Removing observational noise from fisheries-independent time series data using ARIMA models

Abundance indices derived from fishery-independent surveys typically exhibit much higher interannual variability than is consistent with the within-survey variance or the life history of a species. This extra variability is essentially observation noise (i.e. measurement error); it probably reflects environmentally driven factors that affect catchability over time. Unfortunately, high observation noise reduces the ability to detect important changes in the underlying population abundance. In our study, a noise-reduction technique for uncorrelated observation noise that is based on autoregressive integrated moving average (ARIMA) time series modeling is investigated. The approach is applied to 18 time series of finfish abundance, which were derived from trawl survey data from the U.S. northeast continental shelf. Although the a priori assumption of a random-walk-plus-uncorrelated-noise model generally yielded a smoothed result that is pleasing to the eye, we recommend that the most appropriate ARIMA model be identified for the observed time series if the smoothed time series will be used for further analysis of the population dynamics of a species.

Population structure and variance effective size of red snapper (Lutjanus campechanus) in the northern Gulf of Mexico*

We assayed allelic variation at 19 nuclear-encoded microsatellites among 1622 Gulf red snapper (Lutjanus campechanus) sampled from the 1995 and 1997 cohorts at each of three offshore localities in the northern Gulf of Mexico (Gulf). Localities represented western, central, and eastern subregions within the northern Gulf. Number of alleles per microsatellite per sample ranged from four to 23, and gene diversity ranged from 0.170 to 0.917. Tests of conformity to Hardy-Weinberg equilibrium expectations and of genotypic equilibrium between pairs of micro-satellites were generally nonsignificant following Bonferroni correction. Significant genic or genotypic heterogeneity (or both) among samples was detected at four microsatellites and over all microsatellites. Levels of divergence among samples were low (FST ≤0.001). Pairwise exact tests revealed that six of seven “significant” comparisons involved temporal rather than spatial heterogeneity. Contemporaneous or variance effective size (NeV) was estimated from the temporal variance in allele frequencies by using a maximum-likelihood method. Estimates of NeV ranged between 1098 and >75,000 and differed significantly among localities; the NeV estimate for the sample from the northcentral Gulf was >60 times as large as the estimates for the other two localities. The differences in variance effective size could ref lect differences in number of individuals successfully reproducing, differences in patterns and intensity of immigration, or both, and are consistent with the hypothesis, supported by life-history data, that different “demographic stocks” of red snapper are found in the northern Gulf. Estimates of NeV for red snapper in the northern Gulf were at least three orders of magnitude lower than current estimates of census size (N). The ratio of effective to census size (Ne/N) is far below that expected in an ideal population and may reflect high variance in individual reproductive success, high temporal and spatial variance in productivity among subregions or a combination of the two.

BMP treatment technologies, monitoring needs, and knowledge gaps: status of the knowledge and relevance within the Tahoe Basin

This Technical memorandum fulfills Task 2 for Agreement 03-495 between El Dorado County and the Office of Water Programs at California State University Sacramento and their co-authors, Bachand & Associates and the University of California Tahoe Research Group: 1) a review of current stormwater treatment Best Management Practices (BMP) in the Tahoe Basin and their potential effectiveness in removing fine particles and reducing nutrient concentrations; 2) an assessment of the potential for improving the performance of different types of existing BMPs through retrofitting or better maintenance practices; 3) a review of additional promising treatment technologies not currently in use in the Tahoe Basin; and 4) a list of recommendations to help address the knowledge gaps in BMP design and performance. ... (PDF contains 67 pages)

Benthic sampling program in Biscayne Bay, 1981-1982

The Biscayne Bay Benthic Sampling Program was divided into two phases. In Phase I, sixty sampling stations were established in Biscayne Bay (including Dumfoundling Bay and Card Sound) representing diverse habitats. The stations were visited in the wet season (late fall of 1981) and in the dry season (midwinter of 1982). At each station certain abiotic conditions were measured or estimated. These included depth, sources of freshwater inflow and pollution, bottom characteristics, current direction and speed, surface and bottom temperature, salinity and dissolved oxygen, and water clarity was estimated with a secchi disk. Seagrass blades and macroalgae were counted in a 0.1-m2 grid placed so as to best represent the bottom community within a 50-foot radius. Underwater 35-mm photographs were made of the bottom using flash apparatus. Benthic samples were collected using a petite Ponar dredge. These samples were washed through a 5-mm mesh screen, fixed in formalin in the field, and later sorted and identified by experts to a pre-agreed taxonomic level. During the wet season sampling period, a nonquantitative one-meter wide trawl was made of the epibenthic community. These samples were also washed, fixed, sorted and identified. During the dry season sampling period, sediment cores were collected at each station not located on bare rock. These cores were analyzed for sediment size and organic composition by personnel of the University of Miami. Data resulting from the sampling were entered into a computer. These data were subjected to cluster analyses, Shannon-Weaver diversity analysis, multiple regression analysis of variance and covariance, and factor analysis. In Phase II of the program, fifteen stations were selected from among the sixty of Phase I. These stations were sampled quarterly. At each quarter, five Petite Ponar dredge samples were collected from each station. As in Phase I, observations and measurements, including seagrass blade counts, were made at each station. In Phase II, polychaete specimens collected were given to a separate contractor for analysis to the species level. These analyses included mean, standard deviation, coefficient of dispersion, percent of total, and numeric rank for each organism in each station as well as number of species, Shannon-Weaver taxa diversity, and dominance (the compliment of Simpson's Index) for each station. Multiple regression analysis of variance and covariance, and factor analysis were applied to the data to determine effect of abiotic factors measured at each station. (PDF contains 96 pages)

Species and size relationships within schools of yellowfin and skipjack tuna as indicated by catches in the Eastern Tropical Pacific Ocean

ENGLISH: Yellowfin tuna, Neothunnus macropterus, and skipjack tuna, Katsuwonus pelamis, are fished intensively off the west coast of the Americas in an area from about the California-Mexico border in the north to the Peru-Chile border in the south. The historical development of this fishery, and its expansion by the long-range California fleets of bait and purse-seine vessels, are well documented by Godsil (1938), Scofield (1951) and Shimada and Sehaefer (1956). The quarterly distribution of the tuna catches within this area has been reported for some recent years by Alverson (1959). SPANISH: Los atunes aleta amarilla, Neothunnus macropterus, y barrilete, Katsuwonus pelamis, son pescados con intensidad frente a la costa occidental del continente americano, en un área comprendida más o menos entre la frontera California-México en el norte y el límite Perú-Chile en el sur. El desarrollo histórico de esta pesquería y la expansión que le han dado las flotas californianas de largo radio de acción, formadas por los barcos de carnada y rederos, están bien documentados por Godsil (1938), Scofield (1951) y Shimada y Schaefer (1956). La distribución trimestral de las pescas de atún dentro de esta área ha sido tratada por Alverson (1959) con referencia a años recientes.

The distribution and size composition of finfish, American lobster, and long-finned squid in Long Island Sound based on the Connecticut Fisheries Division Bottom Trawl Survey, 1984–1994

The distribution, abundance, and length composition of marine finfish, lobster, and squid in Long Island Sound were examined relative to season and physical features of the Sound, using Connecticut Department of Environmental Protection trawl survey data collected from 1984 to 1994. The following are presented: seasonal distribution maps for 59 species, abundance indices for 41 species, and length frequencies for 26 species. In addition, a broader view of habitat utilization in the Sound was examined by mapping aggregated catches (total catch per tow, demersal catch per tow, and pelagic catch per tow) and by comparing species richness and mean aggregate catch/tow by analysis of variance (ANOVA) among eight habitat types defined by depth interval and bottom type. For many individual species, seasonal migration patterns and preference for particular areas within Long Island Sound were evident. The aggregate distribution maps show that overall abundance was lower in the eastern Sound than the central and western portions. Demersal and pelagic temporal abundance show opposite trends—demersals were abundant in spring and declined through summer and fall, whereas pelagic abundance was low in spring and increased into fall. The analysis of habitat types revealed significant differences for both species richness and mean catch per tow. Generally, species richness was highest in habitats within the central area of the Sound and lowest in eastern habitats. The aggregate mean catch was highest in the western and central habitats, and declined eastward. (PDF file contains 199 pages.)

Variation in size of yellowfin tuna (Thunnus albacares) within individual purse-seine sets

ENGLISH:Length-frequency samples of yellowfin tuna from 276 individual purse-seine sets were examined. Evidence of schooling by size is presented. Yellowfin schooled with skipjack are smaller and more homogeneous in length than are yellowfin from pure schools. Yellowfin in schools associated with porpoise appear to be more variable in size than yellowfin from other types of schools. No relationship was found between the tonnage of yellowfin in a school and the mean length of the yellowfin. Despite the tendency to school by size, the size variation within individual schools was judged to be enough to complicate greatly any program of regulation aimed at maximizing the yield-per-recruit through increasing the minimum size of yellowfin at first capture. SPANISH: Fueron examinadas las muestras frecuencia-longitud de atún aleta amarilla, de 276 lances individuales de redes de cerco. Se presenta la evidencia de agrupación por tamaños. Los atunes aleta amarilla agrupados con barrilete, son más pequeños y más homogéneos en longitud, que los atunes aleta amarilla de cardúmenes puros. El atún aleta amarilla en cardúmenes asociados con delfines parece ser más variable en tamaño, que el atún aleta amarilla proveniente de otros tipos de cardúmenes. No se encontró relac¡'ón entre el tonelaje del atún aleta amarilla en un cardumen y la longitud media de esta especie. A pesar de la tendencia a agruparse por tamaño, se juzgó, que la variación de tamaño en cardúmenes individuales, sería suficiente para complicar grandemente cualquier programa de reglamentación, dirigido a obtener el máximo del rendimiento por recluta a través del incremento del tamaño mínimo del atún aleta amarilla en la primera captura.

"Future fit your catalog" Panel [Presentation]:World Cat Local Implementation as part of a Consortia of Libraries within the University System of Maryland and Affiliated Institutitons

Power Point from Panel presentation giving implementation and search result displays and linking (17 slides)

The lowland dry zone of Sri Lanka: site for study of aquaculture development within farmer-managed irrigation systems and methodology for participatory situation appraisal

The aims of this paper are twofold. Firstly to characterise rural poverty and to give a broad overview of the agro-ecological, climatic and socio-economic conditions in Sri Lanka which shape poverty. Secondly to present the methodology employed to screen suitable field research areas and the techniques subsequently used to carry out Rapid Rural Appraisal in two upper-watersheds villages. Also presented are details of a concurrent stakeholder analysis that aimed to investigate the capacity of secondary stakeholders to promote sustainable aquatic resource development and to invite their participation in the formulation of a participatory research agenda.[PDF contains 58 pages]

An approach to valuing ponds within farming systems for aquaculture

[PDF contains 37 pages]

Estimation of the abundance of yellowfin tuna, Thunnus albacares, by age groups and regions within the Eastern Pacific Ocean

ENGLISH: Monthly estimates of the abundance of yellowfin tuna by age groups and regions within the eastern Pacific Ocean during 1970-1988 are made, using purse-seine catch rates, length-frequency samples, and results from cohort analysis. The numbers of individuals caught of each age group in each logged purse-seine set are estimated, using the tonnage from that set and length-frequency distribution from the "nearest" length-frequency sample(s). Nearest refers to the closest length frequency sample(s) to the purse-seine set in time, distance, and set type (dolphin associated, floating object associated, skipjack associated, none of these, and some combinations). Catch rates are initially calculated as the estimated number of individuals of the age group caught per hour of searching. Then, to remove the effects of set type and vessel speed, they are standardized, using separate weiznted generalized linear models for each age group. The standardized catch rates at the center of each 2.5 0 quadrangle-month are estimated, using locally-weighted least-squares regressions on latitude, longitude and date, and then combined into larger regions. Catch rates within these regions are converted to numbers of yellowfin, using the mean age composition from cohort analysis. The variances of the abundance estimates within regions are large for 0-, 1-, and 5-year-olds, but small for 1.5- to 4-year-olds, except during periods of low fishing activity. Mean annual catch rate estimates for the entire eastern Pacific Ocean are significantly positively correlated with mean abundance estimates from cohort analysis for age groups ranging from 1.5 to 4 years old. Catch-rate indices of abundance by age are expected to be useful in conjunction with data on reproductive biology to estimate total egg production within regions. The estimates may also be useful in understanding geographic and temporal variations in age-specific availability to purse seiners, as well as age-specific movements. SPANISH: Se calculan estimaciones mensuales de la abundancia del atún aleta amarilla por grupos de edad y regiones en el Océano Pacífico oriental durante 1970-1988, usando tasas de captura cerquera, muestras de frecuencia de talla, y los resultados del análisis de cohortes. Se estima el número de individuos capturados de cada grupo de edad en cada lance cerquero registrado, usando el tonelaje del lance en cuestión y la distribución de frecuencia de talla de la(s) muestra(s) de frecuencia de talla "más cercana/s)," "Más cercana" significa la(s) muestra(s) de frecuencia de talla más parecida(s) al lance cerquero en cuanto a fecha, distancia, y tipo de lance (asociado con delfines, con objeto flotante, con barrilete, con ninguno de éstos, y algunas combinaciones). Se calculan inicialmente las tasas de captura como el número estimado de individuos del grupo de edad capturado por hora de búsqueda. A continuación, para eliminar los efectos del tipo de lance y la velocidad del barco, se estandardizan dichas tasas, usando un modelo lineal generalizado ponderado, para cada grupo por separado. Se estima la tasa de captura estandardizada al centro de cada cuadrángulo de 2.5°-mes, usando regresiones de mínimos cuadrados ponderados localmente por latitud, longitud, y fecha, y entonces combinándolas en regiones mayores. Se convierten las tasas de captura dentro de estas regiones en números de aletas amarillas individuales, usando el número promedio por edad proveniente del análisis de cohortes. Las varianzas de las estimaciones de la abundancia dentro de las regiones son grandes para los peces de O, 1, Y5 años de edad, pero pequeñas para aquellos de entre 1.5 Y4 años de edad, excepto durante períodos de poca actividad pesquera. Las estimaciones de la tasa de captura media anual para todo el Océano Pacífico oriental están correlacionadas positivamente de forma significativa con las estimaciones de la abundancia media del análisis de las cohortes para los grupos de edad de entre 1.5 y 4 años. Se espera que los índices de abundancia por edad basados en las tasas de captura sean útiles, en conjunto con datos de la biología reproductiva, para estimar la producción total de huevos por regiones. Las estimaciones podrían asimismo ser útiles para la comprensión de las variaciones geográficas y temporales de la disponibilidad específica por edad a los barcos cerqueros, y también las migraciones específicas por edad. (PDF contains 35 pages.)

Analysis of variance and standardization of longline hook rates of bigeye (Thunnus obesus) and yellowfin (Thunnus albacares) tunas in the Eastern Pacific Ocean during 1975-1987

ENGLISH: Longline hook rates of bigeye and yellowfin tunas in the eastern Pacific Ocean were standardized by maximum depth of fishing, area, and season, using generalized linear models (GLM's). The annual trends of the standardized hook rates differ from the unstandardized, and are more likely to represent the changes in abundance of tunas in the age groups most vulnerable to longliners in the fishing grounds. For both species all of the interactions in the GLM's involving years, depths of fishing, areas, and seasons were significant. This means that the annual trends in hook rates depend on which depths, areas, and seasons are being considered. The overall average hook rates for each were estimated by weighting each 5-degree quadrangle equally and each season by the number of months in it. Since the annual trends in hook rates for each fishing depth category are roughly the same for bigeye, total average annual hook rate estimates are possible with the GLM. For yellowfin, the situation is less clear because of a preponderance of empty cells in the model. The full models explained 55% of the variation in bigeye hook rate and 33% of that of yellowfin. SPANISH: Se estandardizaron las tasas de captura con palangre de atunes patudo y aleta amarilla en el Océano Pacífico oriental por la profunidad máxima de pesca, área, y temporada, usando modelos lineales generalizados (MLG). Las tendencias anuales de las tasas de captura estandardizadas son diferentes a las de las tasas no estandardizadas, y es más que representen los cambios en la abundancia de los atunes en los grupos de edad más vulnerables a los palangreros en las áreas de pesca. Para ambas especies fueron significativas todas las interacciones en los MLG con año, profundidad de pesca, área, y temporada. Esto significa que las tendencias anuales de las tasas de captura dependen de cuál profundidad, área, y temporado se está considerando. Para la estimación de la tasa de captura general media para cada especie se ponderó cada cuadrángulo de 5 grados igualmente y cada temporada por el número de meses que contiene. Ya que las tendencias anuales en las tasas de captura para cada categoría de profundidad de pesca son aproximadamente iguales para el patudo, son posibles estimaciones de la tasa de captura anual media total con el MLG. En el caso del aleta amarilla, la situación es más confusa, debido a una preponderancia de celdas vacías en el modelo. Los modelos completos explican el 55% de la variación de la tasa de captura de patudo y 33% de la del aleta amarilla. (PDF contains 19 pages.)

Poverty alleviation among fishermen within the floodplains of Kaduna River: implication for introducing commercial fish farming at village level in Doko local government area of Niger State, Nigeria

A diagnostic survey was conducted among the fishermen in six selected villages in Doko Local Government Area of Niger State. One hundred and fifty fishermen were randomly selected and interviewed to find out whether or not they had interest in commercial fish farming aimed at improving their livelihood. The dwindling fish catches in the natural flood plain ponds and Ex-bow Lakes continue to have a serious negative effect on the socio-economic well being of the village communities in question. A break on natural regular annual flooding of the plains had resulted into very low natural fish recruitment. Data analysis using simple descriptive statistics revealed that land tenure system, educational status, inadequate infrastructural facilities, religious taboos, existing fish species among others were found to be favourable indices for commercial fish farming. However, serious conflicts among the fishermen concerning the ownership status of these natural fish ponds are found to be major obstacles to commercial fish farming despite that the traditional ownership of the ponds were vested in the lands of individuals and village communities. Extensive fish farming and small-scale fish farming in the ponds and Ex-bow Lake with improved management practices are considered to be profitable venture. Despite the fact that fish seeds supply and extension effort are still inadequate, the fish farmers have indicated willingness to adopt commercial fish farming in the Ex-bow Lakes and flood plains in order to restore abundant fish production thereby providing for their food security and also increasing the daily income

Recruitment pattern and fish production within the Andoni River system in the Niger Delta of Nigeria

Biweekly samples of fish species obtained from five randomly selected Andoni artisanal fisheries within the Andoni River system, Niger Delta of Nigeria were collected between January and December 1999 and their length frequencies analyzed using FISAT (FAO-ICLARM STOCK ASSESSMENT TOOL). The peak recruitment period for Chrysichthys nigrodigitatus, Ethmalosa fimbriata, Eucinostomus melanopterus, Galeodes decadactylus, Pomadasys jubelini and Sarotherodon melanotheron constituting 54.55% was between June and October while Liza grandisquamis and Lutjanus goreensis, Ilisha Africana. Tilapia guinensis and Pseudotolithus elongate constituting 27.27% had two peak recruitment periods including March-May and May- October. In view of this result it is advisable for fishers to intensify fishing effort between May and October for most commercially important fish species for bountiful harvest

1976 step in the Pacific climate: forty environmental changes between 1968-1975 and 1977-1984

Examination of 40 time series of multidisciplinary environmental variables from the Pacific Ocean and the Americas, collected in 1968 to 1984, demonstrated the remarkable consistency of a major climate-related, step-like change in 1976. To combine the 40 variables (e.g., air and water temperatures, Southern Oscillation, chlorophyll, geese, salmon, crabs, glaciers, atmospheric dust, coral, carbon dioxide, winds, ice cover, Bering Strait transport) into a single time series, standard variants of individual annual values (subtracting the mean and dividing by a standard deviation) were averaged. Analysis of the resulting time series showed that the single step in 1976, separating the 1968-1975 period from the 1977-1984 period, accounted for 89% of variance within the composite time series. Apparently, one of the Earth's large ecosystems occasionally undergoes large abrupt shifts.