayes analysis also detected 63 positive sites associated with alternative habitat environments across ten mtDNA proteins. These signatures could be important for studying mitochondrial genetic variation relevant to fish physiology and ecology.

Appearance and possible homing of two species of sculpins in Maine tidepools

USGS Publications Warehouse

Muring, J.R.

2001-01-01

Two species of sculpins (Cottidae), the grubby, Myoxocephalus aenaeus, and the shorthorn sculpin, M. scorpius, were studied in rocky tidepools along the coast of Maine. Fishes were captured and measured during 116 sampling trips between 1979 and 1996. Both of these species of sculpins are from the northwestern Atlantic Ocean and are present in tidepools nearly every month of the year and are the only fish species found in Maine tidepools during winter. Both sculpin species are important components of tidepool ecosystems and dominate the rocky tidepool fish communities from late autumn to early spring, a time when other fish species decline in abundance or are absent. There was no apparent relationship between sculpin abundance and salinity, but the two species of Myoxocephalus were encountered in water temperatures of 1.5 to 18.9??C, with 55.0% of the shorthorn sculpins and 57.3% of the grubbies encountered in tidepools where water temperatures ranged from 12 to 15??C. Between 1988 and 1996, 102 individuals from both species were marked. Of these, 21.3% were recaptured, some repeatedly in the same tidepools and even at specific locations within tidepools over successive tidal cycles - an indication of homing behavior.

Riverine fish diversity varies according to geographical isolation and land use modification.

PubMed

Nicol, Elizabeth; Stevens, Jamie R; Jobling, Susan

2017-10-01

Understanding the environmental factors driving species-genetic diversity correlations (SGDCs) is critical for designing appropriate conservation and management strategies to protect biodiversity. Yet, few studies have explored the impact of changing land use patterns on SGDCs specifically in aquatic communities. This study examined patterns of genetic diversity in roach ( Rutilus rutilus L.) together with fish species composition across 19 locations in a large river catchment, spanning a gradient in land use. Our findings show significant correlations between some, but not all, species and genetic diversity end points. For example, genetic and species differentiation showed a weak but significant linear relationship across the Thames catchment, but additional diversity measures such as allelic richness and fish population abundance did not. Further examination of patterns in species and genetic diversity indicated that land use intensification has a modest effect on fish diversity compared to the combined influence of geographical isolation and land use intensification. These results indicate that environmental changes in riparian habitats have the potential to amplify shifts in the composition of stream fish communities in poorly connected river stretches. Conservation and management strategies for fish populations should, therefore, focus on enhancing connectivity between river stretches and limit conversion of nearby land to arable or urban use to maintain current levels of biodiversity.

Native fishes in the Truckee River: Are in-stream structures and patterns of population genetic structure related?

PubMed

Peacock, Mary M; Gustin, Mae S; Kirchoff, Veronica S; Robinson, Morgan L; Hekkala, Evon; Pizzarro-Barraza, Claudia; Loux, Tim

2016-09-01

In-stream structures are recognized as significant impediments to movement for freshwater fishes. Apex predators such as salmonids have been the focus of much research on the impacts of such barriers to population dynamics and population viability however much less research has focused on native fishes, where in-stream structures may have a greater impact on long term population viability of these smaller, less mobile species. Patterns of genetic structure on a riverscape can provide information on which structures represent real barriers to movement for fish species and under what specific flow conditions. Here we characterize the impact of 41 dam and diversion structures on movement dynamics under varying flow conditions for a suite of six native fishes found in the Truckee River of California and Nevada. Microsatellite loci were used to estimate total allelic diversity, effective population size and assess genetic population structure. Although there is spatial overlap among species within the river there are clear differences in species distributions within the watershed. Observed population genetic structure was associated with in-stream structures, but only under low flow conditions. High total discharge in 2006 allowed fish to move over potential barriers resulting in no observed population genetic structure for any species in 2007. The efficacy of in-stream structures to impede movement and isolate fish emerged only after multiple years of low flow conditions. Our results suggest that restricted movement of fish species, as a result of in-stream barriers, can be mitigated by flow management. However, as flow dynamics are likely to be altered under global climate change, fragmentation due to barriers could isolate stream fishes into small subpopulations susceptible to both demographic losses and losses of genetic variation. Copyright © 2016 Elsevier B.V. All rights reserved.

Meso- and bathy-pelagic fish parasites at the Mid-Atlantic Ridge (MAR): Low host specificity and restricted parasite diversity

NASA Astrophysics Data System (ADS)

Klimpel, Sven; Busch, Markus Wilhelm; Sutton, Tracey; Palm, Harry Wilhelm

2010-04-01

Seven meso- and bathy-pelagic fish species from the Mid-Atlantic Ridge (MAR) were firstly studied for fish parasites and feeding ecology. With a total of seven parasite species, the 247 meso- and bathy-pelagic deep-sea fish specimens belonging to the families Melamphaidae (3 spp.), Myctophidae (3 spp.) and Stomiidae (1 sp.) revealed low parasite diversity. The genetically identified nematodes Anisakis simplex (s.s.) and Anisakis pegreffii from the body cavity, liver and muscles of Myctophum punctatum were the most abundant parasites, reaching a prevalence of 91.4% and mean intensity of 3.1 (1-14). Anisakis sp. (unidentified) infected Chauliodus sloani and Poromitra crassiceps. Bothriocephalidean and tetraphyllidean cestode larvae infected Benthosema glaciale, the latter also occurring in C. sloani and Scopelogadus beanii, at low prevalences. Adult parasites at low infection rates included the digenean Lethadena sp. (2.9%), and the two copepod species Sarcotretes scopeli (5.7%) and Tautochondria dolichoura (5.3-11.4%). The myctophid Lampanyctus macdonaldi and the melamphaid Scopelogadus mizolepis mizolepis were free of parasites. Analyses of the stomach contents revealed crustaceans, especially copepods and euphausiids for the myctophids and also amphipods for the melamphaids as predominant prey items. While all stomachs showing distinct content comprising often unidentified 'tissue' (possibly gelatinous zooplankton), only C. sloani preyed upon fish. Though this feeding habit would enable transfer of a variety of crustacean-transmitted parasites into the fish, the parasite fauna in the meso- and bathy-pelagic fish was species poor. All observed parasites showed low host specificity, demonstrating no distinct pattern of host-parasite co-evolution. The MAR is no barrier for the parasite distribution in the North Atlantic meso- and bathy-pelagial.

Effects of season, sex and body size on the feeding ecology of turtle-headed sea snakes ( Emydocephalus annulatus) on IndoPacific inshore coral reefs

NASA Astrophysics Data System (ADS)

Goiran, C.; Dubey, S.; Shine, R.

2013-06-01

In terrestrial snakes, many cases of intraspecific shifts in dietary habits as a function of predator sex and body size are driven by gape limitation and hence are most common in species that feed on relatively large prey and exhibit a wide body-size range. Our data on sea snakes reveal an alternative mechanism for intraspecific niche partitioning, based on sex-specific seasonal anorexia induced by reproductive activities. Turtle-headed sea snakes ( Emydocephalus annulatus) on coral reefs in the New Caledonian Lagoon feed entirely on the eggs of demersal-spawning fishes. DNA sequence data (cytochrome b gene) on eggs that we palpated from stomachs of 37 snakes showed that despite this ontogenetic stage specialization, the prey comes from a taxonomically diverse array of species including damselfish (41 % of samples, at least 5 species), blennies (41 %, 4 species) and gobies (19 %, 5 species). The composition of snake diets shifted seasonally (with damselfish dominating in winter but not summer), presumably reflecting seasonality of fish reproduction. That seasonal shift affects male and female snakes differently, because reproduction is incompatible with foraging. Adult female sea snakes ceased feeding when they became heavily distended with developing embryos in late summer, and males ceased feeding while they were mate searching in winter. The sex divergence in foraging habits may be amplified by sexual size dimorphism; females grow larger than males, and larger snakes (of both sexes) feed more on damselfish (which often lay their eggs in exposed sites) than on blennies and gobies (whose eggs are hidden within narrow crevices). Specific features of reproductive biology of coral reef fish (seasonality and nest type) have generated intraspecific niche partitioning in these sea snakes, by mechanisms different from those that apply to terrestrial snakes.

Investigating functional redundancy versus complementarity in Hawaiian herbivorous coral reef fishes.

PubMed

Kelly, Emily L A; Eynaud, Yoan; Clements, Samantha M; Gleason, Molly; Sparks, Russell T; Williams, Ivor D; Smith, Jennifer E

2016-12-01

Patterns of species resource use provide insight into the functional roles of species and thus their ecological significance within a community. The functional role of herbivorous fishes on coral reefs has been defined through a variety of methods, but from a grazing perspective, less is known about the species-specific preferences of herbivores on different groups of reef algae and the extent of dietary overlap across an herbivore community. Here, we quantified patterns of redundancy and complementarity in a highly diverse community of herbivores at a reef on Maui, Hawaii, USA. First, we tracked fish foraging behavior in situ to record bite rate and type of substrate bitten. Second, we examined gut contents of select herbivorous fishes to determine consumption at a finer scale. Finally, we placed foraging behavior in the context of resource availability to determine how fish selected substrate type. All species predominantly (73-100 %) foraged on turf algae, though there were differences among the types of macroalgae and other substrates bitten. Increased resolution via gut content analysis showed the composition of turf algae consumed by fishes differed across herbivore species. Consideration of foraging behavior by substrate availability revealed 50 % of herbivores selected for turf as opposed to other substrate types, but overall, there were variable foraging portfolios across all species. Through these three methods of investigation, we found higher complementarity among herbivorous fishes than would be revealed using a single metric. These results suggest differences across species in the herbivore "rain of bites" that graze and shape benthic community composition.

Helminth parasites of South American fishes: current status and characterization as a model for studies of biodiversity.

PubMed

Luque, J L; Pereira, F B; Alves, P V; Oliva, M E; Timi, J T

2017-03-01

The South American subcontinent supports one of the world's most diverse and commercially very important ichthyofauna. In this context, the study of South American fish parasites is of increased relevance in understanding their key roles in ecosystems, regulating the abundance or density of host populations, stabilizing food webs and structuring host communities. It is hard to estimate the number of fish parasites in South America. The number of fish species studied for parasites is still low (less than 10%), although the total number of host-parasite associations (HPAs) found in the present study was 3971. Monogeneans, with 835 species (1123 HPAs, 28.5%), and trematodes, with 662 species (1127 HPAs, 30.9%), are the more diverse groups. Data gathered from the literature are useful to roughly estimate species richness of helminths from South American fish, even though there are some associated problems: the reliability of information depends on accurate species identification; the lack of knowledge about life cycles; the increasing number of discoveries of cryptic species and the geographically biased number of studies. Therefore, the closest true estimations of species diversity and distribution will rely on further studies combining both molecular and morphological approaches with ecological data such as host specificity, geographical distribution and life-cycle data. Research on biodiversity of fish parasites in South America is influenced by problems such as funding, taxonomic impediments and dispersion of research groups. Increasing collaboration, interchange and research networks in the context of globalization will enable a promising future for fish parasitology in South America.

Effects of various cooking methods and food components on bioaccessibility of mercury from fish.

PubMed

Ouédraogo, Ousséni; Amyot, Marc

2011-11-01

Fish consumption is the main source of human exposure to mercury. Studies from specific human populations have reported Hg levels lower than those modeled from consumption data. These discrepancies between expected and measured Hg levels may be explained by differences in dietary habits such as cooking methods and food components on fish Hg bioavailability. We assessed the effects of three cooking methods (no cooking, frying and boiling) and of the co-ingestion of selected food items (tea, coffee and corn starch) on Hg bioaccessibility in three fish species (tuna, shark and mackerel) containing between 1 and 4 μg/g dry weight of Hg. We used in vitro techniques simulating human digestion and each experiment was repeated three times with at least three different individuals for each fish species. For all fish species, Hg concentrations (dry weight) in boiled fish were slightly but not significantly higher than those in fried or raw fish. Boiling and frying reduced Hg bioaccessibility by 40% and 60%, respectively, compared to raw fish Hg bioaccessibility. Black coffee as well as green and black tea significantly reduced raw fish Hg bioaccessibility by 50-60%, whereas, corn starch did not. The combined effect of cooking and addition of tea or coffee led to very low levels of Hg bioaccessibility. This study suggests that Hg bioaccessibilty from fish can be modified by cooking and by the co-ingestion of tea and coffee. These results should be further validated in vitro with different fish species before proceeding with in vivo approaches using animal models. Copyright © 2011 Elsevier Inc. All rights reserved.

An eDNA Assay to Monitor a Globally Invasive Fish Species from Flowing Freshwater.

PubMed

Adrian-Kalchhauser, Irene; Burkhardt-Holm, Patricia

2016-01-01

Ponto-Caspian gobies are a flock of five invasive fish species that have colonized freshwaters and brackish waters in Europe and North America. One of them, the round goby Neogobius melanostomus, figures among the 100 worst invaders in Europe. Current methods to detect the presence of Ponto-Caspian gobies involve catching or sighting the fish. These approaches are labor intense and not very sensitive. Consequently, populations are usually detected only when they have reached high densities and when management or containment efforts are futile. To improve monitoring, we developed an assay based on the detection of DNA traces (environmental DNA, or eDNA) of Ponto-Caspian gobies in river water. The assay specifically detects invasive goby DNA and does not react to any native fish species. We apply the assay to environmental samples and demonstrate that parameters such as sampling depth, sampling location, extraction protocol, PCR protocol and PCR inhibition greatly impact detection. We further successfully outline the invasion front of Ponto-Caspian gobies in a large river, the High Rhine in Switzerland, and thus demonstrate the applicability of the assay to lotic environments. The eDNA assay requires less time, equipment, manpower, skills, and financial resources than the conventional monitoring methods such as electrofishing, angling or diving. Samples can be taken by untrained individuals, and the assay can be performed by any molecular biologist on a conventional PCR machine. Therefore, this assay enables environment managers to map invaded areas independently of fishermen's' reports and fish community monitorings.

Application of denaturing high-performance liquid chromatography (DHPLC) for the identification of fish: a new way to determine the composition of processed food containing multiple species.

PubMed

Le Fresne, Sophie; Popova, Milena; Le Vacon, Françoise; Carton, Thomas

2011-12-14

The identification of fish species in transformed food products is difficult because the existing methods are not adapted to heat-processed products containing more than one species. Using a common to all vertebrates region of the cytochrome b gene, we have developed a denaturing high-performance liquid chromatography (DHPLC) fingerprinting method, which allowed us to identify most of the species in commercial crab sticks. Whole fish and fillets were used for the creation of a library of referent DHPLC profiles. Crab sticks generated complex DHPLC profiles in which the number of contained fish species can be estimated by the number of major fluorescence peaks. The identity of some of the species was predicted by comparison of the peaks with the referent profiles, and others were identified after collection of the peak fractions, reamplification, and sequencing. DHPLC appears to be a quick and efficient method to analyze the species composition of complex heat-processed fish products.

Mercury and omega-3 fatty acid profiles in freshwater fish of the Dehcho Region, Northwest Territories: Informing risk benefit assessments.

PubMed

Laird, Matthew J; Henao, Juan J Aristizabal; Reyes, Ellen S; Stark, Ken D; Low, George; Swanson, Heidi K; Laird, Brian D

2018-10-01

Traditional foods have significant nutritional, sociocultural and economic value in subarctic First Nations communities of the Northwest Territories, and play a crucial role in promoting cultural continuity and sovereignty. Omega-3 polyunsaturated fatty acids (N-3 PUFAs), including eicosapentaenoic (EPA) and docosahexaenoic acid (DHA), carry significant benefits for neurocognitive development and cardiovascular health. However, the health risks posed by methylmercury may serve to undermine the benefits of fish consumption in Northern Indigenous communities. The objective of this study was to characterize profiles for mercury (Hg) and fatty acids in fish species harvested across lakes of the Dehcho Region, in the Mackenzie Valley of the Northwest Territories, to better understand the risks and benefits associated with traditional foods. Hg levels increased with trophic position, with the highest levels found in Burbot, Lake Trout, Walleye, and Northern Pike. Lake Trout, along with planktivorous species including Lake Whitefish, Cisco, and Sucker, demonstrated higher N-3 PUFAs than other species. Negative associations were observed between Hg and N-3 PUFAs in Lake Trout, Northern Pike, Walleye and Burbot. Further stratifying these relationships revealed significant interactions by lake. Significant differences observed in fatty acid and Hg profiles across lakes underscore the importance of considering both species- and lake-specific findings. This growing dataset of freshwater fish of the Dehcho will inform future efforts to characterize human Hg exposure profiles using probabilistic dose reconstruction models. Copyright © 2018 Elsevier B.V. All rights reserved.

[Avoidance of injuries to migrating fish by hydropower and water intake plants].

PubMed

Adam, B

2004-03-01

Every year numerous downstream migrating fish are lethally injured by hydro power plants and inlet works. Especially the katadromous Eel (Anguilla anguilla) and anadromous species like Atlantic Salmon (Salmo salar), which have to migrate downstream into the ocean for closing their life cycle, are highly endangered. Due to their specific migratory behavioral pattern, size and morphology conventional protection techniques, like screens do not properly keep them out from getting into the power plant intakes. Despite of the relevance of this problem for ecology and fishing, there are no protection and downstream migration facilities in Europe available, which can efficiently avoid the damage of all species and sizes of downstream migrating fish. Nevertheless according to protect the fish populations it's necessary to use consequently fish protection and downstream migration facilities, i.e. mechanical barrieres or alternative techniques like early warning systems as a prerequisit for a fish-friendly operational management of hydro power plants.

Climate change vulnerability of native and alien freshwater fishes of California: a systematic assessment approach.

PubMed

Moyle, Peter B; Kiernan, Joseph D; Crain, Patrick K; Quiñones, Rebecca M

2013-01-01

Freshwater fishes are highly vulnerable to human-caused climate change. Because quantitative data on status and trends are unavailable for most fish species, a systematic assessment approach that incorporates expert knowledge was developed to determine status and future vulnerability to climate change of freshwater fishes in California, USA. The method uses expert knowledge, supported by literature reviews of status and biology of the fishes, to score ten metrics for both (1) current status of each species (baseline vulnerability to extinction) and (2) likely future impacts of climate change (vulnerability to extinction). Baseline and climate change vulnerability scores were derived for 121 native and 43 alien fish species. The two scores were highly correlated and were concordant among different scorers. Native species had both greater baseline and greater climate change vulnerability than did alien species. Fifty percent of California's native fish fauna was assessed as having critical or high baseline vulnerability to extinction whereas all alien species were classified as being less or least vulnerable. For vulnerability to climate change, 82% of native species were classified as highly vulnerable, compared with only 19% for aliens. Predicted climate change effects on freshwater environments will dramatically change the fish fauna of California. Most native fishes will suffer population declines and become more restricted in their distributions; some will likely be driven to extinction. Fishes requiring cold water (<22°C) are particularly likely to go extinct. In contrast, most alien fishes will thrive, with some species increasing in abundance and range. However, a few alien species will likewise be negatively affected through loss of aquatic habitats during severe droughts and physiologically stressful conditions present in most waterways during summer. Our method has high utility for predicting vulnerability to climate change of diverse fish species. It should be useful for setting conservation priorities in many different regions.

Climate Change Vulnerability of Native and Alien Freshwater Fishes of California: A Systematic Assessment Approach

PubMed Central

Moyle, Peter B.; Kiernan, Joseph D.; Crain, Patrick K.; Quiñones, Rebecca M.

2013-01-01

Freshwater fishes are highly vulnerable to human-caused climate change. Because quantitative data on status and trends are unavailable for most fish species, a systematic assessment approach that incorporates expert knowledge was developed to determine status and future vulnerability to climate change of freshwater fishes in California, USA. The method uses expert knowledge, supported by literature reviews of status and biology of the fishes, to score ten metrics for both (1) current status of each species (baseline vulnerability to extinction) and (2) likely future impacts of climate change (vulnerability to extinction). Baseline and climate change vulnerability scores were derived for 121 native and 43 alien fish species. The two scores were highly correlated and were concordant among different scorers. Native species had both greater baseline and greater climate change vulnerability than did alien species. Fifty percent of California’s native fish fauna was assessed as having critical or high baseline vulnerability to extinction whereas all alien species were classified as being less or least vulnerable. For vulnerability to climate change, 82% of native species were classified as highly vulnerable, compared with only 19% for aliens. Predicted climate change effects on freshwater environments will dramatically change the fish fauna of California. Most native fishes will suffer population declines and become more restricted in their distributions; some will likely be driven to extinction. Fishes requiring cold water (<22°C) are particularly likely to go extinct. In contrast, most alien fishes will thrive, with some species increasing in abundance and range. However, a few alien species will likewise be negatively affected through loss of aquatic habitats during severe droughts and physiologically stressful conditions present in most waterways during summer. Our method has high utility for predicting vulnerability to climate change of diverse fish species. It should be useful for setting conservation priorities in many different regions. PMID:23717503

The effects of exposure in sandy beach surf zones on larval fishes.

PubMed

Pattrick, P; Strydom, N A

2014-05-01

The influence of wind and wave exposure on larval fish assemblages within a large bay system was investigated. Larval fishes were sampled from two areas with vastly different exposure to waves and wind, namely the windward and leeward sectors of Algoa Bay. In total, 5702 larval fishes were collected using a modified larval seine. Of these, 4391 were collected in the leeward and 1311 in the windward sector of the bay, representing a total of 23 families and 57 species. Dominant fish families included Clinidae, Engraulidae, Kyphosidae, Mugilidae, Soleidae and Sparidae, similar to the situation elsewhere, highlighting continuity in the composition of larval fish assemblages and the utilization of surf zones by a specific group of larval fishes. Nineteen estuary-associated marine species occurred within the surf zones of Algoa Bay and dominated catches (86·7%) in terms of abundance. Postflexion larvae comprised > 80% of the catch, indicating the importance of the seemingly inhospitable surf zone environment for the early life stages of many fish species. The greatest species diversity was observed within the windward sector of the bay. Distance-based linear modelling identified wave period as the environmental variable explaining the largest proportion of the significant variation in the larval fish assemblage. The physical disturbance generated by breaking waves could create a suitable environment for fish larvae, sheltered from predators and with an abundance of food resources. © 2014 The Fisheries Society of the British Isles.

Statistical power to detect change in a mangrove shoreline fish community adjacent to a nuclear power plant.

PubMed

Dolan, T E; Lynch, P D; Karazsia, J L; Serafy, J E

2016-03-01

An expansion is underway of a nuclear power plant on the shoreline of Biscayne Bay, Florida, USA. While the precise effects of its construction and operation are unknown, impacts on surrounding marine habitats and biota are considered by experts to be likely. The objective of the present study was to determine the adequacy of an ongoing monitoring survey of fish communities associated with mangrove habitats directly adjacent to the power plant to detect fish community changes, should they occur, at three spatial scales. Using seasonally resolved data recorded during 532 fish surveys over an 8-year period, power analyses were performed for four mangrove fish metrics (fish diversity, fish density, and the occurrence of two ecologically important fish species: gray snapper (Lutjanus griseus) and goldspotted killifish (Floridichthys carpio). Results indicated that the monitoring program at current sampling intensity allows for detection of <33% changes in fish density and diversity metrics in both the wet and the dry season in the two larger study areas. Sampling effort was found to be insufficient in either season to detect changes at this level (<33%) in species-specific occurrence metrics for the two fish species examined. The option of supplementing ongoing, biological monitoring programs for improved, focused change detection deserves consideration from both ecological and cost-benefit perspectives.

It is the economy, stupid! Projecting the fate of fish populations using ecological-economic modeling.

PubMed

Quaas, Martin F; Reusch, Thorsten B H; Schmidt, Jörn O; Tahvonen, Olli; Voss, Rudi

2016-01-01

Four marine fish species are among the most important on the world market: cod, salmon, tuna, and sea bass. While the supply of North American and European markets for two of these species - Atlantic salmon and European sea bass - mainly comes from fish farming, Atlantic cod and tunas are mainly caught from wild stocks. We address the question what will be the status of these wild stocks in the midterm future, in the year 2048, to be specific. Whereas the effects of climate change and ecological driving forces on fish stocks have already gained much attention, our prime interest is in studying the effects of changing economic drivers, as well as the impact of variable management effectiveness. Using a process-based ecological-economic multispecies optimization model, we assess the future stock status under different scenarios of change. We simulate (i) technological progress in fishing, (ii) increasing demand for fish, and (iii) increasing supply of farmed fish, as well as the interplay of these driving forces under different scenarios of (limited) fishery management effectiveness. We find that economic change has a substantial effect on fish populations. Increasing aquaculture production can dampen the fishing pressure on wild stocks, but this effect is likely to be overwhelmed by increasing demand and technological progress, both increasing fishing pressure. The only solution to avoid collapse of the majority of stocks is institutional change to improve management effectiveness significantly above the current state. We conclude that full recognition of economic drivers of change will be needed to successfully develop an integrated ecosystem management and to sustain the wild fish stocks until 2048 and beyond. © 2015 John Wiley & Sons Ltd.

EFFECTS OF DIOXIN-LIKE COMPOUND CONTAMINATION ON AN ESTUARINE FISH SPECIES: ADAPTIVE CHANGES AT SPECIFIC GENETIC LOCI

EPA Science Inventory

Fish from a highly PCB-contaminated Superfund site (New Bedford, Massachusetts, USA) that show genetically-based tolerance to DLCs (Nacci, D. et al. 1999. Mar.Biol.134: 9-17) also have altered MHC Class II antigen-binding receptor profiles compared to a population of fish from a ...

Exploring Effects of Hypoxia on Fish and Fisheries in the Northern Gulf of Mexico using a Dynamic Spatially-Explicit Ecosystem Model

NASA Astrophysics Data System (ADS)

de Mutsert, K.; Steenbeek, J.; Lewis, K.; Buszowski, J.; Cowan, J. H., Jr.; Christensen, V.

2016-02-01

The formation of an extensive hypoxic area off the Louisiana coast has been well publicized. However, determining the effects of this hypoxic zone on fish and fisheries has proven to be more difficult. The dual effect of nutrient loading on secondary production (positive effects of bottom-up fueling, and negative effects of reduced oxygen levels) impedes the quantification of hypoxia effects on fish and fisheries. The objective of this study was to develop an ecosystem model that is able to separate the two effects, and to evaluate net effects of hypoxia on fish biomass and fisheries landings. An Ecospace model was developed using Ecopath with Ecosim software with an added plug-in to include spatially and temporally dynamic Chlorophyll a (Chl a) and dissolved oxygen (DO) values derived from a coupled physical-biological hypoxia model. Effects of hypoxia were determined by simulating scenarios with DO and Chl a included separately and combined, and a scenario without fish response to Chl a or DO. Fishing fleets were included in the model as well; fleets move to cells with highest revenue following a gravitational model. Results of this model suggest that the increases in total fish biomass and fisheries landings as a result of an increase in primary production outweigh the decreases as a result of hypoxic conditions. However, the results also demonstrated that responses were species-specific, and some species such as red snapper (Lutjanus campechanus) did suffer a net loss in biomass. Scenario-analyses with this model could be used to determine the optimal nutrient load reduction from a fisheries perspective.

Does interspecies hybridization affect the host specificity of parasites in cyprinid fish?

PubMed

Simková, Andrea; Dávidová, Martina; Papoušek, Ivo; Vetešník, Lukáš

2013-04-12

Host specificity varies among parasite species. Some parasites are strictly host-specific, others show a specificity for congeneric or non-congeneric phylogenetically related host species, whilst some others are non-specific (generalists). Two cyprinids, Cyprinus carpio and Carassius gibelio, plus their respective hybrids were investigated for metazoan parasites. The aim of this study was to analyze whether interspecies hybridization affects host specificity. The different degrees of host specificity within a phylogenetic framework were taken into consideration (i.e. strict specialist, intermediate specialist, and intermediate generalist). Fish were collected during harvesting the pond and identified using meristic traits and molecular markers. Metazoan parasite species were collected. Host specificity of parasites was determined using the following classification: strict specialist, intermediate specialist, intermediate generalist and generalist. Parasite species richness was compared between parental species and their hybrids. The effect of host species on abundance of parasites differing in host specificity was tested. Hybrids harbored more different parasite species but their total parasite abundance was lower in comparison with parental species. Interspecies hybridization affected the host specificity of ecto- and endoparasites. Parasite species exhibiting different degrees of host specificity for C. carpio and C. gibelio were also present in hybrids. The abundance of strict specialists of C. carpio was significantly higher in parental species than in hybrids. Intermediate generalists parasitizing C. carpio and C. gibelio as two phylogenetically closely related host species preferentially infected C. gibelio when compared to C. carpio, based on prevalence and maximum intensity of infection. Hybrids were less infected by intermediate generalists when compared to C. gibelio. This finding does not support strict co-adaptation between host and parasite genotypes resulting in narrow host specificity, and showed that hybrid genotypes are susceptible to parasites exhibiting host specificity. The immune mechanisms specific to parental species might represent potential mechanisms explaining the low abundance of parasites in C. gibelio x C. carpio hybrids.

Development of QSAR models for predicting the binding affinity of endocrine disrupting chemicals to eight fish estrogen receptor.

PubMed

He, Junyi; Peng, Tao; Yang, Xianhai; Liu, Huihui

2018-02-01

Endocrine disrupting effect has become a central point of concern, and various biological mechanisms involve in the disruption of endocrine system. Recently, we have explored the mechanism of disrupting hormonal transport protein, through the binding affinity of sex hormone-binding globulin in different fish species. This study, serving as a companion article, focused on the mechanism of activating/inhibiting hormone receptor, by investigating the binding interaction of chemicals with the estrogen receptor (ER) of different fish species. We collected the relative binding affinity (RBA) of chemicals with 17β-estradiol binding to the ER of eight fish species. With this parameter as the endpoints, quantitative structure-activity relationship (QSAR) models were established using DRAGON descriptors. Statistical results indicated that the developed models had satisfactory goodness of fit, robustness and predictive ability. The Euclidean distance and Williams plot verified that these models had wide application domains, which covered a large number of structurally diverse chemicals. Based on the screened descriptors, we proposed an appropriate mechanism interpretation for the binding potency. Additionally, even though the same chemical had different affinities for ER from different fish species, the affinity of ER exhibited a high correlation for fish species within the same Order (i.e., Salmoniformes, Cypriniformes, Perciformes), which consistent with that in our previous study. Hence, when performing the endocrine disrupting effect assessment, the species diversity should be taken into account, but maybe the fish species in the same Order can be grouped together. Copyright © 2017 Elsevier Inc. All rights reserved.

Status and conservation of the fish fauna of the Alabama River system

USGS Publications Warehouse

Freeman, Mary C.; Irwin, E.R.; Burkhead, N.M.; Freeman, B.J.; Bart, H.L.; Rinne, John N.; Hughes, Robert M.; Calamusso, Bob

2005-01-01

The Alabama River system, comprising the Alabama, Coosa, and Tallapoosa subsystems, forms the eastern portion of the Mobile River drainage. Physiographic diversity and geologic history have fostered development in the Alabama River system of globally significant levels of aquatic faunal diversity and endemism. At least 184 fishes are native to the system, including at least 33 endemic species. During the past century, dam construction for hydropower generation and navigation resulted in 16 reservoirs that inundate 44% of the length of the Alabama River system main stems. This extensive physical and hydrologic alteration has affected the fish fauna in three major ways. Diadromous and migratory species have declined precipitously. Fish assemblages persisting downstream from large main-stem dams have been simplified by loss of species unable to cope with altered flow and water quality regimes. Fish populations persisting in the headwaters and in tributaries to the mainstem reservoirs are now isolated and subjected to effects of physical and chemical habitat degradation. Ten fishes in the Alabama River system (including seven endemic species) are federally listed as threatened or endangered. Regional experts consider at least 28 additional species to be vulnerable, threatened, or endangered with extinction. Conserving the Alabama River system fish fauna will require innovative dam management, protection of streams from effects of urbanization and water supply development, and control of alien species dispersal. Failure to manage aggressively for integrity of remaining unimpounded portions of the Alabama River system will result in reduced quality of natural resources for future generations, continued assemblage simplification, and species extinction.

Status and conservation of the fish fauna of the Alabama River system

USGS Publications Warehouse

Freeman, Mary C.; Irwin, E.R.; Burkhead, N.M.; Freeman, B.J.; Bart, H.L.

2005-01-01

The Alabama River system, comprising the Alabama, Coosa, and Tallapoosa subsystems, forms the eastern portion of the Mobile River drainage. Physiographic diversity and geologic history have fostered development in the Alabama River system of globally significant levels of aquatic faunal diversity and endemism. At least 184 fishes are native to the system, including at least 33 endemic species. During the past century, dam construction for hydropower generation and navigation resulted in 16 reservoirs that inundate 44% of the length of the Alabama River system main stems. This extensive physical and hydrologic alteration has affected the fish fauna in three major ways. Diadromous and migratory species have declined precipitously. Fish assemblages persisting downstream from large main-stem dams have been simplified by loss of species unable to cope with altered flow and water quality regimes. Fish populations persisting in the headwaters and in tributaries to the mainstem reservoirs are now isolated and subjected to effects of physical and chemical habitat degradation. Ten fishes in the Alabama River system (including seven endemic species) are federally listed as threatened or endangered. Regional experts consider at least 28 additional species to be vulnerable, threatened, or endangered with extinction. Conserving the Alabama River system fish fauna will require innovative dam management, protection of streams from effects of urbanization and water supply development, and control of alien species dispersal. Failure to manage aggressively for integrity of remaining unimpounded portions of the Alabama River system will result in reduced quality of natural resources for future generations, continued assemblage simplification, and species extinctions. ?? 2005 by the American Fisheries Society.

Ecological energetics of forage fish from the Mediterranean Sea: Seasonal dynamics and interspecific differences

NASA Astrophysics Data System (ADS)

Albo-Puigserver, M.; Muñoz, A.; Navarro, J.; Coll, M.; Pethybridge, H.; Sánchez, S.; Palomera, I.

2017-06-01

Small and medium pelagic fishes play a central role in marine food webs by transferring energy from plankton to top predators. In this study, direct calorimetry was used to analyze the energy density of seven pelagic species collected over four seasons from the western Mediterranean Sea: anchovy Engraulis encrasicolus, sardine Sardina pilchardus, round sardinella Sardinella aurita, horse mackerels Trachurus trachurus and T. mediterraneus, and mackerels Scomber scombrus and S. colias. Inter-specific differences in energy density were linked to spawning period, energy allocation strategies for reproduction and growth, and feeding ecologies. Energy density of each species varied over time, with the exception of S. colias, likely due to its high energetic requirements related to migration throughout the year. In general, higher energy density was observed in spring for all species, regardless of their breeding strategy, probably as a consequence of the late-winter phytoplankton bloom. These results provide new insights into the temporal availability of energy in the pelagic ecosystem of the Mediterranean Sea, which are pivotal for understanding how the population dynamics of small and medium pelagic fishes and their predators may respond to environmental changes and fishing impacts. In addition, the differences found in energy density between species highlighted the importance of using species specific energy-values in ecosystem assessment tools such as bioenergetic and food web models.

DNA barcoding discriminates freshwater fishes from southeastern Nigeria and provides river system-level phylogeographic resolution within some species.

PubMed

Nwani, Christopher D; Becker, Sven; Braid, Heather E; Ude, Emmanuel F; Okogwu, Okechukwu I; Hanner, Robert

2011-10-01

Fishes are the main animal protein source for human beings and play a vital role in aquatic ecosystems and food webs. Fish identification can be challenging, especially in the tropics (due to high diversity), and this is particularly true for larval forms or fragmentary remains. DNA barcoding, which uses the 5' region of the mitochondrial cytochrome c oxidase subunit I (COI) as a target gene, is an efficient method for standardized species-level identification for biodiversity assessment and conservation, pending the establishment of reference sequence libraries. In this study, fishes were collected from three rivers in southeastern Nigeria, identified morphologically, and imaged digitally. DNA was extracted, PCR-amplified, and the standard barcode region was bidirectionally sequenced for 363 individuals belonging to 70 species in 38 genera. All specimen provenance data and associated sequence information were recorded in the barcode of life data systems (BOLD; www.barcodinglife.org ). Analytical tools on BOLD were used to assess the performance of barcoding to identify species. Using neighbor-joining distance comparison, the average genetic distance was 60-fold higher between species than within species, as pairwise genetic distance estimates averaged 10.29% among congeners and only 0.17% among conspecifics. Despite low levels of divergence within species, we observed river system-specific haplotype partitioning within eight species (11.4% of all species). Our preliminary results suggest that DNA barcoding is very effective for species identification of Nigerian freshwater fishes.

Seasonal and spatial variations in fish and macrocrustacean assemblage structure in Mad Island Marsh estuary, Texas

NASA Astrophysics Data System (ADS)

Akin, S.; Winemiller, K. O.; Gelwick, F. P.

2003-05-01

Fish and macrocrustacean assemblage structure was analyzed along an estuarine gradient at Mad Island Marsh (MIM), Matagorda Bay, TX, during March 1998-August 1999. Eight estuarine-dependent fish species accounted for 94% of the individual fishes collected, and three species accounted for 96% of macrocrustacean abundance. Consistent with evidence from other Gulf of Mexico estuarine studies, species richness and abundance were highest during late spring and summer, and lowest during winter and early spring. Sites near the bay supported the most individuals and species. Associations between fish abundance and environmental variables were examined with canonical correspondence analysis. The dominant gradient was associated with water depth and distance from the bay. The secondary gradient reflected seasonal variation and was associated with temperature, salinity, dissolved oxygen, and vegetation cover. At the scales examined, estuarine biota responded to seasonal variation more than spatial variation. Estuarine-dependent species dominated the fauna and were common throughout the open waters of the shallow lake during winter-early spring when water temperature and salinity were low and dissolved oxygen high. During summer-early fall, sub-optimal environmental conditions (high temperature, low DO) in upper reaches accounted for strong spatial variation in assemblage composition. Small estuarine-resident fishes and the blue crab ( Callinectes sapidus) were common in warm, shallow, vegetated inland sites during summer-fall. Estuarine-dependent species were common at deeper, more saline locations near the bay during this period. During summer, freshwater species, such as gizzard shad ( Dorosoma cepedianum) and gars ( Lepisosteus spp.), were positively associated with water depth and proximity to the bay. The distribution and abundance of fishes in MIM appear to result from the combined effects of endogenous, seasonal patterns of reproduction and migration operating on large spatial scales, and species-specific response to local environmental variation.

Rapid development of microsatellite markers for the endangered fish Schizothorax biddulphi (Günther) using next generation sequencing and cross-species amplification.

PubMed

Luo, Wei; Nie, Zhulan; Zhan, Fanbin; Wei, Jie; Wang, Weimin; Gao, Zexia

2012-11-14

Tarim schizothoracin (Schizothorax biddulphi) is an endemic fish species native to the Tarim River system of Xinjiang and has been classified as an extremely endangered freshwater fish species in China. Here, we used a next generation sequencing platform (ion torrent PGM™) to obtain a large number of microsatellites for S. biddulphi, for the first time. A total of 40577 contigs were assembled, which contained 1379 SSRs. In these SSRs, the number of dinucleotide repeats were the most frequent (77.08%) and AC repeats were the most frequently occurring microsatellite, followed by AG, AAT and AT. Fifty loci were randomly selected for primer development; of these, 38 loci were successfully amplified and 29 loci were polymorphic across panels of 30 individuals. The H(o) ranged from 0.15 to 0.83, and H(e) ranged from 0.15 to 0.85, with 3.5 alleles per locus on average. Cross-species utility indicated that 20 of these markers were successfully amplified in a related, also an endangered fish species, S. irregularis. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing microsatellite markers for non-model species and the developed microsatellite markers in this study would be useful in Schizothorax genetic analysis.

Global fishery development patterns are driven by profit but not trophic level.

PubMed

Sethi, Suresh A; Branch, Trevor A; Watson, Reg

2010-07-06

Successful ocean management needs to consider not only fishing impacts but drivers of harvest. Consolidating post-1950 global catch and economic data, we assess which attributes of fisheries are good indicators for fishery development. Surprisingly, year of development and economic value are not correlated with fishery trophic levels. Instead, patterns emerge of profit-driven fishing for attributes related to costs and revenues. Post-1950 fisheries initially developed on shallow ranging species with large catch, high price, and big body size, and then expanded to less desirable species. Revenues expected from developed fisheries declined 95% from 1951 to 1999, and few high catch or valuable fishing opportunities remain. These results highlight the importance of economic attributes of species as leading indicators for harvest-related impacts in ocean ecosystems.

Global fishery development patterns are driven by profit but not trophic level

PubMed Central

Sethi, Suresh A.; Branch, Trevor A.; Watson, Reg

2010-01-01

Successful ocean management needs to consider not only fishing impacts but drivers of harvest. Consolidating post-1950 global catch and economic data, we assess which attributes of fisheries are good indicators for fishery development. Surprisingly, year of development and economic value are not correlated with fishery trophic levels. Instead, patterns emerge of profit-driven fishing for attributes related to costs and revenues. Post-1950 fisheries initially developed on shallow ranging species with large catch, high price, and big body size, and then expanded to less desirable species. Revenues expected from developed fisheries declined 95% from 1951 to 1999, and few high catch or valuable fishing opportunities remain. These results highlight the importance of economic attributes of species as leading indicators for harvest-related impacts in ocean ecosystems. PMID:20566867

Vasotocinergic control of agonistic behavior told by Neotropical fishes.

PubMed

Silva, Ana C; Pandolfi, Matías

2018-04-24

The hypothalamic neuropeptides of the vasopressin-oxytocin family (and their homologs for non-mammalian species) are key modulators of the Social Brain Network, acting via specific receptors reported in all the nuclei of this network. Different conclusive examples have proven the context-dependency actions of hypothalamic nonapeptides on social behavior in several vertebrate taxa. Teleost fishes provide endless possibilities of experimental model systems to explore the underlying mechanisms of nonapeptide actions on social behavior given that they are the most diverse group of vertebrates. Although it has been difficult to identify commonalities of nonapeptide actions across species, indisputable evidence in many teleost species have demonstrated a clear role of vasotocin in the modulation of aggressive and sexual behaviors. Though Neotropical South American fish contribute an important percentage of teleost diversity, most native species remain unexplored as model systems for the study of the neuroendocrine bases of social behavior. In this review, we will revise recent data on the two model systems of Neotropical fish, South American cichlids and weakly electric fish that have contributed to this issue. Copyright © 2018 Elsevier Inc. All rights reserved.

The effectiveness of surrogate taxa to conserve freshwater biodiversity

USGS Publications Warehouse

Stewart, David R.; Underwood, Zachary E.; Rahel, Frank J.; Walters, Annika W.

2018-01-01

Establishing protected areas has long been an effective conservation strategy, and is often based on more readily surveyed species. The potential of any freshwater taxa to be a surrogate of other aquatic groups has not been fully explored. We compiled occurrence data on 72 species of freshwater fish, amphibians, mussels, and aquatic reptiles for the Great Plains, Wyoming. We used hierarchical Bayesian multi-species mixture models and MaxEnt models to describe species distributions, and program Zonation to identify conservation priority areas for each aquatic group. The landscape-scale factors that best characterized aquatic species distributions differed among groups. There was low agreement and congruence among taxa-specific conservation priorities (<20%), meaning that no surrogate priority areas would include or protect the best habitats of other aquatic taxa. We found that common, wide-ranging aquatic species were included in taxa-specific priority areas, but rare freshwater species were not included. Thus, the development of conservation priorities based on a single freshwater aquatic group would not protect all species in the other aquatic groups.

The hypothalamic-pituitary-thyroid (HPT) axis in fish and its role in fish development and reproduction.

PubMed

Blanton, Michael L; Specker, Jennifer L

2007-01-01

Bony fishes represent the largest vertebrate class and are a very diverse animal group. This chapter provides a thorough review of the available scientific literature on the thyroid system in these important vertebrate animals. The molecular components of the hypothalamic-pituitary-thyroid (HPT) axis in this group correspond closely to those of mammals. The thyroid tissue in the fishes is organized as diffuse follicles, with a few exceptions, rather than as an encapsulated gland as is found in most other vertebrate species. The features of this diffuse tissue in fishes are reviewed with an emphasis on feedback relationships within the HPT axis, the molecular biology of the thyroid system in fishes, and comparisons versus the thyroid systems of other vertebrate taxa. A review of the role of thyroid hormone in fish development and reproduction is included. Available information about the HPT axis in fishes is quite detailed for some species and rather limited or absent in others. This review focuses on species that have been intensively studied for their value as laboratory models in assays to investigate disruption in normal function of the thyroid system. In addition, in vitro and in vivo assay methods for screening chemicals for their potential to interfere with the thyroid system are reviewed. It is concluded that there are currently no in vitro or in vivo assays in fish species that are sufficiently developed to warrant recommendation for use to efficiently screen chemicals for thyroid disruption. Methods are available that can be used to measure thyroid hormones, although our ability to interpret the causes and implications of potential alterations in T4 or T3 levels in fishes is nonetheless limited without further research.

Impacts of hypoxia on the structure and processes in the pelagic community (zooplankton, macro-invertebrates and fish)

NASA Astrophysics Data System (ADS)

Ekau, W.; Auel, H.; Pörtner, H.-O.; Gilbert, D.

2009-05-01

Dissolved oxygen (DO) concentration in the water column is an environmental parameter that is crucial for the successful development of many pelagic organisms. Hypoxia tolerance and threshold values are species- and stage-specific and can vary enormously. While some fish species may suffer from oxygen values of less than 3 ml L-1 and show impact on growth, development and behaviour, other organisms such as euphausiids may survive DO levels as low as 0.1 ml L-1. A change in the average or the minimum or maximum DO in an area may have significant impacts on the survival of certain species and hence on the species composition in the ecosystem with consequent changes in trophic pathways and productivity. Evidence of the deleterious effects of oxygen depletion on species of the pelagic realm is scarce, particularly in terms of the effect of low oxygen on development, recruitment and patterns of migration and distribution. While planktonic organisms have to cope with different DOs and find adaptive mechanisms, nektonic species may avoid areas of inconvenient DO and develop adapted migrational strategies. Planktonic organisms may only be able to escape vertically, above or beneath the Oxygen Minimum Zone (OMZ). In shallow areas only the surface layer can serve as a refuge, in deep waters many organisms have developed vertical migration strategies to use, pass and cope with the OMZ. This paper elucidates the role of DO for different taxa in the pelagic realm and the consequences of low oxygen for foodweb structure and system productivity.

Toxicity of ammonia, cadmium, and nitrobenzene to four local fishes in the Liao River, China and the derivation of site-specific water quality criteria.

PubMed

Liu, Zhihong; Li, Xiaojun; Tai, Peidong; Sun, Lizong; Yuan, Honghong; Yang, Xiaonan

2018-01-01

Water quality criteria (WQC) are considered to be an effective management tool for protecting aquatic environments. To derive site-specific WQC for an area, local data based on local species are essential to improve the applicability of WQC derived. Due to the paucity of local fish data available for the development of site-specific WQC for the Liao River, China, four local and widespread fishes (Pseudorasbora parva， Abbottina liaoningensis, Ctenogobius giurinus, and Misgurnus anguillicaudatus) were chosen to test their sensitivities to ammonia, cadmium and nitrobenzene. These compounds are common and regularly-measured pollutants in Chinese rivers. In addition to the published data for species resident in the Liao River, site-specific WQC for the three chemicals were derived using both a log-logistic species sensitivity distribution (SSD) and the method recommended by the USEPA, in line with current best practice, which were then compared with Chinese national WQC. It was found that A. liaoningensis was the most sensitive, followed, in order, by P. parva, C. giurinus and M. anguillicaudatus was the least sensitive, and this trend was the same to all three chemicals tested. When comparing the SSD derived solely from previously-published data with that including our data on local fish, there were significant differences identified among parameters describing the SSD curves for ammonia and nitrobenzene and significant differences were detected for site-specific WQC derived for all of the three chemicals. Based on the dataset with local fish data taxa, site-specific WQC of Liao River for ammonia, cadmium, and nitrobenzene were derived to be 20.53mg/L (at a pH of 7.0 and temperature of 20°C), 3.76μg/L (at a hardness of 100mg/L CaCO 3 ), and 0.49mg/L, respectively. Using the same deriving method for each chemical, the national Chinese WQC were higher than site-specific WQC derived in this study for ammonia (national WQC of 25.16mg/L) and nitrobenzene (national WQC of 0.57mg/L), while the national WQC for cadmium was lower (national WQC of 1.81μg/L). These results indicated that published data can be helpful for use when deriving site-specific WQC but that there were differences between site-specific and national WQC which may lead to either over- or under-protection depending on the pollutant if national WQC were used as the basis for the water management of specific river systems, like the Liao River. Copyright © 2017. Published by Elsevier Inc.

Research in thermal biology: Burning questions for coldwater stream fishes

USGS Publications Warehouse

McCullough, D.A.; Bartholow, J.M.; Jager, H.I.; Beschta, R.L.; Cheslak, E.F.; Deas, M.L.; Ebersole, J.L.; Foott, J.S.; Johnson, S.L.; Marine, K.R.; Mesa, M.G.; Petersen, J.H.; Souchon, Y.; Tiffan, K.F.; Wurtsbaugh, W.A.

2009-01-01

With the increasing appreciation of global warming impacts on ecological systems, in addition to the myriad of land management effects on water quality, the number of literature citations dealing with the effects of water temperature on freshwater fish has escalated in the past decade. Given the many biological scales at which water temperature effects have been studied, and the growing need to integrate knowledge from multiple disciplines of thermal biology to fully protect beneficial uses, we held that a survey of the most promising recent developments and an expression of some of the remaining unanswered questions with significant management implications would best be approached collectively by a diverse research community. We have identified five specific topic areas of renewed research where new techniques and critical thought could benefit coldwater stream fishes (particularly salmonids): molecular, organism, population/species, community and ecosystem, and policy issues in water quality. Our hope is that information gained through examination of recent research fronts linking knowledge at various scales will prove useful in managing water quality at a basin level to protect fish populations and whole ecosystems. Standards of the past were based largely on incipient lethal and optimum growth rate temperatures for fish species, while future standards should consider all integrated thermal impacts to the organism and ecosystem. ?? Taylor and Francis Group, LLC.

Research in thermal biology: Burning questions for coldwater stream fishes

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCullough, Dr. Dale; Bartholow, Dr. John; Jager, Yetta

2009-01-01

With the increasing appreciation of global warming impacts on ecological systems in addition to the myriad of land management effects on water quality, the number of literature citations dealing with the effects of water temperature on freshwater fish has escalated in the past decade. Given the many biological scales at which water temperature effects have been studied and the growing need to integrate knowledge from multiple disciplines of thermal biology to fully protect beneficial uses, we held that a survey of the most promising recent developments and an expression of some of the remaining unanswered questions with significant management implicationsmore » would best be approached collectively by a diverse research community. We have identified five specific topic areas of renewed research where new techniques and critical thought could benefit coldwater stream fishes (particularly salmonids): molecular, organism, population/species, community and ecosystem, and policy issues in water quality. Our hope is that information gained through examination of recent research fronts linking knowledge at various scales will prove useful in managing water quality at a basin level to protect fish populations and whole ecosystems. Standards of the past were based largely on incipient lethal and optimum growth rate temperatures for fish species, while future standards should consider all integrated thermal impacts to the organism and ecosystem.« less

Estimating mercury exposure of piscivorous birds and sport fish using prey fish monitoring

USGS Publications Warehouse

Ackerman, Joshua T.; Hartman, C. Alex; Eagles-Smith, Collin A.; Herzog, Mark P.; Davis, Jay; Ichikawa, Gary; Bonnema, Autumn

2015-01-01

Methylmercury is a global pollutant of aquatic ecosystems, and monitoring programs need tools to predict mercury exposure of wildlife. We developed equations to estimate methylmercury exposure of piscivorous birds and sport fish using mercury concentrations in prey fish. We collected original data on western grebes (Aechmophorus occidentalis) and Clark’s grebes (Aechmophorus clarkii) and summarized the published literature to generate predictive equations specific to grebes and a general equation for piscivorous birds. We measured mercury concentrations in 354 grebes (blood averaged 1.06 ± 0.08 μg/g ww), 101 grebe eggs, 230 sport fish (predominantly largemouth bass and rainbow trout), and 505 prey fish (14 species) at 25 lakes throughout California. Mercury concentrations in grebe blood, grebe eggs, and sport fish were strongly related to mercury concentrations in prey fish among lakes. Each 1.0 μg/g dw (∼0.24 μg/g ww) increase in prey fish resulted in an increase in mercury concentrations of 103% in grebe blood, 92% in grebe eggs, and 116% in sport fish. We also found strong correlations between mercury concentrations in grebes and sport fish among lakes. Our results indicate that prey fish monitoring can be used to estimate mercury exposure of piscivorous birds and sport fish when wildlife cannot be directly sampled.

Water temperature, body mass and fasting heat production of pacu (Piaractus mesopotamicus).

PubMed

Aguilar, Fredy A A; Cruz, Thaline M P DA; Mourão, Gerson B; Cyrino, José Eurico P

2017-01-01

Knowledge on fasting heat production (HEf) of fish is key to develop bioenergetics models thus improving feeding management of farmed species. The core of knowledge on HEf of farmed, neotropical fish is scarce. This study assessed the effect of body mass and water temperature on standard metabolism and fasting heat production of pacu, Piaractus mesopotamicus, an omnivore, Neotropical fresh water characin important for farming and fisheries industries all through South American continent. An automated, intermittent flow respirometry system was used to measure standard metabolic rate (SMR) of pacu (17 - 1,050 g) at five water temperatures: 19, 23, 26, 29 and 33 °C. Mass specific SMR increased with increasing water temperature but decreased as function of body mass. The allometric exponent for scaling HEf was 0.788, and lied in the range recorded for all studied warm-water fish. The recorded van't Hoff factor (Q10) for pacu (2.06) shows the species low response to temperature increases. The model HEf = 0.04643×W0.7882×T1.837 allows to predict HEf (kJ d-1) from body mass (W, kg) and water temperature (T, °C), and can be used in bioenergetical models for the species.

Fishes of Missouri River, chute, and flood plain habitats: Chapter 4 in Initial biotic survey of Lisbon Bottom, Big Muddy National Fish and Wildlife Refuge

USGS Publications Warehouse

Grady, Joanne; Milligan, Jim; Chapman, Duane C.; Ehrhardt, Ellen A.; Dieterman, Douglas J.; Galat, David L.; Hooker, John; Kubisiak, John; DeLonay, Aaron; Little, Edward E.; Robinson, Jack; Tibbs, John

1999-01-01

The Lisbon Bottom Unit of the Big Muddy National Fish and Wildlife Refuge (Refuge) is approximately 2,200 acres and is the first complete unit of the Refuge. Primary objectives of the Refuge are to create and restore diverse riverine aquatic habitats and reconnect the Missouri River to its flood plain where feasible. Management seeks to accomplish these objectives by encouraging natural processes of erosion, deposition, and succession to the greatest extent possible.One of the most salient aquatic features of the Lisbon Bottom Unit is a newly created 2-mile-long free-flowing chute, or side channel (Fig. 1). This chute began forming as a levee breech scour hole during the Great Flood of 1993. The chute continued to develop during the 1995 flood and finally cut through to a flowing side channel during the 1996 flood. Extensive erosion and bank sluffing continued during 1997 due to sustained high flows that occurred throughout most of the year. The chute has progressively become wider and deeper with a developing meander pattern and channel bars have begun to form. Lisbon Bottom also contains several seasonal and permanent wetlands and is subject to periodic flooding at high Missouri River stages.Eight studies have been completed or are ongoing to evaluate Missouri River fishes associated with various habitat components of Lisbon Bottom and adjacent Missouri River reaches (Table 1). Several are part of much larger investigations to evaluate fish use of flood-created habitat features, basinwide fish assessment, and endangered or candidate species concerns.At the Lisbon Bottom Unit or in the Missouri River adjacent to the unit 54 fish species were collected (Table 2). Eight of these species have either a protected status under State or Federal laws or biologists consider them to potentially qualify for protected status. The status of the following fish is listed in Table 2: pallid sturgeon x shovelnose sturgeon hybrid, paddlefish, northern pike, sturgeon chub, sicklefin chub, ghost shiner, western silvery minnow, plains minnow, and blue sucker. Equally important to note are fish species that were not collected. The flathead chub, currently listed as State endangered and proposed for Federal listing, were not collected in any of the studies.Common fish species, collected in all seven sampling studies, included gizzard shad, common carp, river carpsucker, and freshwater drum. Paddlefish, skipjack herring, silver carp, white sucker, redfin shiner, western silvery minnow, bullhead minnow, and black bullhead were each collected in only one of the seven studies.Pflieger (1971) developed a guild system for the fishes of Missouri based on distribution patterns and centers of abundance. Fish were assigned to one of four primary faunal groups: Ozark, Big River, Lowland, and Prairie. Two secondary groups (Ozark-prairie and Ozark-lowland) were defined for species equally abundant and distributed in two of the primary areas. Two Ozark-prairie species, shorthead redhorse and white sucker, were collected on or near the Lisbon Bottom Unit.Big River species are found primarily in the Missouri and Mississippi Rivers. The environmental factors controlling fish distribution in these rivers appear to be substrate, current velocity, and turbidity. On or near the Lisbon Bottom Unit 18 Big River species were collected (Table 2).Lowland species are intolerant of siltation and high turbidity. They inhabit standing or slow-moving water with sand, fine gravel, and organic debris substrates. Two Lowland species, bullhead minnow and mosquitofish, were collected in connected scours on the Lisbon Bottom Unit.Prairie species have broader ecological tolerances than the Ozark and Lowland species. They are largely absent in high gradient streams and cool, clear waters. Prairie species make up a significant proportion of Missouri and Mississippi River fishes. Seven Prairie species were collected on or near the Lisbon Bottom Unit (Table 2).The last group, Wide-ranging, was defined as the species more widespread than the other faunal groups with broader environmental tolerances. Most Wide-ranging species occur at least occasionally in all sections of the state. Nineteen Wide-ranging species were collected on or near the Lisbon Bottom Unit (Table 2).Kubisiak (1997) found that isolated scours in the Lower Missouri River were dominated by Wide-ranging species. Connected scours also held Wideranging species but they contained Prairie species and were dominated by Big River species. Faunal group diversity and species richness were compared between isolated (Study l) and connected (Studies 4, 5, 7, and 8) scours of the Lisbon Bottom Unit. Species richness was similar with 22 species collected in isolated scours and an average of 24.8 species collected in connected scours. Isolated scour fish catches were dominated by Wide-ranging fish (59%) with 14% Big River fishes and 14% Prairie fishes. Connected scours had a larger percentage of Big River fish (32%) and fewer Wide-ranging (36%) and Prairie (13%) species than the isolated scours. In the combined studies, Wide-ranging fish dominated the connected scours.A similar comparison was made of fish from chute habitats and the Missouri River. Chute habitats include the Lisbon Bottom Chute, the chute between the right bank and island located at river mile 219, and a shallow channel running between a large sandbar complex and the channel border adjacent to Lisbon Bottom. Species richness in the chutes (35 species) was greater than that of the adjacent river (23 species). Big River species (40%) dominated the chute samples, followed by Wide-ranging at 31% Cand Prairie Cut 14%.The river samples contained equal numbers of Wide-ranging species (35%) and Big River species (35%) with 17% Prairie species. Differences in fish guild diversity and species richness may be due to numerous factors including sampling effort and sampling season. River samples were collected only in Study 3 in October; chute samples were collected in July, August, and October. Fish may have been using the chute in July and August to spawn, feed, or escape high river levels.The Lisbon Bottom Chute is a truly unique feature of the Lower Missouri River. It is the first naturally created side channel to develop since the U.S. Army Corps of Engineers tamed the river. The Corps eliminated 89% of the islands in the Missouri River between 1879 and 1954 (Funk and Robinson 1974). The chutes between the islands and the shore were shallower with less current than the main channel. These areas provided diversity to the Missouri River fish habitat, serving as nursery and feeding areas. The Lisbon Bottom Unit of the Big Muddy National Fish and Wildlife Refuge will continue to be studied in an effort to understand the complex role these areas play in river systems.

GENETIC ADAPTATION TO CHRONIC CONTAMINANT EXPOSURE BY A SMALL ESTUARINE FISH

EPA Science Inventory

Investigations of the non-migratory fish species Fundulus heteroclitus indigenous to a highly chemically contaminated site is providing novel insights into stressor costs and adaptive strategies. Specifically, we are studying an abundant and persistent population of F. heterocli...

Hierarchical faunal filters: An approach to assessing effects of habitat and nonnative species on native fishes

USGS Publications Warehouse

Quist, M.C.; Rahel, F.J.; Hubert, W.A.

2005-01-01

Understanding factors related to the occurrence of species across multiple spatial and temporal scales is critical to the conservation and management of native fishes, especially for those species at the edge of their natural distribution. We used the concept of hierarchical faunal filters to provide a framework for investigating the influence of habitat characteristics and normative piscivores on the occurrence of 10 native fishes in streams of the North Platte River watershed in Wyoming. Three faunal filters were developed for each species: (i) large-scale biogeographic, (ii) local abiotic, and (iii) biotic. The large-scale biogeographic filter, composed of elevation and stream-size thresholds, was used to determine the boundaries within which each species might be expected to occur. Then, a local abiotic filter (i.e., habitat associations), developed using binary logistic-regression analysis, estimated the probability of occurrence of each species from features such as maximum depth, substrate composition, submergent aquatic vegetation, woody debris, and channel morphology (e.g., amount of pool habitat). Lastly, a biotic faunal filter was developed using binary logistic regression to estimate the probability of occurrence of each species relative to the abundance of nonnative piscivores in a reach. Conceptualising fish assemblages within a framework of hierarchical faunal filters is simple and logical, helps direct conservation and management activities, and provides important information on the ecology of fishes in the western Great Plains of North America. ?? Blackwell Munksgaard, 2004.

Mercury concentrations in water and mercury and selenium concentrations in fish from Brownlee Reservoir and selected sites in the Boise and Snake Rivers, Idaho and Oregon, 2013–15

USGS Publications Warehouse

Williams, Marshall L.; MacCoy, Dorene E.

2016-06-30

Mercury (Hg) analyses were conducted on samples of sport fish and water collected from selected sampling sites in Brownlee Reservoir and the Boise and Snake Rivers to meet National Pollution Discharge and Elimination System (NPDES) permit requirements for the City of Boise, Idaho, between 2013 and 2015. City of Boise personnel collected water samples from six sites between October and November 2013 and 2015, with one site sampled in 2014. Total Hg concentrations in unfiltered water samples ranged from 0.48 to 8.8 nanograms per liter (ng/L), with the highest value in Brownlee Reservoir in 2013. All Hg concentrations in water samples were less than the U.S. Environmental Protection Agency (USEPA) Hg chronic aquatic life criterion of 12 ng/L.The USEPA recommended a water-quality criterion of 0.30 milligrams per kilogram (mg/kg) methylmercury (MeHg) expressed as a fish-tissue residue value (wet-weight MeHg in fish tissue). The Idaho Department of Environmental Quality adopted the USEPA’s fish-tissue criterion and established a reasonable potential to exceed (RPTE) threshold 20 percent lower than the criterion or greater than 0.24 mg/kg Hg based on an average concentration of 10 fish from a receiving waterbody. NPDES permitted discharge to waters with fish having Hg concentrations exceeding 0.24 mg/kg are said to have a reasonable potential to exceed the water-quality criterion and thus are subject to additional permit obligations, such as requirements for increased monitoring and the development of a Hg minimization plan. The Idaho Fish Consumption Advisory Program (IFCAP) issues fish advisories to protect general and sensitive populations of fish consumers and has developed an action level of 0.22 mg/kg Hg in fish tissue. Fish consumption advisories are water body- and species-specific and are used to advise allowable fish consumption from specific water bodies. The geometric mean Hg concentration of 10 fish of a single species collected from a single water body (lake or stream) in Idaho is compared to the action level to determine if a fish consumption advisory should be issued.The U.S. Geological Survey collected and analyzed individual fillets of mountain whitefish (Prosopium williamsoni), rainbow trout (Oncorhynchus mykiss), smallmouth bass (Micropterus dolomieu), and channel catfish (Ictalurus punctatus) for Hg. The 2013 average Hg concentration for small mouth bass (0.32 mg/kg) collected at Brownlee Reservoir and for channel catfish (0.33 mg/kg) collected at the Boise River mouth, exceeded the Idaho water quality criterion (>0.3 mg/kg), the Hg RPTE threshold (>0.24 mg/kg), and the IFCAP action level (>0.22 mg/kg). Average Hg concentrations in fish collected in 2014 or 2015 did not exceed evaluation criteria for any of the species assessed.Selenium (Se) analysis was conducted on one composite fish tissue sample per site to assess general concentrations and to provide information for future risk assessments. Composite concentrations of Se in fish tissue collected between 2013 and 2015 ranged from 0.07 and 0.49 mg/kg wet weight with the highest concentration collected from smallmouth bass from the Snake River near Murphy, and the lowest from mountain whitefish from the Boise River at Eckert Road.

Enhancing fish Underwater Visual Census to move forward assessment of fish assemblages: An application in three Mediterranean Marine Protected Areas

PubMed Central

Thiriet, Pierre; Di Franco, Antonio; Francour, Patrice

2017-01-01

Monitoring fish assemblages is needed to assess whether Marine Protected Areas (MPAs) are meeting their conservation and fisheries management goals, as it allows one to track the progress of recovery of exploited species and associated communities. Underwater Visual Census techniques (UVC) are used to monitor fish assemblages in MPAs. UVCs should be adapted to fish abundance, body-size and behaviour, which can strongly affect fish detectability. In Mediterranean subtidal habitats, however, UVC strip transects of one surface area (25x5 m2) are commonly used to survey the whole fish assemblage, from large shy fish to small crypto-benthic fish. Most high trophic level predators (HTLPs) are large shy fish which rarely swim close to divers and, consequently, their abundance may be under-estimated with commonly used transects. Here, we propose an improvement to traditional transect surveys to better account for differences in behaviour among and within species. First, we compared the effectiveness of combining two transect surface areas (large: 35x20 m2; medium: 25x5 m2) in quantifying large, shy fish within and outside Mediterranean MPAs. We identified species-specific body-size thresholds defining a smaller and a larger size class better sampled by medium and large transects respectively. Combining large and medium transects provided more accurate biomass and species richness estimates for large, shy species than using medium transects alone. We thus combined the new approach with two other transect surface areas commonly used to survey crypto-benthic (10x1 m2) and necto-benthic (25x5 m2) species in order to assess how effectively MPAs protection the whole fish assemblage. We verified that MPAs offer significant protection for HTLPs, their response in terms of biomass and density increase in MPAs was always higher in magnitude than other functional groups. Inside MPAs, the contribution of HTLP reached >25% of total fish biomass, against < 2% outside MPAs. Surveys with multiple transect surface areas allow for a more realistic assessment of the structure of the whole fish assemblage and better assessment of potential recovery of HTLPs within reserves of HTLP. PMID:28594836

Enhancing fish Underwater Visual Census to move forward assessment of fish assemblages: An application in three Mediterranean Marine Protected Areas.

PubMed

Prato, Giulia; Thiriet, Pierre; Di Franco, Antonio; Francour, Patrice

2017-01-01

Monitoring fish assemblages is needed to assess whether Marine Protected Areas (MPAs) are meeting their conservation and fisheries management goals, as it allows one to track the progress of recovery of exploited species and associated communities. Underwater Visual Census techniques (UVC) are used to monitor fish assemblages in MPAs. UVCs should be adapted to fish abundance, body-size and behaviour, which can strongly affect fish detectability. In Mediterranean subtidal habitats, however, UVC strip transects of one surface area (25x5 m2) are commonly used to survey the whole fish assemblage, from large shy fish to small crypto-benthic fish. Most high trophic level predators (HTLPs) are large shy fish which rarely swim close to divers and, consequently, their abundance may be under-estimated with commonly used transects. Here, we propose an improvement to traditional transect surveys to better account for differences in behaviour among and within species. First, we compared the effectiveness of combining two transect surface areas (large: 35x20 m2; medium: 25x5 m2) in quantifying large, shy fish within and outside Mediterranean MPAs. We identified species-specific body-size thresholds defining a smaller and a larger size class better sampled by medium and large transects respectively. Combining large and medium transects provided more accurate biomass and species richness estimates for large, shy species than using medium transects alone. We thus combined the new approach with two other transect surface areas commonly used to survey crypto-benthic (10x1 m2) and necto-benthic (25x5 m2) species in order to assess how effectively MPAs protection the whole fish assemblage. We verified that MPAs offer significant protection for HTLPs, their response in terms of biomass and density increase in MPAs was always higher in magnitude than other functional groups. Inside MPAs, the contribution of HTLP reached >25% of total fish biomass, against < 2% outside MPAs. Surveys with multiple transect surface areas allow for a more realistic assessment of the structure of the whole fish assemblage and better assessment of potential recovery of HTLPs within reserves of HTLP.

Historical changes in Nebraska's lotic fish assemblages: Implications of anthropogenic alterations

USGS Publications Warehouse

Smith, Christopher D.; Fischer, Jesse R.; Quist, Michael C.

2014-01-01

The plains of midwestern North America have undergone significant anthropogenic alterations following European settlement with consequent effects to lotic fish assemblage structure. We examined trends in fish assemblage structure and function in Nebraska's lotic systems using site-specific, presence-absence data from historical (1939–1940) and contemporary surveys (2003–2005; n  =  183). Shifts in fish assemblage structure were characterized by declines of specialist species (e.g., western silvery minnow Hybognathus argyritis) and increases in nonnative, sport, and generalist species (e.g., common carp Cyprinus carpio). Our research illustrates differences between historical and contemporary surveys for both taxonomic and functional metrics. Changes in fish assemblage structure were correlated with a contemporary measure of anthropogenic alteration (Human Threat Index; HTI) and were most pronounced for large-scale threats (i.e., watershed HTI, overall HTI). The HTI is a composite index of cumulative anthropogenic alterations experienced by a stream system and was used to investigate broad-scale implications of anthropogenic activity on fish assemblage structure. Fish assemblages among sites were more similar in contemporary surveys than in historical surveys, such changes might indicate a homogenization of the fish assemblages. Losses of native species and increases in introduced species have occurred in Nebraska's lotic systems across a broad temporal span and shifts are likely related to high levels of human perturbation.

Progress, challenges and perspectives on fish gamete cryopreservation: A mini-review.

PubMed

Asturiano, Juan F; Cabrita, Elsa; Horváth, Ákos

2017-05-01

Protocols for the cryopreservation of fish gametes have been developed for many different fish species, in special, freshwater salmonids and cyprinids. Methods for sperm freezing have progressed during the last decades due to the increasing number of potential applications: aquaculture (genetic improvement programs, broodstock management, helping with species having reproductive problems), biotechnology studies using model fish species (preservation of transgenic or mutant lines), cryobanking of genetic resources from endangered species, etc. This mini-review tries to give an overview of the present situation of this area of research, identifying the main challenges and perspectives, redirecting the reader to more in-depth reviews and papers. Copyright © 2016 Elsevier Inc. All rights reserved.

A regional perspective on the diversity and conservation of tropical Andean fishes.

PubMed

Anderson, Elizabeth P; Maldonado-Ocampo, Javier A

2011-02-01

The tropical Andes harbor an extraordinarily varied concentration of species in a landscape under increasing pressure from human activities. Conservation of the region's native plants and animals has received considerable international attention, but the focus has been on terrestrial biota. The conservation of freshwater fauna, particularly the conservation of fishes, has not been emphasized. Tropical Andean fishes are among the most understudied vertebrates in the world. We estimate that between 400 and 600 fish species inhabit the diverse aquatic environments in the region. Nearly 40% of these species are endemic. Tropical Andean fishes are vulnerable to ongoing environmental changes related to deforestation, water withdrawals, water pollution, species introductions, and hydropower development. Additionally, their distributions and population dynamics may be affected by hydrologic alterations and warmer water temperatures associated with projected climate change. Presently, at least three species are considered extinct, some populations are endangered, and some species are likely to decline or disappear. The long-term persistence of tropical Andean fishes will depend on greater consideration of freshwater systems in regional conservation initiatives. ©2010 Society for Conservation Biology.

The Relationship Between Environment and Nutritional Condition of Arctic Forage Fish

NASA Astrophysics Data System (ADS)

Vollenweider, J.; Heintz, R.; Callahan, M.; Barton, M. B.; Sousa, L.; Danielson, S. L.; Meuter, F.; Moran, J.; Boswell, K. M.

2016-02-01

We describe how marine environmental conditions influence the body condition of forage fish in the Alaskan Arctic. Body condition of fish is a sensitive predictor of fish productivity, with consequences particularly for juvenile survival as well as adult reproduction. For example, body condition of juvenile walleye pollock (Theragra chalcogramma) in the Bering Sea is a significant predictor of survival to recruitment, and a better index than sheer abundance of juveniles. Body condition of fish generally varies with interannual fluctuations in oceanographic conditions such as temperature and wind mixing, which may have cascading effects on food quality and availability, and ultimately fish survival. We use these underlying principles to examine how interannual and spatial variation in environmental conditions affect fish condition of various Arctic species. Specifically, we measured the energy content of some of the most abundant Arctic forage species including Arctic cod (Boreogadus saida), capelin (Mallotus villosus), fourhorn sculpin (Myoxocephalus quadricornis), and saffron cod (Eleginus gracilis) over multiple years and habitats. Fish were sampled from multiple projects (ACES, SHELFZ, Arctic Eis) from three physically distinct waterbodies: the Chukchi and Beaufort Seas, and Elson Lagoon, an extensive, shallow estuary characteristic of the Arctic coastline. Fish condition of the various species responded differently to interannual changes and amongst water bodies. For example, Arctic Cod had energy density in 2014 compared with other years while fourhorn sculpin were unperturbed. These findings will help identify favorable habitats for Arctic species, identify locations and condition contributing the most to fish productivity, and will help predict how Arctic fish and their predators may fare in the face of climate change.

Quantifying seining detection probability for fishes of Great Plains sand‐bed rivers

USGS Publications Warehouse

Mollenhauer, Robert; Logue, Daniel R.; Brewer, Shannon K.

2018-01-01

Species detection error (i.e., imperfect and variable detection probability) is an essential consideration when investigators map distributions and interpret habitat associations. When fish detection error that is due to highly variable instream environments needs to be addressed, sand‐bed streams of the Great Plains represent a unique challenge. We quantified seining detection probability for diminutive Great Plains fishes across a range of sampling conditions in two sand‐bed rivers in Oklahoma. Imperfect detection resulted in underestimates of species occurrence using naïve estimates, particularly for less common fishes. Seining detection probability also varied among fishes and across sampling conditions. We observed a quadratic relationship between water depth and detection probability, in which the exact nature of the relationship was species‐specific and dependent on water clarity. Similarly, the direction of the relationship between water clarity and detection probability was species‐specific and dependent on differences in water depth. The relationship between water temperature and detection probability was also species dependent, where both the magnitude and direction of the relationship varied among fishes. We showed how ignoring detection error confounded an underlying relationship between species occurrence and water depth. Despite imperfect and heterogeneous detection, our results support that determining species absence can be accomplished with two to six spatially replicated seine hauls per 200‐m reach under average sampling conditions; however, required effort would be higher under certain conditions. Detection probability was low for the Arkansas River Shiner Notropis girardi, which is federally listed as threatened, and more than 10 seine hauls per 200‐m reach would be required to assess presence across sampling conditions. Our model allows scientists to estimate sampling effort to confidently assess species occurrence, which maximizes the use of available resources. Increased implementation of approaches that consider detection error promote ecological advancements and conservation and management decisions that are better informed.

Biological baseline data Youngs Bay, Oregon, 1974

DOE Office of Scientific and Technical Information (OSTI.GOV)

McMechan, K.J.; Higley, D.L.; Holton, R.L.

1975-04-01

This report presents biological baseline information gathered during the research project, Physical, Chemical and Biological Studies on Youngs Bay.'' Youngs Bay is a shallow embayment located on the south shore of the Columbia River, near Astoria, Oregon. Research on Youngs Bay was motivated by the proposed construction by Alumax Pacific Aluminum Corporation of an aluminum reduction plant at Warrenton, Oregon. The research was designed to provide biological baseline information on Youngs Bay in anticipation of potential harmful effects from plant effluents. The information collected concerns the kinds of animals found in the Youngs Bay area, and their distribution and seasonalmore » patterns of abundance. In addition, information was collected on the feeding habits of selected fish species, and on the life history and behavioral characteristics of the most abundant benthic amphipod, Corophium salmonis. Sampling was conducted at approximately three-week intervals, using commonly accepted methods of animal collection. Relatively few stations were sampled for fish, because of the need to standardize conditions of capture. Data on fish capture are reported in terms of catch-per-unit effort by a particular sampling gear at a specific station. Methods used in sampling invertebrates were generally more quantitative, and allowed sampling at a greater variety of places, as well as a valid basis for the computation of densities. Checklists of invertebrate species and fish species were developed from these samples, and are referred to throughout the report. The invertebrate checklist is more specific taxonomically than are tables reporting invertebrate densities. This is because the methods employed in identification were more precise than those used in counts. 9 refs., 27 figs., 25 tabs.« less

Iberian fish records in the vertebrate collection of the Museum of Zoology of the University of Navarra

PubMed Central

Rodeles, Amaia A.; Galicia, David; Miranda, Rafael

2016-01-01

The study of freshwater fish species biodiversity and community composition is essential for understanding river systems, the effects of human activities on rivers, and the changes these animals face. Conducting this type of research requires quantitative information on fish abundance, ideally with long-term series and fish body measurements. This Data Descriptor presents a collection of 12 datasets containing a total of 146,342 occurrence records of 41 freshwater fish species sampled in 233 localities of various Iberian river basins. The datasets also contain 148,749 measurement records (length and weight) for these fish. Data were collected in different sampling campaigns (from 1992 to 2015). Eleven datasets represent large projects conducted over several years, and another combines small sampling campaigns. The Iberian Peninsula contains high fish biodiversity, with numerous endemic species threatened by various menaces, such as water extraction and invasive species. These data may support the development of large biodiversity conservation studies. PMID:27727236

Iberian fish records in the vertebrate collection of the Museum of Zoology of the University of Navarra.

PubMed

Rodeles, Amaia A; Galicia, David; Miranda, Rafael

2016-10-11

The study of freshwater fish species biodiversity and community composition is essential for understanding river systems, the effects of human activities on rivers, and the changes these animals face. Conducting this type of research requires quantitative information on fish abundance, ideally with long-term series and fish body measurements. This Data Descriptor presents a collection of 12 datasets containing a total of 146,342 occurrence records of 41 freshwater fish species sampled in 233 localities of various Iberian river basins. The datasets also contain 148,749 measurement records (length and weight) for these fish. Data were collected in different sampling campaigns (from 1992 to 2015). Eleven datasets represent large projects conducted over several years, and another combines small sampling campaigns. The Iberian Peninsula contains high fish biodiversity, with numerous endemic species threatened by various menaces, such as water extraction and invasive species. These data may support the development of large biodiversity conservation studies.

Bioenergetics modeling of the annual consumption of zooplankton by pelagic fish feeding in the Northeast Atlantic

PubMed Central

Utne, Kjell Rong; Jansen, Teunis; Huse, Geir

2018-01-01

The present study uses bioenergetics modeling to estimate the annual consumption of the main zooplankton groups by some of the most commercially important planktivorous fish stocks in the Northeast Atlantic, namely Norwegian spring-spawning (NSS) herring (Clupea harengus), blue whiting (Micromesistius poutassou) and NEA mackerel (Scomber scombrus). The data was obtained from scientific surveys in the main feeding area (Norwegian Sea) in the period 2005–2010. By incorporating novel information about ambient temperature, seasonal growth and changes in the diet from stomach content analyses, annual consumption of the different zooplankton groups by pelagic fish is estimated. The present study estimates higher consumption estimates than previous studies for the three species and suggests that fish might have a greater impact on the zooplankton community as foragers. This way, NEA mackerel, showing the highest daily consumption rates, and NSS herring, annually consume around 10 times their total biomass, whereas blue whiting consume about 6 times their biomass in zooplankton. The three species were estimated to consume an average of 135 million (M) tonnes of zooplankton each year, consisting of 53–85 M tonnes of copepods, 20–32 M tonnes of krill, 8–42 M tonnes of appendicularians and 0.2–1.2 M tonnes of fish, depending on the year. For NSS herring and NEA mackerel the main prey groups are calanoids and appendicularians, showing a peak in consumption during June and June–July, respectively, and suggesting high potential for inter-specific feeding competition between these species. In contrast, blue whiting maintain a low consumption rate from April to September, consuming mainly larger euphausiids. Our results suggest that the three species can coexist regardless of their high abundance, zooplankton consumption rates and overlapping diet. Accordingly, the species might have niche segregation, as they are species specific, showing annual and inter-annual variability in total consumption of the different prey species. These estimates and their inter-annual and inter-specific variation are fundamental for understanding fundamental pelagic predator-prey interactions as well as to inform advanced multispecies ecosystem models. PMID:29293577

Interannual Variability of Fisheries Economic Returns and Energy Ratios Is Mostly Explained by Gear Type

PubMed Central

Trenkel, Verena M.; Daurès, Fabienne; Rochet, Marie-Joëlle; Lorance, Pascal

2013-01-01

According to portfolio theory applied to fisheries management, economic returns are stabilised by harvesting in a portfolio stocks of species whose returns are negatively correlated and for which the portfolio economic return variance is smaller than the sum of stock specific return variances. Also, variability is expected to decrease with portfolio width. Using a range of indicators, these predictions were tested for the French fishing fleets in the Bay of Biscay (Northeast Atlantic) during the period 2001–2009. For this, vessels were grouped into eight fishing fleets based on the gears used and exploited species were grouped into five functional groups. The portfolio width of fleets ranged from 1–3 functional groups, or 4–19 species. Economic fleet returns (sale revenues minus fishing costs) varied strongly between years; the interannual variability was independent of portfolio width (species or functional groups). Energy ratio expressed by the ratio between fuel energy used for fishing and energy contained in landings varied from 0.3 for purse seines to 9.7 for trawlers using bottom trawls alone or in combination with pelagic trawls independent of portfolio width. Interannual variability in total sale revenues was larger than the sum of species specific sales revenue variability, except for fleets using hooks and pelagic trawlers; it increased with the number of species exploited. In conclusion, the interannual variability of economic returns or energy ratios of French fisheries in the Bay of Biscay did not decrease with the number of species or functional groups exploited, though it varied between fleets. PMID:23922951

Observations of the distributions of five fish species in a small Appalachian stream

USGS Publications Warehouse

Larson, Gary L.; Hoffman, Robert L.; Moore, S.E.

2002-01-01

The notion has been growing that resident stream fishes exhibit a greater capacity for movement than was previously thought. In this study, we recorded the distributions of four resident fish species (longnose dace Rhinichthys cataractae, blacknose dace R. atratulus, mottled sculpin Cottus bairdi, and rainbow trout Oncorhynchus mykiss) and one nonresident species (central stoneroller Campostoma anomalum) in Rock Creek, a small tributary of Cosby Creek in Great Smoky Mountains National Park, over the period 1979a??1995. During this study, 1,998 individuals of resident species were collected from stream sections considered to be within a common area of distribution for each species. Forty-five individuals of resident and nonresident species were captured upstream of these areas, and eight of these fish were considered to be larger than individuals considered typical for each species. Small mammal dispersal theory concepts were used to classify and describe fish movements outside of common areas of distribution. These movements were identified as important in maintaining population connectivity within stream drainages, contributing to reducing the potential for local extinctions of populations and to the recolonization of unoccupied habitats. This study highlights the need for continued study of fish movements in stream drainages and for development of appropriate resource management strategies based partly on the spatial dynamics of fish populations and communities.

Risks and benefits of fish consumption for childbearing women.

PubMed

Del Gobbo, Liana C; Archbold, Josephine A; Vanderlinden, Loren D; Eckley, Chris S; Diamond, Miriam L; Robson, Matthew

2010-01-01

Pregnant women's fish consumption provides both benefits and risks to the developing fetus. Docosahexaenoic acid (DHA) from fish may enhance fetal neurodevelopment, while methylmercury (MeHg) can have detrimental effects. Dietitians would benefit from information on the frequency with which fish species may be consumed to increase DHA intake among Canadian women of childbearing age, and on minimizing the risks from MeHg, especially for those who consume fish frequently. Eighteen fish species were selected for DHA and mercury analysis from retail markets in the Toronto area. Consumption scenarios using analytical results for these fish species indicate that women of childbearing age can consume nine of 18 fish species every day (14 servings a week) or often (up to four servings a week) and remain below toxicological benchmarks for mercury. Moreover, women can also attain the recommended DHA level by consuming six of those nine fish: four 75-g servings of smelt, porgie, or bluefish a week, or two 75-g servings of milkfish, silver pomfret, or tilapia a day. Our analysis indicates that the DHA level recommended for childbearing women can be attained through fish consumption alone, without the need for supplementation and without posing a risk to the woman (or the fetus) from mercury.

Patterns of presence and concentration of pesticides in fish and waters of the Júcar River (Eastern Spain).

PubMed

Belenguer, Vicent; Martinez-Capel, Francisco; Masiá, Ana; Picó, Yolanda

2014-01-30

The Júcar River, in a typical Mediterranean Basin, is expected to suffer a decline in water quality and quantity as a consequence of the climate change. This study is focused on the presence and distribution of pesticides in water and fish, using the first extensive optimization and application of the QuEChERS method to determine pesticides in freshwater fish. Majority pesticides in water - in terms of presence and concentration - were dichlofenthion, chlorfenvinphos, imazalil, pyriproxyfen and prochloraz (associated with a frequent use in farming activities), as well as buprofezin, chlorpyriphos and hexythiazox. In fish, the main compounds were azinphos-ethyl, chlorpyriphos, diazinon, dimethoate and ethion. The analysis of bio-concentration in fish indicated differences by species. The maximum average concentration was detected in European eel (a critically endangered fish species). The wide presence of pesticides in water and fish suggests potential severe effects on fish populations and other biota in future scenarios of climate change, in a river basin with several endemic and endangered fish species. The potential effects of pesticides in combination with multiple stressors require further research to prioritize the management of specific chemicals and suggest effective restoration actions at the basin scale. Copyright © 2013 Elsevier B.V. All rights reserved.

The Western Fisheries Research Center studies: threatened and endangered fishes

USGS Publications Warehouse

Parsley, M.; Scoppettone, G.G.; Shively, R.; Gadomski, D.; Becker, D.

2005-01-01

Within historical time, western native fish communities have faced increasing threats from habitat loss, invasive species, and pollution. It should come as no surprise that human development has greatly altered fish habitat in the west because of the importance of water for domestic, agricultural, and industrial uses, power generation, waste disposal, flood protection, and transportation. Fish that were adapted to natural cycles of river flow, lake levels, and water temperatures have been unable to adapt to the changes to these cycles caused by development, leading to the listing as threatened or endangered of 68 species of western native fishes. Rapid expansion of non-native fishes, aquatic plants, and invertebrates has increased competition for food and space while pollutants from past and present degrade our lakes, streams, and rivers.

Investigating phenology of larval fishes in St. Louis River ...

EPA Pesticide Factsheets

As part of the development of an early detection monitoring strategy for non-native fishes, larval fish surveys have been conducted since 2012 in the St. Louis River estuary. Survey data demonstrates there is considerable variability in fish abundance and species assemblages across different habitats and at multiple temporal scales. To optimize early detection monitoring we need to understand temporal and spatial patterns of larval fishes related to their development and dispersion, as well as the environmental factors that influence them. In 2016 we designed an experiment to assess the phenological variability in larval fish abundance and assemblages amongst shallow water habitats. Specifically, we sought to contrast different thermal environments and turbidity levels, as well as assess the importance of vegetation in these habitats. To evaluate phenological differences we sampled larval fish bi-weekly at nine locations from mid-May to mid-July. Sampling locations were split between upper estuary and lower estuary to contrast river versus seiche influenced habitats. To assess differences in thermal environments, temperature was monitored every 15 minutes at each sampling location throughout the study, beginning in early April. Our design also included sampling at both vegetated (or pre-vegetated) and non-vegetated stations within each sampling location throughout the study to assess the importance of this habitat variable. Hydroacoustic surveys (Biosonics) were

Are parasite richness and abundance linked to prey species richness and individual feeding preferences in fish hosts?

PubMed

Cirtwill, Alyssa R; Stouffer, Daniel B; Poulin, Robert; Lagrue, Clément

2016-01-01

Variations in levels of parasitism among individuals in a population of hosts underpin the importance of parasites as an evolutionary or ecological force. Factors influencing parasite richness (number of parasite species) and load (abundance and biomass) at the individual host level ultimately form the basis of parasite infection patterns. In fish, diet range (number of prey taxa consumed) and prey selectivity (proportion of a particular prey taxon in the diet) have been shown to influence parasite infection levels. However, fish diet is most often characterized at the species or fish population level, thus ignoring variation among conspecific individuals and its potential effects on infection patterns among individuals. Here, we examined parasite infections and stomach contents of New Zealand freshwater fish at the individual level. We tested for potential links between the richness, abundance and biomass of helminth parasites and the diet range and prey selectivity of individual fish hosts. There was no obvious link between individual fish host diet and helminth infection levels. Our results were consistent across multiple fish host and parasite species and contrast with those of earlier studies in which fish diet and parasite infection were linked, hinting at a true disconnect between host diet and measures of parasite infections in our study systems. This absence of relationship between host diet and infection levels may be due to the relatively low richness of freshwater helminth parasites in New Zealand and high host-parasite specificity.

Characterization of chitin extracted from fish scales of marine fish species purchased from local markets in North Sulawesi, Indonesia

NASA Astrophysics Data System (ADS)

Rumengan, I. F. M.; Suptijah, P.; Wullur, S.; Talumepa, A.

2017-10-01

Chitin is a biodegradable biopolymer with a variety of commercial applications, including in the food food-supplement industries as a marine-derived nutraceutical. The purpose of this study was to characterize the molecular structure of chitin extracted from fish scales of important marine fish purchased from local markets in North Sulawesi. Chitin compound material was obtained from a specific fish scale, and then sequentially carrying out a boiling treatment to separate it from a complex with collagen. From the scales of two fish species, parrotfish (Chlorurus sordidus) and red snapper (Lutjanus argentimaculatus), the rendemen of chitin obtained were 45 % and 33%, respectively. Structural characteristics of the chitin were discussed by FTIR (Fourier Transform Infrared) analysis data. FTIR analysis was done using infrared spectroscopy, which is the resulting spectrum represents the molecular absorption and transmission, creating a molecular fingerprint of the sample. The molecular structure of chitin, C18H26N2O10, where the hydroxyl group on the second carbon replaced by acetyl amide, was shown by the infrared spectra. In the infrared spectra, chitin from parrot fish scales indicated the amide band at 1627.13 cm-1, and chitin from red snapper fish scales the amide band at 1648.09 cm-1 which are a typical one for marine chitin. The hydroxyl and amino bands at the ranged spectra up to 3500 cm-1. The yields of chitin isolated from fish scale were relatively huge. Some treatments are necessary to confirm the molecular conformation and deacetylation behavior. All products from the extraction of fish scales could be more accessible for structural modifications to develop biocompatible materials for pharmaceutical purposes.

The development of Neoechinorhynchus buttnerae (Eoacanthocephala: Neoechinorhynchidae) in its intermediate host Cypridopsis vidua in Brazil.

PubMed

Lourenço, Felipe de Sousa; Morey, Germán Augusto Murrieta; Malta, José Celso de Oliveira

2018-06-26

The family Neoechinorhynchidae includes seven species of Neoechinorhynchus from freshwater fishes of Brazil. Although several Neoechinorhynchus species are cited infecting different fish species in Brazil, there is a lack of information concerning to their life cycle and the identification of the intermediate hosts. Thus, the aim of the present study was to describe the development of Neoechinorhynchus buttnerae in its intermediate host collected in a fish farm located in Rio Preto da Eva, Amazonas, Brazil. To verify the presence of N. buttnerae in the fish pond, twenty Colossoma macropomum were captured and analyzed, being corroborated the presence of this parasite species. Samples of plankton were also collected, finding the ostracod Cypridopsis vidua as the intermediate host. For the description of the larvae development, a laboratory experimental procedure was conducted by feeding the collected ostracods with the eggs of the adult specimens taken from the sampled fish. To observe the stages of development an artificial hatch was performed. Every stage of development was photographed, measured, drawn and described. The time of development of the immature stages of N. buttnerae was 29 days, reporting the stages: acanthor, acanthella (with eight developmental changes) and cystacanth. As high infections by N. buttnerae causes morphological damages to the intestine and may compromise the quality of C. macropomum and in consequence the production of fish farmers in the Brazilian Amazon region, the knowledge of its intermediate host and the understanding of its life cycle represents a useful information to prevent and combat infections by this parasite.

Considerations for Treatment of Large Zoologic Collections: Fish.

PubMed

Erlacher-Reid, Claire D

2018-05-01

Aquatic species live most or all their lives in water; therefore, the health of the environment is intimately connected to their health and medical care. Understanding and maintaining appropriate husbandry and nutrition for the housed aquarium species are essential to sustain health. Most diseases of fish are secondary opportunistic infections; prevention and early diagnosis are recommended. Treatments involve environmental and/or nutritional management first, followed by targeted pharmacologic treatment to control a specific pathogen. Pharmacokinetic research evaluating the effects and safety of medications in fish are greatly needed in the peer-reviewed literature. Copyright © 2018 Elsevier Inc. All rights reserved.

Detecting fish parvalbumin with commercial mouse monoclonal anti-frog parvalbumin IgG.

PubMed

Chen, Lingyun; Hefle, Sue L; Taylor, Steve L; Swoboda, Ines; Goodman, Richard E

2006-07-26

Parvalbumin is a calcium-binding muscle protein that is highly conserved across fish species and amphibians. It is the major cross-reactive allergen associated with both fish and frog allergy. We used two-dimensional electrophoretic and immunoblotting techniques to investigate the utility of a commercial monoclonal anti-frog parvalbumin IgG for detecting parvalbumin present in some commonly consumed fish species. The 2D electrophoresis and immunoblots revealed species-specific differences in proteins that appear to represent various numbers of isoforms of parvalbumin in carp (5), catfish (3), cod (1) and tilapia (2). No parvalbumin was detected in yellowfin tuna. Based on minor differences in relative intensities of protein staining and immunodetection, parvalbumin isoforms may have slight differences in the epitope region recognized by the anti-frog parvalbumin antibody. These results suggest that the frog anti-parvalbumin antibody can be used as a valuable tool to detect parvalbumins from the fish tested in this study, except yellowfin tuna.

Qualitative variation of photolabelled benzodiazepine receptors in different species.

PubMed

Hebebrand, J; Friedl, W; Lentes, K U; Propping, P

1986-01-01

In order to examine whether species differences of benzodiazepine receptor subunits exist, we compared the fluorographic pattern of photoaffinity labelled subunits after SDS-PAGE in five species: fish, frog, chicken, mouse and calf. Each species showed a distinct pattern of specifically labelled proteins. We conclude that species variation of benzodiazepine receptor does indeed exist.

Why are freshwater fish so threatened?

USGS Publications Warehouse

Closs, Gerard P.; Angermeier, Paul; Darwall, William R.T.; Balcombe, Stephen R.

2015-01-01

Understanding why so many freshwater fish species are threatened requires some understanding of their biology, diversity, distribution, biogeography and ecology, but also some appreciation of the social, economic and political forces that are causing humans to destroy the natural ecosystems upon which we all ultimately depend. To begin to understand the diversity of freshwater fishes, we first need to consider the processes that generated and continue to sustain the diversity of species we see today. Based on an understanding of how freshwater fish diversity is generated and sustained, we consider how vulnerable or resilient various freshwater fishes are to the range of anthropogenic impacts that impinge on freshwater ecosystems. Finally, we discuss how social, political and economic drivers influence human impacts on natural systems, and the changes needed to current models of development that can lead to a sustainable future for humans and the diverse range of freshwater fish species with which we share our planet. The aim of this chapter is to provide an overview of the key issues and threats driving the declines in freshwater fish diversity identified in Chapter 1; subsequent chapters provide more detail on the key issues and address our options for developing a sustainable future for freshwater fishes.

Investigation of sensory profiles and hedonic drivers of emerging aquaculture fish species.

PubMed

Alexi, Niki; Byrne, Derek V; Nanou, Evangelia; Grigorakis, Kriton

2018-02-01

The aquaculture sector needs to increase the diversity fish species and their processed products to cover rising consumer demands. Candidates for this diversification have been identified to be meagre, greater amberjack, pikeperch and wreckfish. Yet scientific knowledge on their sensory profiles and consumer hedonic responses is scarce. The aim of the current study was to investigate these aspects, since they are essential for product development and market targeting. Species exhibited different sensory profiles with the exception of the odor/flavor profiles of meagre and greater amberjack, which were similar. Texture was more important than odor/flavor in explaining interspecies differences. Yet the hedonic responses were equally related to texture and odor/flavor. None of the species received negative hedonic scores. Both positive and negative hedonic drivers were identified within the odor/flavor and texture modalities. The distinct profiles of meagre, greater amberjack, pikeperch and wreckfish make these fish species valuable first materials for new product development and for covering markets with different sensory preferences. Differences in fish texture are more easily perceivable, yet small variations in fish odor/flavor can have a great impact on consumers' hedonic responses. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries.

PubMed

Balasingham, Katherine D; Walter, Ryan P; Mandrak, Nicholas E; Heath, Daniel D

2018-01-01

The extraction and characterization of DNA from aquatic environmental samples offers an alternative, noninvasive approach for the detection of rare species. Environmental DNA, coupled with PCR and next-generation sequencing ("metabarcoding"), has proven to be very sensitive for the detection of rare aquatic species. Our study used a custom-designed group-specific primer set and next-generation sequencing for the detection of three species at risk (Eastern Sand Darter, Ammocrypta pellucida; Northern Madtom, Noturus stigmosus; and Silver Shiner, Notropis photogenis), one invasive species (Round Goby, Neogobius melanostomus) and an additional 78 native species from two large Great Lakes tributary rivers in southern Ontario, Canada: the Grand River and the Sydenham River. Of 82 fish species detected in both rivers using capture-based and eDNA methods, our eDNA method detected 86.2% and 72.0% of the fish species in the Grand River and the Sydenham River, respectively, which included our four target species. Our analyses also identified significant positive and negative species co-occurrence patterns between our target species and other identified species. Our results demonstrate that eDNA metabarcoding that targets the fish community as well as individual species of interest provides a better understanding of factors affecting the target species spatial distribution in an ecosystem than possible with only target species data. Additionally, eDNA is easily implemented as an initial survey tool, or alongside capture-based methods, for improved mapping of species distribution patterns. © 2017 John Wiley & Sons Ltd.

Development and Application of Camelid Molecular Cytogenetic Tools

PubMed Central

Avila, Felipe; Das, Pranab J.; Kutzler, Michelle; Owens, Elaine; Perelman, Polina; Rubes, Jiri; Hornak, Miroslav; Johnson, Warren E.

2014-01-01

Cytogenetic chromosome maps offer molecular tools for genome analysis and clinical cytogenetics and are of particular importance for species with difficult karyotypes, such as camelids (2n = 74). Building on the available human–camel zoo-fluorescence in situ hybridization (FISH) data, we developed the first cytogenetic map for the alpaca (Lama pacos, LPA) genome by isolating and identifying 151 alpaca bacterial artificial chromosome (BAC) clones corresponding to 44 specific genes. The genes were mapped by FISH to 31 alpaca autosomes and the sex chromosomes; 11 chromosomes had 2 markers, which were ordered by dual-color FISH. The STS gene mapped to Xpter/Ypter, demarcating the pseudoautosomal region, whereas no markers were assigned to chromosomes 14, 21, 22, 28, and 36. The chromosome-specific markers were applied in clinical cytogenetics to identify LPA20, the major histocompatibility complex (MHC)-carrying chromosome, as a part of an autosomal translocation in a sterile male llama (Lama glama, LGL; 2n = 73,XY). FISH with LPAX BACs and LPA36 paints, as well as comparative genomic hybridization, were also used to investigate the origin of the minute chromosome, an abnormally small LPA36 in infertile female alpacas. This collection of cytogenetically mapped markers represents a new tool for camelid clinical cytogenetics and has applications for the improvement of the alpaca genome map and sequence assembly. PMID:23109720

Zoogeography of the shorefish fauna of Clipperton Atoll

NASA Astrophysics Data System (ADS)

Robertson, D. R.; Allen, G. R.

1996-06-01

One hundred and fifteen species of fishes (14 oceanic, plus 101 shore and nearshore species) are known from Clipperton Island, a small, remote coral atoll in the tropical eastern Pacific (TEP). This fish fauna includes only ˜ 14% of the region's shallow-water species, and also is depauperate relative to the fish faunas of other isolated tropical islands. The island's isolation, small size, reduced habitat diversity, and oceanic environment contribute to this paucity of species. Fifty-two species at Clipperton can be identified as TEP; these include 37 widespread species, six species shared only with the Revillagigedo Islands [the nearest (950 km) offshore shoals], and eight endemic to Clipperton. Endemics species apparently have a mix of west and east Pacific origins. Sixty-three species are transpacific; they include three new records (of Naso surgeonfishes) that maybe vagrants recruited > 4,000 km from Oceania. Clipperton is situated at the juncture between the TEP and Oceania. Its fish fauna contains about equal numbers of TEP and transpacific species. This faunal structure reflects the relative influence of surface currents from Oceania and the TEP. Although most of Clipperton's transpacific shorefishes are widespread in eastern Oceania, the Clipperton fauna has specific affinities to the fauna of the Line Islands, which are located within the main eastbound current from Oceania. Clipperton may therefore be a major stepping stone for dispersal between Oceania and the remainder of the TEP. About 50% of the non-oceanic, tropical transpacific fishes occur there, and at least 75 % of those species apparently have resident populations at the island.

Helminth parasites of fish and shellfish from the Santa Gilla Lagoon in southern Sardinia, Italy.

PubMed

Culurgioni, J; Sabatini, A; De Murtas, R; Mattiucci, S; Figus, V

2014-12-01

An extensive survey of helminth parasites in fish and shellfish species from Santa Gilla, a brackish water lagoon in southern Sardinia (western Mediterranean), resulted in the identification of 69 helminth parasite taxa and/or species from 13 fish species (n= 515) and seven bivalve species (n= 2322) examined between September 2001 and July 2011. The list summarizes information on the helminth parasites harboured by fish and molluscs contained in the available literature. Digenea species (37), both adults and larvae, dominated the parasite fauna, whereas Cestoda were the least represented class (three species). Monogenea, Nematoda and Acanthocephala were present with 17, 6 and 6 species, respectively, which were mainly adults. The most widespread parasite species was the generalist Contracaecum rudolphii A (Nematoda). Other species, such as the Haploporidae and Ascocotyle (Phagicola) spp. 1 and 2 (Digenea), showed a high family specificity in Mugilidae. Importantly, the study recorded the occurrence of potential zoonotic agents, such as Heterophyes heterophyes, Ascocotyle (Phagicola) spp. and C. rudolphii A, the latter two reaching the highest indices of infection in the highly marketed fish grey mullet and sea bass, respectively. The highest parasite richness was detected in Dicentrarchus labrax, which harboured 17 helminth species, whereas the lowest value was observed in Atherina boyeri, infected by only three species. The list includes the first geographical record in Italian coastal waters of Robinia aurata and Stictodora sawakinensis, and 30 reports of new host-parasite complexes, including the larval stages of Ascocotyle (Ascocotyle) sp. and Southwellina hispida in D. labrax.

Separate and combined effects of habitat-specific fish predation on the survival of invasive and native gammarids

NASA Astrophysics Data System (ADS)

Kotta, Jonne; Orav-Kotta, Helen; Herkül, Kristjan

2010-10-01

The North-American amphipod Gammarus tigrinus was observed for the first time in the northern Baltic Sea in 2003. The invasive amphipod has been particularly successful in some habitats (e.g. on pebbles) where it has become one of the most abundant gammarid species. We studied experimentally if the dominant fish Gasterosteus aculeatus preyed differentially on the exotic G. tigrinus and the native Gammarus salinus, if predation differed among habitats, and if one gammarid species facilitated predation on the other. The experiment demonstrated that (1) fish preyed more on the exotic G. tigrinus than the native G. salinus. (2) Predation did not differ among habitats. (3) Gammarus tigrinus facilitated the predation on G. salinus and this facilitation varied among habitats with significant effects on pebbles. Thus, the combined effect of habitat-specific fish predation and competition between gammarid amphipods is a possible explanation of the current range of G. tigrinus in the northern Baltic Sea. G. tigrinus seems to establish in habitats where it can significantly increase fish predation on the native gammarids.

Biotechnology applied to fish reproduction: tools for conservation.

PubMed

de Siqueira-Silva, Diógenes Henrique; Saito, Taiju; Dos Santos-Silva, Amanda Pereira; da Silva Costa, Raphael; Psenicka, Martin; Yasui, George Shigueki

2018-04-29

This review discusses the new biotechnological tools that are arising and promising for conservation and enhancement of fish production, mainly regarding the endangered and the most economically important species. Two main techniques, in particular, are available to avoid extinction of endangered fish species and to improve the production of commercial species. Germ cell transplantation technology includes a number of approaches that have been studied, such as the transplantation of embryo-to-embryo blastomere, embryo-to-embryo differentiated PGC, larvae to larvae and embryo differentiated PGC, transplantation of spermatogonia from adult to larvae or between adults, and oogonia transplantation. However, the success of germ cell transplantation relies on the prior sterilization of fish, which can be performed at different stages of fish species development by means of several protocols that have been tested in order to achieve the best approach to produce a sterile fish. Among them, fish hybridization and triploidization, germline gene knockdown, hyperthermia, and chemical treatment deserve attention based on important results achieved thus far. This review currently used technologies and knowledge about surrogate technology and fish sterilization, discussing the stronger and the weaker points of each approach.

Marine protected area and the spatial distribution of the gill net fishery in Copacabana, Rio de Janeiro, RJ, Brazil.

PubMed

Amorim, R B; Monteiro-Neto, C

2016-02-01

This study characterizes the gill net fishery at Colônia de Pescadores Z13 (CPZ13), in Copacabana, Rio de Janeiro, and its relationship with the marine protected area 'Monumento Natural do Arquipélago das Ilhas Cagarras - MoNa Cagarras', describing the fleet and fishing gears, identifying fishing spots, species and their associations by gillnet type. From June 2012 to May 2013, every Tuesday to Sunday, gill net landings were monitored and fishers interviewed regarding their catch. Small boats (dory whaleboats) are used to set three types of gillnets: "Corvineira" (target species - whitemouth croaker), "linguadeira" (target species - flounders) and "rede-alta" (target species - bluefish). Fifty-nine species within 37 families were captured at 14 fishing spots, showing association with bottom type and distance from shore. The use of fisher's local ecological knowledge defines gear placement at specific sites targeting fisheries resources. All fishing sites are not within the limits of MoNa Cagarras but would benefit from management plans including an MPA buffering zone.

Development of a real-time PCR assay for rapid detection and quantification of Photobacterium damselae subsp. piscicida in fish tissues.

PubMed

Carraro, R; Dalla Rovere, G; Ferraresso, S; Carraro, L; Franch, R; Toffan, A; Pascoli, F; Patarnello, T; Bargelloni, L

2018-02-01

The availability of a rapid and accurate method for the diagnosis of Photobacterium damselae subsp. piscicida (Phdp), able to discriminate its strictly correlated subsp. damselae (Phdd), formally known as Vibrio damsela, is essential for managing fish pasteurellosis outbreaks in farmed fish. A single-step, high-sensitivity real-time PCR assay for simultaneous detection and quantification of P. damselae was designed targeting partial of the sequence of the bamB gene and tested for specificity and sensitivity on laboratory-generated samples as well as on experimentally infected seabream tissue samples. With a limit of detection (LOD) of one copy in pure bacterial DNA, the sensitivity was higher than all methods previously reported. Validation in target and non-target bacterial species proved the assay was able to discriminate Phdd-Phdp subspecies from diverse hosts/geographical origins and between non-target species. In addition, two SNPs in the target amplicon region determine two distinctive qPCR dissociation curves distinguishing between Phdp-Phdd. This is the first time that a molecular method for P. damselae diagnosis combines detection, quantification and subspecies identification in one step. The assay holds the potential to improve the knowledge of infection dynamics and the development of better strategies to control an important fish disease. © 2017 John Wiley & Sons Ltd.

Structure and variation of the mitochondrial genome of fishes.

PubMed

Satoh, Takashi P; Miya, Masaki; Mabuchi, Kohji; Nishida, Mutsumi

2016-09-07

The mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well understood. A potential strategy for improving our understanding is to conduct a comprehensive comparative study of large mt genome data. The aim of this study was to characterize the structure and variability of the fish mt genome through comparative analysis of large datasets. An analysis of the secondary structure of proteins for 250 fish species (248 ray-finned and 2 cartilaginous fishes) illustrated that cytochrome c oxidase subunits (COI, COII, and COIII) and a cytochrome bc1 complex subunit (Cyt b) had substantial amino acid conservation. Among the four proteins, COI was the most conserved, as more than half of all amino acid sites were invariable among the 250 species. Our models identified 43 and 58 stems within 12S rRNA and 16S rRNA, respectively, with larger numbers than proposed previously for vertebrates. The models also identified 149 and 319 invariable sites in 12S rRNA and 16S rRNA, respectively, in all fishes. In particular, the present result verified that a region corresponding to the peptidyl transferase center in prokaryotic 23S rRNA, which is homologous to mt 16S rRNA, is also conserved in fish mt 16S rRNA. Concerning the gene order, we found 35 variations (in 32 families) that deviated from the common gene order in vertebrates. These gene rearrangements were mostly observed in the area spanning the ND5 gene to the control region as well as two tRNA gene cluster regions (IQM and WANCY regions). Although many of such gene rearrangements were unique to a specific taxon, some were shared polyphyletically between distantly related species. Through a large-scale comparative analysis of 250 fish species mt genomes, we elucidated various structural aspects of the fish mt genome and the encoded genes. The present results will be important for understanding functions of the mt genome and developing programs for nucleotide sequence analysis. This study demonstrated the significance of extensive comparisons for understanding the structure of the mt genome.

Threats, conservation strategies, and prognosis for suckers (Catostomidae) in North America: insights from regional case studies of a diverse family of non-game fishes

USGS Publications Warehouse

Cooke, Steven J.; Bunt, Christopher M.; Hamilton, Steven J.; Jennings, Cecil A.; Pearson, Micheal P.; Cooperman, Michael S.; Markle, Douglas F.

2005-01-01

Catostomid fishes are a diverse family of 76+ freshwater species that are distributed across North America in many different habitats. This group of fish is facing a variety of impacts and conservation issues that are somewhat unique relative to more economically valuable and heavily managed fish species. Here, we present a brief series of case studies to highlight the threats such as migration barriers, flow regulation, environmental contamination, habitat degradation, exploitation and impacts from introduced (non-native) species that are facing catostomids in different regions. Collectively, the case studies reveal that individual species usually are not threatened by a single, isolated factor. Instead, species in general face numerous stressors that threaten multiple stages of their life history. Several factors have retarded sucker conservation including widespread inabilities of field workers to distinguish some species, lack of basic natural history and ecological knowledge of life history, and the misconception that suckers are tolerant of degraded conditions and are of little social or ecological value. Without a specific constituent group lobbying for conservation of non-game fishes, all such species, including members of the catostomid family, will continue to face serious risks because of neglect, ignorance, and misunderstanding. We suggest that conservation strategies should incorporate research and education/outreach components. Other conservation strategies that would be effective for protecting suckers include freshwater protected areas for critical habitat, restoration of degraded habitat, and design of catostomid-friendly fish bypass facilities. We believe that the plight of the catostomids is representative of the threats facing many other non-game freshwater fishes with diverse life-history strategies globally.

[Rapid ecological assessment of tropical fish communities in a gold mine area of Costa Rica].

PubMed

Espinoza Mendiola, Mario

2008-12-01

Gold mining impacts have generated a great concern regarding aquatic systems and habitat fragmentation. Anthropogenic disturbances on the structure and heterogeneity of a system can have an important effect on aquatic community stability. Ecological rapid assessments (1996, 2002, and 2007) were employed to determine the structure, composition and distribution of tropical fish communities in several rivers and smaller creeks from a gold mining area in Cerro Crucitas, Costa Rica. In addition, species composition and relative abundance were related with habitat structure. A total of 35 species were registered, among which sardine Astyanax aeneus (Characidae) and livebearer Alfaro cultratus (Poeciliidae) were the most abundant fish (71%). The highest species richness was observed in Caño Crucitas (s=19) and Minas Creek (s=18). Significant differences in fish communities structure and composition from Infiernillo river and Minas creek were observed (lamda = 0.0, F(132, 66) = 2.24, p < 0.001). Presence and/or absence of certain species such as Dormitor gobiomorus, Rhamdia nicaraguensis, Parachromis loiseillei and Atractosteus tropicus explained most of the spatial variation among sites. Habitat structure also contributed to explain differences among sites (lamda = 0.004, F(60.183) = 5.52, p < 0.001). Substratum (soft and hard bottom types) and habitat attributes (elevation, width and depth) explained most of the variability observed in Infiernillo River, Caño Crucitas and Tamagá Creek. In addition, a significant association between fish species and habitat structure was observed. This study reveals a high complexity in tropical fish communities that inhabit a gold mine area. Furthermore, it highlights the importance of habitat heterogeneity in fish community dynamics. The loss and degradation of aquatic systems in Cerro Crucitas can have a strong negative effect on fish community structure and composition of local species. A better understanding of the use of specific habitats that serve as essential fish habitats can improve tropical fish conservation and management strategies, thus increasing local diversity, and thereby, the biological importance of the area.

Helminth communities of four commercially important fish species from Chetumal Bay, Mexico.

PubMed

Aguirre-Macedo, M L; Vidal-Martínez, V M; González-Solís, D; Caballero, P I

2007-03-01

The relative importance of ecology and evolution as factors determining species richness and composition of the helminth communities of fish is a matter of current debate. Theoretical studies use host-parasite lists, but these do not include studies on a temporal or spatial scale. Local environmental conditions and host biological characteristics are shown to influence helminth species richness and composition in four fish species (Eugerres plumieri, Hexanematichthys assimilis, Oligoplites saurus, and Scomberomorus maculatus) in Chetumal Bay, Mexico. With the exception of H. assimilis, the helminth communities had not been previously studied and possible associations between environmental and host biological characteristics as factors determining helminth species richness and composition using redundancy analysis (RDA) are described. Thirty-four helminth species are identified, with the highest number of species (19 total (mean = 6.3 +/- 2.1)) and the lowest (9 (4.0 +/- 1.0)) occurring in H. assimilis and S. maculatus, respectively. The larval nematodes Contracaecum sp. and Pseudoterranova sp. were not only the helminth species shared by all four host species but also were the most prevalent and abundant. Statistical associations between helminth community parameters and local ecological variables such as host habitat use, feeding habits, mobility, and time of residence in coastal lagoons are identified. Phylogeny is important because it clearly separates all four host species by their specialist parasites, although specific habitat and feeding habits also significantly influence the differentiation between the four fish species.

Fish assemblages

USGS Publications Warehouse

McGarvey, Daniel J.; Falke, Jeffrey A.; Li, Hiram W.; Li, Judith; Hauer, F. Richard; Lamberti, G.A.

2017-01-01

Methods to sample fishes in stream ecosystems and to analyze the raw data, focusing primarily on assemblage-level (all fish species combined) analyses, are presented in this chapter. We begin with guidance on sample site selection, permitting for fish collection, and information-gathering steps to be completed prior to conducting fieldwork. Basic sampling methods (visual surveying, electrofishing, and seining) are presented with specific instructions for estimating population sizes via visual, capture-recapture, and depletion surveys, in addition to new guidance on environmental DNA (eDNA) methods. Steps to process fish specimens in the field including the use of anesthesia and preservation of whole specimens or tissue samples (for genetic or stable isotope analysis) are also presented. Data analysis methods include characterization of size-structure within populations, estimation of species richness and diversity, and application of fish functional traits. We conclude with three advanced topics in assemblage-level analysis: multidimensional scaling (MDS), ecological networks, and loop analysis.

Biofluorescence as a survey tool for cryptic marine species.

PubMed

De Brauwer, Maarten; Hobbs, Jean-Paul A; Ambo-Rappe, Rohani; Jompa, Jamaluddin; Harvey, Euan S; McIlwain, Jennifer L

2017-10-06

As ecosystems come under increasing anthropogenic pressure, rare species face the highest risk of extinction. Paradoxically, data necessary to evaluate the conservation status of rare species are often lacking because of the challenges of detecting species with low abundance. One group of fishes subject to this undersampling bias are those with cryptic body patterns. Twenty-one percent of cryptic fish species assessed for their extinction risk (International Union for Conservation of Nature [IUCN]) are data deficient. We developed a nondestructive method for surveying cryptically patterned marine fishes based on the presence of biofluorescence (underwater biofluorescence census, UBC). Blue LED torches were used to investigate how widespread biofluorescence was in cryptic reef fishes in the Coral Triangle region. The effectiveness of UBC to generate abundance data was tested on a data-deficient pygmy seahorse species (Hippocampus bargibanti) and compared with data obtained from standard underwater visual census (UVC) surveys. We recorded 95 reef fish species displaying biofluorescence, 73 of which had not been previously described as biofluorescent. Of those fish with cryptic patterns, 87% were biofluorescent compared with 9% for noncryptic fishes. The probability of species displaying biofluorescence was 70.9 times greater for cryptic species than for noncryptic species. Almost twice the number of H. bargibanti was counted using the UBC compared with UVC. For 2 triplefin species (Ucla xenogrammus, Enneapterygius tutuilae), the abundance detected with UBC was triple that detected with UVC. The UBC method was effective at finding cryptic species that would otherwise be difficult to detect and thus will reduce interobserver variability inherent to UVC surveys. Biofluorescence is ubiquitous in cryptic fishes, making this method applicable across a wide range of species. Data collected using UBC could be used with multiple IUCN criteria to assess the extinction risk of cryptic species. Adopting this technique will enhance researchers' ability to survey cryptic species and facilitate management and conservation of cryptic marine species. © 2017 Society for Conservation Biology.

Toward fish and seafood traceability: anchovy species determination in fish products by molecular markers and support through a public domain database.

PubMed

Jérôme, Marc; Martinsohn, Jann Thorsten; Ortega, Delphine; Carreau, Philippe; Verrez-Bagnis, Véronique; Mouchel, Olivier

2008-05-28

Traceability in the fish food sector plays an increasingly important role for consumer protection and confidence building. This is reflected by the introduction of legislation and rules covering traceability on national and international levels. Although traceability through labeling is well established and supported by respective regulations, monitoring and enforcement of these rules are still hampered by the lack of efficient diagnostic tools. We describe protocols using a direct sequencing method based on 212-274-bp diagnostic sequences derived from species-specific mitochondria DNA cytochrome b, 16S rRNA, and cytochrome oxidase subunit I sequences which can efficiently be applied to unambiguously determine even closely related fish species in processed food products labeled "anchovy". Traceability of anchovy-labeled products is supported by the public online database AnchovyID ( http://anchovyid.jrc.ec.europa.eu), which provided data obtained during our study and tools for analytical purposes.

Diversity of trypanorhynch metacestodes in teleost fishes from coral reefs off eastern Australia and New Caledonia

PubMed Central

Beveridge, Ian; Bray, Rodney A.; Cribb, Thomas H.; Justine, Jean-Lou

2014-01-01

Trypanorhynch metacestodes were examined from teleosts from coral reefs in eastern Australia and from New Caledonia. From over 12,000 fishes examined, 33 named species of trypanorhynchs were recovered as well as three species of tentacularioids which are described but not named. Host-parasite and parasite-host lists are provided, including more than 100 new host records. Lacistorhynchoid and tentacularioid taxa predominated with fewer otobothrioid and gymnorhynchoids. Five species, Callitetrarhynchus gracilis, Floriceps minacanthus, Pseudotobothrium dipsacum, Pseudolacistorhynchus heroniensis and Ps. shipleyi, were particularly common and exhibited low host specificity. Limited data suggested a higher diversity of larval trypanorhynchs in larger piscivorous fish families. Several fish families surveyed extensively (Blenniidae, Chaetodontidae, Gobiidae, Kyphosidae and Scaridae) yielded no trypanorhynch larvae. The overall similarity between the fauna of the Great Barrier Reef and New Caledonia was 45%. Where available, information on the adult stages in elasmobranchs has been included. PMID:25402635

Kudoa spp. (Myxozoa, Multivalvulida) parasitizing fish caught in Aracaju, Sergipe, Brazil.

PubMed

Eiras, Jorge Costa; Fujimoto, Rodrigo Yudi; Madi, Rubens Riscala; Jeraldo, Veronica de Lourdes Sierpe; Melo, Cláudia Moura de; Souza, Jônatas Dos Santos de; Diniz, José Antonio Picanço; Diniz, Daniel Guerreiro

2016-01-01

This study reports on Kudoa spp. (Myxozoa, Multivalvulida) from the fish species Lutjanus analis, Bagre marinus, Aspistor luniscutis and Lutjanus jocu, which were caught in Aracaju, state of Sergipe, Brazil. The parasites formed oval plasmodia around the esophagus of L. analis, and elongated plasmodia inside the skeletal muscle of B. marinus, A. luniscutis and L. jocu. Host myoliquefaction was not observed in all the cases studied. The current study provides a morphological and morphometric description of each parasite as well as a comparison with all the species described worldwide. Lack of molecular data impaired specific identification of the parasites. The importance of these parasites is discussed and the need for further studies on infections in Brazilian fish is emphasized because of the high economic impact of some Kudoa species which cause liquefaction in hosts' muscles and render these fish unsuitable for consumption.

Ecological limit functions relating fish community response to hydrologic departures of the ecological flow regime in the Tennessee River basin, United States

USGS Publications Warehouse

Knight, Rodney R.; Murphy, Jennifer C.; Wolfe, William J.; Saylor, Charles F.; Wales, Amy K.

2014-01-01

Ecological limit functions relating streamflow and aquatic ecosystems remain elusive despite decades of research. We investigated functional relationships between species richness and changes in streamflow characteristics at 662 fish sampling sites in the Tennessee River basin. Our approach included the following: (1) a brief summary of relevant literature on functional relations between fish and streamflow, (2) the development of ecological limit functions that describe the strongest discernible relationships between fish species richness and streamflow characteristics, (3) the evaluation of proposed definitions of hydrologic reference conditions, and (4) an investigation of the internal structures of wedge-shaped distributions underlying ecological limit functions.Twenty-one ecological limit functions were developed across three ecoregions that relate the species richness of 11 fish groups and departures from hydrologic reference conditions using multivariate and quantile regression methods. Each negatively sloped function is described using up to four streamflow characteristics expressed in terms of cumulative departure from hydrologic reference conditions. Negative slopes indicate increased departure results in decreased species richness.Sites with the highest measured fish species richness generally had near-reference hydrologic conditions for a given ecoregion. Hydrology did not generally differ between sites with the highest and lowest fish species richness, indicating that other environmental factors likely limit species richness at sites with reference hydrology.Use of ecological limit functions to make decisions regarding proposed hydrologic regime changes, although commonly presented as a management tool, is not as straightforward or informative as often assumed. We contend that statistical evaluation of the internal wedge structure below limit functions may provide a probabilistic understanding of how aquatic ecology is influenced by altered hydrology and may serve as the basis for evaluating the potential effect of proposed hydrologic changes.

Fish Ecology and Evolution in the World's Oxygen Minimum Zones and Implications of Ocean Deoxygenation.

PubMed

Gallo, N D; Levin, L A

Oxygen minimum zones (OMZs) and oxygen limited zones (OLZs) are important oceanographic features in the Pacific, Atlantic, and Indian Ocean, and are characterized by hypoxic conditions that are physiologically challenging for demersal fish. Thickness, depth of the upper boundary, minimum oxygen levels, local temperatures, and diurnal, seasonal, and interannual oxycline variability differ regionally, with the thickest and shallowest OMZs occurring in the subtropics and tropics. Although most fish are not hypoxia-tolerant, at least 77 demersal fish species from 16 orders have evolved physiological, behavioural, and morphological adaptations that allow them to live under the severely hypoxic, hypercapnic, and at times sulphidic conditions found in OMZs. Tolerance to OMZ conditions has evolved multiple times in multiple groups with no single fish family or genus exploiting all OMZs globally. Severely hypoxic conditions in OMZs lead to decreased demersal fish diversity, but fish density trends are variable and dependent on region-specific thresholds. Some OMZ-adapted fish species are more hypoxia-tolerant than most megafaunal invertebrates and are present even when most invertebrates are excluded. Expansions and contractions of OMZs in the past have affected fish evolution and diversity. Current patterns of ocean warming are leading to ocean deoxygenation, causing the expansion and shoaling of OMZs, which is expected to decrease demersal fish diversity and alter trophic pathways on affected margins. Habitat compression is expected for hypoxia-intolerant species, causing increased susceptibility to overfishing for fisheries species. Demersal fisheries are likely to be negatively impacted overall by the expansion of OMZs in a warming world. © 2016 Elsevier Ltd. All rights reserved.

Examining the Impact of a Public Health Message on Fish Consumption in Bermuda

PubMed Central

McLean Pirkle, Catherine; Peek-Ball, Cheryl; Outerbridge, Eugene; Rouja, Philippe Max

2015-01-01

Background In 2003 mean cord blood mercury concentrations in pregnant Bermudian women exceeded levels associated with adverse health outcomes in children. The principal mercury source was local fish species. Public health messages were developed suggesting pregnant women reduce consumption of fish species with higher mercury concentrations (e.g. swordfish), substituting species containing lower mercury concentrations, and elevated omega-3 fatty acids (e.g. anchovies). Recent evidence indicates mercury concentrations in Bermuda’s pregnant women have fallen five- fold. Objectives Assess whether changes in women’s fish eating patterns during pregnancy are consistent with the public health messaging. Determine who is making changes to their diet during pregnancy and why. Methods Mixed methods study with a cross-sectional survey of 121 pregnant women, including 13 opened-ended interviews. Health system, social vulnerability, public health messaging, and socio-demographic variables were characterized and related to changes in fish consumption during pregnancy. Qualitative data were coded according to nutritional advice messages, comprehension of communication strategies, and sources of information. Results 95% of women surveyed encountered recommendations about fish consumption during pregnancy. 75% reported modifying fish eating behaviors because of recommendations. Principal sources of information about fish consumption in pregnancy were health care providers and the Internet. 71% of women reported reducing consumption of large fish species with greater mercury levels, but 60% reported reduced consumption of smaller, low mercury fish. No participant mentioned hearing about the benefits of fish consumption. More frequent exposure to public health messages during pregnancy was associated with lower reported consumption. Bermudian born women were less likely to reduce consumption of large fish species during pregnancy. Conclusions In Bermuda, public health messages advocating reduced consumption of larger, higher mercury-containing fish species appear effective, but masked the nutritional value message of small fish species, with low mercury concentration. Adjustment is needed to better balance the risk communication. PMID:26426692

Examining the Impact of a Public Health Message on Fish Consumption in Bermuda.

PubMed

McLean Pirkle, Catherine; Peek-Ball, Cheryl; Outerbridge, Eugene; Rouja, Philippe Max

2015-01-01

In 2003 mean cord blood mercury concentrations in pregnant Bermudian women exceeded levels associated with adverse health outcomes in children. The principal mercury source was local fish species. Public health messages were developed suggesting pregnant women reduce consumption of fish species with higher mercury concentrations (e.g. swordfish), substituting species containing lower mercury concentrations, and elevated omega-3 fatty acids (e.g. anchovies). Recent evidence indicates mercury concentrations in Bermuda's pregnant women have fallen five- fold. Assess whether changes in women's fish eating patterns during pregnancy are consistent with the public health messaging. Determine who is making changes to their diet during pregnancy and why. Mixed methods study with a cross-sectional survey of 121 pregnant women, including 13 opened-ended interviews. Health system, social vulnerability, public health messaging, and socio-demographic variables were characterized and related to changes in fish consumption during pregnancy. Qualitative data were coded according to nutritional advice messages, comprehension of communication strategies, and sources of information. 95% of women surveyed encountered recommendations about fish consumption during pregnancy. 75% reported modifying fish eating behaviors because of recommendations. Principal sources of information about fish consumption in pregnancy were health care providers and the Internet. 71% of women reported reducing consumption of large fish species with greater mercury levels, but 60% reported reduced consumption of smaller, low mercury fish. No participant mentioned hearing about the benefits of fish consumption. More frequent exposure to public health messages during pregnancy was associated with lower reported consumption. Bermudian born women were less likely to reduce consumption of large fish species during pregnancy. In Bermuda, public health messages advocating reduced consumption of larger, higher mercury-containing fish species appear effective, but masked the nutritional value message of small fish species, with low mercury concentration. Adjustment is needed to better balance the risk communication.

The Covert World of Fish Biofluorescence: A Phylogenetically Widespread and Phenotypically Variable Phenomenon

PubMed Central

Schelly, Robert C.; Smith, W. Leo; Davis, Matthew P.; Tchernov, Dan; Pieribone, Vincent A.

2014-01-01

The discovery of fluorescent proteins has revolutionized experimental biology. Whereas the majority of fluorescent proteins have been identified from cnidarians, recently several fluorescent proteins have been isolated across the animal tree of life. Here we show that biofluorescence is not only phylogenetically widespread, but is also phenotypically variable across both cartilaginous and bony fishes, highlighting its evolutionary history and the possibility for discovery of numerous novel fluorescent proteins. Fish biofluorescence is especially common and morphologically variable in cryptically patterned coral-reef lineages. We identified 16 orders, 50 families, 105 genera, and more than 180 species of biofluorescent fishes. We have also reconstructed our current understanding of the phylogenetic distribution of biofluorescence for ray-finned fishes. The presence of yellow long-pass intraocular filters in many biofluorescent fish lineages and the substantive color vision capabilities of coral-reef fishes suggest that they are capable of detecting fluoresced light. We present species-specific emission patterns among closely related species, indicating that biofluorescence potentially functions in intraspecific communication and evidence that fluorescence can be used for camouflage. This research provides insight into the distribution, evolution, and phenotypic variability of biofluorescence in marine lineages and examines the role this variation may play. PMID:24421880

The covert world of fish biofluorescence: a phylogenetically widespread and phenotypically variable phenomenon.

PubMed

Sparks, John S; Schelly, Robert C; Smith, W Leo; Davis, Matthew P; Tchernov, Dan; Pieribone, Vincent A; Gruber, David F

2014-01-01

The discovery of fluorescent proteins has revolutionized experimental biology. Whereas the majority of fluorescent proteins have been identified from cnidarians, recently several fluorescent proteins have been isolated across the animal tree of life. Here we show that biofluorescence is not only phylogenetically widespread, but is also phenotypically variable across both cartilaginous and bony fishes, highlighting its evolutionary history and the possibility for discovery of numerous novel fluorescent proteins. Fish biofluorescence is especially common and morphologically variable in cryptically patterned coral-reef lineages. We identified 16 orders, 50 families, 105 genera, and more than 180 species of biofluorescent fishes. We have also reconstructed our current understanding of the phylogenetic distribution of biofluorescence for ray-finned fishes. The presence of yellow long-pass intraocular filters in many biofluorescent fish lineages and the substantive color vision capabilities of coral-reef fishes suggest that they are capable of detecting fluoresced light. We present species-specific emission patterns among closely related species, indicating that biofluorescence potentially functions in intraspecific communication and evidence that fluorescence can be used for camouflage. This research provides insight into the distribution, evolution, and phenotypic variability of biofluorescence in marine lineages and examines the role this variation may play.

Stable isotope evidence of terrestrial organic matter incorporation into coastal marine food webs: impact of Rhone River inputs on five NW Mediterranean marine flatfish species.

NASA Astrophysics Data System (ADS)

Darnaude, A. M.; Salen-Picard, C.; Harmelin-Vivien, M.

2003-04-01

The positive influence of land-based run-off on coastal fishery production is thought to be of particular importance for oligotrophic seas such as the Mediterranean. In order to estimate the impact of the Rhone River inputs of particulate organic matter (POM) on exploited demersal fish populations, stable isotope signature in nitrogen (δ15N) and carbon (δ13C) were determined for both juveniles and adults of the five main flatfish species living off the Rhone delta (Arnoglossus laterna, Buglossidium luteum, Citharus linguatula, Solea impar and Solea solea) and the main components of their food webs. The five flatfish species showed inter and intra-specific differences in isotopic signatures. The δ15N significantly increased from the smallest species to the largest ones and, in all species, from juveniles to adults (P<0.05), which indicated a global increase in trophic level with fish body size. Concerning the carbon signature, the δ13C obtained indicated an incorporation of organic material from terrestrial origin in the flesh of all the species. This incorporation was minimum for C. linguatula and reduced for all the species with the exception of S. solea for which a significantly (P<0.001) lower δ13C indicated an important use of organic matter from terrestrial origin. Mean δ13C values also differed significantly between juveniles and adults of B. luteum and S. impar (P<0.05), suggesting changes in terrestrial organic matter use with growth in these two species. To explain inter and intra-specific differences in δ13C, stable isotope data were compared with gut content analyses (prey % total contents mass, W%) performed on the same fishes. The δ13C signature of fishes was inversely related to the W% of polychaetes in their diet, and not to other prey categories. The common sole S. solea, that fed mainly on polychaetes (W% > 50% at all benthic stages of life), exhibited the most negative mean δ13C for both juveniles and adults among all the fish species studied. The isotopic analyses of the Rhone River water, the marine phytoplankton, the sediment and the main fish prey, confirmed that polychaetes represented the major pathway of terrestrial POM transfer up to fishes into coastal trophic webs. The effect of terrestrial inputs in enhancing the population dynamics of the five flatfish species studied differed thus according to their diet. Keywords : river run-off, food webs, stable isotopes, gut contents, flatfishes, fisheries, NW Mediterranean.

Molecular and morphological evidence for three species of Diplostomum (Digenea: Diplostomidae), parasites of fishes and fish-eating birds in Spain.

PubMed

Pérez-del-Olmo, Ana; Georgieva, Simona; Pula, Héctor J; Kostadinova, Aneta

2014-11-12

Recent molecular studies have revealed high species diversity of Diplostomum in central and northern Europe. However, our knowledge of the distribution of Diplostomum spp. in the southern distributional range in Europe of the snail intermediate hosts (Lymnaea stagnalis and Radix spp.) is rather limited. This study aims to fill this gap in our knowledge using molecular and morphological evidence. Nineteen fish species and six fish-eating bird species were sampled opportunistically in three regions (Catalonia, Extremadura and Aragon) in Spain. All isolates of Diplostomum spp. were characterised morphologically and molecularly. Partial sequences of the barcode region of the cox1 mitochondrial gene and complete sequences of the ribosomal ITS1-5.8S-ITS2 gene cluster were used for molecular identification of the isolates. Integrated morphological and molecular analyses demonstrated the presence of three species among the larval and adult isolates of Diplostomum spp. sampled in Spain: Diplostomum spathaceum (in fish and birds), D. pseudospathaceum (in birds) and Diplostomum sp. (in fish) referred to as Clade Q sensu Georgieva et al. (Int J Parasitol, 43:57-72, 2013). We detected ten cox1 haplotypes among the isolates of D. spathaceum with only one haplotype shared with adult isolates from central and northern Europe. No specific geographic pattern of the distribution of the novel haplotypes was found. This first molecular exploration of the diversity of Diplostomum spp. in southern Europe indicates much lower species richness compared with the northern regions of Europe.

Sand lance: A review of biology and predator relations and annotated bibliography

USGS Publications Warehouse

Robards, Martin D.; Willson, Mary F.; Armstrong, Robert H.; Piatt, John F.

1999-01-01

Six species of sand lance (Ammodytes) in temperate and boreal regions are currently recognized. Sand lance can occupy a wide range of environmental conditions, but all appear to be dormant predominantly in winter, and one species is in summer also. They lack a swim bladder and spend much of their time buried in specific substrates. Copepods are the primary food. Spawning usually occurs in fall or winter (although some species also spawn in spring), eggs are demersal, and larvae may hatch at times of low food abundance. Sand lance usually occur in schools and are regarded as a relatively high-quality forage fish.Sand lance constitute a major prey for at least some populations of over 100 species of consumer, including 40 species of birds, 12 species of marine mammals, 45 species of fishes, and some invertebrates. Variation in the availability of sand lance (and other forage fishes) can have major effects on the breeding success and survival of their predators. Commercial fishing and other pressures on sand lance populations potentially have ramifying effects on many species of wildlife.The bibliography contains over 1,700 references on the family Ammodytidae, with an emphasis on the genus Ammodytes. Keywords are provided for each reference and have been further organized into taxonomic, geographic, subject, and predator indexes.

Fish Ontology framework for taxonomy-based fish recognition

PubMed Central

Ali, Najib M.; Khan, Haris A.; Then, Amy Y-Hui; Ving Ching, Chong; Gaur, Manas

2017-01-01

Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval. Automated classification for unknown specimens is a unique feature that currently does not appear to exist in other known ontologies. Examples of automated classification for major groups of fish are demonstrated, showing the inferred information by introducing several restrictions at the species or specimen level. The current version of FO has 1,830 classes, includes widely used fisheries terminology, and models major aspects of fish taxonomy, grouping, and character. With more than 30,000 known fish species globally, the FO will be an indispensable tool for fish scientists and other interested users. PMID:28929028

Effects of acoustic alarms, designed to reduce small cetacean bycatch in gillnet fisheries, on the behaviour of North Sea fish species in a large tank.

PubMed

Kastelein, Ronald A; van der Heul, Sander; van der Veen, Jan; Verboom, Willem C; Jennings, Nancy; de Haan, Dick; Reijnders, Peter J H

2007-08-01

World-wide many cetaceans drown incidentally in fishing nets. To reduce the unwanted bycatch in gillnets, pingers (acoustic alarms) have been developed that are attached to the nets. In the European Union, pingers will be made compulsory in some areas in 2005 and in others in 2007. However, pingers may effect non-target marine fauna such as fish. Therefore in this study, the effects of seven commercially-available pingers on the behaviour of five North Sea fish species in a large tank were quantified. The species tested were: sea bass (Dicentrarchus labrax), pout (Trisopterus luscus), thicklip mullet (Chelon labrosus), herring (Clupea harengus), and cod (Gadus morhua). The fish were housed as single-species schools of 9-13 individuals in a tank. The behaviour of fish in quiet periods was compared with their behaviour during periods with active pingers. The results varied both between pingers and between fish species. Sea bass decreased their speed in response to one pinger and swam closer to the surface in response to another. Thicklip mullet swam closer to the bottom in response to two pingers and increased their swimming speed in response to one pinger. Herring swam faster in response to one pinger, and pout and cod (close relatives) showed no behavioural responses to any of the pingers. Of the seven pingers tested, four elicited responses in at least one fish species, and three elicited no responses. Whether similar responses would be elicited in these fish species in the wild, and if so, whether such responses would influence the catch rate of fisheries, cannot be derived from the results of this study. However, the results indicate the need for field studies with pingers and fish. Based on the small number of fish species tested, the present study suggests that the higher the frequency of a pinger, the less likely it is to affect the behaviour of marine fish.

No evidence for host specialization or host-race formation in the European bitterling (Rhodeus amarus), a fish that parasitizes freshwater mussels.

PubMed

Reichard, M; Bryja, J; Polačik, M; Smith, C

2011-09-01

Coevolutionary relationships between parasites and hosts can elevate the rate of evolutionary changes owing to reciprocal adaptations between coevolving partners. Such relationships can result in the evolution of host specificity. Recent methodological advances have permitted the recognition of cryptic lineages, with important consequences for our understanding of biological diversity. We used the European bitterling (Rhodeus amarus), a freshwater fish that parasitizes unionid mussels, to investigate host specialization across regions of recent and ancient sympatry between coevolving partners. We combined genetic data (12 microsatellite and 2 mitochondrial markers) from five populations with experimental data for possible mechanisms of host species recognition (imprinting and conditioning). We found no strong evidence for the existence of cryptic lineages in R. amarus, though a small proportion of variation among individuals in an area of recent bitterling-mussel association was statistically significant in explaining host specificity. No other measures supported the existence of host-specific lineages. Behavioural data revealed a weak effect of conditioning that biased behavioural preferences towards specific host species. Host imprinting had no effect on oviposition behaviour. Overall, we established that populations of R. amarus show limited potential for specialization, manifested as weak effects of host conditioning and genetic within-population structure. Rhodeus amarus is the only species of mussel-parasitizing fish in Europe, which contrasts with the species-rich communities of bitterling in eastern Asia where several host-specific bitterling occur. We discuss costs and constraints on the evolution of host-specific lineages in our study system and more generally. © 2011 Blackwell Publishing Ltd.

Acid phosphatase activity in liver macrophage aggregates as a marker for pollution-induced immunomodulation of the non-specific immune response in fish

NASA Astrophysics Data System (ADS)

Broeg, Katja

2003-10-01

The activity of acid phosphatase in liver macrophage aggregates (MA-AP) of different fish species was used as a marker for a pollution-induced modulation of the digestive capacity of phagocytes, since functions of the non-specific immune response play a central role in the maintenance of animals' health. Based upon the investigation of more than 900 individual flounders (Platichthys flesus) and mullets (Liza aurata), natural variations, gender-specific differences and pollution-induced alterations in AP activity are demonstrated in this study. MA-AP activity was dependent on temperature and season but, nevertheless, distinctions between differently polluted areas were visible in all sampling campaigns with lowest MA-AP activity in fish from the polluted areas of the German Bight and the Israeli coast of the Mediterranean Sea. For organochlorine contaminants, as well as for mercury and copper, a significant correlation could be observed between residue concentrations in fish tissues and MA-AP activity. In all cases, except mercury which showed a positive correlation, AP activity was suppressed in animals with a high contaminant burden. MA-AP activity turned out to give reliable and consistent results for a quantification of immunomodulation in both fish species.

MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

PubMed Central

Miya, M.; Sato, Y.; Fukunaga, T.; Sado, T.; Poulsen, J. Y.; Sato, K.; Minamoto, T.; Yamamoto, S.; Yamanaka, H.; Araki, H.; Kondoh, M.; Iwasaki, W.

2015-01-01

We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163–185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales. PMID:26587265

MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species.

PubMed

Miya, M; Sato, Y; Fukunaga, T; Sado, T; Poulsen, J Y; Sato, K; Minamoto, T; Yamamoto, S; Yamanaka, H; Araki, H; Kondoh, M; Iwasaki, W

2015-07-01

We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163-185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.

Characterisation of transcriptional responses to dioxins and dioxin-like contaminants in roach (Rutilus rutilus) using whole transcriptome analysis.

PubMed

Brinkmann, Markus; Koglin, Sven; Eisner, Bryanna; Wiseman, Steve; Hecker, Markus; Eichbaum, Kathrin; Thalmann, Beat; Buchinger, Sebastian; Reifferscheid, Georg; Hollert, Henner

2016-01-15

There is significant concern regarding the contamination of riverine sediments with dioxins and dioxin-like compounds (DLCs), including polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), polychlorinated biphenyls (PCBs) and some polycyclic aromatic hydrocarbons (PAHs). The majority of studies investigating the ecotoxicology of DLCs in fish have focused on a few standard model species. However, there is significant uncertainty as to whether these model species are representative of native river fish, particularly in Europe. In this study, the transcriptional responses following exposure to equipotent concentrations of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), PCB 156 or the dioxin-like PAH, benzo[k]fluoranthene (BkF), were investigated in juvenile roach (Rutilus rutilus), a fish species that constitutes a large proportion of the fish biomass in freshwater bodies throughout Europe. To this end, RNA sequencing analysis was used to comprehensively characterise the molecular mechanisms and pathways of toxicity of these DLCs. Whole transcriptome analyses using ClueGO software revealed that DLCs have the potential to disrupt a number of important processes, including energy metabolism, oogenesis, the immune system, apoptosis and the response to oxidative stress. However, despite using equipotent concentrations, there was very little conservation of the transcriptional responses observed in fish exposed to different DLCs. TCDD provoked significant specific changes in the levels of transcripts related to immunotoxicity and carbohydrate metabolism, while PCB 156 caused virtually no specific effects. Exposure to BkF affected the most diverse suite of molecular functions and biological processes, including blood coagulation, oxidative stress responses, unspecific responses to organic or inorganic substances/stimuli, cellular redox homeostasis and specific receptor pathways. To our knowledge, this is the first study of the transcriptome-wide effects of different classes of DLCs in fish. These findings represent an important step towards describing complete toxicity pathways of DLCs, which will be important in the context of informing risk assessments of DLC toxicity in native fish species. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular identification, morphological characterization and new insights into the ecology of larval Pseudoterranova cattani in fishes from the Argentine coast with its differentiation from the Antarctic species, P. decipiens sp. E (Nematoda: Anisakidae).

PubMed

Timi, Juan T; Paoletti, Michela; Cimmaruta, Roberta; Lanfranchi, Ana L; Alarcos, Ana J; Garbin, Lucas; George-Nascimento, Mario; Rodríguez, Diego H; Giardino, Gisela V; Mattiucci, Simonetta

2014-01-17

Larvae of the genus Pseudoterranova constitute a risk for human health when ingested through raw or undercooked fish. They can provoke pseudoterranovosis in humans, a fish-borne zoonotic disease whose pathogenicity varies with the species involved, making their correct specific identification a necessary step in the knowledge of this zoonosis. Larvae of Pseudoterranova decipiens s.l. have been reported in several fish species from off the Argentine coasts; however, there are no studies dealing with their specific identification in this region. Here, a genetic identification and morphological characterization of larval Pseudoterranova spp. from three fish species sampled from Argentine waters and from Notothenia coriiceps from Antarctic waters was carried out. Larvae were sequenced for their genetic/molecular identification, including the mitochondrial cytochrome c oxidase subunit II (mtDNA cox2), the first (ITS-1) and the second (ITS-2) internal transcribed spacers of the nuclear ribosomal DNA, and compared with all species of the P. decipiens (sensu lato) species complex (sequences available in GenBank). Further, adults of Pseudoterranova spp. from the definitive host, the southern sea lion, Otaria flavescens, from Argentine and Chilean coasts were sequenced at the same genes. The sequences obtained at the ITS-1 and ITS-2 genes from all the larvae examined from fish of Argentine waters, as well as the adult worms, matched 100% the sequences for the species P. cattani. The sequences obtained at mtDNA cox2 gene for Antarctic larvae matched 99% those available in GenBank for the sibling P. decipiens sp. E. Both MP and BI phylogenetic trees strongly supported P. cattani and P. decipiens sp. E as two distinct phylogenetic lineages and depicted the species P. decipiens sp. E as sister taxon to the remaining taxa of the P. decipiens complex. Larval morphometry was similar between specimens of P. cattani from Argentina, but significantly different from those of P. decipiens sp. E, indicating that larval forms can be distinguished based on their morphology. Pseudoterranova cattani is common and abundant in a variety of fish species from Chile, whereas few host species harbour these larvae in Argentina where they show low levels of parasitism. This pattern could arise from a combination of factors, including environmental conditions, density and dietary preferences of definitive hosts and life-cycle pathways of the parasite. Finally, this study revealed that the life-cycle of P. cattani involves mainly demersal and benthic organisms, with a marked preference by large-sized benthophagous fish. Copyright © 2013 Elsevier B.V. All rights reserved.

What are we missing? Advantages of more than one viewpoint to estimate fish assemblages using baited video

PubMed Central

Huveneers, Charlie; Fairweather, Peter G.

2018-01-01

Counting errors can bias assessments of species abundance and richness, which can affect assessments of stock structure, population structure and monitoring programmes. Many methods for studying ecology use fixed viewpoints (e.g. camera traps, underwater video), but there is little known about how this biases the data obtained. In the marine realm, most studies using baited underwater video, a common method for monitoring fish and nekton, have previously only assessed fishes using a single bait-facing viewpoint. To investigate the biases stemming from using fixed viewpoints, we added cameras to cover 360° views around the units. We found similar species richness for all observed viewpoints but the bait-facing viewpoint recorded the highest fish abundance. Sightings of infrequently seen and shy species increased with the additional cameras and the extra viewpoints allowed the abundance estimates of highly abundant schooling species to be up to 60% higher. We specifically recommend the use of additional cameras for studies focusing on shyer species or those particularly interested in increasing the sensitivity of the method by avoiding saturation in highly abundant species. Studies may also benefit from using additional cameras to focus observation on the downstream viewpoint. PMID:29892386

Predictive models for fish assemblages in eastern USA streams: implications for assessing biodiversity

USGS Publications Warehouse

Meador, Michael R.; Carlisle, Daren M.

2009-01-01

Management and conservation of aquatic systems require the ability to assess biological conditions and identify changes in biodiversity. Predictive models for fish assemblages were constructed to assess biological condition and changes in biodiversity for streams sampled in the eastern United States as part of the U.S. Geological Survey's National Water Quality Assessment Program. Separate predictive models were developed for northern and southern regions. Reference sites were designated using land cover and local professional judgment. Taxonomic completeness was quantified based on the ratio of the number of observed native fish species expected to occur to the number of expected native fish species. Models for both regions accurately predicted fish species composition at reference sites with relatively high precision and low bias. In general, species that occurred less frequently than expected (decreasers) tended to prefer riffle areas and larger substrates, such as gravel and cobble, whereas increaser species (occurring more frequently than expected) tended to prefer pools, backwater areas, and vegetated and sand substrates. In the north, the percentage of species identified as increasers and the percentage identified as decreasers were equal, whereas in the south nearly two-thirds of the species examined were identified as decreasers. Predictive models of fish species can provide a standardized indicator for consistent assessments of biological condition at varying spatial scales and critical information for an improved understanding of fish species that are potentially at risk of loss with changing water quality conditions.

Assessment of nonlethal methods for predicting muscle tissue mercury concentrations in coastal marine fishes

PubMed Central

Piraino, Maria N.; Taylor, David L.

2013-01-01

Caudal fin clips and dorsolateral scales were analyzed in this study as a potential nonlethal approach for predicting muscle tissue mercury (Hg) concentrations in marine fishes. Target fishes were collected from the Narragansett Bay (RI, USA), and included black sea bass Centropristis striata (n = 54, 14–55 cm total length, TL), bluefish Pomatomus saltatrix (n = 113, 31–73 cm TL), striped bass Morone saxatilis (n = 40, 34–102 cm TL), summer flounder Paralichthys dentatus (n = 64, 18–55 cm TL), and tautog Tautoga onitis (n = 102, 27–61 cm TL). For all fish species, Hg concentrations were greatest in muscle tissue (mean muscle Hg = 0.47–1.18 mg/kg dry weight), followed by fin clips (0.03–0.09 mg/kg dry weight) and scales (0.01–0.07 mg/kg dry weight). The coefficient of determination (R2) derived from power regressions of intra-species muscle Hg against fin and scale Hg ranged between 0.35–0.78 (mean R2 = 0.57) and 0.14–0.37 (mean R2 = 0.30), respectively. The inclusion of fish body size interaction effects in the regression models improved the predictive ability of fins (R2 = 0.63–0.80; mean = 0.71) and scales (R2 = 0.33–0.71; mean = 0.53). According to the high level of uncertainty within the regression models (R2 values) and confidence interval widths, scale analysis was deemed an ineffective tool for estimating muscle tissue Hg concentrations in the target species. In contrast, the examination of fin clips as predictors of muscle Hg had value as a cursory screening tool, but this method should not be the foundation for developing human consumption advisories. It is also noteworthy that the efficacy of these nonlethal techniques was highly variable across fishes, and likely depends on species-specific life history characteristics. PMID:23929385

Encephalization in tropical teleost fishes and comparison with their mode of life.

PubMed

Bauchot, R; Randall, J E; Ridet, J M; Bauchot, M L

1989-01-01

The brains were dissected from a total of 1225 fishes representing 737 species, 310 genera and 113 families of tropical and subtropical teleosts. Each fish was weighed before brain dissection, and each brain weighed after its removal. The encephalization coefficient k was determined for each fish from a quadratic formula; to conveniently compare brain size of one species with that of another, we used an encephalization index so that an encephalization index of 100 is the average for all the species investigated. The encephalization indices for the families of fishes studied varied from 7 for the Moringuidae to 233 for the Coryphaenidae. There is no strong correlation in relative brain size with phylogenetic position. Although there is a general trend for the more highly evolved fishes to have larger brains, this is partially obscured by some high values in certain primitive groups and low ones in the more advanced. Elongate fishes have lower encephalization indices in general. This may in part be related to low phylogenetic position of most elongate species (anguilliform fishes, for example), in part to the greater relative body weight due to the longer vertebral column (and usually more numerous fin rays as as well), and to their usual mode of swimming by lateral undulations of the body (the most primitive type of aquatic locomotion--one in which the spinal cord plays a major role). No difference could be noted in the encephalization indices of herbivorous families of fishes compared to carnivorous ones. Within a genus, among medium to large-size fishes, those species of larger size tend to have lower encephalization indices. This may be related to larger fishes having less to fear of predators. Fishes which in some passive way avoid predation have low indices in general. This is particularly true of benthic species which conceal themselves by flattened form, fleshy protuberances or protective coloration, or which bury in the sediment or take refuge in burrows. Also correlated with low indices is some form of predator deterence such as production of skin toxins, presence of venomous spines or ability to enlarge the body by inflation. Fishes which have more than a single sense highly developed exhibit a larger relative brain size than those with only one well developed sense. Fishes which live in a complex community of high species diversity, such as a coral reef, have higher indices, in general, than those which dwell on mud and sand flat. Pelagic fishes, such as scombrids and carangids, are among those with the highest indices.(ABSTRACT TRUNCATED AT 400 WORDS)

Annual and Spatial Variation of the Kelp Forest Fish Assemblage at San Nicolas Island, California

USGS Publications Warehouse

Cowen, R.J.; Bodkin, James L.

1993-01-01

The kelp forest fishes of San Nicolas Island, California were studied from 1981-1986 to examine the causes of among-site and among-year variation in the fish assemblages. Fish counts and seven physical and biological variables were recorded at six sites around the island every spring and fall. Over the study period, a total of 45 fish species from 18 families were recorded, though members of nive families dominated at all sites. Among-site variation was considereable with two sites on the south side of the island having two to four times as many non-schooling fishes as the other four sites. Three variables, based on stepwise multiple regression techniques, were important predictors of site-specific fish abundance: 1) vertical relief; 2) sand cover and 3) understory algal cover. The total number of fishes varied interannually by a factor of three. Due to recruitment occuring each spring, there was a strong seasonal component to the variation in fish abundance. The extent of seasonal and interannual variaton of fish abundance is an indication of the variable nature of recruitment to this area. Over the 6 yr period, there were three distinct groupings of fish assemblages correspondong to pre- (Fall 1981 - Fall 1982), during spring (Spring 1983 - Spring 1984) and post El Nino (Fall 1984 - Fall 1986) sampling dates. During El Nino sampling period, there was considerable recruitment of southern affinity fish species, increasing both the abundance and diversity of the fish assemblages. Large-scale oceanographic processes, coupled with site-specific features of the reef habitat, produce a moderately diverse, though relatively abundant fish fauna at San Nicolas Island.

Fish sound production in the presence of harmful algal blooms in the eastern Gulf of Mexico.

PubMed

Wall, Carrie C; Lembke, Chad; Hu, Chuanmin; Mann, David A

2014-01-01

This paper presents the first known research to examine sound production by fishes during harmful algal blooms (HABs). Most fish sound production is species-specific and repetitive, enabling passive acoustic monitoring to identify the distribution and behavior of soniferous species. Autonomous gliders that collect passive acoustic data and environmental data concurrently can be used to establish the oceanographic conditions surrounding sound-producing organisms. Three passive acoustic glider missions were conducted off west-central Florida in October 2011, and September and October 2012. The deployment period for two missions was dictated by the presence of red tide events with the glider path specifically set to encounter toxic Karenia brevis blooms (a.k.a red tides). Oceanographic conditions measured by the glider were significantly correlated to the variation in sounds from six known or suspected species of fish across the three missions with depth consistently being the most significant factor. At the time and space scales of this study, there was no detectable effect of red tide on sound production. Sounds were still recorded within red tide-affected waters from species with overlapping depth ranges. These results suggest that the fishes studied here did not alter their sound production nor migrate out of red tide-affected areas. Although these results are preliminary because of the limited measurements, the data and methods presented here provide a proof of principle and could serve as protocol for future studies on the effects of algal blooms on the behavior of soniferous fishes. To fully capture the effects of episodic events, we suggest that stationary or vertically profiling acoustic recorders and environmental sampling be used as a complement to glider measurements.

Fish Sound Production in the Presence of Harmful Algal Blooms in the Eastern Gulf of Mexico

PubMed Central

Wall, Carrie C.; Lembke, Chad; Hu, Chuanmin; Mann, David A.

2014-01-01

This paper presents the first known research to examine sound production by fishes during harmful algal blooms (HABs). Most fish sound production is species-specific and repetitive, enabling passive acoustic monitoring to identify the distribution and behavior of soniferous species. Autonomous gliders that collect passive acoustic data and environmental data concurrently can be used to establish the oceanographic conditions surrounding sound-producing organisms. Three passive acoustic glider missions were conducted off west-central Florida in October 2011, and September and October 2012. The deployment period for two missions was dictated by the presence of red tide events with the glider path specifically set to encounter toxic Karenia brevis blooms (a.k.a red tides). Oceanographic conditions measured by the glider were significantly correlated to the variation in sounds from six known or suspected species of fish across the three missions with depth consistently being the most significant factor. At the time and space scales of this study, there was no detectable effect of red tide on sound production. Sounds were still recorded within red tide-affected waters from species with overlapping depth ranges. These results suggest that the fishes studied here did not alter their sound production nor migrate out of red tide-affected areas. Although these results are preliminary because of the limited measurements, the data and methods presented here provide a proof of principle and could serve as protocol for future studies on the effects of algal blooms on the behavior of soniferous fishes. To fully capture the effects of episodic events, we suggest that stationary or vertically profiling acoustic recorders and environmental sampling be used as a complement to glider measurements. PMID:25551564

Development of a Life History Database for Upper Mississippi River Fishes

DTIC Science & Technology

2007-05-01

prevailing ecological and river theories with existing empirical data, investigating anthropogenic controls on functional attributes of ecosystems...2001; 2005a). database closely reflect the ecological attributes Finally, the life history database will allow the of UMRS fish species. These...34 Functional Feeding Guilds attribute class provide information on reproductive capacity, timing and mode for UMRS fish species. Our first example used the

Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna?

PubMed Central

2013-01-01

Background The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region. Results Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (<2%), application of a complementary character-based nucleotide diagnostic approach proved useful in discriminating them. Additionally, 14 species displayed high intra-specific genetic divergence (>2%), pointing to at least 23 strong candidates for new species. Conclusions Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications. PMID:23497346

Fish assemblage structure and habitat associations in a large western river system

USGS Publications Warehouse

Smith, C.D.; Quist, Michael C.; Hardy, R. S.

2016-01-01

Longitudinal gradients of fish assemblage and habitat structure were investigated in the Kootenai River of northern Idaho. A total of 43 500-m river reaches was sampled repeatedly with several techniques (boat-mounted electrofishing, hoop nets and benthic trawls) in the summers of 2012 and 2013. Differences in habitat and fish assemblage structure were apparent along the longitudinal gradient of the Kootenai River. Habitat characteristics (e.g. depth, substrate composition and water velocity) were related to fish assemblage structure in three different geomorphic river sections. Upper river sections were characterized by native salmonids (e.g. mountain whitefish Prosopium williamsoni), whereas native cyprinids (peamouth Mylocheilus caurinus, northern pikeminnow Ptychocheilus oregonensis) and non-native fishes (pumpkinseed Lepomis gibbosus, yellow perch Perca flavescens) were common in the downstream section. Overall, a general pattern of species addition from upstream to downstream sections was discovered and is likely related to increased habitat complexity and additions of non-native species in downstream sections. Assemblage structure of the upper sections were similar, but were both dissimilar to the lower section of the Kootenai River. Species-specific hurdle regressions indicated the relationships among habitat characteristics and the predicted probability of occurrence and relative abundance varied by species. Understanding fish assemblage structure in relation to habitat could improve conservation efforts of rare fishes and improve management of coldwater river systems.

Risk assessment and toxic effects of metal pollution in two cultured and wild fish species from highly degraded aquatic habitats.

PubMed

Omar, Wael A; Zaghloul, Khalid H; Abdel-Khalek, Amr A; Abo-Hegab, S

2013-11-01

Lake Qaroun is an inland lake at the lowest part of El-Fayoum depression, Egypt. It receives agricultural and domestic non-treated drainage waters, which are also used for aquaculture in Qaroun area. The results of the present study aimed to provide comparable data between wild (collected from Lake Qaroun) and cultured (collected from Qaroun fish farms and the reference site) Nile tilapia Oreochromis niloticus and mullet Mugil cephalus, as indicators of natural and anthropogenic impacts on aquatic ecosystem as well as to evaluate the human hazard index associated with fish consumption. Metal concentrations in fish tissues showed a species-specific bioaccumulation pattern. Statistically significant differences were observed in the mean metal concentrations with lower bioavailability in M. cephalus compared with O. niloticus in internal vital organs (liver, kidney, and muscle) but much higher in external organs (gill and skin). Histopathological alterations and evident damages were observed in gill, liver, and kidney of both species collected from Lake Qaroun and Qaroun fish farms compared with those from the reference site. The results showed significant increase of plasma aspartate aminotransferase and alanine aminotransferase activity as well as creatinine and uric acid concentration in both fish species from polluted locations. The human health hazard index showed that the cumulative risk greatly increases with increasing fish consumption rate, thus yielding an alarming concern for consumer health.

Functional redundancy and sensitivity of fish assemblages in European rivers, lakes and estuarine ecosystems.

PubMed

Teichert, Nils; Lepage, Mario; Sagouis, Alban; Borja, Angel; Chust, Guillem; Ferreira, Maria Teresa; Pasquaud, Stéphanie; Schinegger, Rafaela; Segurado, Pedro; Argillier, Christine

2017-12-14

The impact of species loss on ecosystems functioning depends on the amount of trait similarity between species, i.e. functional redundancy, but it is also influenced by the order in which species are lost. Here we investigated redundancy and sensitivity patterns across fish assemblages in lakes, rivers and estuaries. Several scenarios of species extinction were simulated to determine whether the loss of vulnerable species (with high propensity of extinction when facing threats) causes a greater functional alteration than random extinction. Our results indicate that the functional redundancy tended to increase with species richness in lakes and rivers, but not in estuaries. We demonstrated that i) in the three systems, some combinations of functional traits are supported by non-redundant species, ii) rare species in rivers and estuaries support singular functions not shared by dominant species, iii) the loss of vulnerable species can induce greater functional alteration in rivers than in lakes and estuaries. Overall, the functional structure of fish assemblages in rivers is weakly buffered against species extinction because vulnerable species support singular functions. More specifically, a hotspot of functional sensitivity was highlighted in the Iberian Peninsula, which emphasizes the usefulness of quantitative criteria to determine conservation priorities.

Nodavirus infections in Israeli mariculture.

PubMed

Ucko, M; Colorni, A; Diamant, A

2004-08-01

Viral encephalopathy and retinopathy (VER) infections were diagnosed in five fish species: Epinephelus aeneus, Dicentrarchus labrax, Sciaenops ocellatus, Lates calcarifer and Mugil cephalus cultured on both the Red Sea and Mediterranean coasts of Israel during 1998-2002. Spongiform vacuolation of nervous tissue was observed in histological sections of all examined species. With transmission electron microscopy, paracrystalline arrays and pieces of membrane-associated non-enveloped virions measuring approximately 30 nm in diameter were observed in the brain and retina of all species. At the molecular level, the nodavirus was detected by using a primer set that amplified the T4 region of the coat protein gene. When the same set of primers was used to search for VER in an additional fish species, Sparus aurata, it was found to produce non-specific amplicons, giving rise to false-positive results. This problem was overcome by using a different primer set (F1/VR3), designed on a highly conserved region of the virus gene, which amplified a fragment of 254 bp, and confirmed that S. aurata was nodavirus-free. This set was validated on all five species of infected fish, as well as clinically healthy fish. Comparison of the coat protein genes from the Israeli isolated sequences indicated that more than one viral strain was involved. No strict host-specificity was evident. Red Sea and Mediterranean isolated sequences grouped in distinct clusters, together with several foreign isolates from the Mediterranean area and the Far East, as phylogenetically close to the Epinephelus akaara RGNNV type.

The standardized fish bioassay procedure for detecting and culturing actively toxic Pfiesteria, used by two reference laboratories for atlantic and gulf coast states.

PubMed Central

Burkholder, J M; Marshall, H G; Glasgow, H B; Seaborn, D W; Deamer-Melia, N J

2001-01-01

In the absence of purified standards of toxins from Pfiesteria species, appropriately conducted fish bioassays are the "gold standard" that must be used to detect toxic strains of Pfiesteria spp. from natural estuarine water or sediment samples and to culture actively toxic Pfiesteria. In this article, we describe the standardized steps of our fish bioassay as an abbreviated term for a procedure that includes two sets of trials with fish, following the Henle-Koch postulates modified for toxic rather than infectious agents. This procedure was developed in 1991, and has been refined over more than 12 years of experience in research with toxic Pfiesteria. The steps involve isolating toxic strains of Pfiesteria (or other potentially, as-yet-undetected, toxic Pfiesteria or Pfiesteria-like species) from fish-killing bioassays with natural samples; growing the clones with axenic algal prey; and retesting the isolates in a second set of fish bioassays. The specific environmental conditions used (e.g., temperature, salinity, light, other factors) must remain flexible, given the wide range of conditions from which natural estuarine samples are derived. We present a comparison of information provided for fish culture conditions, reported in international science journals in which such research is routinely published, and we provide information from more than 2,000 fish bioassays with toxic Pfiesteria, along with recommendations for suitable ranges and frequency of monitoring of environmental variables. We present data demonstrating that algal assays, unlike these standardized fish bioassays, should not be used to detect toxic strains of Pfiesteria spp. Finally, we recommend how quality control/assurance can be most rapidly advanced among laboratories engaged in studies that require research-quality isolates of toxic Pfiesteria spp. PMID:11677184

Chemical Ototoxicity of the Fish Inner Ear and Lateral Line.

PubMed

Coffin, Allison B; Ramcharitar, John

2016-01-01

Hair cell-driven mechanosensory systems are crucial for successful execution of a number of behaviors in fishes, and have emerged as good models for exploring questions relevant to human hearing. This review focuses on ototoxic effects in the inner ear and lateral line system of fishes. We specifically examine studies where chemical ototoxins such as aminoglycoside antibiotics have been employed as tools to disable the lateral line. Lateral line ablation results in alterations to feeding behavior and orientation to water current in a variety of species. However, neither behavior is abolished in the presence of additional sensory cues, supporting the hypothesis that many fish behaviors are driven by multisensory integration. Within biomedical research, the larval zebrafish lateral line has become an important model system for understanding signaling mechanisms that contribute to hair cell death and for developing novel pharmacological therapies that protect hair cells from ototoxic damage. Furthermore, given that fishes robustly regenerate damaged hair cells, ototoxin studies in fishes have broadened our understanding of the molecular and genetic events in an innately regenerative system, offering potential targets for mammalian hair cell regeneration. Collectively, studies of fish mechanosensory systems have yielded insight into fish behavior and in mechanisms of hair cell death, protection, and regeneration.

Fish trophic level and the similarity of non-specific larval parasite assemblages.

PubMed

Timi, J T; Rossin, M A; Alarcos, A J; Braicovich, P E; Cantatore, D M P; Lanfranchi, A L

2011-03-01

Whereas the effect of parasites on food webs is increasingly recognised and has been extensively measured and modelled, the effect of food webs on the structure of parasite assemblages has not been quantified in a similar way. Here, we apply the concept of decay in community similarity with increasing distance, previously used for parasites in geographical, phylogenetic and ontogenetic contexts, to differences in the trophic level (TL) based on diet composition of fishes. It is proposed as an accurate quantitative method to measure rates of assemblage change as a function of host feeding habits and is applied, to our knowledge for the first time, across host species in marine waters. We focused on a suite of 15 species of trophically-transmitted and non-specific larval helminths across 16 fish species (1783 specimens, six orders, 14 families) with different sizes and TLs, gathered from the same ecosystem. Not all host species harboured the same number and types of parasites, reflecting the differences in their ecological characteristics. Using differences in TL and body length as measurements of size and trophic distances, we found that similarity at both infracommunity and component community levels showed a very clear decay pattern, based on parasite abundance and relative abundance, with increasing distance in TL, but was not related to changes in fish size, with TL thus emerging as the main explanatory factor for similarity of parasite assemblages. Furthermore, the relationships between host TL and assemblage similarity allowed identification of fishes for which the TL was under- or over-estimated and prediction of the TL of host species based on parasite data alone. Copyright © 2010 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

A new specific reference gene based on growth hormone gene (GH1) used for detection and relative quantification of Aquadvantage® GM salmon (Salmo salar L.) in food products.

PubMed

Hafsa, Ahmed Ben; Nabi, Nesrine; Zellama, Mohamed Salem; Said, Khaled; Chaouachi, Maher

2016-01-01

Genetic transformation of fish is mainly oriented towards the improvement of growth for the benefit of the aquaculture. Actually, Atlantic salmon (Salmo salar) is the species most transformed to achieve growth rates quite large compared to the wild. To anticipate the presence of contaminations with GM salmon in fish markets and the lack of labeling regulations with a mandatory threshold, the proper methods are needed to test the authenticity of the ingredients. A quantitative real-time polymerase chain reaction (QRT-PCR) method was used in this study. Ct values were obtained and validated using 15 processed food containing salmon. The relative and absolute limits of detection were 0.01% and 0.01 ng/μl of genomic DNA, respectively. Results demonstrate that the developed QRT-PCR method is suitable specifically for identification of S. salar in food ingredients based on the salmon growth hormone gene 1 (GH1). The processes used to develop the specific salmon reference gene case study are intended to serve as a model for performing quantification of Aquadvantage® GM salmon on future genetically modified (GM) fish to be commercialized. Copyright © 2015 Elsevier Ltd. All rights reserved.

An eDNA Assay to Monitor a Globally Invasive Fish Species from Flowing Freshwater

PubMed Central

Adrian-Kalchhauser, Irene; Burkhardt-Holm, Patricia

2016-01-01

Ponto-Caspian gobies are a flock of five invasive fish species that have colonized freshwaters and brackish waters in Europe and North America. One of them, the round goby Neogobius melanostomus, figures among the 100 worst invaders in Europe. Current methods to detect the presence of Ponto-Caspian gobies involve catching or sighting the fish. These approaches are labor intense and not very sensitive. Consequently, populations are usually detected only when they have reached high densities and when management or containment efforts are futile. To improve monitoring, we developed an assay based on the detection of DNA traces (environmental DNA, or eDNA) of Ponto-Caspian gobies in river water. The assay specifically detects invasive goby DNA and does not react to any native fish species. We apply the assay to environmental samples and demonstrate that parameters such as sampling depth, sampling location, extraction protocol, PCR protocol and PCR inhibition greatly impact detection. We further successfully outline the invasion front of Ponto-Caspian gobies in a large river, the High Rhine in Switzerland, and thus demonstrate the applicability of the assay to lotic environments. The eDNA assay requires less time, equipment, manpower, skills, and financial resources than the conventional monitoring methods such as electrofishing, angling or diving. Samples can be taken by untrained individuals, and the assay can be performed by any molecular biologist on a conventional PCR machine. Therefore, this assay enables environment managers to map invaded areas independently of fishermen’s’ reports and fish community monitorings. PMID:26814998

Phylogenetic resolution and habitat specificity of members of the Photobacterium phosphoreum species group.

PubMed

Ast, Jennifer C; Dunlap, Paul V

2005-10-01

Substantial ambiguity exists regarding the phylogenetic status of facultatively psychrophilic luminous bacteria identified as Photobacterium phosphoreum, a species thought to be widely distributed in the world's oceans and believed to be the specific bioluminescent light-organ symbiont of several deep-sea fishes. Members of the P. phosphoreum species group include luminous and non-luminous strains identified phenotypically from a variety of different habitats as well as phylogenetically defined lineages that appear to be evolutionarily distinct. To resolve this ambiguity and to begin developing a meaningful knowledge of the geographic distributions, habitats and symbiotic relationships of bacteria in the P. phosphoreum species group, we carried out a multilocus, fine-scale phylogenetic analysis based on sequences of the 16S rRNA, gyrB and luxABFE genes of many newly isolated luminous strains from symbiotic and saprophytic habitats, together with previously isolated luminous and non-luminous strains identified as P. phosphoreum from these and other habitats. Parsimony analysis unambiguously resolved three evolutionarily distinct clades, phosphoreum, iliopiscarium and kishitanii. The tight phylogenetic clustering within these clades and the distinct separation between them indicates they are different species, P. phosphoreum, Photobacterium iliopiscarium and the newly recognized 'Photobacterium kishitanii'. Previously reported non-luminous strains, which had been identified phenotypically as P. phosphoreum, resolved unambiguously as P. iliopiscarium, and all examined deep-sea fishes (specimens of families Chlorophthalmidae, Macrouridae, Moridae, Trachichthyidae and Acropomatidae) were found to harbour 'P. kishitanii', not P. phosphoreum, in their light organs. This resolution revealed also that 'P. kishitanii' is cosmopolitan in its geographic distribution. Furthermore, the lack of phylogenetic variation within 'P. kishitanii' indicates that this facultatively symbiotic bacterium is not cospeciating with its phylogenetically divergent host fishes. The results of this fine-scale phylogenetic analysis support the emerging view that bacterial species names should designate singular historical entities, i.e. discrete lineages diagnosed by a significant divergence of shared derived nucleotide characters.

Projected shifts in fish species dominance in Wisconsin lakes under climate change.

PubMed

Hansen, Gretchen J A; Read, Jordan S; Hansen, Jonathan F; Winslow, Luke A

2017-04-01

Temperate lakes may contain both coolwater fish species such as walleye (Sander vitreus) and warmwater fish species such as largemouth bass (Micropterus salmoides). Recent declining walleye and increasing largemouth bass populations have raised questions regarding the future trajectories and management actions for these species. We developed a thermodynamic model of water temperatures driven by downscaled climate data and lake-specific characteristics to estimate daily water temperature profiles for 2148 lakes in Wisconsin, US, under contemporary (1989-2014) and future (2040-2064 and 2065-2089) conditions. We correlated contemporary walleye recruitment and largemouth bass relative abundance to modeled water temperature, lake morphometry, and lake productivity, and projected lake-specific changes in each species under future climate conditions. Walleye recruitment success was negatively related and largemouth bass abundance was positively related to water temperature degree days. Both species exhibited a threshold response at the same degree day value, albeit in opposite directions. Degree days were predicted to increase in the future, although the magnitude of increase varied among lakes, time periods, and global circulation models (GCMs). Under future conditions, we predicted a loss of walleye recruitment in 33-75% of lakes where recruitment is currently supported and a 27-60% increase in the number of lakes suitable for high largemouth bass abundance. The percentage of lakes capable of supporting abundant largemouth bass but failed walleye recruitment was predicted to increase from 58% in contemporary conditions to 86% by mid-century and to 91% of lakes by late century, based on median projections across GCMs. Conversely, the percentage of lakes with successful walleye recruitment and low largemouth bass abundance was predicted to decline from 9% of lakes in contemporary conditions to only 1% of lakes in both future periods. Importantly, we identify up to 85 resilient lakes predicted to continue to support natural walleye recruitment. Management resources could target preserving these resilient walleye populations. © 2016 The Authors. Global Change Biology published by John Wiley & Sons Ltd.

Ontogenetic, spatial and temporal variation in trophic level and diet of Chukchi Sea fishes

NASA Astrophysics Data System (ADS)

Marsh, Jennifer M.; Mueter, Franz J.; Iken, Katrin; Danielson, Seth

2017-01-01

Climate warming and increasing development are expected to alter the ecosystem of the Chukchi Sea, including its fish communities. As a component of the Arctic Ecosystem Integrated Survey, we assessed the ontogenetic, spatial and temporal variability of the trophic level and diet of key fish species in the Chukchi Sea using N and C stable isotopes. During August and September of 2012 and 2013, 16 common fish species and two primary, invertebrate consumers were collected from surface, midwater and bottom trawls within the eastern Chukchi Sea. Linear mixed-effects models were used to detect possible variation in the relationship between body length and either δ13C or δ15N values among water masses and years for 13 fish species with an emphasis on Arctic cod (Boreogadus saida). We also examined the fish community isotopic niche space, trophic redundancy, and trophic separation within each water mass as measures of resiliency of the fish food web. Ontogenetic shifts in trophic level and diet were observed for most species and these changes tended to vary by water mass. As they increased in length, most fish species relied more on benthic prey with the exception of three forage fish species (walleye pollock, Gadus chalcogrammus, capelin, Mallotus villosus, and Pacific sandlance, Ammodytes hexapterus). Species that exhibited interannual differences in diet and trophic level were feeding at lower trophic levels and consumed a more pelagic diet in 2012 when zooplankton densities were higher. Fish communities occupied different isotopic niche spaces depending on water mass association. In more northerly Arctic waters, the fish community occupied the smallest isotopic niche space and relied heavily on a limited range of intermediate δ13C prey, whereas in warmer, nutrient-rich Bering Chukchi Summer Water, pelagic prey was important. In the warmest, Pacific-derived coastal water, fish consumed both benthic and pelagic prey. Examining how spatial gradients in trophic position are linked to environmental drivers can provide insight into potential fish community shifts with a changing climate.

Rapid differentiation of Francisella species and subspecies by fluorescent in situ hybridization targeting the 23S rRNA

PubMed Central

2010-01-01

Background Francisella (F.) tularensis is the causative agent of tularemia. Due to its low infectious dose, ease of dissemination and high case fatality rate, F. tularensis was the subject in diverse biological weapons programs and is among the top six agents with high potential if misused in bioterrorism. Microbiological diagnosis is cumbersome and time-consuming. Methods for the direct detection of the pathogen (immunofluorescence, PCR) have been developed but are restricted to reference laboratories. Results The complete 23S rRNA genes of representative strains of F. philomiragia and all subspecies of F. tularensis were sequenced. Single nucleotide polymorphisms on species and subspecies level were confirmed by partial amplification and sequencing of 24 additional strains. Fluorescent In Situ Hybridization (FISH) assays were established using species- and subspecies-specific probes. Different FISH protocols allowed the positive identification of all 4 F. philomiragia strains, and more than 40 F. tularensis strains tested. By combination of different probes, it was possible to differentiate the F. tularensis subspecies holarctica, tularensis, mediasiatica and novicida. No cross reactivity with strains of 71 clinically relevant bacterial species was observed. FISH was also successfully applied to detect different F. tularensis strains in infected cells or tissue samples. In blood culture systems spiked with F. tularensis, bacterial cells of different subspecies could be separated within single samples. Conclusion We could show that FISH targeting the 23S rRNA gene is a rapid and versatile method for the identification and differentiation of F. tularensis isolates from both laboratory cultures and clinical samples. PMID:20205957

Eco-Design of River Fishways for Upstream Passage: Application for Hanfeng Dam, Pengxi River, China

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Gary E.; Rainey, William S.

2012-05-20

This paper provides a scientific approach to eco-design of river fishways to allow upstream movement of fish past new and existing dams in China. This eco-design approach integrates principles of fish ecology/behavior and engineering, a scientific field also known as bio-engineering or eco-hydraulics. We define a fishway as a structure or mechanism to convey fish upstream past a dam. Man-made or natural stream beds can be part of the fishway mechanism. Fish include bony and non-bony fishes, and upstream passage is the concern here, not downstream passage. The problem is dams block access to upstream habitat used for spawning, rearing,more » and refuge, i.e., dams decrease habitat connectivity. A solution to alleviate this problem is to design fishways, preferably while the dam is being designed, but if necessary, as retrofits afterward to provide a route that fish can and will use to pass safely upstream without undue delay. Our eco-design approach for fishways involves eight steps: 1) identify the primary species of importance; 2) understand basic ecology and behavior of these fish; 3) characterize the environmental conditions where passage is or will be blocked; 4 identify fishway alternatives and select a preferred alternative; 5) establish eco-design criteria for the fishway, either from management agencies or, if necessary, developed specifically for the given site; 6) where needed, identify and perform research required to resolve critical uncertainties and finalize the eco-design criteria; 7) apply the eco-design criteria and site-specific considerations to design the fishway, involving peer-review by local stakeholders in the process; 8) build the fishway, monitor its effectiveness, and apply the lessons learned. Example fishways are described showing a range of eco-designs depending on the dam site and fish species of concern. We apply the eco-design principles to recommend an approach and next steps for a fishway to pass fish upstream at Hanfeng Dam, an existing regulating dam forming Hanfeng Lake on the Pengxi River near Kaixian, China.« less

Bayesian estimation of diagnostic sensitivity and specificity of a nervous necrosis virus antibody ELISA.

PubMed

Jaramillo, Diana; Dürr, Salome; Hick, Paul; Whittington, Richard

2016-01-01

Diagnosis of nervous necrosis virus (NNV) infection in susceptible fish species is mostly performed post-mortem due to the neurotropism of the causative agent and the only validated diagnostic assays require samples from brain and retinal tissue. However, a non-lethal alternative to test for exposure of fish to NNV is needed. An indirect ELISA for the detection of anti-NNV antibodies in was recently developed and evaluated to detect responses in the sera from immunized fish. For this study, we assessed the accuracy of the assay at detecting specific antibodies from naturally exposed fish using field samples from populations with differing infection status. We applied a Bayesian model, using RTqPCR as a second test. Median estimates of the diagnostic sensitivity and specificity of the VNN ELISA were 81.8% and 86.7%, respectively. We concluded that the assay was fit for the purpose of identifying animals in naturally exposed populations. With further evaluation in larger populations the test might be used to inform implementation of control measures, and for estimating infection prevalence to facilitate risk analysis. To our knowledge this is the first report on the diagnostic accuracy of an antibody ELISA for an infectious disease in finfish. Copyright © 2015 Elsevier B.V. All rights reserved.

Body size, trophic level, and the use of fish as transmission routes by parasites.

PubMed

Poulin, R; Leung, T L F

2011-07-01

Within food webs, trophically transmitted helminth parasites use predator-prey links for their own transfer from intermediate prey hosts, in which they occur as larval or juvenile stages, to predatory definitive hosts, in which they reach maturity. In large taxa that can be used as intermediate and/or definitive hosts, such as fish, a host species' position within a trophic network should determine whether its parasite fauna consists mostly of adult or larval helminths, since vulnerability to predation determines an animal's role in predator-prey links. Using a large database on the helminth parasites of 303 fish species, we tested whether the proportion of parasite species in a host that occur as larval or juvenile stages is best explained by their trophic level or by their body size. Independent of fish phylogeny or habitat, only fish body length emerged as a significant predictor of the proportion of parasites in a host that occur as larval stages from our multivariate analyses. On average, the proportion of larval helminth taxa in fish shorter than 20 cm was twice as high as that for fish over 100 cm in length. This is consistent with the prediction that small fishes, being more vulnerable to predation, make better hosts for larval parasites. However, trophic level and body length are strongly correlated among fish species, and they may have separate though confounded effects on the parasite fauna exploiting a given species. Helminths show varying levels of host specificity toward their intermediate host when the latter is the downstream host involved in trophic transmission toward an upstream definitive host. Given this broad physiological compatibility of many helminths with fish hosts, our results indicate that fish body length, as a proxy for vulnerability to predators, is a better predictor of their use by helminth larvae than their trophic level based on diet content.

Stability and generalization in seed dispersal networks: a case study of frugivorous fish in Neotropical wetlands.

PubMed

Correa, Sandra Bibiana; Arujo, Joisiane K; Penha, Jerry; Nunes da Cunha, Catia; Bobier, Karen E; Anderson, Jill T

2016-08-31

When species within guilds perform similar ecological roles, functional redundancy can buffer ecosystems against species loss. Using data on the frequency of interactions between fish and fruit, we assessed whether co-occurring frugivores provide redundant seed dispersal services in three species-rich Neotropical wetlands. Our study revealed that frugivorous fishes have generalized diets; however, large-bodied fishes had greater seed dispersal breadth than small species, in some cases, providing seed dispersal services not achieved by smaller fish species. As overfishing disproportionately affects big fishes, the extirpation of these species could cause larger secondary extinctions of plant species than the loss of small specialist frugivores. To evaluate the consequences of frugivore specialization for network stability, we extracted data from 39 published seed dispersal networks of frugivorous birds, mammals and fish (our networks) across ecosystems. Our analysis of interaction frequencies revealed low frugivore specialization and lower nestedness than analyses based on binary data (presence-absence of interactions). In that case, ecosystems may be resilient to loss of any given frugivore. However, robustness to frugivore extinction declines with specialization, such that networks composed primarily of specialist frugivores are highly susceptible to the loss of generalists. In contrast with analyses of binary data, recently developed algorithms capable of modelling interaction strengths provide opportunities to enhance our understanding of complex ecological networks by accounting for heterogeneity of frugivore-fruit interactions. © 2016 The Author(s).

Stability and generalization in seed dispersal networks: a case study of frugivorous fish in Neotropical wetlands

PubMed Central

Arujo, Joisiane K.; Penha, Jerry; Nunes da Cunha, Catia

2016-01-01

When species within guilds perform similar ecological roles, functional redundancy can buffer ecosystems against species loss. Using data on the frequency of interactions between fish and fruit, we assessed whether co-occurring frugivores provide redundant seed dispersal services in three species-rich Neotropical wetlands. Our study revealed that frugivorous fishes have generalized diets; however, large-bodied fishes had greater seed dispersal breadth than small species, in some cases, providing seed dispersal services not achieved by smaller fish species. As overfishing disproportionately affects big fishes, the extirpation of these species could cause larger secondary extinctions of plant species than the loss of small specialist frugivores. To evaluate the consequences of frugivore specialization for network stability, we extracted data from 39 published seed dispersal networks of frugivorous birds, mammals and fish (our networks) across ecosystems. Our analysis of interaction frequencies revealed low frugivore specialization and lower nestedness than analyses based on binary data (presence–absence of interactions). In that case, ecosystems may be resilient to loss of any given frugivore. However, robustness to frugivore extinction declines with specialization, such that networks composed primarily of specialist frugivores are highly susceptible to the loss of generalists. In contrast with analyses of binary data, recently developed algorithms capable of modelling interaction strengths provide opportunities to enhance our understanding of complex ecological networks by accounting for heterogeneity of frugivore–fruit interactions. PMID:27581879

Characterization of Diet using Stomach Contents and Multivariate Statistics of four Beaufort Sea Eelpout Species

NASA Astrophysics Data System (ADS)

Apsens, S. J.; Norcross, B.

2016-02-01

Eelpouts of the genus Lycodes are a group of demersal fish commonly found in the U.S. Beaufort Sea. They are relatively numerous, having composed a significant proportion of fish catches during trawl surveys, and they are consumed by marine mammals and birds. Eelpouts themselves may also potentially feed on, or compete for resources with, other fish species. Currently, however, their exact role in the Arctic food web is still poorly understood. Percent number (%N) and percent weight (%W) were used to describe diet, and multivariate techniques were used to look for patterns across environmental (depth and longitude) and biological (length) gradients. Fish were collected in August and September of 2012 and 2014 as part of the U.S.-Canada Transboundary cruises. Stomachs from four eelpout species were examined: Adolf's Eelpout Lycodes adolfi, Canadian Eelpout L. polaris, Archers Eelpout L. sagittarius, and Longear Eelpout L. seminudus. Polychaetes, benthic amphipods, brittle stars, and harpacticoid copepods composed a large part of the observed diet for all four Lycodes species, but proportions differed by species. Intraspecific similarity was low, suggesting these fish have diverse diets even among individuals of the same species. Fish total length was found to be correlated with diet composition for all fish species examined except L. seminudus. Longitude and depth were found to be correlated with diet for L. sagittarius. Identifying prey and factors influencing diet are initial steps towards characterizing the ecological role of this fish genus in the U.S. Arctic food web. Ecological information on abundant fish species is needed for the development of ecosystem-based management practices. Establishing a benchmark for this group is important for understanding their current and future role in the rapidly changing Arctic food web.

Underappreciated species in ecology: "ugly fish" in the northwest Atlantic Ocean.

PubMed

Link, Jason S

2007-10-01

Species shifts and replacements are common in ecological studies. Observations thereof serve as the impetus for many ecological endeavors. Many of the species now known to dominate ecosystem functioning were largely ignored until studies of those underappreciated species elucidated their critical roles. Recognizing the potential importance of underappreciated species has implications for functional redundancies in ecosystems and should alter our approach to long-term monitoring. One example of an applied ecological system containing species shifts, underappreciated species, and potential changes in functional redundancies is the topic of fisheries. The demersal component of many fish communities usually consists of high-profile and commercially valuable species that are targets of fisheries, plus a diverse group of lesser known species that have minimal commercial value and focus. Yet ecologically these traditionally nontargeted species are often a major biomass sink in marine ecosystems and can also be critical in the functioning of bentho-demersal food webs. I examined the biomass trajectories of several species of skates, cottids, lophiids, anarhichadids, zooarcids, and similar species in the northeast U.S. Atlantic ecosystem to determine whether their relative abundance has changed across the past four decades. Distribution and stomach contents of these species were also evaluated over time to further elucidate the relative importance of these species. Landings of these underappreciated bentho-demersal fish were also examined in comparison to those species that historically have been commercially targeted. Of particular emphasis was the evaluation of evidence for sequential stock depletion and the ramifications for functional redundancy for this ecosystem. Results indicate that some of these fish species are now the dominant piscivores, benthivores, and scavengers in this ecosystem. These formerly under-studied species generally have either maintained a consistent population size or have increased in abundance (and expanded in distribution) over the past several decades. Nontraditionally targeted fish species are an often overlooked but important component of bentho-demersal fish communities. Implications for the energy flow and resilience specifically for future fisheries and generally for harvesting biological resources are significant, remaining critical issues for the world's ecosystems.

Trait-based diet selection: prey behaviour and morphology predict vulnerability to predation in reef fish communities.

PubMed

Green, Stephanie J; Côté, Isabelle M

2014-11-01

Understanding how predators select their prey can provide important insights into community structure and dynamics. However, the suite of prey species available to a predator is often spatially and temporally variable. As a result, species-specific selectivity data are of limited use for predicting novel predator-prey interactions because they are assemblage specific. We present a method for predicting diet selection that is applicable across prey assemblages, based on identifying general morphological and behavioural traits of prey that confer vulnerability to predation independent of species identity. We apply this trait-based approach to examining prey selection by Indo-Pacific lionfish (Pterois volitans and Pterois miles), invasive predators that prey upon species-rich reef fish communities and are rapidly spreading across the western Atlantic. We first generate hypotheses about morphological and behavioural traits recurring across fish species that could facilitate or deter predation by lionfish. Constructing generalized linear mixed-effects models that account for relatedness among prey taxa, we test whether these traits predict patterns of diet selection by lionfish within two independent data sets collected at different spatial scales: (i) in situ visual observations of prey consumption and availability for individual lionfish and (ii) comparisons of prey abundance in lionfish stomach contents to availability on invaded reefs at large. Both analyses reveal that a number of traits predicted to affect vulnerability to predation, including body size, body shape, position in the water column and aggregation behaviour, are important determinants of diet selection by lionfish. Small, shallow-bodied, solitary fishes found resting on or just above reefs are the most vulnerable. Fishes that exhibit parasite cleaning behaviour experience a significantly lower risk of predation than non-cleaning fishes, and fishes that are nocturnally active are at significantly greater risk. Together, vulnerable traits heighten the risk of predation by a factor of nearly 200. Our study reveals that a trait-based approach yields insights into predator-prey interactions that are robust across prey assemblages. Importantly, in situ observations of selection yield similar results to broadscale comparisons of prey use and availability, which are more typically gathered for predator species. A trait-based approach could therefore be of use across predator species and ecosystems to predict the outcomes of changing predator-prey interactions on community dynamics. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

Long-term monitoring data provide evidence of declining species richness in a river valued for biodiversity conservation

USGS Publications Warehouse

Freeman, Mary C.; Hagler, Megan M.; Bumpers, Phillip M.; Wheeler, Kit; Wengerd, Seth J.; Freeman, Byron J.

2017-01-01

Free-flowing river segments provide refuges for many imperiled aquatic biota that have been extirpated elsewhere in their native ranges. These biodiversity refuges are also foci of conservation concerns because species persisting within isolated habitat fragments may be particularly vulnerable to local environmental change. We have analyzed long-term (14- and 20-y) survey data to assess evidence of fish species declines in two southeastern U.S. rivers where managers and stakeholders have identified potentially detrimental impacts of current and future land uses. The Conasauga River (Georgia and Tennessee) and the Etowah River (Georgia) form free-flowing headwaters of the extensively dammed Coosa River system. These rivers are valued in part because they harbor multiple species of conservation concern, including three federally endangered and two federally threatened fishes. We used data sets comprising annual surveys for fish species at multiple, fixed sites located at river shoals to analyze occupancy dynamics and temporal changes in species richness. Our analyses incorporated repeated site-specific surveys in some years to estimate and account for incomplete species detection, and test for species-specific (rarity, mainstem-restriction) and year-specific (elevated frequencies of low- or high-flow days) covariates on occupancy dynamics. In the Conasauga River, analysis of 26 species at 13 sites showed evidence of temporal declines in colonization rates for nearly all taxa, accompanied by declining species richness. Four taxa (including one federally endangered species) had reduced occupancy across the Conasauga study sites, with three of these taxa apparently absent for at least the last 5 y of the study. In contrast, a similar fauna of 28 taxa at 10 sites in the Etowah River showed no trends in species persistence, colonization, or occupancy. None of the tested covariates showed strong effects on persistence or colonization rates in either river. Previous studies and observations identified contaminants, nutrient loading, or changes in benthic habitat as possible causes for fish species declines in the Conasauga River. Our analysis provides baseline information that could be used to assess effectiveness of future management actions in the Conasauga or Etowah rivers, and illustrates the use of dynamic occupancy models to evaluate evidence of faunal decline from time-series data.

In Brief: Europe's freshwater fish threatened

NASA Astrophysics Data System (ADS)

Showstack, Randy

2007-11-01

Two hundred of Europe's 522 freshwater fish species are threatened with extinction and 12 are already extinct, according to the Handbook of European Freshwater Fishes, published in collaboration with the World Conservation Union (IUCN) and released on 1 November 2007. IUCN notes that the main threats to fish species stem from development and population growth and include water withdrawals, large dams, and inappropriate fisheries management that has led to overfishing and the introduction of alien species. Authors Maurice Kottelat, former president of the European Ichthyological Society, and Jörg Freyhof, scientist from Leibniz Institute of Freshwater Ecology, noted that fish conservation should be managed by agencies in charge of conservation, and not as a crop by agencies in charge of agriculture. William Darwall, senior program officer with IUCN's Species Program, said the species ``are critical to the freshwater ecosystems upon which we do depend, such as for water purification and flood control.'' For more information, visit the Web site: http://www.iucn.org.

Effect of parasites on resistance to oxygen starvation in the ruff (sic) (Gymnocephalus cernuus)

USGS Publications Warehouse

Pronin, N.M.; Selgeby, J.; Pronina, S.V.; Darland, T.

1997-01-01

Ruffe (Gymnocephalus cernuus) occur widely in Eurasia. This species was accidentally introduced into Lake Superior and rapidly occupied the western part of the lake. Ruffe had a strong impact on populations of commercially important fish species and on commercial fishing. Our studies show that ruffe from Lake Superior are strongly infested by parasites specific to North America. These parasites cause severe pathology in ruffe because this host is less adapted to them.

Diversity of fish sound types in the Pearl River Estuary, China

PubMed Central

Wang, Zhi-Tao; Nowacek, Douglas P.; Akamatsu, Tomonari; Liu, Jian-Chang; Duan, Guo-Qin; Cao, Han-Jiang

2017-01-01

Background Repetitive species-specific sound enables the identification of the presence and behavior of soniferous species by acoustic means. Passive acoustic monitoring has been widely applied to monitor the spatial and temporal occurrence and behavior of calling species. Methods Underwater biological sounds in the Pearl River Estuary, China, were collected using passive acoustic monitoring, with special attention paid to fish sounds. A total of 1,408 suspected fish calls comprising 18,942 pulses were qualitatively analyzed using a customized acoustic analysis routine. Results We identified a diversity of 66 types of fish sounds. In addition to single pulse, the sounds tended to have a pulse train structure. The pulses were characterized by an approximate 8 ms duration, with a peak frequency from 500 to 2,600 Hz and a majority of the energy below 4,000 Hz. The median inter-pulsepeak interval (IPPI) of most call types was 9 or 10 ms. Most call types with median IPPIs of 9 ms and 10 ms were observed at times that were exclusive from each other, suggesting that they might be produced by different species. According to the literature, the two section signal types of 1 + 1 and 1 + N10 might belong to big-snout croaker (Johnius macrorhynus), and 1 + N19 might be produced by Belanger’s croaker (J. belangerii). Discussion Categorization of the baseline ambient biological sound is an important first step in mapping the spatial and temporal patterns of soniferous fishes. The next step is the identification of the species producing each sound. The distribution pattern of soniferous fishes will be helpful for the protection and management of local fishery resources and in marine environmental impact assessment. Since the local vulnerable Indo-Pacific humpback dolphin (Sousa chinensis) mainly preys on soniferous fishes, the fine-scale distribution pattern of soniferous fishes can aid in the conservation of this species. Additionally, prey and predator relationships can be observed when a database of species-identified sounds is completed. PMID:29085746

Diversity of fish sound types in the Pearl River Estuary, China.

PubMed

Wang, Zhi-Tao; Nowacek, Douglas P; Akamatsu, Tomonari; Wang, Ke-Xiong; Liu, Jian-Chang; Duan, Guo-Qin; Cao, Han-Jiang; Wang, Ding

2017-01-01

Repetitive species-specific sound enables the identification of the presence and behavior of soniferous species by acoustic means. Passive acoustic monitoring has been widely applied to monitor the spatial and temporal occurrence and behavior of calling species. Underwater biological sounds in the Pearl River Estuary, China, were collected using passive acoustic monitoring, with special attention paid to fish sounds. A total of 1,408 suspected fish calls comprising 18,942 pulses were qualitatively analyzed using a customized acoustic analysis routine. We identified a diversity of 66 types of fish sounds. In addition to single pulse, the sounds tended to have a pulse train structure. The pulses were characterized by an approximate 8 ms duration, with a peak frequency from 500 to 2,600 Hz and a majority of the energy below 4,000 Hz. The median inter-pulsepeak interval (IPPI) of most call types was 9 or 10 ms. Most call types with median IPPIs of 9 ms and 10 ms were observed at times that were exclusive from each other, suggesting that they might be produced by different species. According to the literature, the two section signal types of 1 + 1 and 1 + N 10 might belong to big-snout croaker ( Johnius macrorhynus ), and 1 + N 19 might be produced by Belanger's croaker ( J. belangerii ). Categorization of the baseline ambient biological sound is an important first step in mapping the spatial and temporal patterns of soniferous fishes. The next step is the identification of the species producing each sound. The distribution pattern of soniferous fishes will be helpful for the protection and management of local fishery resources and in marine environmental impact assessment. Since the local vulnerable Indo-Pacific humpback dolphin ( Sousa chinensis ) mainly preys on soniferous fishes, the fine-scale distribution pattern of soniferous fishes can aid in the conservation of this species. Additionally, prey and predator relationships can be observed when a database of species-identified sounds is completed.

Molecular responses differ between sensitive silver carp and tolerant bighead carp and bigmouth buffalo exposed to rotenone

USGS Publications Warehouse

Amberg, Jon J.; Schreier, Theresa M.; Gaikowski, Mark P.

2012-01-01

Some species of fish are more tolerant of rotenone, a commonly used non-specific piscicide, than others. This species-specific tolerance to rotenone has been thought to be associated with the uptake and the efficiency at which the chemical is detoxified. However, rotenone stimulates oxidative stress and superoxides, which are also toxic. Understanding the modes in which fish physiologically respond to rotenone is important in developing improved protocols for its application in controlling aquatic nuisance species. Using a molecular approach, we investigated the physiological and molecular mechanisms of rotenone resistance. Species-specific responses were observed when rotenone-sensitive silver, Hypophthalmichthys molitrix, and both rotenone-resistant bighead carp, Hypophthalmichthys nobilis, and bigmouth buffalo, Ictiobus cyprinellus, were exposed to rotenone. Rotenone levels in plasma were highest 90 min after exposure in both silver carp and bigmouth buffalo, but bigmouth buffalo tolerated over twice the burden (ng mL-1 g-1) than silver carp. Expression of genes related with detoxification (cyp1a and gst) increased in silver carp, but either decreased or remained the same in bighead carp. Genes linked with oxidative stress in the cytosol (gpx, cat and sod1) and hsp70 increased only in silver carp after a 6-h exposure. Expression of genes associated with oxidative stress in the mitochondria (sod2 and ucp2) differed between silver carp and bighead carp. Expression of sod2 changed minimally in bighead carp, but expression of ucp2 linearly increased to nearly 85-fold of the level prior to exposure. Expression of sod2 and ucp2 did not change until 6 h in silver carp. Use of sod1 and sod2 to combat oxidative stress results in hydrogen peroxide production, while use of ucp2 produces nitric oxide, a chemical known to inhibit apoptosis. We conclude that the mechanism at which a fish handles oxidative stress plays an important role in the tolerance to rotenone.

Guiding out-migrating juvenile sea lamprey (Petromyzon marinus) with pulsed direct current

USGS Publications Warehouse

Johnson, Nicholas S.; Miehls, Scott M.

2014-01-01

Non-physical stimuli can deter or guide fish without affecting water flow or navigation and therefore have been investigated to improve fish passage at anthropogenic barriers and to control movement of invasive fish. Upstream fish migration can be blocked or guided without physical structure by electrifying the water, but directional downstream fish guidance with electricity has received little attention. We tested two non-uniform pulsed direct current electric systems, each having different electrode orientations (vertical versus horizontal), to determine their ability to guide out-migrating juvenile sea lamprey (Petromyzon marinus) and rainbow trout (Oncorhynchus mykiss). Both systems guided significantly more juvenile sea lamprey to a specific location in our experimental raceway when activated than when deactivated, but guidance efficiency decreased at the highest water velocities tested. At the electric field setting that effectively guided sea lamprey, rainbow trout were guided by the vertical electrode system, but most were blocked by the horizontal electrode system. Additional research should characterize the response of other species to non-uniform fields of pulsed DC and develop electrode configurations that guide fish over a range of water velocity.

Improving non-native fish larvae detection based on temporal habitat use.

EPA Science Inventory

As part of the development of an early detection monitoring strategy for non-native fishes, larval fish surveys have been conducted since 2012 in the St. Louis River estuary. Survey data demonstrates considerable variability in fish abundance and species assemblages across habit...

Impacts of hypoxia on the structure and processes in pelagic communities (zooplankton, macro-invertebrates and fish)

NASA Astrophysics Data System (ADS)

Ekau, W.; Auel, H.; Pörtner, H.-O.; Gilbert, D.

2010-05-01

Dissolved oxygen (DO) concentration in the water column is an environmental parameter that is crucial for the successful development of many pelagic organisms. Hypoxia tolerance and threshold values are species- and stage-specific and can vary enormously. While some fish species may suffer from oxygen values of less than 3 mL O2 L-1 through impacted growth, development and behaviour, other organisms such as euphausiids may survive DO levels as low as 0.1 mL O2 L-1. A change in the average or the range of DO may have significant impacts on the survival of certain species and hence on the species composition in the ecosystem with consequent changes in trophic pathways and productivity. Evidence for the deleterious effects of oxygen depletion on pelagic species is scarce, particularly in terms of the effect of low oxygen on development, recruitment and patterns of migration and distribution. While planktonic organisms have to cope with variable DOs and exploit adaptive mechanisms, nektonic species may avoid areas of unfavourable DO and develop adapted migration strategies. Planktonic organisms may only be able to escape vertically, above or beneath the Oxygen Minimum Zone (OMZ). In shallow areas only the surface layer can serve as a refuge, but in deep waters many organisms have developed vertical migration strategies to use, pass through and cope with the OMZ. This paper elucidates the role of DO for different taxa in the pelagic realm and the consequences of low oxygen for foodweb structure and system productivity. We describe processes in two contrasting systems, the semi-enclosed Baltic Sea and the coastal upwelling system of the Benguela Current to demonstrate the consequences of increasing hypoxia on ecosystem functioning and services.

Vast assembly of vocal marine mammals from diverse species on fish spawning ground.

PubMed

Wang, Delin; Garcia, Heriberto; Huang, Wei; Tran, Duong D; Jain, Ankita D; Yi, Dong Hoon; Gong, Zheng; Jech, J Michael; Godø, Olav Rune; Makris, Nicholas C; Ratilal, Purnima

2016-03-17

Observing marine mammal (MM) populations continuously in time and space over the immense ocean areas they inhabit is challenging but essential for gathering an unambiguous record of their distribution, as well as understanding their behaviour and interaction with prey species. Here we use passive ocean acoustic waveguide remote sensing (POAWRS) in an important North Atlantic feeding ground to instantaneously detect, localize and classify MM vocalizations from diverse species over an approximately 100,000 km(2) region. More than eight species of vocal MMs are found to spatially converge on fish spawning areas containing massive densely populated herring shoals at night-time and diffuse herring distributions during daytime. We find the vocal MMs divide the enormous fish prey field into species-specific foraging areas with varying degrees of spatial overlap, maintained for at least two weeks of the herring spawning period. The recorded vocalization rates are diel (24 h)-dependent for all MM species, with some significantly more vocal at night and others more vocal during the day. The four key baleen whale species of the region: fin, humpback, blue and minke have vocalization rate trends that are highly correlated to trends in fish shoaling density and to each other over the diel cycle. These results reveal the temporospatial dynamics of combined multi-species MM foraging activities in the vicinity of an extensive fish prey field that forms a massive ecological hotspot, and would be unattainable with conventional methodologies. Understanding MM behaviour and distributions is essential for management of marine ecosystems and for accessing anthropogenic impacts on these protected marine species.

Post-Disturbance Stability of Fish Assemblages Measured at Coarse Taxonomic Resolution Masks Change at Finer Scales.

PubMed

Ceccarelli, Daniela M; Emslie, Michael J; Richards, Zoe T

2016-01-01

Quantifying changes to coral reef fish assemblages in the wake of cyclonic disturbances is challenging due to spatial variability of damage inherent in such events. Often, fish abundance appears stable at one spatial scale (e.g. reef-wide), but exhibits substantial change at finer scales (e.g. site-specific decline or increase). Taxonomic resolution also plays a role; overall stability at coarse taxonomic levels (e.g. family) may mask species-level turnover. Here we document changes to reef fish communities after severe Tropical Cyclone Ita crossed Lizard Island, Great Barrier Reef. Coral and reef fish surveys were conducted concurrently before and after the cyclone at four levels of exposure to the prevailing weather. Coral cover declined across all exposures except sheltered sites, with the largest decline at exposed sites. There was no significant overall reduction in the total density, biomass and species richness of reef fishes between 2011 and 2015, but individual fish taxa (families and species) changed in complex and unpredictable ways. For example, more families increased in density and biomass than decreased following Cyclone Ita, particularly at exposed sites whilst more fish families declined at lagoon sites even though coral cover did not decline. All sites lost biomass of several damselfish species, and at most sites there was an increase in macroinvertivores and grazers. Overall, these results suggest that the degree of change measured at coarse taxonomic levels masked high species-level turnover, although other potential explanations include that there was no impact of the storm, fish assemblages were impacted but underwent rapid recovery or that there is a time lag before the full impacts become apparent. This study confirms that in high-complexity, high diversity ecosystems such as coral reefs, species level analyses are essential to adequately capture the consequences of disturbance events.

Post-Disturbance Stability of Fish Assemblages Measured at Coarse Taxonomic Resolution Masks Change at Finer Scales

PubMed Central

Ceccarelli, Daniela M.

2016-01-01

Quantifying changes to coral reef fish assemblages in the wake of cyclonic disturbances is challenging due to spatial variability of damage inherent in such events. Often, fish abundance appears stable at one spatial scale (e.g. reef-wide), but exhibits substantial change at finer scales (e.g. site-specific decline or increase). Taxonomic resolution also plays a role; overall stability at coarse taxonomic levels (e.g. family) may mask species-level turnover. Here we document changes to reef fish communities after severe Tropical Cyclone Ita crossed Lizard Island, Great Barrier Reef. Coral and reef fish surveys were conducted concurrently before and after the cyclone at four levels of exposure to the prevailing weather. Coral cover declined across all exposures except sheltered sites, with the largest decline at exposed sites. There was no significant overall reduction in the total density, biomass and species richness of reef fishes between 2011 and 2015, but individual fish taxa (families and species) changed in complex and unpredictable ways. For example, more families increased in density and biomass than decreased following Cyclone Ita, particularly at exposed sites whilst more fish families declined at lagoon sites even though coral cover did not decline. All sites lost biomass of several damselfish species, and at most sites there was an increase in macroinvertivores and grazers. Overall, these results suggest that the degree of change measured at coarse taxonomic levels masked high species-level turnover, although other potential explanations include that there was no impact of the storm, fish assemblages were impacted but underwent rapid recovery or that there is a time lag before the full impacts become apparent. This study confirms that in high-complexity, high diversity ecosystems such as coral reefs, species level analyses are essential to adequately capture the consequences of disturbance events. PMID:27285160

Male-mediated species recognition among African weakly electric fishes

PubMed Central

Nagel, Rebecca; Kirschbaum, Frank; Engelmann, Jacob; Hofmann, Volker; Pawelzik, Felix

2018-01-01

Effective communication among sympatric species is often instrumental for behavioural isolation, where the failure to successfully discriminate between potential mates could lead to less fit hybrid offspring. Discrimination between con- and heterospecifics tends to occur more often in the sex that invests more in offspring production, i.e. females, but males may also mediate reproductive isolation. In this study, we show that among two Campylomormyrus African weakly electric fish species, males preferentially associate with conspecific females during choice tests using live fish as stimuli, i.e. when all sensory modalities potentially used for communication were present. We then conducted playback experiments to determine whether the species-specific electric organ discharge (EOD) used for electrocommunication serves as the cue for this conspecific association preference. Interestingly, only C. compressirostris males associated significantly more with the conspecific EOD waveform when playback stimuli were provided, while no such association preference was observed in C. tamandua males. Given our results, the EOD appears to serve, in part, as a male-mediated pre-zygotic isolation mechanism among sympatric species. However, the failure of C. tamandua males to discriminate between con- and heterospecific playback discharges suggests that multiple modalities may be necessary for species recognition in some African weakly electric fish species. PMID:29515818

Proteomics for the authentication of fish species.

PubMed

Mazzeo, Maria Fiorella; Siciliano, Rosa Anna

2016-09-16

Assessment of seafood authenticity and origin, mainly in the case of processed products (fillets, sticks, baby food) represents the crucial point to prevent fraudulent deceptions thus guaranteeing market transparency and consumers health. The most dangerous practice that jeopardies fish safety is intentional or unintentional mislabeling, originating from the substitution of valuable fish species with inferior ones. Conventional analytical methods for fish authentication are becoming inadequate to comply with the strict regulations issued by the European Union and with the increase of mislabeling due to the introduction on the market of new fish species and market globalization. This evidence prompts the development of high-throughput approaches suitable to identify unambiguous biomarkers of authenticity and screen a large number of samples with minimal time consumption. Proteomics provides suitable and powerful tools to investigate main aspects of food quality and safety and has given an important contribution in the field of biomarkers discovery applied to food authentication. This report describes the most relevant methods developed to assess fish identity and offers a perspective on their potential in the evaluation of fish quality and safety thus depicting the key role of proteomics in the authentication of fish species and processed products. The assessment of fishery products authenticity is a main issue in the control quality process as deceptive practices could imply severe health risks. Proteomics based methods could significantly contribute to detect falsification and frauds, thus becoming a reliable operative first-line testing resource in food authentication. Copyright © 2016 Elsevier B.V. All rights reserved.

Use of classification trees to apportion single echo detections to species: Application to the pelagic fish community of Lake Superior

USGS Publications Warehouse

Yule, Daniel L.; Adams, Jean V.; Hrabik, Thomas R.; Vinson, Mark R.; Woiak, Zebadiah; Ahrenstroff, Tyler D.

2013-01-01

Acoustic methods are used to estimate the density of pelagic fish in large lakes with results of midwater trawling used to assign species composition. Apportionment in lakes having mixed species can be challenging because only a small fraction of the water sampled acoustically is sampled with trawl gear. Here we describe a new method where single echo detections (SEDs) are assigned to species based on classification tree models developed from catch data that separate species based on fish size and the spatial habitats they occupy. During the summer of 2011, we conducted a spatially-balanced lake-wide acoustic and midwater trawl survey of Lake Superior. A total of 51 sites in four bathymetric depth strata (0–30 m, 30–100 m, 100–200 m, and >200 m) were sampled. We developed classification tree models for each stratum and found fish length was the most important variable for separating species. To apply these trees to the acoustic data, we needed to identify a target strength to length (TS-to-L) relationship appropriate for all abundant Lake Superior pelagic species. We tested performance of 7 general (i.e., multi-species) relationships derived from three published studies. The best-performing relationship was identified by comparing predicted and observed catch compositions using a second independent Lake Superior data set. Once identified, the relationship was used to predict lengths of SEDs from the lake-wide survey, and the classification tree models were used to assign each SED to a species. Exotic rainbow smelt (Osmerus mordax) were the most common species at bathymetric depths 100 m (384 million; 6.0 kt). Cisco (Coregonus artedi) were widely distributed over all strata with their population estimated at 182 million (44 kt). The apportionment method we describe should be transferable to other large lakes provided fish are not tightly aggregated, and an appropriate TS-to-L relationship for abundant pelagic fish species can be determined.

Stable multilineage xenogeneic replacement of definitive hematopoiesis in adult zebrafish.

PubMed

Hess, Isabell; Boehm, Thomas

2016-01-18

Bony fishes are the most numerous and phenotypically diverse group of vertebrates inhabiting our planet, making them an ideal target for identifying general principles of tissue development and function. However, lack of suitable experimental platforms prevents the exploitation of this rich source of natural phenotypic variation. Here, we use a zebrafish strain lacking definitive hematopoiesis for interspecific analysis of hematopoietic cell development. Without conditioning prior to transplantation, hematopoietic progenitor cells from goldfish stably engraft in adult zebrafish homozygous for the c-myb(I181N) mutation. However, in competitive repopulation experiments, zebrafish hematopoietic cells exhibit an advantage over their goldfish counterparts, possibly owing to subtle species-specific functional differences in hematopoietic microenvironments resulting from over 100 million years of independent evolution. Thus, our unique animal model provides an unprecedented opportunity to genetically and functionally disentangle universal and species-specific contributions of the microenvironment to hematopoietic progenitor cell maintenance and development.

Fine-scale spatial patterns in the demersal fish and invertebrate community in a northwest Atlantic ecosystem

NASA Astrophysics Data System (ADS)

Malek, Anna J.; Collie, Jeremy S.; Gartland, James

2014-06-01

The abundance, biomass, diversity, and species composition of the demersal fish and invertebrate community in Rhode Island Sound and Block Island Sound, an area identified for offshore renewable energy development, were evaluated for spatial and seasonal structure. We conducted 58 otter trawls and 51 beam trawls in the spring, summer and fall of 2009-2012, and incorporated additional data from 88 otter trawls conducted by the Northeast Area Monitoring and Assessment Program. We used regionally-grouped abundance, biomass, diversity, and size spectra to assess spatial patterns in the aggregate fish community, and hierarchical cluster analysis to evaluate trends in species assemblages. Our analyses revealed coherent gradients in fish community biomass, diversity and species composition extending from inshore to offshore waters, as well as patterns related to the differing bathymetry of Rhode Island and Block Island Sounds. The fish communities around Block Island and Cox's Ledge are particularly diverse, suggesting that the proximity of hard bottom habitat may be important in structuring fish communities in this area. Species assemblages in Rhode Island and Block Island Sounds are characterized by a combination of piscivores (silver hake, summer flounder, spiny dogfish), benthivores (American lobster, black sea bass, Leucoraja spp. skates, scup) and planktivores (sea scallop), and exhibit geographic patterns that are persistent from year to year, yet variable by season. Such distributions reflect the cross-shelf migration of fish and invertebrate species in the spring and fall, highlighting the importance of considering seasonal fish behavior when planning construction schedules for offshore development projects. The fine spatial scale (10 s of kms) of this research makes it especially valuable for local marine spatial planning efforts by identifying local-scale patterns in fish community structure that will enable future assessment of the ecological impacts of offshore development. As such, this knowledge of the spatial and temporal structure of the demersal fish community in Rhode Island and Block Island Sounds will help to guide the placement of offshore structures so as to preserve the ecological and economic value of the area.

Quantifying avian predation on fish populations: integrating predator-specific deposition probabilities in tag-recovery studies

USGS Publications Warehouse

Hostetter, Nathan J.; Evans, Allen F.; Cramer, Bradley M.; Collis, Ken; Lyons, Donald E.; Roby, Daniel D.

2015-01-01

Accurate assessment of specific mortality factors is vital to prioritize recovery actions for threatened and endangered species. For decades, tag recovery methods have been used to estimate fish mortality due to avian predation. Predation probabilities derived from fish tag recoveries on piscivorous waterbird colonies typically reflect minimum estimates of predation due to an unknown and unaccounted-for fraction of tags that are consumed but not deposited on-colony (i.e., deposition probability). We applied an integrated tag recovery modeling approach in a Bayesian context to estimate predation probabilities that accounted for predator-specific tag detection and deposition probabilities in a multiple-predator system. Studies of PIT tag deposition were conducted across three bird species nesting at seven different colonies in the Columbia River basin, USA. Tag deposition probabilities differed significantly among predator species (Caspian ternsHydroprogne caspia: deposition probability = 0.71, 95% credible interval [CRI] = 0.51–0.89; double-crested cormorants Phalacrocorax auritus: 0.51, 95% CRI = 0.34–0.70; California gulls Larus californicus: 0.15, 95% CRI = 0.11–0.21) but showed little variation across trials within a species or across years. Data from a 6-year study (2008–2013) of PIT-tagged juvenile Snake River steelhead Oncorhynchus mykiss (listed as threatened under the Endangered Species Act) indicated that colony-specific predation probabilities ranged from less than 0.01 to 0.17 and varied by predator species, colony location, and year. Integrating the predator-specific deposition probabilities increased the predation probabilities by a factor of approximately 1.4 for Caspian terns, 2.0 for double-crested cormorants, and 6.7 for California gulls compared with traditional minimum predation rate methods, which do not account for deposition probabilities. Results supported previous findings on the high predation impacts from strictly piscivorous waterbirds nesting in the Columbia River estuary (i.e., terns and cormorants), but our findings also revealed greater impacts of a generalist predator species (i.e., California gulls) than were previously documented. Approaches used in this study allow for direct comparisons among multiple fish mortality factors and considerably improve the reliability of tag recovery models for estimating predation probabilities in multiple-predator systems.

Macroecological analysis of the fish fauna inhabiting Cymodocea nodosa seagrass meadows.

PubMed

Espino, F; Brito, A; Haroun, R; Tuya, F

2015-10-01

In this study, patterns in the taxonomic richness and composition of the fish fauna inhabiting Cymodocea nodosa seagrass meadows were described across their entire distribution range in the Mediterranean Sea and adjacent Atlantic Ocean. Specifically, the study tested whether there are differences in the composition of fish assemblages between those ecoregions encompassed by the distribution range of C. nodosa, and whether these differences in composition are connected with differences in bioclimatic affinities of the fish faunas. A literature review resulted in a total of 19 studies, containing 22 fish assemblages at 18 locations. The ichthyofauna associated with C. nodosa seagrass meadows comprises 59 families and 188 species. The western Mediterranean (WM) Sea has the highest species richness (87 species). Fish assemblages from the Macaronesia-Canary Islands, the Sahelian Upwelling, South European Atlantic Shelf and the WM differ, in terms of assemblage composition, relative to other ecoregions. In contrast, the composition of the fish fauna from the central and eastern Mediterranean overlaps. There is a significant serial correlation in fish assemblage composition between adjacent ecoregions along the distribution range of C. nodosa. Dissimilarities in assemblage composition are connected with the geographical separation between locations, and the mean minimum annual seawater temperature is the environmental factor that explains most variation in fish assemblage composition. © 2015 The Fisheries Society of the British Isles.

Sex-specific evolution during the diversification of live-bearing fishes.

PubMed

Culumber, Zachary W; Tobler, Michael

2017-08-01

Natural selection is often assumed to drive parallel functional diversification of the sexes. But males and females exhibit fundamental differences in their biology, and it remains largely unknown how sex differences affect macroevolutionary patterns. On microevolutionary scales, we understand how natural and sexual selection interact to give rise to sex-specific evolution during phenotypic diversification and speciation. Here we show that ignoring sex-specific patterns of functional trait evolution misrepresents the macroevolutionary adaptive landscape and evolutionary rates for 112 species of live-bearing fishes (Poeciliidae). Males and females of the same species evolve in different adaptive landscapes. Major axes of female morphology were correlated with environmental variables but not reproductive investment, while male morphological variation was primarily associated with sexual selection. Despite the importance of both natural and sexual selection in shaping sex-specific phenotypic diversification, species diversification was overwhelmingly associated with ecological divergence. Hence, the inter-predictability of mechanisms of phenotypic and species diversification may be limited in many systems. These results underscore the importance of explicitly addressing sex-specific diversification in empirical and theoretical frameworks of evolutionary radiations to elucidate the roles of different sources of selection and constraint.

Trophic structure of a coastal fish community determined with diet and stable isotope analyses.

PubMed

Malek, A J; Collie, J S; Taylor, D L

2016-09-01

A combination of dietary guild analysis and nitrogen (δ(15) N) and carbon (δ(13) C) stable-isotope analysis was used to assess the trophic structure of the fish community in Rhode Island and Block Island Sounds, an area off southern New England identified for offshore wind energy development. In the autumn of 2009, 2010 and 2011, stomach and tissue samples were taken from 20 fish and invertebrate species for analysis of diet composition and δ(15) N and δ(13) C signatures. The food chain in Rhode Island and Block Island Sounds comprises approximately four trophic levels within which the fish community is divided into distinct dietary guilds, including planktivores, benthivores, crustacivores and piscivores. Within these guilds, inter-species isotopic and dietary overlap is high, suggesting that resource partitioning or competitive interactions play a major role in structuring the fish community. Carbon isotopes indicate that most fishes are supported by pelagic phytoplankton, although there is evidence that benthic production also plays a role, particularly for obligate benthivores such as skates Leucoraja spp. This type of analysis is useful for developing an ecosystem-based approach to management, as it identifies species that act as direct links to basal resources as well as species groups that share trophic roles. © 2016 The Fisheries Society of the British Isles.

New insights into the factors mediating the onset of puberty in sea bass.

PubMed

Espigares, F; Rocha, A; Molés, G; Gómez, A; Carrillo, M; Zanuy, S

2015-12-01

In populations of 1-year-old male European sea bass (Dicentrarchus labrax), only large males are able to acquire for the first time a functional competence of their reproductive axis; in other words, to attain puberty. To examine the causes and mechanisms involved in the onset of puberty in this species, a size sorting sampling was carried out to obtain two experimental groups of small and large male fish exhibiting different growth rates. As expected, only large fish reached full spermiogenesis (stage V of testicular development) by the end of the experiment. Our study suggests that fish size is a permissive condition to ensure full effectiveness of the hormonal (Gnrh1, gonadotropins and sexual steroids) actions. Thus, though small fish had endocrine profiles similar to those of large fish, their amplitude was much lower, and was most likely the reason why functional competence of the reproductive axis was not achieved. Moreover, this work provides evidence of the involvement of kisspeptin and Gnrh1 systems in the onset of puberty in a marine teleost fish. It also indicates that very likely kisspeptin and Gnrh1 may regulate gonadotropins and sex steroids at specific stages of testicular development. Copyright © 2015 Elsevier Inc. All rights reserved.

Inter-habitat variation in density and size composition of reef fishes from the Cuban Northwestern shelf.

PubMed

Aguilar, Consuelo; González-Sansón, Gaspar; Cabrera, Yureidy; Ruiz, Alexei; Curry, R Allen

2014-06-01

Movement and exchange of individuals among habitats is critical for the dynamics and success of reef fish populations. Size segregation among habitats could be taken as evidence for habitat connectivity, and this would be a first step to formulate hypotheses about ontogenetic inter-habitat migrations. The primary goal of our research was to find evidence of inter-habitat differences in size distributions and density of reef fish species that can be classified a priori as habitat-shifters in an extensive (-600km2) Caribbean shelf area in NW Cuba. We sampled the fish assemblage of selected species using visual census (stationary and transect methods) in 20 stations (sites) located in mangrove roots, patch reefs, inner zone of the crest and fore reef (12-16m depth). In each site, we performed ten censuses for every habitat type in June and September 2009. A total of 11 507 individuals of 34 species were counted in a total of 400 censuses. We found significant differences in densities and size compositions among reef and mangrove habitats, supporting the species-specific use of coastal habitats. Adults were found in all habitats. Reef habitats, mainly patch reefs, seem to be most important for juvenile fish of most species. Mangroves were especially important for two species of snappers (Lutjanus apodus and L. griseus), providing habitat for juveniles. These species also displayed well defined gradients in length composition across the shelf.

Normal development of the tomato clownfish Amphiprion frenatus: live imaging and in situ hybridization analyses of mesodermal and neurectodermal development.

PubMed

Ghosh, J; Wilson, R W; Kudoh, T

2009-12-01

The normal embryonic development of the tomato clownfish Amphiprion frenatus was analysed using live imaging and by in situ hybridization for detection of mesodermal and neurectodermal development. Both morphology of live embryos and tissue-specific staining revealed significant differences in the gross developmental programme of A. frenatus compared with better-known teleost fish models, in particular, initiation of somitogenesis before complete epiboly, initiation of narrowing of the neurectoderm (neurulation) before somitogenesis, relatively early pigmentation of melanophores at the 10-15 somite stage and a distinctive pattern of melanophore distribution. These results suggest evolutionary adaptability of the teleost developmental programme. The ease of obtaining eggs, in vitro culture of the embryo, in situ staining analyses and these reported characteristics make A. frenatus a potentially important model marine fish species for studying embryonic development, physiology, ecology and evolution.

The fish and fisheries of Jones Bank and the wider Celtic Sea

NASA Astrophysics Data System (ADS)

Martinez, I.; Ellis, J. R.; Scott, B.; Tidd, A.

2013-10-01

The Celtic Sea is a diverse fishing ground that supports important commercial fisheries for a range of demersal fish, large and small-bodied pelagic fish and a variety of cephalopods and other shellfish. A regional overview of the main commercial fish stocks of the Celtic Sea and of the fish that occur in the vicinity of Jones Bank are provided through analyses of landings data from English and Welsh vessels, and from scientific trawl surveys. Dedicated smaller scale sampling via trawl surveys combined with baited cameras on and around the Jones Bank were also analysed to investigate the importance of sandbank habitats with attention paid to the differences in the species occurring on the top of the bank in comparison to adjacent off-bank habitats. Official landing statistics for UK (English and Welsh) vessels indicated that the predominant commercial demersal species in ICES Divisions VIIg,h (in terms of quantities landed) were anglerfish, megrim, pollack and skates (Rajidae). There were, however, regional differences in the distribution of fish and fisheries, and the area surrounding Jones Bank (ICES Rectangles 28E1 and 28E2) supports fisheries for megrim, anglerfish, skates, hake, ling and turbot, with otter trawl, gillnet and beam trawl the main gears used. Recent survey data collected with GOV (Grande Ouverture Verticale) trawl from the Celtic Sea (ICES Divisions VIIe-h, 2007-2010) were used to highlight the broad scale distribution of the main fish assemblages in the Celtic Sea. Analyses of the fish and cephalopod catches from these surveys indicated that there were four broad assemblages in the area, including (i) a region around the Cornwall (which will also be partly influenced by the necessity to use rockhopper ground gear on these rough grounds), (ii) the shallower regions of the north-western Celtic Sea (including parts of the Bristol Channel), (iii) the deeper parts of the outer shelf and (iv) the central Celtic Sea. These data also provided information on the ichthyofauna of the Jones Bank. Further site-specific data for bank and off-bank habitats were collected during dedicated surveys on the Jones Bank in 2008 using commercial trawlers and baited camera deployments. Twenty-three species were recorded on the top of the bank, where horse mackerel, haddock and boarfish were the most abundant species; 18 species were found along the slope of the bank (with blue whiting, poor cod, hake and horse mackerel predominant) and 18 species observed off the bank (where catches were dominated by blue whiting, poor cod and hake). The differences between camera and trawls were important with cameras only picking up 28% of the species seen in the trawls. However both camera and trawl results suggest that some species are very habitat specific, with species such as haddock only observed on the top of the bank, whilst Nephrops norvegicus was abundant on the flat areas off the bank but was infrequent on the top of the bank. These results suggest that future surveys of offshore sandbank habitats should stratify sampling more specifically to deal with smaller scale features that may play an important role in providing a greater range of habitats than just their relative size would suggest.

A biomonitoring plan for assessing potential radionuclide exposure using Amchitka Island in the Aleutian chain of Alaska as a case study.

PubMed

Burger, Joanna; Gochfeld, Michael; Kosson, D S; Powers, Charles W

2007-01-01

With the ending of the Cold War, the US and other nations were faced with a legacy of nuclear wastes. For some sites where hazardous nuclear wastes will remain in place, methods must be developed to protect human health and the environment. Biomonitoring is one method of assessing the status and trends of potential radionuclide exposure from nuclear waste sites, and of providing the public with early warning of any potential harmful exposure. Amchitka Island (51 degrees N lat, 179 degrees E long) was the site of three underground nuclear tests from 1965 to 1971. Following a substantive study of radionuclide levels in biota from the marine environment around Amchitka and a reference site, we developed a suite of bioindicators (with suggested isotopes) that can serve as a model for other sites contaminated with radionuclides. Although the species selection was site-specific, the methods can provide a framework for other sites. We selected bioindicators using five criteria: (1) occurrence at all three test shots (and reference site), (2) receptor groups (subsistence foods, commercial species, and food chain nodes), (3) species groups (plants, invertebrates, fish, and birds), (4) trophic levels, and (5) an accumulator of one or several radionuclides. Our major objective was to identify bioindicators that could serve for both human health and the ecosystem, and were abundant enough to collect adjacent to the three test sites and at the reference site. Site-specific information on both biota availability and isotope levels was essential in the final selection of bioindicators. Actinides bioaccumulated in algae and invertebrates, while radiocesium accumulated in higher trophic level birds and fish. Thus, unlike biomonitoring schemes developed for heavy metals or other contaminants, top-level predators are not sufficient to evaluate potential radionuclide exposure at Amchitka. The process described in this paper resulted in the selection of Fucus, Alaria fistulosa, blue mussel (Mytilus trossulus), dolly varden (Salvelinus malma), black rockfish (Sebastes melanops), Pacific cod (Gadus macrocephalus), Pacific halibut (Hippoglossus stenolepis), and glaucous-winged gull (Larus glaucescens) as bioindicators. This combination of species included mainly subsistence foods, commercial fish, and nodes on different food chains.

Verification of responses of Japanese medaka (Oryzias latipes) to anti-androgens, vinclozolin and flutamide, in short-term assays.

PubMed

Nakamura, Ataru; Takanobu, Hitomi; Tamura, Ikumi; Yamamuro, Masumi; Iguchi, Taisen; Tatarazako, Norihisa

2014-05-01

Various testing methods for the detection of the endocrine disruptive activities of chemicals have been developed in freshwater fish species. However, a few relatively easier specific methods for detecting anti-androgenic activities are available for fish. The aim of this study was to verify the papillary process in Japanese medaka (Oryzias latipes) as an indicator of the anti-androgenic activity of chemicals. Japanese medaka were exposed to two types of anti-androgenic compounds, vinclozolin and flutamide, using two short-term assays; one was conformed to the existing short-term reproduction assay using adult fish (adult test) and the other was a test based on the same methods but using juvenile fish at the beginning of exposure (juvenile test). Significant decreases in male papillary processes were observed in the juvenile test treated with the highest concentration of both antiandrogens (640 µg l(-1) vinclozolin and 1000 µg l(-1) flutamide); however, no significant effects were observed in the adult test. Consequently, our results indicate that papillary processes in Japanese medaka can be used as the end-point for screening the anti-androgenic activity of chemicals using juvenile fish for a specific period based on the existing short-term reproduction assay. Copyright © 2013 John Wiley & Sons, Ltd.

FishTraits: a database of ecological and life-history traits of freshwater fishes of the United States

USGS Publications Warehouse

Angermeier, Paul L.; Frimpong, Emmanuel A.

2011-01-01

The need for integrated and widely accessible sources of species traits data to facilitate studies of ecology, conservation, and management has motivated development of traits databases for various taxa. In spite of the increasing number of traits-based analyses of freshwater fishes in the United States, no consolidated database of traits of this group exists publicly, and much useful information on these species is documented only in obscure sources. The largely inaccessible and unconsolidated traits information makes large-scale analysis involving many fishes and/or traits particularly challenging. We have compiled a database of > 100 traits for 809 (731 native and 78 nonnative) fish species found in freshwaters of the conterminous United States, including 37 native families and 145 native genera. The database, named Fish Traits, contains information on four major categories of traits: (1) trophic ecology; (2) body size, reproductive ecology, and life history; (3) habitat preferences; and (4) salinity and temperature tolerances. Information on geographic distribution and conservation status was also compiled. The database enhances many opportunities for conducting research on fish species traits and constitutes the first step toward establishing a central repository for a continually expanding set of traits of North American fishes.

Blood flukes Cardicola parvus and C. laruei (Trematoda: Aporocotylidae): life cycles and cryptic infection in spotted seatrout, Cynoscion nebulosus (Teleost: Sciaenidae).

PubMed

Siegel, Sasha V; Rivero, Andrea V; Oberstaller, Jenna; Colon, Beatrice L; de Buron, Isaure; Kyle, Dennis E

2018-04-01

Aporocotylidae comprises a diverse family of fish blood flukes, with adults found in blood or body cavity of marine, brackish, or freshwater fish. Aporocotylids are unique among the Digenea with many developing in polychaetes. The life cycle has been elucidated for only a few species that develop in polychaetes from marine/brackish environments and none for western Atlantic aporocotylids. The basis for this study was observations of blood fluke larvae in annelids from South Carolina, USA in 1982 prior to possible usage of molecular tools to specifically identify parasite larvae. Recent description of aporocotylid species and genotyping tools prompted revisiting original collection sites to examine polychaetes and fish as potential hosts. Polycirrid Enoplobranchus sanguineus and terebellids Amphitrite ornata, and Terebella lapidaria revealed infections with aporocotylid larvae. Adult blood flukes were also collected from fish commonly encountered in the same habitat: spotted seatrout (Cynoscion nebulosus), red drum (Sciaenops ocellatus), black drum (Pogonias cromis), and Atlantic croaker (Micropogonias undulatus). Sporocysts containing cercariae were found in individuals of each annelid species. Adult Cardicola parvus were found in spotted seatrout and Atlantic croaker, C. laruei in spotted seatrout, C. currani in red drum, and C. palmeri in black drum. Genotype analysis of ITS-2 and lsrDNA of all forms confirmed conspecific infections by C. parvus in E. sanguineus and A. ornata and C. laruei in T. lapidaria. This is the first description of complete life cycles of aporocotylids in the Western Atlantic and first evidence of cryptic infections of Cy. nebulosus with C. parvus. Copyright © 2017 Elsevier B.V. All rights reserved.

Fish communities associated with cold-water corals vary with depth and substratum type

NASA Astrophysics Data System (ADS)

Milligan, Rosanna J.; Spence, Gemma; Roberts, J. Murray; Bailey, David M.

2016-08-01

Understanding the processes that drive the distribution patterns of organisms and the scales over which these processes operate are vital when considering the effective management of species with high commercial or conservation value. In the deep sea, the importance of scleractinian cold-water corals (CWCs) to fish has been the focus of several studies but their role remains unclear. We propose this may be due to the confounding effects of multiple drivers operating over multiple spatial scales. The aims of this study were to investigate the role of CWCs in shaping fish community structure and individual species-habitat associations across four spatial scales in the NE Atlantic ranging from "regions" (separated by >500 km) to "substratum types" (contiguous). Demersal fish and substratum types were quantified from three regions: Logachev Mounds, Rockall Bank and Hebrides Terrace Seamount (HTS). PERMANOVA analyses showed significant differences in community composition between all regions which were most likely caused by differences in depths. Within regions, significant variation in community composition was recorded at scales of c. 20-3500 m. CWCs supported significantly different fish communities to non-CWC substrata at Rockall Bank, Logachev and the HTS. Single-species analyses using generalised linear mixed models showed that Sebastes sp. was strongly associated with CWCs at Rockall Bank and that Neocyttus helgae was more likely to occur in CWCs at the HTS. Depth had a significant effect on several other fish species. The results of this study suggest that the importance of CWCs to fish is species-specific and depends on the broader spatial context in which the substratum is found. The precautionary approach would be to assume that CWCs are important for associated fish, but must acknowledge that CWCs in different depths will not provide redundancy or replication within spatially-managed conservation networks.

Why are there so few freshwater fish species in most estuaries?

PubMed

Whitfield, A K

2015-04-01

The freshwater fish assemblage in most estuaries is not as species rich as the marine assemblage in the same systems. Coupled with this differential richness is an apparent inability by most freshwater fish species to penetrate estuarine zones that are mesohaline (salinity: 5·0-17·9), polyhaline (salinity: 18·0-29·9) or euhaline (salinity: 30·0-39·9). The reason why mesohaline waters are avoided by most freshwater fishes is difficult to explain from a physiological perspective as many of these species would be isosmotic within this salinity range. Perhaps, a key to the poor penetration of estuarine waters by freshwater taxa is an inability to develop chloride cells in gill filament epithelia, as well as a lack of other osmoregulatory adaptations present in euryhaline fishes. Only a few freshwater fish species, especially some of those belonging to the family Cichlidae, have become fully euryhaline and have successfully occupied a wide range of estuaries, sometimes even dominating in hyperhaline systems (salinity 40+). Indeed, this review found that there are few fish species that can be termed holohaline (i.e. capable of occupying waters with a salinity range of 0-100+) and, of these taxa, there is a disproportionally high number of freshwater species (e.g. Cyprinodon variegatus, Oreochromis mossambicus and Sarotherodon melanotheron). Factors such as increased competition for food and higher predation rates by piscivorous fishes and birds may also play an important role in the low species richness and abundance of freshwater taxa in estuaries. Added to this is the relatively low species richness of freshwater fishes in river catchments when compared with the normally higher diversity of marine fish species for potential estuarine colonization from the adjacent coastal waters. The almost complete absence of freshwater fish larvae from the estuarine ichthyoplankton further reinforces the poor representation of this guild within these systems. An explanation as to why more freshwater fish species have not become euryhaline and occupied a wide range of estuaries similar to their marine counterparts is probably due to a combination of the above described factors, with physiological restrictions pertaining to limited salinity tolerances probably playing the most important role. © 2015 The Fisheries Society of the British Isles.

GENETIC DIVERSITY OF STREAM FISH IN THE MID-ATLANTIC INTEGRATED ASSESSMENT AREA

EPA Science Inventory

In this report, we describe the results of research to assess the genetics of three stream fish species in the Mid-Atlantic region. This research had three specific goals. First, we sought to examine the utility of genetic analysis for purposes of taxonomic identification. Bioa...

Quantitative estimate of commercial fish enhancement by seagrass habitat in southern Australia

NASA Astrophysics Data System (ADS)

Blandon, Abigayil; zu Ermgassen, Philine S. E.

2014-03-01

Seagrass provides many ecosystem services that are of considerable value to humans, including the provision of nursery habitat for commercial fish stock. Yet few studies have sought to quantify these benefits. As seagrass habitat continues to suffer a high rate of loss globally and with the growing emphasis on compensatory restoration, valuation of the ecosystem services associated with seagrass habitat is increasingly important. We undertook a meta-analysis of juvenile fish abundance at seagrass and control sites to derive a quantitative estimate of the enhancement of juvenile fish by seagrass habitats in southern Australia. Thirteen fish of commercial importance were identified as being recruitment enhanced in seagrass habitat, twelve of which were associated with sufficient life history data to allow for estimation of total biomass enhancement. We applied von Bertalanffy growth models and species-specific mortality rates to the determined values of juvenile enhancement to estimate the contribution of seagrass to commercial fish biomass. The identified species were enhanced in seagrass by 0.98 kg m-2 y-1, equivalent to ˜$A230,000 ha-1 y-1. These values represent the stock enhancement where all fish species are present, as opposed to realized catches. Having accounted for the time lag between fish recruiting to a seagrass site and entering the fishery and for a 3% annual discount rate, we find that seagrass restoration efforts costing $A10,000 ha-1 have a potential payback time of less than five years, and that restoration costing $A629,000 ha-1 can be justified on the basis of enhanced commercial fish recruitment where these twelve fish species are present.

Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms

PubMed Central

2011-01-01

Background The purpose of this study was to design and evaluate fluorescent in situ hybridization (FISH) probes for the single-cell detection and enumeration of lactic acid bacteria, in particular organisms belonging to the major phylogenetic groups and species of oral lactobacilli and to Abiotrophia/Granulicatella. Results As lactobacilli are known for notorious resistance to probe penetration, probe-specific assay protocols were experimentally developed to provide maximum cell wall permeability, probe accessibility, hybridization stringency, and fluorescence intensity. The new assays were then applied in a pilot study to three biofilm samples harvested from variably demineralized bovine enamel discs that had been carried in situ for 10 days by different volunteers. Best probe penetration and fluorescent labeling of reference strains were obtained after combined lysozyme and achromopeptidase treatment followed by exposure to lipase. Hybridization stringency had to be established strictly for each probe. Thereafter all probes showed the expected specificity with reference strains and labeled the anticipated morphotypes in dental plaques. Applied to in situ grown biofilms the set of probes detected only Lactobacillus fermentum and bacteria of the Lactobacillus casei group. The most cariogenic biofilm contained two orders of magnitude higher L. fermentum cell numbers than the other biofilms. Abiotrophia/Granulicatella and streptococci from the mitis group were found in all samples at high levels, whereas Streptococcus mutans was detected in only one sample in very low numbers. Conclusions Application of these new group- and species-specific FISH probes to oral biofilm-forming lactic acid bacteria will allow a clearer understanding of the supragingival biome, its spatial architecture and of structure-function relationships implicated during plaque homeostasis and caries development. The probes should prove of value far beyond the field of oral microbiology, as many of them detect non-oral species and phylogenetic groups of importance in a variety of medical conditions and the food industry. PMID:21247450

Assessing the feasibility of native fish reintroductions: a framework and example applied to bull trout in the Clackamas River, Oregon

USGS Publications Warehouse

Dunham, Jason B.; Gallo, Kirsten

2008-01-01

In a species conservation context, translocations can be an important tool, but they frequently fail to successfully establish new populations. We consider the case of reintroductions for bull trout (Salvelinus confluentus), a federally-listed threatened species with a widespread but declining distribution in western North America. Our specific objectives in this work were to: 1) develop a general framework for assessing the feasibility of reintroduction for bull trout, 2) provide a detailed example of implementing this framework to assess the feasibility of reintroducing bull trout in the Clackamas River, Oregon, and 3) discuss the implications of this effort in the more general context of fish reintroductions as a conservation tool. Review of several case histories and our assessment of the Clackamas River suggest that an attempt to reintroduce bull trout could be successful, assuming adequate resources are committed to the subsequent stages of implementation, monitoring, and evaluation.

A demonstration of the instream flow incremental methodology, Shenandoah River

USGS Publications Warehouse

Zappia, Humbert; Hayes, Donald C.

1998-01-01

Current and projected demands on the water resources of the Shenandoah River have increased concerns for the potential effect of these demands on the natural integrity of the Shenandoah River system. The Instream Flow Incremental Method (IFIM) process attempts to integrate concepts of water-supply planning, analytical hydraulic engineering models, and empirically derived habitat versus flow functions to address water-use and instream-flow issues and questions concerning life-stage specific effects on selected species and the general well being of aquatic biological populations.The demonstration project also sets the stage for the identification and compilation of the major instream-flow issues in the Shenandoah River Basin, development of the required multidisciplinary technical team to conduct more detailed studies, and development of basin specific habitat and flow requirements for fish species, species assemblages, and various water uses in the Shenandoah River Basin. This report presents the results of an IFIM demonstration project, conducted on the main stem Shenandoah River in Virginia, during 1996 and 1997, using the Physical Habitat Simulation System (PHABSIM) model.Output from PHABSIM is used to address the general flow requirements for water supply and recreation and habitat for selected life stages of several fish species. The model output is only a small part of the information necessary for effective decision making and management of river resources. The information by itself is usually insufficient for formulation of recommendations regarding instream-flow requirements. Additional information, for example, can be obtained by analysis of habitat time-series data, habitat duration data, and habitat bottlenecks. Alternative-flow analysis and habitat-duration curves are presented.

Co-adaptation of Electric Organ Discharges and Chirps in South American Ghost Knifefishes (Apteronotidae)

PubMed Central

Petzold, Jacquelyn M.; Marsat, Gary; Smith, G. Troy

2016-01-01

Animal communication signals that simultaneously share the same sensory channel are likely to coevolve to maximize the transmission of each signal component. Weakly electric fish continuously produce a weakly electric field that functions in communication. Fish modulate the electric organ discharge (EOD) on short timescales to produce context-specific signals called chirps. EODs and chirps are simultaneously detected by electroreceptors and processed in the electrosensory system. We analyzed these signals, first to explore whether EOD waveform is encoded in the signal received by electroreceptors and then to examine how EODs and chirps interact to influence conspicuousness. Our findings show that gross discrimination of sinusoidal from complex EOD waveforms is feasible for all species, but fine discrimination of waveform may be possible only for species with waveforms of intermediate complexity. The degree of chirp frequency modulation and chirp relative decay strongly influenced chirp conspicuousness, but other chirp parameters were less influential. The frequency difference between the interacting EODs also strongly impacted chirp conspicuousness. Finally, we developed a method for creating hybrid chirp/EOD combinations to independently analyze the impact of chirp species, EOD species, and EOD difference frequency on chirp conspicuousness. All three components and their interactions strongly influenced chirp conspicuousness, which suggests that evolutionary changes in parameters of either chirps or EODs are likely to influence chirp detection. Examining other environmental factors such as noise created by fish movement and species-typical patterns of sociality may enrich our understanding of how interacting EODs affect the detection and discrimination of chirps across species. PMID:27989653

Identifying sources of stress to native aquatic fauna using a watershed ecological risk assessment framework.

PubMed

Diamond, J M; Serveiss, V B

2001-12-15

The free-flowing Clinch and Powell River Basin, located in southwestern Virginia, United States, historically had one of the richest assemblages of native fish and freshwater mussels in the world. Nearly half of the species once residing here are now extinct, threatened, or endangered. The United States Environmental Protection Agency's framework for conducting an ecological risk assessment was used to structure a watershed-scale analysis of human land use, in-stream habitat quality, and their relationship to native fish and mussel populations in order to develop future management strategies and prioritize areas in need of enhanced protection. Our analyses indicate that agricultural and urban land uses as well as proximity to mining activities and transportation corridors are inversely related to fish index of biotic integrity (IBI) and mussel species diversity. Forward stepwise multiple regression analyses indicated that coal mining had the most impact on fish IBI followed by percent cropland and urban area in the riparian corridor (R2 = 0.55, p = 0.02); however, these analyses suggest that other site-specific factors are important. Habitat quality measures accounted for as much as approximately half of the variability in fish IBI values if the analysis was limited to sites within a relatively narrow elevation range. These results, in addition to other data collected in this watershed, suggest that nonhabitat-related stressors (e.g., accidental chemical spills) also have significant effects on biota in this basin. The number of co-occurring human land uses was inversely related to fish IBI (r = -0.49, p < 0.01). Sites with > or = 2 co-occurring land uses had >90% probability of having <2 mussel species present. Our findings predict that many mussel concentration sites are vulnerable to future extirpation. In addition, our results suggest that protection and enhancement of naturally vegetated riparian corridors, better controls of mine effluents and urban runoff, and increased safeguards against accidental chemical spills, as well as reintroduction or augmentation of threatened and endangered species, may help sustain native fish and mussel populations in this watershed.

Use of an autonomous sensor to evaluate the biological performance of the advanced turbine at Wanapum Dam

DOE PAGES

Deng, Zhiqun; Carlson, Thomas J.; Duncan, Joanne P.; ...

2010-10-13

Hydropower is the largest renewable energy resource in the United States and the world. However, hydropower dams have adverse ecological impacts because migrating fish may be injured or killed when they pass through hydroturbines. In the Columbia and Snake River basins, dam operators and engineers are required to make those hydroelectric facilities more fish-friendly through changes in hydroturbine design and operation after fish population declines and the subsequent listing of several species of Pacific salmon under the Endangered Species Act of 1973. Public Utility District No. 2 of Grant County, Washington, requested authorization from the Federal Energy Regulatory Commission tomore » replace the ten turbines at Wanapum Dam with advanced hydropower turbines designed to improve survival for fish passing through the turbines while improving operation efficiency and increasing power generation. As an additional measure to the primary metric of direct injury and mortality rates of juvenile Chinook salmon using balloon tag-recapture methodology, this study used an autonomous sensor device - the Sensor Fish - to provide insight into the specific hydraulic conditions and physical stresses experienced by the fish as well as the specific causes of fish biological response. We found that the new hydroturbine blade shape and the corresponding reduction of turbulence in the advanced hydropower turbine were effective in meeting the objectives of improving fish survival while enhancing operational efficiency of the dam. The frequency of severe events based on Sensor Fish pressure and acceleration measurements showed trends similar to those of fish survival determined by the balloon tag-recapture methodology. In addition, the new turbine provided a better pressure and rate of pressure change environment for fish passage. Altogether, the Sensor Fish data indicated that the advanced hydroturbine design improved passage of juvenile salmon at Wanapum Dam.« less

Predators shape distribution and promote diversification of morphological defenses in Leucorrhinia , Odonata

USGS Publications Warehouse

Petrin, Zlatko; Schilling, Emily Gaenzle; Loftin, Cyndy; Johansson, Frank

2010-01-01

Predators strongly influence species assemblages and shape morphological defenses of prey. Interestingly, adaptations that constitute effective defenses against one type of predator may render the prey susceptible to other types of predators. Hence, prey may evolve different strategies to escape predation, which may facilitate adaptive radiation of prey organisms. Larvae of different species in the dragonfly genus Leucorrhinia have various morphological defenses. We studied the distribution of these larvae in relation to the presence of predatory fish. In addition, we examined the variation in morphological defenses within species with respect to the occurrence of fish. We found that well-defended species, those with more and longer spines, were more closely associated with habitats inhabited by predatory fish and that species with weakly developed morphological defenses were more abundant in habitats without fish. The species predominantly connected to lakes with or without fish, respectively, were not restricted to a single clade in the phylogeny of the genus. Our data is suggestive of phenotypic plasticity in morphological defense in three of the studied species since these species showed longer spines in lakes with fish. We suggest that adaptive phenotypic plasticity may have broadened the range of habitats accessible to Leucorrhinia. It may have facilitated colonization of new habitats with different types of predators, and ultimately, speciation through adaptive radiation.

Colorimetric Method of Loop-Mediated Isothermal Amplification with the Pre-Addition of Calcein for Detecting Flavobacterium columnare and its Assessment in Tilapia Farms.

PubMed

Suebsing, Rungkarn; Kampeera, Jantana; Sirithammajak, Sarawut; Withyachumnarnkul, Boonsirm; Turner, Warren; Kiatpathomchai, Wansika

2015-03-01

Flavobacterium columnare, the causative agent of columnaris disease in fish, affects many economically important freshwater fish species. A colorimetric method of loop-mediated isothermal amplification with the pre-addition of calcein (LAMP-calcein) was developed and used to detect the presence of F. columnare in farmed tilapia (Nile Tilapia Oreochromis niloticus and red tilapia [Nile Tilapia × Mozambique Tilapia O. mossambicus]) and rearing water. The detection method, based on a change in color from orange to green, could be performed within 45 min at 63°C. The method was highly specific, as it had no cross-detections with 14 other bacterial species, including other fish pathogens and two Flavobacterium species. The method has a minimum detection limit of 2.2 × 10(2) F. columnare CFU; thus, it is about 10 times more sensitive than conventional PCR. With this method, F. columnare was detected in gonad, gill, and blood samples from apparently healthy tilapia broodstock as well as in samples of fertilized eggs, newly hatched fry, and rearing water. The bacteria isolated from the blood were further characterized biochemically and found to be phenotypically identical to F. columnare. The amplified products from the LAMP-calcein method had 97% homology with the DNA sequence of F. columnare.

[The main radionuclides and dose formation in fish of the Chernobyl NPP exclusion zone].

PubMed

Gudkov, D I; Kaglian, A E; Kireev, S I; Nazarov, A B; Klenus, V G

2008-01-01

The results of the researches of spices-specificity, accumulation dynamics and distribution of 90Sr, of 137Cs and of transuranic elements in fish of the Chernobyl NPP exclusion zone are analysed. The data of estimations of absorbed doze rate from incorporated radionuclides for pray fish and predatory species are given. For the fish from the lake of the left-bank floodplain of the Pripyat River the increase of 90Sr specific activity is registered which is presumably connected with the dynamics of the physical-chemical forms of the radionuclide in soils and their wash out in water bodies from the catchment basin. Now about 90% of internal dose rate of fish from closed aquatic ecosystems within the Chernobyl NPP exclusion zone is caused by 90Sr incorporation.

Proposing priorities of intervention for the recovery of native fish populations using hierarchical ranking of environmental and exotic species impact.

PubMed

Aschonitis, V G; Gavioli, A; Lanzoni, M; Fano, E A; Feld, C; Castaldelli, G

2018-03-15

The freshwater populations of native fish species (Ns) have reached critical levels in many parts of the world due to combined habitat deterioration by human interventions and exotic fish species (Es) invasions. These alarming conditions require combined and well-designed interventions for restoring environmental quality and restricting Es invasion. The aim of the study is to propose a method to design spatially explicit priorities of intervention for the recovery of Ns populations in highly impacted freshwater systems by exotic multi-species invasion and water quality (WQ) degradation. WQ and Es are used as Ns descriptors, which require intervention. The method uses gradient analysis (ordination method of Canonical Correspondence Analysis) for assessing the weights of Ns descriptors' effects, which are further used to develop weighted severity indices; the severity index of WQ (Swq) and Es invasion (Se), respectively. Swq and Se are further merged to one combined total severity index St. The proposed method provides a) a ranking of the sites, based on the values of S t , which denotes the priority for combined intervention in space and can be visualized in maps, b) a ranking of the most important Ns descriptors for each site to perform site-specific interventions, and c) Es rankings based on their potential threat on Ns for species-specific interventions. WQ, Es and Ns data from 208 sampling sites located in the Emilia-Romagna Region (Northern Italy) were used as a case study for the presentation of the proposed method. The application of the method showed that the north and northwestern lowland areas of Emilia-Romagna region presented the higher priority for intervention since the Ns of these areas are the most impacted from combined Es invasions and WQ degradation. Specific Es belonging to cyprinids, which are mostly responsible for the decline of aquatic vegetation and the increase of water turbidity, and a top Es predator (Wels catfish) were mostly present in these areas. Additionally, the most important WQ stressors of Ns were found to be COD, BOD and temperature that are all connected to oxygen depletion. The aforementioned conditions in the areas described by high priority for intervention can be used as a basis for the development of specific Ns conservation practices targeting the containment of the most harmful Es, the restoration of aquatic vegetation and the improvement of oxygen conditions. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Camera-Based Assessment Survey System (C-BASS): A towed camera platform for reef fish abundance surveys and benthic habitat characterization in the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Lembke, Chad; Grasty, Sarah; Silverman, Alex; Broadbent, Heather; Butcher, Steven; Murawski, Steven

2017-12-01

An ongoing challenge for fisheries management is to provide cost-effective and timely estimates of habitat stratified fish densities. Traditional approaches use modified commercial fishing gear (such as trawls and baited hooks) that have biases in species selectivity and may also be inappropriate for deployment in some habitat types. Underwater visual and optical approaches offer the promise of more precise and less biased assessments of relative fish abundance, as well as direct estimates of absolute fish abundance. A number of video-based approaches have been developed and the technology for data acquisition, calibration, and synthesis has been developing rapidly. Beginning in 2012, our group of engineers and researchers at the University of South Florida has been working towards the goal of completing large scale, video-based surveys in the eastern Gulf of Mexico. This paper discusses design considerations and development of a towed camera system for collection of video-based data on commercially and recreationally important reef fishes and benthic habitat on the West Florida Shelf. Factors considered during development included potential habitat types to be assessed, sea-floor bathymetry, vessel support requirements, personnel requirements, and cost-effectiveness of system components. This regional-specific effort has resulted in a towed platform called the Camera-Based Assessment Survey System, or C-BASS, which has proven capable of surveying tens of kilometers of video transects per day and has the ability to cost-effective population estimates of reef fishes and coincident benthic habitat classification.

Fish is Fish: the use of experimental model species to reveal causes of skeletal diversity in evolution and disease

PubMed Central

Harris, M. P.; Henke, K.; Hawkins, M. B.; Witten, P. E.

2014-01-01

Summary Fishes are wonderfully diverse. This variety is a result of the ability of ray-finned fishes to adapt to a wide range of environments, and has made them more specious than the rest of vertebrates combined. With such diversity it is easy to dismiss comparisons between distantly related fishes in efforts to understand the biology of a particular fish species. However, shared ancestry and the conservation of developmental mechanisms, morphological features and physiology provide the ability to use comparative analyses between different organisms to understand mechanisms of development and physiology. The use of species that are amenable to experimental investigation provides tools to approach questions that would not be feasible in other ‘non-model’ organisms. For example, the use of small teleost fishes such as zebrafish and medaka has been powerful for analysis of gene function and mechanisms of disease in humans, including skeletal diseases. However, use of these fish to aid in understanding variation and disease in other fishes has been largely unexplored. This is especially evident in aquaculture research. Here we highlight the utility of these small laboratory fishes to study genetic and developmental factors that underlie skeletal malformations that occur under farming conditions. We highlight several areas in which model species can serve as a resource for identifying the causes of variation in economically important fish species as well as to assess strategies to alleviate the expression of the variant phenotypes in farmed fish. We focus on genetic causes of skeletal deformities in the zebrafish and medaka that closely resemble phenotypes observed both in farmed as well as natural populations of fishes. PMID:25221374

Scaling mimesis: Morphometric and ecomorphological similarities in three sympatric plant-mimetic fish of the family Carangidae (Teleostei).

PubMed

Queiroz, Alexya Cunha de; Vallinoto, Marcelo; Sakai, Yoichi; Giarrizzo, Tommaso; Barros, Breno

2018-01-01

The mimetic juveniles of a number of carangid fish species resemble plant parts floating near the water surface, such as leaves, seeds and other plant debris. The present study is the first to verify the morphological similarities and ecomorphological relationships between three carangids (Oligoplites saurus, Oligoplites palometa and Trachinotus falcatus) and their associated plant models. Behavioral observations were conducted in the estuary of Curuçá River, in northeastern Pará (Brazil) between August 2015 and July 2016. Individual fishes and associated floating objects (models) were sampled for comparative analysis using both geometric and morphometric approaches. While the mimetic fish and their models retain their own distinct, intrinsic morphological features, a high degree of morphological similarity was found between each fish species and its model. The morphometric analyses revealed a general tendency of isometric development in all three fish species, probably related to their pelagic habitats, during all ontogenetic stages.

Extinction vulnerability of coral reef fishes.

PubMed

Graham, Nicholas A J; Chabanet, Pascale; Evans, Richard D; Jennings, Simon; Letourneur, Yves; Aaron Macneil, M; McClanahan, Tim R; Ohman, Marcus C; Polunin, Nicholas V C; Wilson, Shaun K

2011-04-01

With rapidly increasing rates of contemporary extinction, predicting extinction vulnerability and identifying how multiple stressors drive non-random species loss have become key challenges in ecology. These assessments are crucial for avoiding the loss of key functional groups that sustain ecosystem processes and services. We developed a novel predictive framework of species extinction vulnerability and applied it to coral reef fishes. Although relatively few coral reef fishes are at risk of global extinction from climate disturbances, a negative convex relationship between fish species locally vulnerable to climate change vs. fisheries exploitation indicates that the entire community is vulnerable on the many reefs where both stressors co-occur. Fishes involved in maintaining key ecosystem functions are more at risk from fishing than climate disturbances. This finding is encouraging as local and regional commitment to fisheries management action can maintain reef ecosystem functions pending progress towards the more complex global problem of stabilizing the climate. © 2011 Blackwell Publishing Ltd/CNRS.

Food web dynamics in a seasonally varying wetland

USGS Publications Warehouse

DeAngelis, D.L.; Trexler, J.C.; Donalson, D.D.

2008-01-01

A spatially explicit model is developed to simulate the small fish community and its underlying food web, in the freshwater marshes of the Everglades. The community is simplified to a few small fish species feeding on periphyton and invertebrates. Other compartments are detritus, crayfish, and a piscivorous fish species. This unit food web model is applied to each of the 10,000 spatial cells on a 100 x 100 pixel landscape. Seasonal variation in water level is assumed and rules are assigned for fish movement in response to rising and falling water levels, which can cause many spatial cells to alternate between flooded and dry conditions. It is shown that temporal variations of water level on a spatially heterogeneous landscape can maintain at least three competing fish species. In addition, these environmental factors can strongly affect the temporal variation of the food web caused by top-down control from the piscivorous fish.

Extinction vulnerability of coral reef fishes

PubMed Central

Graham, Nicholas A J; Chabanet, Pascale; Evans, Richard D; Jennings, Simon; Letourneur, Yves; Aaron MacNeil, M; McClanahan, Tim R; Öhman, Marcus C; Polunin, Nicholas V C; Wilson, Shaun K

2011-01-01

With rapidly increasing rates of contemporary extinction, predicting extinction vulnerability and identifying how multiple stressors drive non-random species loss have become key challenges in ecology. These assessments are crucial for avoiding the loss of key functional groups that sustain ecosystem processes and services. We developed a novel predictive framework of species extinction vulnerability and applied it to coral reef fishes. Although relatively few coral reef fishes are at risk of global extinction from climate disturbances, a negative convex relationship between fish species locally vulnerable to climate change vs. fisheries exploitation indicates that the entire community is vulnerable on the many reefs where both stressors co-occur. Fishes involved in maintaining key ecosystem functions are more at risk from fishing than climate disturbances. This finding is encouraging as local and regional commitment to fisheries management action can maintain reef ecosystem functions pending progress towards the more complex global problem of stabilizing the climate. PMID:21320260

Pressure-specific and multiple pressure response of fish assemblages in European running waters☆

PubMed Central

Schinegger, Rafaela; Trautwein, Clemens; Schmutz, Stefan

2013-01-01

We classified homogenous river types across Europe and searched for fish metrics qualified to show responses to specific pressures (hydromorphological pressures or water quality pressures) vs. multiple pressures in these river types. We analysed fish taxa lists from 3105 sites in 16 ecoregions and 14 countries. Sites were pre-classified for 15 selected pressures to separate unimpacted from impacted sites. Hierarchical cluster analysis was used to split unimpacted sites into four homogenous river types based on species composition and geographical location. Classification trees were employed to predict associated river types for impacted sites with four environmental variables. We defined a set of 129 candidate fish metrics to select the best reacting metrics for each river type. The candidate metrics represented tolerances/intolerances of species associated with six metric types: habitat, migration, water quality sensitivity, reproduction, trophic level and biodiversity. The results showed that 17 uncorrelated metrics reacted to pressures in the four river types. Metrics responded specifically to water quality pressures and hydromorphological pressures in three river types and to multiple pressures in all river types. Four metrics associated with water quality sensitivity showed a significant reaction in up to three river types, whereas 13 metrics were specific to individual river types. Our results contribute to the better understanding of fish assemblage response to human pressures at a pan-European scale. The results are especially important for European river management and restoration, as it is necessary to uncover underlying processes and effects of human pressures on aquatic communities. PMID:24003262

Beyond Biodiversity: Fish Metagenomes

PubMed Central

Ardura, Alba; Planes, Serge; Garcia-Vazquez, Eva

2011-01-01

Biodiversity and intra-specific genetic diversity are interrelated and determine the potential of a community to survive and evolve. Both are considered together in Prokaryote communities treated as metagenomes or ensembles of functional variants beyond species limits. Many factors alter biodiversity in higher Eukaryote communities, and human exploitation can be one of the most important for some groups of plants and animals. For example, fisheries can modify both biodiversity and genetic diversity (intra specific). Intra-specific diversity can be drastically altered by overfishing. Intense fishing pressure on one stock may imply extinction of some genetic variants and subsequent loss of intra-specific diversity. The objective of this study was to apply a metagenome approach to fish communities and explore its value for rapid evaluation of biodiversity and genetic diversity at community level. Here we have applied the metagenome approach employing the Barcoding target gene COI as a model sequence in catch from four very different fish assemblages exploited by fisheries: freshwater communities from the Amazon River and northern Spanish rivers, and marine communities from the Cantabric and Mediterranean seas. Treating all sequences obtained from each regional catch as a biological unit (exploited community) we found that metagenomic diversity indices of the Amazonian catch sample here examined were lower than expected. Reduced diversity could be explained, at least partially, by overexploitation of the fish community that had been independently estimated by other methods. We propose using a metagenome approach for estimating diversity in Eukaryote communities and early evaluating genetic variation losses at multi-species level. PMID:21829636

Beyond biodiversity: fish metagenomes.

PubMed

Ardura, Alba; Planes, Serge; Garcia-Vazquez, Eva

2011-01-01

Biodiversity and intra-specific genetic diversity are interrelated and determine the potential of a community to survive and evolve. Both are considered together in Prokaryote communities treated as metagenomes or ensembles of functional variants beyond species limits.Many factors alter biodiversity in higher Eukaryote communities, and human exploitation can be one of the most important for some groups of plants and animals. For example, fisheries can modify both biodiversity and genetic diversity (intra specific). Intra-specific diversity can be drastically altered by overfishing. Intense fishing pressure on one stock may imply extinction of some genetic variants and subsequent loss of intra-specific diversity. The objective of this study was to apply a metagenome approach to fish communities and explore its value for rapid evaluation of biodiversity and genetic diversity at community level. Here we have applied the metagenome approach employing the barcoding target gene coi as a model sequence in catch from four very different fish assemblages exploited by fisheries: freshwater communities from the Amazon River and northern Spanish rivers, and marine communities from the Cantabric and Mediterranean seas.Treating all sequences obtained from each regional catch as a biological unit (exploited community) we found that metagenomic diversity indices of the Amazonian catch sample here examined were lower than expected. Reduced diversity could be explained, at least partially, by overexploitation of the fish community that had been independently estimated by other methods.We propose using a metagenome approach for estimating diversity in Eukaryote communities and early evaluating genetic variation losses at multi-species level.

Compensatory mechanisms in fish populations: Literature reviews: Volume 2, Compensation in fish populations subject to catastrophic impact: Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jude, D.J.; Mansfield, P.J.; Schneeberger, P.J.

1987-05-01

This study comprises an extensive literature review, critical evaluations of case histories, and considered recommendations for future research on the mechanisms and extent of compensation by various fish species subject to catastrophic impacts. ''Catastrophic impact'' was defined as an event which removes some limitation (such as food or space) on a fish population. Those events studied included new species introduction, toxic spills, exploitation of specific fish populations, and drawdown. The fish studied each had more than one compensatory mechanism available, and thus were able to respond to a catastrophic event even if an option was removed. Predation, overfishing, competition, disease,more » and parasitism are all potential catastrophies, but were found not to cause a catastrophic impact (except in special cases). In general, compensatory responses were determined to vary widely, even for species which perform fairly similar functions in an ecosystem. The extensive nature of this study, however, pointed up the many data gaps in the existing literature; recommendations are therefore made for followup research and expansion of ongoing monitoring programs, based on an evaluation of their relative importance.« less

Case Study: Sensitivity Analysis of the Barataria Basin Barrier Shoreline Wetland Value Assessment Model

DTIC Science & Technology

2014-07-01

wetlands in providing resting, foraging , breeding, and nursery habitat to a diverse assemblage of fish and wildlife species in coastal Louisiana (EWG...services, including fish and wildlife production, storm damage reduction, and recreation. Federal, state, and local partners have jointly pursued large...habitat units” (HU) provided by a given alternative. Whereas traditional HEP models focused on specific taxa, WVA assesses the fish and wildlife community

Effects of body mass and water temperature on routine metabolism of American paddlefish Polyodon spathula.

PubMed

Patterson, J T; Mims, S D; Wright, R A

2013-04-01

This study quantified the effects of temperature and fish mass on routine metabolism of the American paddlefish Polyodon spathula. Thermal sensitivity, as measured by Q(10) value, was low in P. spathula. Mean Q(10) was 1·78 while poikilotherms are generally expected to have Q(10) values in the 2·00-2·50 range. Mass-specific metabolism did not decrease with increased fish size to the extent that this phenomenon is observed in teleosts, as evidenced by a mass exponent (β) value of 0·92 for P. spathula compared with 0·79 in a review of teleost species. Other Acipenseriformes have exhibited relatively high β values for mass-specific respiration. Overall P. spathula metabolism appears to be more dependent on body mass and less dependent on temperature than for many other fishes. An equation utilizing temperature and fish mass to estimate gross respiration for P. spathula was derived and this equation was applied to respiratory data from other Acipenseriformes to assess inter-species variation. Polyodon spathula respiration rates across water temperature and fish mass appear most similar to those of Atlantic sturgeon Acipenser naccarii and white sturgeon Acipenser transmontanus. © 2013 The Authors. Journal of Fish Biology © 2013 The Fisheries Society of the British Isles.

Review of fish diversity in the Lake Huron basin

USGS Publications Warehouse

Roseman, E.F.; Schaeffer, J.S.; Steen, P.J.

2009-01-01

Lake Huron has a rich aquatic habitat diversity that includes shallow embayments, numerous tributaries, shallow mid-lake reef complexes, archipelagos, and profundal regions. These habitats provide support for warm, cool, and cold water fish communities. Diversity of fishes in Lake Huron reflects post-glaciation colonization events, current climate conditions, accidental and intentional introductions of non-indigenous species, and extinctions. Most extinction events have been largely associated with habitat alterations, exploitation of fisheries, and interactions with non-indigenous species. The most recent historical survey of extirpated and imperiled species conducted in the late 1970s identified 79 fish species in Lake Huron proper and about 50 additional species in tributaries. Of those 129 species, 20 are now considered extirpated or imperiled. Extirpated species include Arctic grayling, paddlefish, weed shiner, deepwater cisco, blackfin cisco, shortnose cisco, and kiyi. Six species have declined appreciably due to loss of clear-water stream habitat: the river redhorse, river darter, black redhorse, pugnose shiner, lake chubsucker, redside dace, eastern sand darter, and channel darter. While numerous agencies, universities, and other organizations routinely monitor nearshore and offshore fish distribution and abundance, there is a need for more rigorous examination of the distribution and abundance of less-common species to better understand their ecology. This information is critical to the development of management plans aimed at ecosystem remediation and restoration.

Prey fish returned to Forster's tern colonies suggest spatial and temporal differences in fish composition and availability.

PubMed

Peterson, Sarah H; Ackerman, Joshua T; Eagles-Smith, Collin A; Herzog, Mark P; Hartman, C Alex

2018-01-01

Predators sample the available prey community when foraging; thus, changes in the environment may be reflected by changes in predator diet and foraging preferences. We examined Forster's tern (Sterna forsteri) prey species over an 11-year period by sampling approximately 10,000 prey fish returned to 17 breeding colonies in south San Francisco Bay, California. We compared the species composition among repeatedly-sampled colonies (≥ 4 years), using both relative species abundance and the composition of total dry mass by species. Overall, the relative abundances of prey species at seven repeatedly-sampled tern colonies were more different than would be expected by chance, with the most notable differences in relative abundance observed between geographically distant colonies. In general, Mississippi silverside (Menidia audens) and topsmelt silverside (Atherinops affinis) comprised 42% of individuals and 40% of dry fish mass over the study period. Three-spined stickleback (Gasterosteus aculeatus) comprised the next largest proportion of prey species by individuals (19%) but not by dry mass (6%). Five additional species each contributed ≥ 4% of total individuals collected over the study period: yellowfin goby (Acanthogobius flavimanus; 10%), longjaw mudsucker (Gillichthys mirabilis; 8%), Pacific herring (Clupea pallasii; 6%), northern anchovy (Engraulis mordax; 4%), and staghorn sculpin (Leptocottus armatus; 4%). At some colonies, the relative abundance and biomass of specific prey species changed over time. In general, the abundance and dry mass of silversides increased, whereas the abundance and dry mass of three-spined stickleback and longjaw mudsucker decreased. As central place foragers, Forster's terns are limited in the distance they forage; thus, changes in the prey species returned to Forster's tern colonies suggest that the relative availability of some fish species in the environment has changed, possibly in response to alteration of the available habitat.

Prey fish returned to Forster’s tern colonies suggest spatial and temporal differences in fish composition and availability

USGS Publications Warehouse

Peterson, Sarah; Ackerman, Joshua T.; Eagles-Smith, Collin A.; Herzog, Mark; Hartman, C. Alex

2018-01-01

Predators sample the available prey community when foraging; thus, changes in the environment may be reflected by changes in predator diet and foraging preferences. We examined Forster’s tern (Sterna forsteri) prey species over an 11-year period by sampling approximately 10,000 prey fish returned to 17 breeding colonies in south San Francisco Bay, California. We compared the species composition among repeatedly-sampled colonies (≥ 4 years), using both relative species abundance and the composition of total dry mass by species. Overall, the relative abundances of prey species at seven repeatedly-sampled tern colonies were more different than would be expected by chance, with the most notable differences in relative abundance observed between geographically distant colonies. In general, Mississippi silverside (Menidia audens) and topsmelt silverside (Atherinops affinis) comprised 42% of individuals and 40% of dry fish mass over the study period. Three-spined stickleback (Gasterosteus aculeatus) comprised the next largest proportion of prey species by individuals (19%) but not by dry mass (6%). Five additional species each contributed ≥ 4% of total individuals collected over the study period: yellowfin goby (Acanthogobius flavimanus; 10%), longjaw mudsucker (Gillichthys mirabilis; 8%), Pacific herring (Clupea pallasii; 6%), northern anchovy (Engraulis mordax; 4%), and staghorn sculpin (Leptocottus armatus; 4%). At some colonies, the relative abundance and biomass of specific prey species changed over time. In general, the abundance and dry mass of silversides increased, whereas the abundance and dry mass of three-spined stickleback and longjaw mudsucker decreased. As central place foragers, Forster’s terns are limited in the distance they forage; thus, changes in the prey species returned to Forster’s tern colonies suggest that the relative availability of some fish species in the environment has changed, possibly in response to alteration of the available habitat.

So Long and Thanks for All the Fish: Overexploitation of the Regionally Endemic Galapagos Grouper Mycteroperca olfax (Jenyns, 1840).

PubMed

Usseglio, Paolo; Friedlander, Alan M; Koike, Haruko; Zimmerhackel, Johanna; Schuhbauer, Anna; Eddy, Tyler; Salinas-de-León, Pelayo

2016-01-01

The regionally endemic Galapagos Grouper, locally known as bacalao, is one of the most highly prized finfish species within the Galapagos Marine Reserve (GMR). Concerns of overfishing, coupled with a lack of fishing regulations aimed at this species raises concerns about the current population health. We assessed changes in population health over a 30-year period using three simple indicators: (1) percentage of fish below reproductive size (Lm); (2) percentage of fish within the optimum length interval (Lopt); and (3) percentage of mega-spawners in the catch. Over the assessed period, none of the indicators reached values associated with healthy populations, with all indicators declining over time. Furthermore, the most recent landings data show that the vast majority of the bacalao caught (95.7%,) were below Lm, the number of fish within the Lopt interval was extremely low (4.7%), and there were virtually no mega-spawners (0.2%). Bacalao fully recruit to the fishery 15 cm below the size at which 50% of the population matures. The Spawning Potential Ratio is currently 5% of potential unfished fecundity, strongly suggesting severe overfishing. Our results suggest the need for bacalao-specific management regulations that should include minimum (65 cm TL) and maximum (78 cm TL) landing sizes, slot limits (64-78 cm TL), as well as a closed season during spawning from October to January. It is recognized that these regulations are harsh and will certainly have negative impacts on the livelihoods of fishers in the short term, however, continued inaction will likely result in a collapse of this economically and culturally valuable species. Alternative sources of income should be developed in parallel with the establishment of fishing regulations to limit the socio-economic disruption to the fishing community during the transition to a more sustainable management regime.

So Long and Thanks for All the Fish: Overexploitation of the Regionally Endemic Galapagos Grouper Mycteroperca olfax (Jenyns, 1840)

PubMed Central

Friedlander, Alan M.; Koike, Haruko; Zimmerhackel, Johanna; Schuhbauer, Anna; Eddy, Tyler; Salinas-de-León, Pelayo

2016-01-01

The regionally endemic Galapagos Grouper, locally known as bacalao, is one of the most highly prized finfish species within the Galapagos Marine Reserve (GMR). Concerns of overfishing, coupled with a lack of fishing regulations aimed at this species raises concerns about the current population health. We assessed changes in population health over a 30-year period using three simple indicators: (1) percentage of fish below reproductive size (Lm); (2) percentage of fish within the optimum length interval (Lopt); and (3) percentage of mega-spawners in the catch. Over the assessed period, none of the indicators reached values associated with healthy populations, with all indicators declining over time. Furthermore, the most recent landings data show that the vast majority of the bacalao caught (95.7%,) were below Lm, the number of fish within the Lopt interval was extremely low (4.7%), and there were virtually no mega-spawners (0.2%). Bacalao fully recruit to the fishery 15 cm below the size at which 50% of the population matures. The Spawning Potential Ratio is currently 5% of potential unfished fecundity, strongly suggesting severe overfishing. Our results suggest the need for bacalao-specific management regulations that should include minimum (65 cm TL) and maximum (78 cm TL) landing sizes, slot limits (64–78 cm TL), as well as a closed season during spawning from October to January. It is recognized that these regulations are harsh and will certainly have negative impacts on the livelihoods of fishers in the short term, however, continued inaction will likely result in a collapse of this economically and culturally valuable species. Alternative sources of income should be developed in parallel with the establishment of fishing regulations to limit the socio-economic disruption to the fishing community during the transition to a more sustainable management regime. PMID:27780213

Proximate composition, energetic value, and relative abundance of prey fish from the inshore eastern Bering Sea: Implications for piscivorous predators

USGS Publications Warehouse

Ball, J.R.; Esler, Daniel N.; Schmutz, J.A.

2007-01-01

Changing ocean conditions and subsequent shifts in forage fish communities have been linked to numerical declines of some piscivorous marine birds and mammals in the North Pacific. However, limited information about fish communities is available for some regions, including nearshore waters of the eastern Bering Sea, where many piscivores reside. We determined proximate composition and energetic value of a suite of potential forage fish collected from an estuary on the Yukon-Kuskokwim Delta, Alaska, during 2002 and 2003. Across species, energy density ranged from 14.5 to 20.7 kJ g−1 dry mass and varied primarily as a function of lipid content. Total energy content was strongly influenced by body length and we provide species-specific predictive models of total energy based on this relationship; some models may be improved further by incorporating year and date effects. Based on observed energetic differences, we conclude that variation in fish size, quantity, and species composition of the prey community could have important consequences for piscivorous predators.

Development of a multimetric index for assessing the biological condition of the Ohio River

USGS Publications Warehouse

Emery, E.B.; Simon, T.P.; McCormick, F.H.; Angermeier, P.L.; Deshon, J.E.; Yoder, C.O.; Sanders, R.E.; Pearson, W.D.; Hickman, G.D.; Reash, R.J.; Thomas, J.A.

2003-01-01

The use of fish communities to assess environmental quality is common for streams, but a standard methodology for large rivers is as yet largely undeveloped. We developed an index to assess the condition of fish assemblages along 1,580 km of the Ohio River. Representative samples of fish assemblages were collected from 709 Ohio River reaches, including 318 "least-impacted" sites, from 1991 to 2001 by means of standardized nighttime boat-electrofishing techniques. We evaluated 55 candidate metrics based on attributes of fish assemblage structure and function to derive a multimetric index of river health. We examined the spatial (by river kilometer) and temporal variability of these metrics and assessed their responsiveness to anthropogenic disturbances, namely, effluents, turbidity, and highly embedded substrates. The resulting Ohio River Fish Index (ORFIn) comprises 13 metrics selected because they responded predictably to measures of human disturbance or reflected desirable features of the Ohio River. We retained two metrics (the number of intolerant species and the number of sucker species [family Catostomidae]) from Karr's original index of biotic integrity. Six metrics were modified from indices developed for the upper Ohio River (the number of native species; number of great-river species; number of centrarchid species; the number of deformities, eroded fins and barbels, lesions, and tumors; percent individuals as simple lithophils; and percent individuals as tolerant species). We also incorporated three trophic metrics (the percent of individuals as detritivores, invertivores, and piscivores), one metric based on catch per unit effort, and one metric based on the percent of individuals as nonindigenous fish species. The ORFIn declined significantly where anthropogenic effects on substrate and water quality were prevalent and was significantly lower in the first 500 m below point source discharges than at least-impacted sites nearby. Although additional research on the temporal stability of the metrics and index will likely enhance the reliability of the ORFIn, its incorporation into Ohio River assessments still represents an improvement over current physicochemical protocols.

Model for Predicting Passage of Invasive Fish Species Through Culverts

NASA Astrophysics Data System (ADS)

Neary, V.

2010-12-01

Conservation efforts to promote or inhibit fish passage include the application of simple fish passage models to determine whether an open channel flow allows passage of a given fish species. Derivations of simple fish passage models for uniform and nonuniform flow conditions are presented. For uniform flow conditions, a model equation is developed that predicts the mean-current velocity threshold in a fishway, or velocity barrier, which causes exhaustion at a given maximum distance of ascent. The derivation of a simple expression for this exhaustion-threshold (ET) passage model is presented using kinematic principles coupled with fatigue curves for threatened and endangered fish species. Mean current velocities at or above the threshold predict failure to pass. Mean current velocities below the threshold predict successful passage. The model is therefore intuitive and easily applied to predict passage or exclusion. The ET model’s simplicity comes with limitations, however, including its application only to uniform flow, which is rarely found in the field. This limitation is addressed by deriving a model that accounts for nonuniform conditions, including backwater profiles and drawdown curves. Comparison of these models with experimental data from volitional swimming studies of fish indicates reasonable performance, but limitations are still present due to the difficulty in predicting fish behavior and passage strategies that can vary among individuals and different fish species.

Development of Solar Drying Model for Selected Cambodian Fish Species

PubMed Central

Hubackova, Anna; Kucerova, Iva; Chrun, Rithy; Chaloupkova, Petra; Banout, Jan

2014-01-01

A solar drying was investigated as one of perspective techniques for fish processing in Cambodia. The solar drying was compared to conventional drying in electric oven. Five typical Cambodian fish species were selected for this study. Mean solar drying temperature and drying air relative humidity were 55.6°C and 19.9%, respectively. The overall solar dryer efficiency was 12.37%, which is typical for natural convection solar dryers. An average evaporative capacity of solar dryer was 0.049 kg·h−1. Based on coefficient of determination (R 2), chi-square (χ 2) test, and root-mean-square error (RMSE), the most suitable models describing natural convection solar drying kinetics were Logarithmic model, Diffusion approximate model, and Two-term model for climbing perch and Nile tilapia, swamp eel and walking catfish and Channa fish, respectively. In case of electric oven drying, the Modified Page 1 model shows the best results for all investigated fish species except Channa fish where the two-term model is the best one. Sensory evaluation shows that most preferable fish is climbing perch, followed by Nile tilapia and walking catfish. This study brings new knowledge about drying kinetics of fresh water fish species in Cambodia and confirms the solar drying as acceptable technology for fish processing. PMID:25250381

External and internal controls of lunar-related reproductive rhythms in fishes.

PubMed

Takemura, A; Rahman, M S; Park, Y J

2010-01-01

Reproductive activities of many fish species are, to some extent, entrained to cues from the moon. During the spawning season, synchronous spawning is repeated at intervals of c. 1 month (lunar spawning cycle) and 2 weeks (semi-lunar spawning cycle) or daily according to tidal changes (tidal spawning cycle). In species showing lunar-related spawning cycles, oocytes in the ovary develop towards and mature around a specific moon phase for lunar spawners, around spring tides for semi-lunar spawners and at daytime high tides for tidal spawners. The production of sex steroid hormones also changes in accordance with synchronous oocyte development. Since the production of the steroid hormones with lunar-related reproductive periodicity is regulated by gonadotropins, it is considered that the higher parts of the hypothalamus-pituitary-gonad axis play important roles in the perception and regulation of lunar-related periodicity. It is likely that fishes perceive cues from the moon by sensory organs; however, it is still unknown how lunar cues are transduced as an endogenous rhythm exerting lunar-related spawning rhythmicity. Recent research has revealed that melatonin fluctuated according to the brightness at night, magnetic fields and the tidal cycle. In addition, cyclic changes in hydrostatic pressure had an effect on monoamine contents in the brain. These factors may be indirectly related to the exertion of lunar-related periodicity. Molecular approaches have revealed that mRNA expressions of light-sensitive clock genes change with moonlight, suggesting that brightness at night plays a role in phase-shifting or resetting of biological clocks. Some species may have evolved biological clocks in relation to lunar cycles, although it is still not known how lunar periodicities are endogenously regulated in fishes. This review demonstrates that lunar-related periodicity is utilized and incorporated by ecological and physiological mechanisms governing the reproductive success of fishes.

Effects of Kraft Mill effluent on the sexuality of fishes: An environmental early warning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davis, W.P.; Bortone, S.A.

1992-01-01

Arrhenoid or masculinized female fish species of the live-bearing family, Poeciliidae, have been observed for over thirteen years in specific southern streams which receive waste effluents from pulping mills. The complex mixture of organic compounds in kraft mill effluent (KME) has inhibited specific identification of causal agent(s). However, microbially degraded phytosterols (e.g. sitosterol or stigmastanol) in experimental exposures induce the same intersexual states that characterize affected female poeciliids sampled from KME streams. KME-polluted streams often exhibit a drastic reduction of fish species diversity and degrees of physiological stress, all of which suggests reduced reproduction in surviving forms. A potential ontogeneticmore » or developmental response is demonstrated in American eels captured in one of these streams as well. The authors examine available information, including laboratory and experimental field exposures, and suggest directions for additional research as well as the need for environmental concern.« less

Characterizing lentic freshwater fish assemblages using multiple sampling methods

USGS Publications Warehouse

Fischer, Jesse R.; Quist, Michael C.

2014-01-01

Characterizing fish assemblages in lentic ecosystems is difficult, and multiple sampling methods are almost always necessary to gain reliable estimates of indices such as species richness. However, most research focused on lentic fish sampling methodology has targeted recreationally important species, and little to no information is available regarding the influence of multiple methods and timing (i.e., temporal variation) on characterizing entire fish assemblages. Therefore, six lakes and impoundments (48–1,557 ha surface area) were sampled seasonally with seven gear types to evaluate the combined influence of sampling methods and timing on the number of species and individuals sampled. Probabilities of detection for species indicated strong selectivities and seasonal trends that provide guidance on optimal seasons to use gears when targeting multiple species. The evaluation of species richness and number of individuals sampled using multiple gear combinations demonstrated that appreciable benefits over relatively few gears (e.g., to four) used in optimal seasons were not present. Specifically, over 90 % of the species encountered with all gear types and season combinations (N = 19) from six lakes and reservoirs were sampled with nighttime boat electrofishing in the fall and benthic trawling, modified-fyke, and mini-fyke netting during the summer. Our results indicated that the characterization of lentic fish assemblages was highly influenced by the selection of sampling gears and seasons, but did not appear to be influenced by waterbody type (i.e., natural lake, impoundment). The standardization of data collected with multiple methods and seasons to account for bias is imperative to monitoring of lentic ecosystems and will provide researchers with increased reliability in their interpretations and decisions made using information on lentic fish assemblages.

Integrating Stomach Content and Stable Isotope Analyses to Quantify the Diets of Pygoscelid Penguins

PubMed Central

Polito, Michael J.; Trivelpiece, Wayne Z.; Karnovsky, Nina J.; Ng, Elizabeth; Patterson, William P.; Emslie, Steven D.

2011-01-01

Stomach content analysis (SCA) and more recently stable isotope analysis (SIA) integrated with isotopic mixing models have become common methods for dietary studies and provide insight into the foraging ecology of seabirds. However, both methods have drawbacks and biases that may result in difficulties in quantifying inter-annual and species-specific differences in diets. We used these two methods to simultaneously quantify the chick-rearing diet of Chinstrap (Pygoscelis antarctica) and Gentoo (P. papua) penguins and highlight methods of integrating SCA data to increase accuracy of diet composition estimates using SIA. SCA biomass estimates were highly variable and underestimated the importance of soft-bodied prey such as fish. Two-source, isotopic mixing model predictions were less variable and identified inter-annual and species-specific differences in the relative amounts of fish and krill in penguin diets not readily apparent using SCA. In contrast, multi-source isotopic mixing models had difficulty estimating the dietary contribution of fish species occupying similar trophic levels without refinement using SCA-derived otolith data. Overall, our ability to track inter-annual and species-specific differences in penguin diets using SIA was enhanced by integrating SCA data to isotopic mixing modes in three ways: 1) selecting appropriate prey sources, 2) weighting combinations of isotopically similar prey in two-source mixing models and 3) refining predicted contributions of isotopically similar prey in multi-source models. PMID:22053199

Diagnostic criteria for proliferative hepatic lesions in brown bullhead Ameiurus nebulosus

USGS Publications Warehouse

Blazer, V.S.; Fournie, J.W.; Wolf, J.C.; Wolfe, M.J.

2006-01-01

Brown bullhead Ameiurus nebulosus is used as indicator species for contaminant effects at areas of concern (AOC) in the Great Lakes and other areas. One of the beneficial use impairments at numerous AOC is 'fish tumors and other deformities'. An impairment occurs when the prevalence of fish tumors and other deformities exceeds those at unimpacted or control sites or when survey data confirm the presence of neoplastic or preneoplastic liver lesions in bullhead or white sucker Catostomus commersonii. Numerous surveys have been conducted over the years assessing neoplasia in these fishes, both liver and skin tumors. However, a major problem in comparing the results has been a lack of consistent criteria for evaluating histological changes in bullhead livers. As individual AOC develop and implement remedial action plans, realistic and attainable delisting targets need to be specified. For this to occur and be consistent from site to site there must be standardization of the criteria being used to evaluate specific impairments. In this report, specific diagnostic criteria are provided for both non-neoplastic and neoplastic proliferative hepatocellular and biliary lesions. These criteria should assist fish pathologists in describing and categorizing proliferative liver lesions from brown bullhead. ?? Inter-Research 2006.

Fully-automated identification of fish species based on otolith contour: using short-time Fourier transform and discriminant analysis (STFT-DA).

PubMed

Salimi, Nima; Loh, Kar Hoe; Kaur Dhillon, Sarinder; Chong, Ving Ching

2016-01-01

Background. Fish species may be identified based on their unique otolith shape or contour. Several pattern recognition methods have been proposed to classify fish species through morphological features of the otolith contours. However, there has been no fully-automated species identification model with the accuracy higher than 80%. The purpose of the current study is to develop a fully-automated model, based on the otolith contours, to identify the fish species with the high classification accuracy. Methods. Images of the right sagittal otoliths of 14 fish species from three families namely Sciaenidae, Ariidae, and Engraulidae were used to develop the proposed identification model. Short-time Fourier transform (STFT) was used, for the first time in the area of otolith shape analysis, to extract important features of the otolith contours. Discriminant Analysis (DA), as a classification technique, was used to train and test the model based on the extracted features. Results. Performance of the model was demonstrated using species from three families separately, as well as all species combined. Overall classification accuracy of the model was greater than 90% for all cases. In addition, effects of STFT variables on the performance of the identification model were explored in this study. Conclusions. Short-time Fourier transform could determine important features of the otolith outlines. The fully-automated model proposed in this study (STFT-DA) could predict species of an unknown specimen with acceptable identification accuracy. The model codes can be accessed at http://mybiodiversityontologies.um.edu.my/Otolith/ and https://peerj.com/preprints/1517/. The current model has flexibility to be used for more species and families in future studies.

Investigating phenology of larval fishes in St. Louis River estuary shallow water habitats

EPA Science Inventory

As part of the development of an early detection monitoring strategy for non-native fishes, larval fish surveys have been conducted since 2012 in the St. Louis River estuary. Survey data demonstrates there is considerable variability in fish abundance and species assemblages acro...

Selective fishing and analysis of xanthine oxidase binders from two Fabaceae species by coupling enzyme functionalized core-shell magnetic nanoparticles with HPLC-MS.

PubMed

Liu, Liangliang; Shi, Shuyun; Zhao, Huading; Yu, Jingang; Jiang, Xinyu; Chen, Xiaoqing

2014-01-15

Xanthine oxidase (XOD) immobilized core-shell magnetic silica (Fe3O4@SiO2-XOD) nanoparticles coupled with high performance liquid chromatography-mass spectrometry (HPLC-MS) was developed to fish out and analyze XOD binders from two Fabaceae species, Puerariae lobata flower and Glycyrrhiza uralensis root. The prepared Fe3O4@SiO2-XOD nanoparticles exhibited good specificity for XOD binders, better dispersion in aqueous solution and reusability than those of Fe3O4-XOD nanoparticles. The amount of XOD immobilized onto Fe3O4@SiO2 nanoparticles was 339.9μg/mg and the activity of Fe3O4@SiO2-XOD nanoparticles remained 95% after ten times usage. The optimum conditions of selective fishing were optimized, and finally incubating pH was set at 7, incubating temperature at 25°C and adsorption time at 30min. Twelve XOD binders were successfully identified from ethyl acetate extract of P. lobata flower and G. uralensis root. The developed method provides a rapid, purposeful and effective way to identify active compounds from natural complex mixtures. Copyright © 2013 Elsevier B.V. All rights reserved.