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.

Modelling algal blooms

This is the final report on the research project to develop predictive models to quantify algal blooms in relation to environmental variables. The project's objectives were to develop models simulating the impact of vertical structure and mass transfer upon the dynamics of planktonic algae, including cyanobacteria, in lakes and reservoirs, to assess the potential of sedimentary phosphorus to sustain algal growth following reduction in external loading and to expand and enhance formulations to predict behaviour of blue-green algal populations and to incorporate these into a model software package. As part of the project a strategy for the production of a user-friendly packaging for the modelling software PROTEC-2 adaptable to particular sites was developed.

Use of macroinvertebrate communities to detect environmental stress in running waters

This paper presents an account of some current uses of RIVPACS (River Invertebrate Prediction and Classification System), a software package developed by the Institute of Freshwater Ecology (UK). Background information is also given on the unique data-set on which the system is based. Before discussing RIVPACS, we consider the range of environmental stresses encountered in flowing-water systems and some of the ways in which stresses may affect macroinvertebrate communities. The wide application and relevance of the RIVPACS approach was recognised when it was chosen as the biological method for use throughout the UK in the 1990 River Quality Survey (RQS). In the concluding section we list some lessons learnt both from the 1990 survey and from our own testing exercise, and we outline current developments which will lead to a new version of RIVPACS for use in the 1995 RQS.

An introduction to RIVPACS

RIVPACS (River InVertebrate Prediction And Classification System) is a software package developed by the Institute of Freshwater Ecology (IFE). The primary application is to assess the biological quality of rivers within the UK. RIVPACS offers site-specific predictions of the macroinvertebrate fauna to be expected in the absence of major environmental stress. The expected fauna is derived by RIVPACS using a small suite of environmental characteristics. The biological evaluation is then obtained by comparing the fauna observed at the site with the expected fauna. RIVPACS also includes a site classification based on the macroinvertebrate fauna of the component reference sites. New sites, judged by their fauna to be of high biological quality, may be allocated to classification groups within the fixed RIVPACS classification. This has potential for evaluating sites for conservation. In this chapter, the origins and history of the RIVPACS approach are described, including major scientific and operational developments over the life of the project. RIVPACS III is described in detail and predictions at different taxonomic levels are demonstrated. The value of the reference dataset for river management and conservation is examined, and the chapter concludes with a brief consideration of some future challenges.

Estimating the food consumption of fishes: one step in linking a species with its ecosystem

Details are given of a new software package MAXIMS which may be used to estimate the daily food consumption of fish. The software estimates the feeding times, the rates of ingestion and evacuation and related parameters. Two applications of the program are described. The first pertains to anchovy (Engraulis ringens ) with one feeding period per day, and the second one to juvenile cod (Gadus morhua ), which feed during dawn and dusk.

Population dynamics and exploitation of Metapenaeus affinis in Kuwaiti waters

Length-frequency data of Metapenaeus affinis collected from the trawl catches of R/V Bahith in Kuwaiti waters from 1985 to 1989 were combined with estimates of monthly total catch by the commercial and small-scale fleets operating in Kuwait, and analyzed using the Compleat ELEFAN software package. A major recruitment pulse of M. affinis occurs in spring and a minor one in autumn. Optimum relative yield per recruit (Y'/R) is obtained with the length-at-first capture (L sub(c)) of 24.4 cm CL for females and < 17.6 m CL for males. Virtual population analysis results indicated that the biomasses have decreased during the last three-year period for which data were available.

Growth and length-weight parameters of Pacific mackerel (Scomber japonicus) in the Gulf of Guayaquil, Ecuador

The seasonally oscillating growth parameters and length-weight relationships for Scomber japonicus caught in the Gulf of Guayaquil, Ecuador, were determined based on length-frequency data from 1989 to 1996, using the FiSAT software package of Gayanilo et al. (1996). Estimates of growth parameters are in general agreement with previous studies on the same species. Results also imply that the growth of Scomber japonicus slows down during the cold season by approximately 50% with respect to the average growth. The mean value of the power b is significantly larger than 3, indicating that the model of allometric growth should be used for the length-weight relationship and calculation of the condition factor.

Seasonal growth of five commercially important fishes at Sofala Bank, Mozambique

An analysis of growth of scad and mackerels on Sofala Bank, Mozambique, was performed using data collected from commercial vessels during the year 1986-87, using the "Compleat Elefan" software package. Updated estimates of growth parameters of Decapterus russelli, D. macrosoma (Carangidae), and Rastrelliger kanagurta (Scombridae) were obtained which take seasonal growth oscillations into account. Preliminary growth parameter estimates are also presented for Selar crumenophthalmus (Carangidae) and Saurida undosquamis (Synodontidae).

Biology of the penaeid shrimp populations exploited by Estuarine Set Bagnet

Results of analysis of part of the data collected during October, 1989 to December, 1990 are given on the biology and catch assessment studies on the Estuarine Set Bagnet (ESBN) from six sampling stations covering the entire coast line of Bangladesh. Length frequency analysis of seven most commonly occurring penaeid shrimp species have been done with complete ELEFAN software package. The result of exploitation patterns indicate that all penaeids except P. stylifera are being over exploited on their way back to the Sea from the nursery ground. This appeared to be the instances of serious growth over fishing. These species are exploited at a size much lower than the length at first maturity, which strongly suggests a complete withdrawal of the bagnet fishery from the coast of Bangladesh.

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.