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.

Lionfish dissection: techniques and applications

Dissection can provide unique information on the physiology, biology and ecology of organisms. This document describes protocols for dissecting lionfish (Pterois volitans and P. miles). Protocols were developed to provide guidance to trained research personnel. Lionfish are native to the Indo-Pacific, but have become established in marine habitats within the Western Atlantic, Gulf of Mexico and Caribbean. The protocols described within this document were designed to help standardize handling and dissection methodologies for these species, with the goal of improving the coordination of research (e.g., Lionfish Tissue Repository; Appendix V). We focus on dissection methods, which yield data that contribute to our understanding of lionfish biology and ecology. By pairing dissection information with environmental and biotic data, researchers and managers can better understand lionfish population structure and dynamics, age and growth, reproductive biology, and food web ecology on various temporal and spatial scales.

NMFS / Interagency Working Group Evaluation of CITES Criteria and Guidelines.

EXECUTIVE SUMMARY: At present, the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) criteria used to assess whether a population qualifies for inclusion in the CITES Appendices relate to (A) size of the population, (B) area of distribution of the population, and (C) declines in the size of the population. Numeric guidelines are provided as indicators of a small population (less than 5,000 individuals), a small subpopulation (less than 500 individuals), a restricted area of distribution for a population (less than 10,000 km2), a restricted area of distribution for a subpopula-tion (less than 500 km2), a high rate of decline (a decrease of 50% or more in total within 5 years or two generations whichever is longer or, for a small wild population, a decline of 20% or more in total within ten years or three generations whichever is longer), large fluctuations (population size or area of distribution varies widely, rapidly and frequently, with a variation greater than one order of magnitude), and a short-term fluctuation (one of two years or less). The Working Group discussed several broad issues of relevance to the CITES criteria and guidelines. These included the importance of the historical extent of decline versus the recent rate of decline; the utility and validity of incorporating relative population productivity into decline criteria; the utility of absolute numbers for defining small populations or small areas; the appropriateness of generation times as time frames for examining declines; the importance of the magnitude and frequency of fluctuations as factors affecting risk of extinction; and the overall utility of numeric thresh-olds or guidelines.

Our living oceans: report on the status of U.S. living marine resources, 6th edition

The National Marine Fisheries Service (NMFS) is dedicated to the stewardship of living marine resources (LMR’s). This is accomplished through science-based conservation and management, and the promotion of healthy ecosystems. As a steward, NMFS has an obligation to conserve, protect, and manage these resources in a way that ensures their continuation as functioning components of healthy marine ecosystems, affords economic opportunities, and enhances the quality of life for the American public. In addition to its responsibilities within the U.S. Exclusive Economic Zone (EEZ), NMFS plays a supportive and advisory role in the management of LMR’s in the coastal areas under state jurisdiction and provides scientific and policy leadership in the international arena. NMFS also implements international measures for the conservation and management of LMR’s, as appropriate.NMFS receives its stewardship responsibilities under a number of Federal laws. These include the Nation’s primary fisheries law, the Magnuson Fishery Conservation and Management Act. This law was first passed in 1976, later reauthorized as the Magnuson-Stevens Fishery Conservation and Management Act in 1996, and reauthorized again on 12 January 2007 as the Magnuson-Stevens Fishery Conservation and Management Reauthorization Act (MSRA). The MSRA mandates strong action to conserve and manage fishery resources and requires NMFS to end overfishing by 2010 in all U.S. commercial and recreational fisheries, rebuild all overfished stocks, and conserve essential fish habitat.

Marine and estuarine ecosystem and habitat classification

The Ecological Society of America and NOAA's Offices of Habitat Conservation and Protected Resources sponsored a workshop to develop a national marine and estuarine ecosystem classification system. Among the 22 people involved were scientists who had developed various regional classification systems and managers from NOAA and other federal agencies who might ultimately use this system for conservation and management. The objectives were to: (1) review existing global and regional classification systems; (2) develop the framework of a national classification system; and (3) propose a plan to expand the framework into a comprehensive classification system. Although there has been progress in the development of marine classifications in recent years, these have been either regionally focused (e.g., Pacific islands) or restricted to specific habitats (e.g., wetlands; deep seafloor). Participants in the workshop looked for commonalties across existing classification systems and tried to link these using broad scale factors important to ecosystem structure and function.

Marine Fisheries Stock Assessment Improvement Plan: report of the National Marine Fisheries Service National Task Force for Improving Fish Stock Assessments

This report argues for greatly increased resources in terms of data collection facilities and staff to collect, process, and analyze the data, and to communicate the results, in order for NMFS to fulfill its mandate to conserve and manage marine resources. In fact, the authors of this report had great difficulty defining the "ideal" situation to which fisheries stock assessments and management should aspire. One of the primary objectives of fisheries management is to develop sustainable harvest policies that minimize the risks of overfishing both target species and associated species. This can be achieved in a wide spectrum of ways, ranging between the following two extremes. The first is to implement only simple management measures with correspondingly simple assessment demands, which will usually mean setting fishing mortality targets at relatively low levels in order to reduce the risk of unknowingly overfishing or driving ecosystems towards undesirable system states. The second is to expand existing data collection and analysis programs to provide an adequate knowledge base that can support higher fishing mortality targets while still ensuring low risk to target and associated species and ecosystems. However, defining "adequate" is difficult, especially when scientists have not even identified all marine species, and information on catches, abundances, and life histories of many target species, and most associated species, is sparse. Increasing calls from the public, stakeholders, and the scientific community to implement ecosystem-based stock assessment and management make it even more difficult to define "adequate," especially when "ecosystem-based management" is itself not well-defined. In attempting to describe the data collection and assessment needs for the latter, the authors took a pragmatic approach, rather than trying to estimate the resources required to develop a knowledge base about the fine-scale detailed distributions, abundances, and associations of all marine species. Thus, the specified resource requirements will not meet the expectations of some stakeholders. In addition, the Stock Assessment Improvement Plan is designed to be complementary to other related plans, and therefore does not duplicate the resource requirements detailed in those plans, except as otherwise noted.

An ecological characterization of the Stellwagen Bank National Marine Sanctuary Region: oceanographic, biogeographic, and contaminants assessment

The mission of NOAA’s National Marine Sanctuary Program (NMSP) is to serve as the trustee for a system of marine protected areas, to conserve, protect, and enhance their biodiversity, ecological integrity, and cultural legacy while facilitating compatible uses. Since 1972, thirteen National Marine Sanctuaries, representing a wide variety of ocean environments, have been established, each with management goals tuned to their unique diversity. Extending from Cape Ann to Cape Cod across the mouth of Massachusetts Bay, Stellwagen Bank National Marine Sanctuary (NMS) encompasses 2,181 square kilometers of highly productive, diverse, and culturally unique Federal waters. As a result of its varied seafloor topography, oceanographic conditions, and high primary productivity, Stellwagen Bank NMS is utilized by diverse assemblages of seabirds, marine mammals, invertebrates, and fish species, as well as containing a number of maritime heritage resources. Furthermore, it is a region of cultural significance, highlighted by the recent discovery of several historic shipwrecks. Officially designated in 1992, Stellwagen Bank became the Nation’s twelfth National Marine Sanctuary in order to protect these and other unique biological, geological, oceanographic, and cultural features of the region. The Stellwagen Bank NMS is in the midst of its first management plan review since designation. The management plan review process, required by law, is designed to evaluate, enhance, and guide the development of future research efforts, education and outreach, and the management approaches used by Sanctuaries. Given the ecological and physical complexity of Stellwagen Bank NMS, burgeoning anthropogenic impacts to the region, and competing human and biological uses, the review process was challenged to assimilate and analyze the wealth of existing scientific knowledge in a framework which could enhance management decision-making. Unquestionably, the Gulf of Maine, Massachusetts Bay, and Stellwagen Bank-proper are extremely well studied systems, and in many regards, the scientific information available greatly exceeds that which is available for other Sanctuaries. However, the propensity of scientific information reinforces the need to utilize a comprehensive analytical approach to synthesize and explore linkages between disparate information on physical, biological, and chemical processes, while identifying topics needing further study. Given this requirement, a partnership was established between NOAA’s National Marine Sanctuary Program (NMSP) and the National Centers for Coastal Ocean Science (NCCOS) so as to leverage existing NOAA technical expertise to assist the Sanctuary in developing additional ecological assessment products which would benefit the management plan review process.

Characterization and monitoring of temperature, chlorophyll, and light availability patterns in National Marine Sanctuary waters: final report

This project provides a framework for developing the capabilities of using satellite and related oceanographic and climatological data to improve environmental monitoring and characterization of physical, biological, and water quality parameters in the National Marine Sanctuaries (NMS). The project sought to: 1) assemble satellite imagery datasets in order to extract spatially explicit time series information on temperature, chlorophyll, and light availability for the Cordell Bank, Gulf of the Farallones, and Monterey Bay National Marine Sanctuaries. 2) perform preliminary analyses with these data in order to identify seasonal, annual, inter-annual, and event-driven patterns.

An ecological characterization of Salt River Bay National Historical Park and Ecological Preserve, U.S. Virgin Islands

Salt River Bay National Historical Park and Ecological Preserve (hereafter, SARI or the park) was created in 1992 to preserve, protect, and interpret nationally significant natural, historical, and cultural resources (United States Congress 1992). The diverse ecosystem within it includes a large mangrove forest, a submarine canyon, coral reefs, seagrass beds, coastal forests, and many other natural and developed landscape elements. These ecosystem components are, in turn, utilized by a great diversity of flora and fauna. A comprehensive spatial inventory of these ecosystems is required for successful management. To meet this need, the National Oceanic and Atmospheric Administration (NOAA) Biogeography Program, in consultation with the National Park Service (NPS) and the Government of the Virgin Islands Department of Planning and Natural Resources (VIDPNR), conducted an ecological characterization. The characterization consists of three complementary components: a text report, digital habitat maps, and a collection of historical aerial photographs. This ecological characterization provides managers with a suite of tools that, when coupled with the excellent pre-existing body of work on SARI resources, enables improved research and monitoring activities within the park (see Appendix F for a list of data products).

A pilot survey of deepwater coral/sponge assemblages and their susceptibility to fishing/harvest impacts at the Olympic Coast National Marine Sanctuary (OCNMS). Cruise report for NOAA Ship McARTHUR II Cruise AR-04-04: Leg 2 (June 1-12, 2004)

The offshore shelf and canyon habitats of the OCNMS are areas of high primary productivity and biodiversity that support extensive groundfish fisheries. Recent acoustic surveys conducted in these waters have indicated the presence of hard-bottom substrates believed to harbor unique deep-sea coral and sponge assemblages. Such fauna are often associated with shallow tropical waters, however an increasing number of studies around the world have recorded them in deeper, cold-water habitats in both northern and southern latitudes. These habitats are of tremendous value as sites of recruitment for commercially important fishes. Yet, ironically, studies have shown how the gear used in offshore demersal fishing, as well as other commercial operations on the seafloor, can cause severe physical disturbances to resident benthic fauna. Due to their exposed structure, slow growth and recruitment rates, and long life spans, deep-sea corals and sponges may be especially vulnerable to such disturbances, requiring very long periods to recover. Potential effects of fishing and other commercial operations in such critical habitats, and the need to define appropriate strategies for the protection of these resources, have been identified as a high-priority management issue for the sanctuary.

The use of large artificial reefs to enhance fish populations at different depths in the Florida Keys

This study showed that large prefabricated units and concrete rubble patch reefs, placed as artificial marine habitats on sand bottom, greatly enhance the abundance, diversity, and biomass of fish in an area. Densities of individuals and biomass were found considerably higher at artificial reefs than at nearby, natural, bank reefs, a result consistent with other studies. Location, depth, and vertical profile are important factors determining fish assemblages at artificial habitats in the Keys. Fishes were both produced at artificial reefs and attracted from the surrounding area. Fish assemblages at the Hawk Channel artificial reefs were considerably different from those on the offshore reef tract, particularly in terms of dominant species. Rescue of the original 1992 work in 2005 was funded by the South Florida Ecosystem Restoration Prediction and Modeling Program.

Mapping the shallow-water coral ecosystems of the Freely Associated States: an implementation plan

This Freely Associated States Shallow-water Coral Ecosystem Mapping Implementation Plan (FAS MIP) presents a framework for the development of shallow-water (~0–40 m; 0–22 fm) benthic habitat and possibly bathymetric maps of critical areas of the Freely Associated States (FAS). The FAS is made up of three self-governing groups of islands and atolls—the Republic of Palau (Palau), the Federated States of Micronesia (FSM), and the Republic of the Marshall Islands (RMI)—that are affiliated with the United States through Compacts of Free Association. This MIP was developed with extensive input from colleges, national and state regulatory and management agencies, federal agencies, non-governmental organizations, and individuals involved in or supporting the conservation and management of the FAS’s coral ecosystems. A list of organizations and individuals that provided input to the development of this MIP is provided in Appendix 1. This MIP has been developed to complement the Coral Reef Mapping Implementation Plan (2nd Draft) released in 1999 by the U.S. Coral Reef Task Force’s Mapping and Information Synthesis Working Group. That plan focused on mapping United States and FAS shallow-water (then defined as <30 m) coral reefs by 2009, based on available funding and geographic priorities, using primarily visual interpretation of aerial photography and satellite imagery. This MIP focuses on mapping the shallow-water (now defined as 0–40 m, rather than 0–30 m) coral ecosystems of the FAS using a suite of technologies and map development procedures. Both this FAS MIP and the 1999 Coral Reef Mapping Implementation Plan (2nd Draft) support to goals of the National Action Plan to Conserve Coral Reefs (U.S. Coral Reef Task Force, 2000). This FAS MIP presents a framework for mapping the coral ecosystems of the FAS and should be considered an evolving document. As priorities change, funding opportunities arise, new data are collected, and new technologies become available, the information presented herein will change.

Mapping southern Florida's shallow-water coral ecosystems: an implementation plan

The Southern Florida Shallow-water Coral Ecosystem Mapping Implementation Plan (MIP) discusses the need to produce shallow-water (~0-40 m; 0-22 fm) benthic habitat and bathymetric maps of critical areas in southern Florida and moderate-depth (~40-200 m; 22 -109 fm) bathymetric maps for all of Florida. The ~0-40 m depth regime generally represents where most hermatypic coral species are found and where most direct impacts from pollution and coastal development occur. The plan was developed with extensive input from over 90 representatives of state regulatory and management agencies, federal agencies, universities, and non-governmental organizations involved in the conservation and management of Florida’s coral ecosystems. Southern Florida’s coral ecosystems are extensive. They extend from the Dry Tortugas in the Florida Keys as far north as St Lucie Inlet on the Atlantic Ocean coast and Tarpon Springs on the Gulf of Mexico coast. Using 10 fm (18 m) depth curves on nautical charts as a guide, southern Florida has as much as 84 percent (30,801 sq km) of 36,812 sq km of potential shallow-water (<10 fm; <18 m) coral ecosystems the tropical and subtropical U.S. Moreover, southern Florida’s coral ecosystems contribute greatly to the regional economy. Coral ecosystem-related expenditures generated $4.4 billion in sales, income, and employment and created over 70,000 full-time and part-time jobs in the region during the recent 12-month periods when surveys were conducted.

A biogeographic assessment of the Channel Islands National Marine Sanctuary: a review of boundary expansion concepts for NOAA’s National Marine Sanctuary Program

The priority management goal of the National Marine Sanctuaries Program (NMSP) is to protect marine ecosystems and biodiversity. This goal requires an understanding of broad-scale ecological relationships and linkages between marine resources and physical oceanography to support an ecosystem management approach. The Channel Islands National Marine Sanctuary (CINMS) is currently reviewing its management plan and investigating boundary expansion. A management plan study area (henceforth, Study Area) was described that extends from the current boundary north to the mainland, and extends north to Point Sal and south to Point Dume. Six additional boundary concepts were developed that vary in area and include the majority of the Study Area. The NMSP and CINMS partnered with NOAA’s National Centers for Coastal Ocean Science Biogeography Team to conduct a biogeographic assessment to characterize marine resources and oceanographic patterns within and adjacent to the sanctuary. This assessment includes a suite of quantitative spatial and statistical analyses that characterize biological and oceanographic patterns in the marine region from Point Sal to the U.S.-Mexico border. These data were analyzed using an index which evaluates an ecological “cost-benefit” within the proposed boundary concepts and the Study Area. The sanctuary resides in a dynamic setting where two oceanographic regimes meet. Cold northern waters mix with warm southern waters around the Channel Islands creating an area of transition that strongly influences the regions oceanography. In turn, these processes drive the biological distributions within the region. This assessment analyzes bathymetry, benthic substrate, bathymetric life-zones, sea surface temperature, primary production, currents, submerged aquatic vegetation, and kelp in the context of broad-scale patterns and relative to the proposed boundary concepts and the Study Area. Boundary cost-benefit results for these parameters were variable due to their dynamic nature; however, when analyzed in composite the Study Area and Boundary Concept 2 were considered the most favorable. Biological data were collected from numerous resource agencies and university scientists for this assessment. Fish and invertebrate trawl data were used to characterize community structure. Habitat suitability models were developed for 15 species of macroinvertebrates and 11 species of fish that have significant ecological, commercial, or recreational importance in the region and general patterns of ichthyoplankton distribution are described. Six surveys of ship and plane at-sea surveys were used to model marine bird diversity from Point Arena to the U.S.-Mexico border. Additional surveys were utilized to estimate density and colony counts for nine bird species. Critical habitat for western snowy plover and the location of California least tern breeding pairs were also analyzed. At-sea surveys were also used to describe the distribution of 14 species of cetaceans and five species of pinnipeds. Boundary concept cost-benefit indices revealed that Boundary Concept 2 and the Study Area were most favorable for the majority of the species-specific analyses. Boundary Concept 3 was most favorable for bird diversity across the region. Inadequate spatial resolution for fish and invertebrate community data and incompatible sampling effort information for bird and mammal data precluded boundary cost-benefit analysis.