Assessment of cobia, Rachycentron canadum, in the waters of the U.S. Gulf of Mexico

This assessment applies to cobia (Rachycentron canadum) located in the territorial waters of the U.S. Gulf of Mexico. Separation of the Gulf of Mexico and Atlantic Ocean is defined by the seaward extension of the Dade/Monroe county line in south Florida. Mixing of fish between the Atlantic and Gulf of Mexico occurs in the Florida Keys during winter months. Cobia annually migrate north in early spring in the Gulf to spawning grounds in the northern Gulf of Mexico, returning to the Florida Keys by winter. Catches of cobia in the Gulf of Mexico are dominated by recreational landings, accounting for nearly 90% of the total. Since 1980, the landings of cobia in the recreational fishery have remained fairly stable at around 400-600 mt with a slight peak of 1,014 mt in 1997. The recreational fishery was estimated to have landed 471 mt in 2000. The landings from the commercial fishery have shown a steady increase from 45 mt in 1980 to a peak of 120 mt in 1994, followed by a decline to 62 mt in 2000. The previous assessment of cobia occurred in 1996 using a virtual population analysis (VPA) model. For this analysis a surplus-production model (ASPIC) and a forward-projecting, age-structured population model programmed in the AD Model Builder (ADMB) software were applied to cobia data from the Gulf of Mexico. The primary data consisted of four catch-per-unit-effort (CPUE) indices derived from the Marine Recreational Fisheries Statistics Survey (MRFSS) (1981-1999), Southeast region headboat survey (1986-1999), Texas creel survey (1983-1999), and shrimp bycatch estimates (1980-1999). Length samples were available from the commercial (1983-2000) and recreational (1981-2000) fisheries. The ASPIC model applied to the cobia data provided unsatisfactory results. The ADMB model fit described the observed length composition data and fishery landings fairly well based on graphical examination of model residuals. The CPUE indices indicated some disagreement for various years, but the model fit an overall increasing trend from 1992-1997 for the MRFSS, headboat, and Texas creel indices. The shrimp bycatch CPUE was treated as a recruitment index in the model. The fit to these data followed an upward trend in recruitment from 1988-1997, but did not fit the 1994-1997 data points very well. This was likely the result of conflicting information from other data sources. Natural mortality (M) for cobia is unknown. As a result, a range of values for M from 0.2-0.4, based on longevity and growth parameters, were selected for use in the age-structured model. The choice of natural mortality appears to greatly influence the perceived status of the population. Population status as measured by spawning stock biomass in the last year relative to the value at maximum sustainable yield (SSB2000/SSBMSY), spawning stock biomass in the last year relative to virgin spawning stock biomass (SSB2000/S0), and static spawning stock biomass per recruit (SSBR) all indicate the population is either depleted, near MSY, or well above MSY depending on the choice of M. The variance estimates for these benchmarks are very large and in most cases ranges from depleted to very healthy status. The only statement that can be made with any degree of certainty about cobia in the Gulf of Mexico is that the population has increased since the 1980s. (PDF contains 61 pages)

Networking for Rural Development: a closer look at the evolution of communications in the STREAM Initiative

What began as a general desire to share messages about processes, technologies, lives and opportunities – among farming and fishing communities and those who work with them – has evolved into a network that shares meanings and lessons learnt. Now instead of relying on core funding or catalytic support, the STREAM Initiative is self-funded through the services its network provides to academic, development and other organizations. (Pdf contains 8 pages).

Final report of the Support to Regional Aquatic Resources Management (STREAM): a NACA networking initiative

The governing council of Naca has resolved to effect a shift in emphasis from aquaculture development to aquaculture for development. This will require engaging partners from a broad spectrum of government and development agencies, the nature of the information that will need to be gathered and the strategies used for disseminating information and initiating action. The vehicle for operationalising this shift is STREAM - Support to Regional Aquatic Resources Management. This report outlines the nature of the STREAM network, its relationship to NACA's vision, mission, objectives and operating principles, and how STREAM differs from previous NACA's networks. Because STREAM is different, a theoretical basis for network communication is presented along with an outline of the preliminary steps in getting the network up and running. (Pdf contains 33 pages).

Technologies for Measuring Currents in Coastal Environments, Portland, Maine, October 26-28, 2005:workshop proceedings

The Alliance for Coastal Technologies (ACT) Workshop entitled "Technologies for Measuring Currents in Coastal Environments" was held in Portland, Maine, October 26-28, 2005, with sponsorship by the Gulf of Maine Ocean Observing System (GoMOOS), an ACT partner organization. The primary goals of the event were to summarize recent trends in nearshore research and management applications for current meter technologies, identify how current meters can assist coastal managers to fulfill their regulatory and management objectives, and to recommend actions to overcome barriers to use of the technologies. The workshop was attended by 25 participants representing state and federal environmental management agencies, manufacturers of current meter technologies, and researchers from academic institutions and private industry. Common themes that were discussed during the workshop included 1) advantages and limitations of existing current measuring equipment, 2) reliability and ease of use with each instrument type, 3) data decoding and interpretation procedures, and 4) mechanisms to facilitate better training and guidance to a broad user group. Seven key recommendations, which were ranked in order of importance during the last day of the workshop are listed below. 1. Forums should be developed to facilitate the exchange of information among users and industry: a) On-line forums that not only provide information on specific instruments and technologies, but also provide an avenue for the exchange of user experiences with various instruments (i.e. problems encountered, cautions, tips, advantages, etc). (see References for manufacturer websites with links to application and technical forums at end of report) b) Regional training/meetings for operational managers to exchange ideas on methods for measuring currents and evaluating data. c) Organize mini-meetings or tutorial sessions within larger conference venues. 2. A committee of major stakeholders should be convened to develop common standards (similar to the Institute of Electrical and Electronics Engineers (IEEE) committee) that enable users to switch sensors without losing software or display capabilities. (pdf contains 28 pages)

IBM PC Data Acquisition and Processing Software Evaluation

Commercially available software packages for IBM PC-compatibles are evaluated to use for data acquisition and processing work. Moss Landing Marine Laboratories (MLML) acquired computers since 1978 to use on shipboard data acquisition (Le. CTD, radiometric, etc.) and data processing. First Hewlett-Packard desktops were used then a transition to the DEC VAXstations, with software developed mostly by the author and others at MLML (Broenkow and Reaves, 1993; Feinholz and Broenkow, 1993; Broenkow et al, 1993). IBM PC were at first very slow and limited in available software, so they were not used in the early days. Improved technology such as higher speed microprocessors and a wide range of commercially available software made use of PC more reasonable today. MLML is making a transition towards using the PC for data acquisition and processing. Advantages are portability and available outside support.

Dividing population genetic distance data with the software Partitioning Optimization with Restricted Growth Strings (PORGS): an application for Chinook salmon (Oncorhynchus tshawytscha), Vancouver Island, British Columbia

A new method of finding the optimal group membership and number of groupings to partition population genetic distance data is presented. The software program Partitioning Optimization with Restricted Growth Strings (PORGS), visits all possible set partitions and deems acceptable partitions to be those that reduce mean intracluster distance. The optimal number of groups is determined with the gap statistic which compares PORGS results with a reference distribution. The PORGS method was validated by a simulated data set with a known distribution. For efficiency, where values of n were larger, restricted growth strings (RGS) were used to bipartition populations during a nested search (bi-PORGS). Bi-PORGS was applied to a set of genetic data from 18 Chinook salmon (Oncorhynchus tshawytscha) populations from the west coast of Vancouver Island. The optimal grouping of these populations corresponded to four geographic locations: 1) Quatsino Sound, 2) Nootka Sound, 3) Clayoquot +Barkley sounds, and 4) southwest Vancouver Island. However, assignment of populations to groups did not strictly reflect the geographical divisions; fish of Barkley Sound origin that had strayed into the Gold River and close genetic similarity between transferred and donor populations meant groupings crossed geographic boundaries. Overall, stock structure determined by this partitioning method was similar to that determined by the unweighted pair-group method with arithmetic averages (UPGMA), an agglomerative clustering algorithm.

The ECOPATH II software

Problems involved in the development of ecosystem models are discussed, considering in particular the use of the ECOPATH II software and the approach used at ICLARM in the project Global comparisons of trophic aquatic ecosystem models designed to support modelling efforts of research groups throughout the world.

ICLARM software projects: back to the future

The different computer softwares developed by the International Center for Living Aquatic Resources (ICLARM) and its functions and uses in fisheries science are presented.

A computer software package for assessing and managing risks posed by experiments with genetically modified fish and shellfish

Assessment and management of risk is needed for sustainable use of genetically modified aquatic organisms (aquatic GMOs). A computer software package for safely conducting research with genetically modified fish and shellfish is described. By answering a series of questions about the organism and the accessible aquatic ecosystem, a researcher or oversight authority can either identify specific risks or conclude that there is a specific reason for safety of the experiment. Risk assessment protocols with examples involving transgenic coho salmon, triploid grass carp and hybrid tilapia are described. In case a specific risk is identified, the user is led to consider risk management measures, involving culture methods, facilities design and operations management, to minimize the risk. Key features of the software are its user-friendly organization; easy access to explanatory text, literature citations and glossary; and automated completion of a worksheet. Documented completion of the Performance Standards can facilitate approval of a well designed experiment by oversight authorities.

Invasionsoft: a web-enabled tool for invasive species colonization predictions

Predicting and averting the spread of invasive species is a core focus of resource managers in all ecosystems. Patterns of invasion are difficult to forecast, compounded by a lack of user-friendly species distribution model (SDM) tools to help managers focus control efforts. This paper presents a web-based cellular automata hybrid modeling tool developed to study the invasion pattern of lionfish (Pterois volitans/miles) in the western Atlantic and is a natural extension our previous lionfish study. Our goal is to make publically available this hybrid SDM tool and demonstrate both a test case (P. volitans/miles) and a use case (Caulerpa taxifolia). The software derived from the model, titled Invasionsoft, is unique in its ability to examine multiple default or user-defined parameters, their relation to invasion patterns, and is presented in a rich web browser-based GUI with integrated results viewer. The beta version is not species-specific and includes a default parameter set that is tailored to the marine habitat. Invasionsoft is provided as copyright protected freeware at http://www.invasionsoft.com.

Bibliography of synthesis documents on selected coastal ocean topics

This compilation of references to works which synthesize information on coastal topics is intended to be useful to resource managers in decision making processes. However, the utility must be understand in terms of its limited coverage. The bibliography is not inclusive of all the published materials on the topics selected. Coverage is clearly defined in the following paragraph. The time span of the bibliography is limited to references that were published from I983 to 1993, except for a last-minute addition of a few 1994 publications. All searches were done in mid- to late-1993. The bibliography was compiled from searches done on the following DIALOG electronic databases: Aquatic Sciences and Fisheries Abstracts, BlOSlS Previews, Dissertation Abstracts Online, Life Sciences Collection, NTlS (National Technical lnformation Service), Oceanic Abstracts, Pollution Abstracts, SciSearch, and Water Resources Abstracts. In addition, two NOAA electronic datases were searched: the NOAA Library and lnformation Catalog and the NOAA Sea Grant Depository Database. Synthesis of information is not an ubiquitous term used in database development. In order to locate syntheses of required coastal topics, 89 search terms were used in combinations which required 10 searches from each file. From the nearly 6,000 citations which resulted from the electronic searches, the most appropriate were selected to produce this bibliography. The document was edited and indexed using Wordperfect software. When available, an abstract has been included. Every abstract was edited. The bibliography is subdivided into four main topics or sections: ecosystems, coastal water body conditions, natural disasters, and resource management. In the ecosystems section, emphasis is placed on organisms in their environment on the major coastlines of the U.S. In the second section, coastal water body conditions, the environment itself is emphasized. References were found for the Alaskan coast, but none were found for Hawaii. The third section, on natural disasters, emphasizes environmental impacts resulting from natural phenomena. Guidelines, planning and management reports, modelling documents, strategic and restoration plans, and environmental economics related to sustainability are included in the fourth section, resource management. Author, geographic, and subject indices indices are provided. The authors would like to thank Victor Omelczenko and Terry Seldon of the NOAA Sea Grant Office for access to and training on the NOAA Sea Grant Depository Database. We are grateful also to Dorothy Anderson, Philip Keavey, and Elizabeth Petersen who reviewed the draft document.

Scientific statistics and graphics on the Macintosh

The personal computer has become commonplace on the desk of most scientists. As hardware costs have plummeted, software capabilities have expanded enormously, permitting the scientist to examine extremely large datasets in novel ways. Advances in networking now permit rapid transfer of large datasets, which can often be used unchanged from one machine to the next. In spite of these significant advances, many scientists still use their personal computers only for word processing or e-mail, or as "dumb terminals". Many are simply unaware of the richness of software now available to statistically analyze and display scientific data in highly innovative ways. This paper presents several examples drawn from actual climate data analysis that illustrate some novel and practical features of several widely-used software packages for Macintosh computers.