An ecological characterization of the marine resources of Vieques, Puerto Rico. Part I: Historical data synthesis

From the 1940s until 2003, portions of the island of Vieques, a municipality within the Commonwealth of Puerto Rico, were used by the US Navy as a base and training facility, resulting in development and zoning history that differ in comparison to other Caribbean islands. The majority of former Navy lands are now under the jurisdiction of the Department of the Interior’s Fish and Wildlife Service as a National Wildlife Refuge, while a smaller percentage of land was transferred to the Vieques municipality and the Puerto Rico Conservation Trust. An analysis of the distribution and status of the marine resources is timely in light of the recent land transfer, increases in development and tourism, and potential changes in marine zoning around the island. To meet this need, NOAA’s Biogeography Branch, in cooperation with the Office of Response and Restoration and other local and regional partners, conducted Part I of an ecological characterization to integrate historical data and research into a synthesis report. The overall objective of this report is to provide resource managers and residents a comprehensive characterization of the marine resources of Vieques to support research, monitoring, and management. For example, knowledge of the spatial distribution of physical features, habitats, and biological communities is necessary to make an informed decision of the establishment and placement of a marine protected area (MPA). The report is divided into chapters based on the physical environment (e.g., climate, geology, bathymetry), habitat types (e.g., reefs and hardbottom, seagrasses, mangroves) and major faunal groups (e.g. fish, turtles, birds). Each section includes five subsections: an overview, description of the relevant literature, methods of analysis, information on the distribution, status and trends of the particular resource, and a discussion of ecological linkages with other components of the Vieques marine ecosystem and surrounding environment. The physical environment of Vieques is similar to other islands within the Greater Antilles chain, with some distinctions. The warm, tropical climate of Vieques, mediated by the northeasterly trade winds, is characterized by a dry season (December-April) and a rainy season (May-November), the latter of which is characterized by the occasional passage of tropical cyclones. Compared to mainland Puerto Rico, Vieques is characterized by lower elevation, less annual precipitation, and higher average temperatures. The amount of annual precipitation also varies spatially within Vieques, with the western portion of the island receiving higher amounts of rainfall than further east. While the North Equatorial Current dominates the circulation pattern in the Greater Antilles region, small scale current patterns specific to Vieques are not as well characterized. These physical processes are important factors mitigating the distribution and composition of marine benthic habitats around Vieques. In general, the topography of Vieques is characterized by rolling hills. Mt. Pirata, the tallest point at 301 m, is located near the southwest coast. In the absence of island wide sedimentation measurements, information on land cover, slope, precipitation, and soil type were used to estimate relative erosion potential and sediment delivery for each watershed. While slope and precipitation amount are the primary driving factors controlling runoff, land use practices such as urban development, military activity, road construction, and agriculture can increase the delivery of pollution and sediments to coastal waters. Due to the recent land transfer, increased development and tourism is expected, which may result in changes in the input of sediments to the coastal environment.

Simple data analysis for biologists

This document provides a simple introduction to research methods and analysis tools for biologists or environmental scientists, with particular emphasis on fish biology in devleoping countries.

An evaluation of length-frequency sampling procedures and subsequent data analysis for purse seine-caught yellowfin tuna in the Eastern Pacific Ocean

ENGLISH: A two-stage sampling design is used to estimate the variances of the numbers of yellowfin in different age groups caught in the eastern Pacific Ocean. For purse seiners, the primary sampling unit (n) is a brine well containing fish from a month-area stratum; the number of fish lengths (m) measured from each well are the secondary units. The fish cannot be selected at random from the wells because of practical limitations. The effects of different sampling methods and other factors on the reliability and precision of statistics derived from the length-frequency data were therefore examined. Modifications are recommended where necessary. Lengths of fish measured during the unloading of six test wells revealed two forms of inherent size stratification: 1) short-term disruptions of existing pattern of sizes, and 2) transition zones between long-term trends in sizes. To some degree, all wells exhibited cyclic changes in mean size and variance during unloading. In half of the wells, it was observed that size selection by the unloaders induced a change in mean size. As a result of stratification, the sequence of sizes removed from all wells was non-random, regardless of whether a well contained fish from a single set or from more than one set. The number of modal sizes in a well was not related to the number of sets. In an additional well composed of fish from several sets, an experiment on vertical mixing indicated that a representative sample of the contents may be restricted to the bottom half of the well. The contents of the test wells were used to generate 25 simulated wells and to compare the results of three sampling methods applied to them. The methods were: (1) random sampling (also used as a standard), (2) protracted sampling, in which the selection process was extended over a large portion of a well, and (3) measuring fish consecutively during removal from the well. Repeated sampling by each method and different combinations indicated that, because the principal source of size variation occurred among primary units, increasing n was the most effective way to reduce the variance estimates of both the age-group sizes and the total number of fish in the landings. Protracted sampling largely circumvented the effects of size stratification, and its performance was essentially comparable to that of random sampling. Sampling by this method is recommended. Consecutive-fish sampling produced more biased estimates with greater variances. Analysis of the 1988 length-frequency samples indicated that, for age groups that appear most frequently in the catch, a minimum sampling frequency of one primary unit in six for each month-area stratum would reduce the coefficients of variation (CV) of their size estimates to approximately 10 percent or less. Additional stratification of samples by set type, rather than month-area alone, further reduced the CV's of scarce age groups, such as the recruits, and potentially improved their accuracy. The CV's of recruitment estimates for completely-fished cohorts during the 198184 period were in the vicinity of 3 to 8 percent. Recruitment estimates and their variances were also relatively insensitive to changes in the individual quarterly catches and variances, respectively, of which they were composed. SPANISH: Se usa un diseño de muestreo de dos etapas para estimar las varianzas de los números de aletas amari11as en distintos grupos de edad capturados en el Océano Pacifico oriental. Para barcos cerqueros, la unidad primaria de muestreo (n) es una bodega de salmuera que contenía peces de un estrato de mes-área; el numero de ta11as de peces (m) medidas de cada bodega es la unidad secundaria. Limitaciones de carácter practico impiden la selección aleatoria de peces de las bodegas. Por 10 tanto, fueron examinados los efectos de distintos métodos de muestreo y otros factores sobre la confiabilidad y precisión de las estadísticas derivadas de los datos de frecuencia de ta11a. Se recomiendan modificaciones donde sean necesarias. Las ta11as de peces medidas durante la descarga de seis bodegas de prueba revelaron dos formas de estratificación inherente por ta11a: 1) perturbaciones a corto plazo en la pauta de ta11as existente, y 2) zonas de transición entre las tendencias a largo plazo en las ta11as. En cierto grado, todas las bodegas mostraron cambios cíclicos en ta11a media y varianza durante la descarga. En la mitad de las bodegas, se observo que selección por ta11a por los descargadores indujo un cambio en la ta11a media. Como resultado de la estratificación, la secuencia de ta11as sacadas de todas las bodegas no fue aleatoria, sin considerar si una bodega contenía peces de un solo lance 0 de mas de uno. El numero de ta11as modales en una bodega no estaba relacionado al numero de lances. En una bodega adicional compuesta de peces de varios lances, un experimento de mezcla vertical indico que una muestra representativa del contenido podría estar limitada a la mitad inferior de la bodega. Se uso el contenido de las bodegas de prueba para generar 25 bodegas simuladas y comparar los resultados de tres métodos de muestreo aplicados a estas. Los métodos fueron: (1) muestreo aleatorio (usado también como norma), (2) muestreo extendido, en el cual el proceso de selección fue extendido sobre una porción grande de una bodega, y (3) medición consecutiva de peces durante la descarga de la bodega. EI muestreo repetido con cada método y distintas combinaciones de n y m indico que, puesto que la fuente principal de variación de ta11a ocurría entre las unidades primarias, aumentar n fue la manera mas eficaz de reducir las estimaciones de la varianza de las ta11as de los grupos de edad y el numero total de peces en los desembarcos. El muestreo extendido evito mayormente los efectos de la estratificación por ta11a, y su desempeño fue esencialmente comparable a aquel del muestreo aleatorio. Se recomienda muestrear con este método. El muestreo de peces consecutivos produjo estimaciones mas sesgadas con mayores varianzas. Un análisis de las muestras de frecuencia de ta11a de 1988 indico que, para los grupos de edad que aparecen con mayor frecuencia en la captura, una frecuencia de muestreo minima de una unidad primaria de cada seis para cada estrato de mes-área reduciría los coeficientes de variación (CV) de las estimaciones de ta11a correspondientes a aproximadamente 10% 0 menos. Una estratificación adicional de las muestras por tipo de lance, y no solamente mes-área, redujo aun mas los CV de los grupos de edad escasos, tales como los reclutas, y mejoró potencialmente su precisión. Los CV de las estimaciones del reclutamiento para las cohortes completamente pescadas durante 1981-1984 fueron alrededor de 3-8%. Las estimaciones del reclutamiento y sus varianzas fueron también relativamente insensibles a cambios en las capturas de trimestres individuales y las varianzas, respectivamente, de las cuales fueron derivadas. (PDF contains 70 pages)

Workshop on turtle bycatch mitigation for longline fisheries: experimental design and data analysis, 7-8 November 2007, San Ramón de Alajuela, Costa Rica

Large numbers of fishing vessels operating from ports in Latin America participate in surface longline fisheries in the eastern Pacific Ocean (EPO), and several species of sea turtles inhabit the grounds where these fleets operate. The endangered status of several sea turtle species, and the success of circle hooks (‘treatment’ hooks) in reducing turtle hookings in other ocean areas, as compared to J-hooks and Japanese-style tuna hooks (‘control’ hooks), prompted the initiation of a hook exchange program on the west coast of Latin America, the Eastern Pacific Regional Sea Turtle Program (EPRSTP)1. One of the goals of the EPRSTP is to determine if circle hooks would be effective at reducing turtle bycatch in artisanal fisheries of the EPO without significantly reducing the catch of marketable fish species. Participating fishers were provided with circle hooks at no cost and asked to replace the J/Japanese-style tuna hooks on their longlines with circle hooks in an alternating manner. Data collected by the EPRSTP show differences in longline gear and operational characteristics within and among countries. These aspects of the data, in addition to difficulties encountered with implementation of the alternating-hook design, pose challenges for analysis of these data.

A report on the population structure of adult salmon and sea trout in the River Lune using scale samples - with reference to historical data.

During 1993, a comprehensive data set of scale readings, length and weight measurements was established for migratory salmonids on the River Lune. This information was collected using three methods of fish capture: 1. The Lune estuary commercial nets. 2. River Lune Forge weir fish trap. 3. River Lune rod catch scale returns. Additional information was contributed by the Kent, Leven and Duddon rod and commercial fisheries. The data shows that the salmon stock in 1993 was dominated by two year old smolts. This varies from year to year. The sea trout population displays a normal population curve in terms of numbers of fish in each age and weight class. The growth rate of salmon and sea trout is very similar even though salmon have the benefit of high sea feeding.

Report on BOBLME Indian mackerel genetic data analysis including final workshop, Phuket, Thailand, 17-19 February 2015

This workshop followed on from two previous workshops held in Colombo, Sri Lanka, 2012 and Kochi, India in 2013. The 14 microsattellite markers had previously been developed for Indian Mackerel (Rastrelliger kanagurta) were used on 31 tissue collections from all eight countries were genotyped in India.

Techniques for spatial analysis and visualization of benthic mapping data: final report

The mapping and geospatial analysis of benthic environments are multidisciplinary tasks that have become more accessible in recent years because of advances in technology and cost reductions in survey systems. The complex relationships that exist among physical, biological, and chemical seafloor components require advanced, integrated analysis techniques to enable scientists and others to visualize patterns and, in so doing, allow inferences to be made about benthic processes. Effective mapping, analysis, and visualization of marine habitats are particularly important because the subtidal seafloor environment is not readily viewed directly by eye. Research in benthic environments relies heavily, therefore, on remote sensing techniques to collect effective data. Because many benthic scientists are not mapping professionals, they may not adequately consider the links between data collection, data analysis, and data visualization. Projects often start with clear goals, but may be hampered by the technical details and skills required for maintaining data quality through the entire process from collection through analysis and presentation. The lack of technical understanding of the entire data handling process can represent a significant impediment to success. While many benthic mapping efforts have detailed their methodology as it relates to the overall scientific goals of a project, only a few published papers and reports focus on the analysis and visualization components (Paton et al. 1997, Weihe et al. 1999, Basu and Saxena 1999, Bruce et al. 1997). In particular, the benthic mapping literature often briefly describes data collection and analysis methods, but fails to provide sufficiently detailed explanation of particular analysis techniques or display methodologies so that others can employ them. In general, such techniques are in large part guided by the data acquisition methods, which can include both aerial and water-based remote sensing methods to map the seafloor without physical disturbance, as well as physical sampling methodologies (e.g., grab or core sampling). The terms benthic mapping and benthic habitat mapping are often used synonymously to describe seafloor mapping conducted for the purpose of benthic habitat identification. There is a subtle yet important difference, however, between general benthic mapping and benthic habitat mapping. The distinction is important because it dictates the sequential analysis and visualization techniques that are employed following data collection. In this paper general seafloor mapping for identification of regional geologic features and morphology is defined as benthic mapping. Benthic habitat mapping incorporates the regional scale geologic information but also includes higher resolution surveys and analysis of biological communities to identify the biological habitats. In addition, this paper adopts the definition of habitats established by Kostylev et al. (2001) as a “spatially defined area where the physical, chemical, and biological environment is distinctly different from the surrounding environment.” (PDF contains 31 pages)

The Ragfish, Icosteus aenigmaticus Lockington, 1880: A Synthesis of Historical and Recent Records From the North Pacific Ocean and the Bering Sea

Knowledge of the distribution and biology of the ragfish, Icosteus aenigmaticus, an aberrant deepwater perciform of the North Pacific Ocean, has increased slowly since the first description of the species in the 1880’s which was based on specimens retrieved from a fish monger’s table in San Francisco, Calif. As a historically rare, and subjectively unattractive appearing noncommercial species, ichthyologists have only studied ragfish from specimens caught and donated by fishermen or by the general public. Since 1958, I have accumulated catch records of >825 ragfish. Specimens were primarily from commercial fishermen and research personnel trawling for bottom and demersal species on the continental shelves of the eastern North Pacific Ocean, Gulf of Alaska, Bering Sea, and the western Pacific Ocean, as well as from gillnet fisheries for Pacific salmon, Oncorhynchus spp., in the north central Pacific Ocean. Available records came from four separate sources: 1) historical data based primarily on published and unpublished literature (1876–1990), 2) ragfish delivered fresh to Humboldt State University or records available from the California Department of Fish and Game of ragfish caught in northern California and southern Oregon bottom trawl fisheries (1950–99), 3) incidental catches of ragfish observed and recorded by scientific observers of the commercial fisheries of the eastern Pacific Ocean and catches in National Marine Fisheries Service trawl surveys studying these fisheries from 1976 to 1999, and 4) Japanese government research on nearshore fisheries of the northwestern Pacific Ocean (1950–99). Limited data on individual ragfish allowed mainly qualitative analysis, although some quantitative analysis could be made with ragfish data from northern California and southern Oregon. This paper includes a history of taxonomic and common names of the ragfish, types of fishing gear and other techniques recovering ragfish, a chronology of range extensions into the North Pacific and Bering Sea, reproductive biology of ragfish caught by trawl fisheries off northern California and southern Oregon, and topics dealing with early, juvenile, and adult life history, including age and growth, food habits, and ecology. Recommendations for future study are proposed, especially on the life history of juvenile ragfish (5–30 cm FL) which remains enigmatic.

Recent changes in the efficiency of vessels fishing for yellowfin tuna in the eastern Pacific Ocean

ENGLISH: Since the inception of the Inter-American Tropical Tuna Commission in 1950, one of the primary tasks of its scientific staff has been the collection and analysis of the statistics of total catch, effort expended in obtaining this catch, and the apparent abundance of yellowfin tuna (Neothunnus macropterus) and the skipjack tuna (Katsuwonus pelamis) in the Eastern Pacific Ocean. A concentrated effort by the staff during 1951 and 1952 resulted in the compilation of a series of historical data on the catch and catch-per-effort of tropical tunas for the years 1934-1950, and in the establishment of a detailed logbook system to monitor the current activities of the tuna fleets. Schaefer (1953) and Shimada and Schaefer (1956) have reviewed in detail the methods of collection and analysis of these data. Further studies, based on these and subsequently collected records, are contained in publications by Schaefer (1957), Shimada (1958), Alverson (1959, 1960), Griffiths (1960) and Calkins (1961). SPANISH: Desde que la Comisión Interamericana del Atún Tropical comenzó sus funciones en 1950, entre las más importantes tareas de su personal científico incluyó la recolección y análisis de las estadísticas de la captura total, del esfuerzo empleado en obtener esta captura y de la abundancia aparente de los atunes aleta amarilla (Neothunnus macropterus) y barriletes (Katsutvonus pelamis) en el Océano Pacífico Oriental. El concentrado esfuerzo del personal científico de la Comisión durante 1951 y 1952 dió como resultado la compilación de una serie de datos históricos sobre la captura de atunes tropicales y sobre la captura según el esfuerzo durante los años 1934 a 1950, así como el establecimiento de un sistema detallado de registro de las anotaciones en los cuadernos de bitácora para vigilar las actividades diarias de las flotas atuneras. Schaefer (1953) y Shimada y Schaefer (1956) han expuesto detalladamente los métodos de recolección y análisis de dichos datos. Otros estudios, basados en estos registros y en los recolectados posteriormente, se encuentran en las publicaciones de Schaefer (1957), Shimada (1958), Alverson (1959, 1960), Griffiths (1960) y Calkins (1961).

Growth, recruitment, and abundance of juvenile striped mullet (Mugil cephalus) in South Carolina estuaries

Growth, recruitment, and abundance of young-of-the-year (YOY) striped mullet (Mugil cephalus L.) in estuarine habitats in South Carolina from 1998 to 2000 were examined and compared to historical data (1986–91) of growth, recruitment, and abundance. Daily growth increments from the sagittal otoliths of juvenile striped mullet were validated by using fish immersed in oxytetracycline hydrochloride (OTC) for five hours from the Charleston Harbor Estuary system. The distribution of back-calculated birthdates indicated that striped mullet spawn from October to late April and estuarine recruitment occurs from January through May. Juveniles were more abundant in mesohaline and polyhaline salinity regimes but were found throughout the estuary. Juvenile growth after recruitment into the estuary can be described by the relationship Total length (mm) = 0.341 (Age)1.04 (r2=0.741, P=0.001). Growth of juveniles according to the analysis of size-frequency data from historical surveys (1986 to 1991) in the same estuaries gave the relationship Total length (mm) = 8.77 (month)1.12 (r2=0.950, P=0.001). The similarity in the growth curves for both groups of fish suggests that juvenile striped mullet in South Carolina have consistent annual growth during the first year of life.