A model of the pelagic ecossystem in the eastern tropical Pacific Ocean

English: Recent calls for a more holistic approach to fisheries management have motivated development of trophic mass-balance models of ecosystems that underlie fisheries production. We developed a model hypothesis of the pelagic ecosystem in the eastern tropical Pacific Ocean (ETP) to gain insight into the relationships among the various species in the system and to explore the ecological implications of alternative methods of harvesting tunas. We represented the biomasses of and fluxes between the principal elements in the ecosystem with Ecopath, and examined the ecosystem's dynamic, time-series behavior with Ecosim. We parameterized the model for 38 species or groups of species, and described the sources, justifications, assumptions, and revisions of our estimates of the various parameters, diet relations, fisheries landings, and fisheries discards in the model. We conducted sensitivity analyses with an intermediate version of the model, for both the Ecopath mass-balance and the dynamic trajectories predicted by Ecosim. The analysis showed that changes in the basic parameters for two components at middle trophic levels, Cephalopods and Auxis spp., exert the greatest influence on the system. When the Cephalopod Q/B and Auxis spp. P/B were altered from their initial values and the model was rebalanced, the trends of the biomass trajectories predicted by Ecosim were not sensitive, but the scaling was sensitive for several components. We described the review process the model was subjected to, which included reviews by the IATTC Purse-seine Bycatch Working Group and by a working group supported by the National Center for Ecological Analysis and Synthesis. We fitted the model to historical time series of catches per unit of effort and mortality rates for yellowfin and bigeye tunas in simulations that incorporated historical fishing effort and a climate driver to represent the effect of El Niño-Southern Oscillation-scale variation on the system. The model was designed to evaluate the possible ecological implications of fishing for tunas in various ways. We recognize that a model cannot possibly represent all the complexity of a pelagic ocean ecosystem, but we believe that the ETP model provides insight into the structure and function of the pelagic ETP. Spanish: Llamamientos recientes hacia un enfoque más holístico al ordenamiento de la pesca han motivado el desarrollo de modelos tróficos de balance de masas de los ecosistemas que sostienen la producción pesquera. Desarrollamos una hipótesis modelo del ecosistema pelágico en el Océano Pacífico oriental tropical (POT) con miras a mejorar los conocimientos de las relaciones entre las distintas especies en el sistema y explorar las implicaciones ecológicas de métodos alternativos de capturar atunes. Con Ecopath representamos las biomasas de los elementos principales en el ecosistema, y los flujos entre los mismos, y con Ecosim examinamos el comportamiento dinámico del ecosistema con el tiempo. Parametrizamos el modelo para 38 especies o grupos de especies (denominados “componentes” del modelo), y describimos las fuentes, justificaciones, supuestos, y revisiones de nuestras estimaciones de los distintos parámetros, relaciones basadas en dieta, capturas retenidas de las pesquerías, y descartes de las mismas en el modelo. Realizamos análisis de sensibilidad con una versión intermedia del modelo, para el balance de masas de Ecopath y las trayectorias dinámicas predichas por Ecosim también. El análisis demostró que cambios en los parámetros básicos para dos componentes en niveles tróficos medianos, Cefalópodos y Auxis spp., ejercieron la mayor influencia sobre el sistema. Cuando se alteraron el Q/B de los Cefalópodos y el P/B de los Auxis spp. de sus valores iniciales y se balanceó el modelo de nuevo, las tendencias de las trayectorias de la biomasa predichas por Ecosim no fueron sensibles, pero la escala fue sensible para varios componentes. Describimos el proceso de revisión al que fue sujeto el modelo, inclusive revisiones por el Grupo de Trabajo sobre Captura Incidental de la CIAT y un grupo de trabajo apoyado por el Centro Nacional para Síntesis y Análisis Ecológicos. Ajustamos el modelo a series de tiempo históricas de capturas por unidad de esfuerzo y tasas de mortalidad de atunes aleta amarilla y patudo en simulaciones que incorporaron esfuerzo de pesca histórico e impulsos climáticos para representar el efecto de variaciones a escala de El Niño-Oscilación del Sur sobre el sistema. El modelo fue diseñado para evaluar las posibles implicaciones ecológicas de la pesca atunera de varias formas. Reconocemos la imposibilidad de que el modelo represente toda la complejidad de un ecosistema oceánico pelágico, pero creemos que el modelo del POT mejora los conocimientos de la estructura y función del POT pelágico.

Viral metagenomic analysis of feces of wild small carnivores

Background: Recent studies have clearly demonstrated the enormous virus diversity that exists among wild animals. This exemplifies the required expansion of our knowledge of the virus diversity present in wildlife, as well as the potential transmission of these viruses to domestic animals or humans. Methods: In the present study we evaluated the viral diversity of fecal samples (n = 42) collected from 10 different species of wild small carnivores inhabiting the northern part of Spain using random PCR in combination with next-generation sequencing. Samples were collected from American mink (Neovison vison), European mink (Mustela lutreola), European polecat (Mustela putorius), European pine marten (Martes martes), stone marten (Martes foina), Eurasian otter (Lutra lutra) and Eurasian badger (Meles meles) of the family of Mustelidae; common genet (Genetta genetta) of the family of Viverridae; red fox (Vulpes vulpes) of the family of Canidae and European wild cat (Felis silvestris) of the family of Felidae. Results: A number of sequences of possible novel viruses or virus variants were detected, including a theilovirus, phleboviruses, an amdovirus, a kobuvirus and picobirnaviruses. Conclusions: Using random PCR in combination with next generation sequencing, sequences of various novel viruses or virus variants were detected in fecal samples collected from Spanish carnivores. Detected novel viruses highlight the viral diversity that is present in fecal material of wild carnivores.

Generation of 210 fs laser pulses at 1093 nm by a self-starting mode-locked Yb:GYSO laser

We report the first demonstration, to our knowledge, of the femtosecond laser operation by using a new alloyed Yb:GYSO crystal as the gain medium. With a 5 at. % Yb3+-doped sample and chirped mirrors for dispersion compensation, we obtained pulses as short as 210 fs at the center wavelength of 1093 nm. The average mode-locking power is 300 mW, and the pulse repetition frequency is 80 MHz. (C) 2008 Optical Society of America

Spatial and temporal distribution of grouper larvae (Serranidae: Epinephelinae: Epinephelini) in the Gulf of Mexico and Straits of Florida

Little is known about the seasonality and distribution of grouper larvae (Serranidae: Epinephelini) in the Gulf of Mexico and Atlantic Ocean off the coast of the southeast United States. Grouper larvae were collected from a transect across the Straits of Florida in 2003 and 2004 and during the Southeast Area Monitoring and Assessment Program spring and fall surveys from 1982 through 2005. Analysis of these larval data provided information on location and timing of spawning, larval distribution patterns, and interannual occurrence for a group of species not easily studied as adults. Our analyses indicated that shelf-edge habitat is important for spawning of many species of grouper—some species for which data were not previously available. Spawning for some species may occur year-round, but two peak seasons are evident: late winter and late summer through early fall. Interannual variability in the use of three important subregions by species or groups of species was partially explained by environmental factors (surface temperature, surface salinity, and water depth). A shift in species dominance over the last three decades from spring-spawned species (most of the commercial species) to fall-spawned species also was documented. The results of these analyses expand our understanding of the basic distribution and spawning patterns of northwest Atlantic grouper species and indicate a need for further examination of the changing population structure of individual species and species dominance in the region.

The trophic dynamics of summer flounder (Paralichthys dentatus) in Chesapeake Bay

Data on the trophic dynamics of fishes are needed for management of ecosystems such as Chesapeake Bay. Summer flounder (Paralichthys dentatus) are an abundant seasonal resident of the bay and have the potential to impact foodweb dynamics. Analyses of diet data for late juvenile and adult summer flounder collected from 2002−2006 in Chesapeake Bay were conducted to characterize the role of this flatfish in this estuary and to contribute to our understanding of summer flounder trophic dynamics throughout its range. Despite the diversity of prey, nearly half of the diet comprised mysid shrimp (Neomysis spp.) and bay anchovy (Anchoa mitchilli). Ontogenetic differences in diet and an increase in diet diversity with increasing fish size were documented. Temporal (inter- and intra-annual) changes were also detected, as well as trends in diet reflecting peaks in abundance and diversity of prey. The preponderance of fishes in the diet of summer flounder indicates that this species is an important piscivorous predator in Chesapeake Bay.

Transitions in the morphological features, habitat use, and diet of young-of-the-year goosefish (Lophius americanus)

This study was designed to improve our understanding of transitions in the early life history and the distribution, habitat use, and diets for young-of-the-year (YOY) goosefish (Lophius americanus) and, as a result, their role in northeastern U.S. continental shelf ecosystems. Pelagic juveniles (>12 to ca. 50 mm total length [TL]) were distributed over most portions of the continental shelf in the Middle Atlantic Bight, Georges Bank, and into the Gulf of Maine. Most individuals settled by 50−85 mm TL and reached approximately 60−120 mm TL by one year of age. Pelagic YOY fed on chaetognaths, hyperiid amphipods, calanoid copepods, and ostracods, and benthic YOY had a varied diet of fishes and benthic crustaceans. Goosefish are widely scattered on the continental shelf in the Middle Atlantic Bight during their early life history and once settled, are habitat generalists, and thus play a role in many continental shelf habit

Effects of Spring Temperatures on the Strength of Selection on Timing of Reproduction in a Long-Distance Migratory Bird

Climate change has differentially affected the timing of seasonal events for interacting trophic levels, and this has often led to increased selection on seasonal timing. Yet, the environmental variables driving this selection have rarely been identified, limiting our ability to predict future ecological impacts of climate change. Using a dataset spanning 31 years from a natural population of pied flycatchers (Ficedula hypoleuca), we show that directional selection on timing of reproduction intensified in the first two decades (1980-2000) but weakened during the last decade (2001-2010). Against expectation, this pattern could not be explained by the temporal variation in the phenological mismatch with food abundance. We therefore explored an alternative hypothesis that selection on timing was affected by conditions individuals experience when arriving in spring at the breeding grounds: arriving early in cold conditions may reduce survival. First, we show that in female recruits, spring arrival date in the first breeding year correlates positively with hatch date; hence, early-hatched individuals experience colder conditions at arrival than late-hatched individuals. Second, we show that when temperatures at arrival in the recruitment year were high, early-hatched young had a higher recruitment probability than when temperatures were low. We interpret this as a potential cost of arriving early in colder years, and climate warming may have reduced this cost. We thus show that higher temperatures in the arrival year of recruits were associated with stronger selection for early reproduction in the years these birds were born. As arrival temperatures in the beginning of the study increased, but recently declined again, directional selection on timing of reproduction showed a nonlinear change. We demonstrate that environmental conditions with a lag of up to two years can alter selection on phenological traits in natural populations, something that has important implications for our understanding of how climate can alter patterns of selection in natural populations.

Age, growth, mortality, and radiometric age validation of gray snapper (Lutjanus griseus) from Louisiana

The gray snapper (Lutjanus griseus) is a temperate and tropical reef fish that is found along the Gulf of Mexico and Atlantic coasts of the southeastern United States. The recreational fishery for gray snapper has developed rapidly in south Louisiana with the advent of harvest and seasonal restrictions on the established red snapper (L. campechanus) fishery. We examined the age and growth of gray snapper in Louisiana with the use of cross-sectioned sagittae. A total of 833 specimens, (441 males, 387 females, and 5 of unknown sex) were opportunistically sampled from the recreational fishery from August 1998 to August 2002. Males ranged in size from 222 to 732 mm total length (TL) and from 280 g to 5700 g total weight (TW) and females ranged from 254 to 756 mm TL and from 340 g to 5800 g TW. Both edge analysis and bomb radiocarbon analyses were used to validate otolith-based age estimates. Ages were estimated for 718 individuals; both males and females ranged from 1 to 28 years. The von Bertalanffy growth models derived from TL at age were Lt = 655.4{1–e[–0.23(t)]} for males, Lt = 657.3{1–e[– 0.21(t)]} for females, and L t = 656.4{1–e[– 0.22 (t)]} for all specimens of known sex. Catch curves were used to produce a total mortality (Z) estimate of 0.17. Estimates of M calculated with various methods ranged from 0.15 to 0.50; however we felt that M= 0.15 was the most appropriate estimate based on our estimate of Z. Full recruitment to the gray snapper recreational fishery began at age 4, was completed by age 8, and there was no discernible peak in the catch curve dome.

The U.S. Gulf of Mexico Pink Shrimp, Farfantepenaeus duorarum, Fishery: 50 Years of Commercial Catch Statistics

U.S. Gulf of Mexico, pink shrimp, Farfantepenaeus duorarum, catch statistics have been collected by NOAA’s National Marine Fisheries Service, or its predecessor agency, for over 50 years. Recent events, including hurricanes and oil spills within the ecosystem of the fishery, have shown that documentation of these catch data is of primary importance. Fishing effort for this stock has fluctuated over the 50-year period analyzed, ranging from 3,376 to 31,900 days fished, with the most recent years on record, 2008 and 2009, exhibiting declines up to 90% relative to the high levels recorded in the mid 1990’s. Our quantification of F. duorarum landings and catch rates (CPUE) indicates catch have been below the long-term average of about 12 million lb for all of the last 10 years on record. In contrast to catch and effort, catch rates have increased in recent years, with record CPUE levels measured in 2008 and 2009, of 1,340 and 1,144 lb per day fished, respectively. Our regression results revealed catch was dependent upon fishing effort (F=98.48df=1, 48, p<0.001, r2=0.67), (Catch=1,623,378 + (520) × (effort)). High CPUE’s measured indicate stocks were not in decline prior to 2009, despite the decline in catch. The decrease in catch is attributed in large part to low effort levels caused by economical and not biological or habitat related conditions. Future stock assessments using these baseline data will provide further insights and management advice concerning the Gulf of Mexic

Human Dimensions of Marine Fisheries: Using GIS to Illustrate Land-Sea Connections in the Northeast U.S. Herring, Clupea harengus, Fishery

Geographic Information Systems can help improve ocean literacy and inform our understanding of the human dimensions of marine resource use. This paper describes a pilot project where GIS is used to illustrate the connections between fish stocks and the social, cultural, and economic components of the fishery on land. This method of presenting and merging qualitative and quantitative data represents a new approach to assist fishery managers, participants, policy-makers, and other stakeholders in visualizing an often confusing and poorly understood web of interactions. The Atlantic herring fishery serves as a case study and maps from this pilot project are presented and methods reviewed.

A Review of Stock Identification of Haddock, Melanogrammus aeglefinus, in the Northwest Atlantic Ocean

Haddock, Melanogrammus aeglefinus, is a principal commercial species distributed throughout the northwest Atlantic Ocean, with major aggregations occurring on Georges Bank and on the Scotian Shelf. This review examines all available information on stock structure of haddock to evaluate the suitability of current stock units and to investigate areas that require further research. Combined information from tag-recapture, demographic, recruitment, meristic, parasitic, and genetic studies provide evidence for the identification of haddock stocks, with major population divisions occurring between New England, Nova Scotia, and Newfoundland waters. Within each of these major divisions a number of discrete stocks appear to exist, although uncertainty remains in the amount of separation found within each region. Research utilizing more recent stock identification techniques should refine and improve our understanding of haddock stock structure in the northwest Atlantic.

The review of recent advances in fish genetics and biotechnology

Great advances have been, and are being made in our knowledge of the genetics and molecular biology (including genomics, proteomics and structural biology). Global molecular profiling technologies such as microassays using DNA or oligonucleotide chip, and protein and lipid chips are being developed. The application of such biotechnological advances are inevitable in aquaculture in the areas of improvement of aquaculture stocks where many molecular markers such as RFLPs, AFLDs and RAPD are now available for genome analysis, finger printing and genetic linkage mapping. Transgenic technology has been developed in a number of fish species and research is being pursed to produce transgenic fish carrying genes that encode antimicrobial peptides such as lysozyme thereby achieving disease resistance in fish. Also it is a short cut to achieving genetic change for fast growth and other desirable traits like early sexual maturity, temperature tolerance and feed conversion efficiency. KEYWORDS: Fish genetics, transgenesis, monoploidy, diploidy, polyploidy,gynogenesis, androgenesis, cryopreservation.

High-resolution natural recording systems: intercomparisons of the response to interannual climatic variability [abstract]

The goal of this work is to examine the properties of recording mechanisms which are common to continuously recording high-resolution natural systems in which climatic signals are imprinted and preserved as proxy records. These systems produce seasonal structures as an indirect response to climatic variability over the annual cycle. We compare the proxy records from four different high-resolution systems: the Quelccaya ice cap of the Peruvian Andes; composite tree ring growth from southern California and the southwestern United States; and the marine varve sedimentation systems in the Santa Barbara basin (off California, United States) and in the Gulf of California, Mexico. An important focus of this work is to indicate how the interannual climatic signal is recorded in a variety of different natural systems with vastly different recording mechanisms and widely separated in space. These high-resolution records are the products of natural processes which should be comparable, to some degree, to human-engineered systems developed to transmit and record physical quantities. We therefore present a simple analogy of a data recording system as a heuristic model to provide some unifying concepts with which we may better understand the formation of the records. This analogy assumes special significance when we consider that natural proxy records are the principal means to extend our knowledge of climatic variability into the past, beyond the limits of instrumentally recorded data.

Seascape ecology of coastal biogenic habitats: advances, gaps, and challenges

We review the progress made in the emerging field of coastal seascape ecology, i.e. the application of landscape ecology concepts and techniques to the coastal marine environment. Since the early 1990s, the landscape ecology approach has been applied in several coastal subtidal and intertidal biogenic habitats across a range of spatial scales. Emerging evidence indicates that animals in these seascapes respond to the structure of patches and patch mosaics in different ways and at different spatial scales, yet we still know very little about the ecological significance of these relationships and the consequences of change in seascape patterning for ecosystem functioning and overall biodiversity. Ecological interactions that occur within patches and among different types of patches (or seascapes) are likely to be critically important in maintaining primary and secondary production, trophic transfer, biodiversity, coastal protection, and supporting a wealth of ecosystem goods and services. We review faunal responses to patch and seascape structure, including effects of fragmentation on 5 focal habitats: seagrass meadows, salt marshes, coral reefs, mangrove forests, and oyster reefs. Extrapolating and generalizing spatial relationships between ecological patterns and processes across scales remains a significant challenge, and we show that there are major gaps in our understanding of these relationships. Filling these gaps will be crucial for managing and responding to an inevitably changing coastal environment. We show that critical ecological thresholds exist in the structural patterning of biogenic ecosystems that, when exceeded, cause abrupt shifts in the distribution and abundance of organisms. A better understanding of faunal–seascape relationships, including the identifications of threshold effects, is urgently needed to support the development of more effective and holistic management actions in restoration, site prioritization, and forecasting the impacts of environmental change.

Nocturnal migration patterns of two Caribbean reef fishes, Haemulon sciurus and Lutjanus apodus [Poster]

In the Caribbean, many coral reef associated fishes have been observed making diel migrations, yet little is known about the detailed movement pathways and space use patterns of individual fish. Often these migrations occur along temporally or spatially consistent corridors that connect preferred resting and foraging habitats. Recent analysis of gut contents from Haemulids and Lutjanids, has provided evidence that these species forage in seagrass beds and other habitats near their coral reef refuges. Few studies have provided direct and spatially explicit evidence of nocturnal migrations and detailed day and night space use patterns for individual fish. This study integrated manual acoustic telemetry to track two common reef species, the bluestriped grunt (Haemulon sciurus) and schoolmaster snapper (Lutjanus apodus) throughout their daily home range. Space use patterns of these species were then examined using Geographical Information System (GIS) tools to link movement behavior to seascape structure derived in a benthic habitat map. This study represents a novel integration of spatial technologies to enhance our understanding of the movement ecology of adult H. sciurus and L. apodus.