Introduction to MLML_DBASE Programs

The MLML DBASE family of programs described here provides many of the. algorithms used in oceanographic data reduction, general data manipulation and line graphs. These programs provide a consistent file structure for serial data typically encountered in oceanography. This introduction should provide enough general knowledge to explain the scope of the program and to run the basic MLML_DBASE programs. It is not intended as a programmer's guide. (PDF contains 50 pages)

Social structure and underwater behavior of harbor seals in southern Monterey Bay, California

To understand harbor seal social and mating strategies, I examined site fidelity, seasonal abundance and distribution, herd integrity, and underwater behavior of individual harbor seals in southern Monterey Bay. Individual harbor seals (n = 444) were identified by natural markings and represented greater than 80% of an estimated 520 seals within this community. Year to year fidelity of individual harbor seals to southern Monterey Bay coastline was 84% (n = 388), and long-term associations (>2 yrs) among individuals were common (>40%). Consistent with these long-term associations, harbor seals were highly social underwater throughout the year. Underwater social behavior included three primary types: (1) visual and acoustic displays, such as vocalizing, surface splashing, and bubble-blowing; (2) playful or agonistic social behavior such as rolling, mounting, attending, and biting; and (3) signal gestures such as head-thrusting, fore-flipper scratch~ng, and growling. Frequency of these types of behavior was related to seal age, gender, season, and resource availability. Underwater behavior had a variety of functions, including promotion of learning and social development, reduction of aggression and preservation of social bonds by maintaining social hierarchy, and facilitation of mate selection during breeding season. Social behavior among adult males was significantly correlated with vocalization characteristics (r = 0.99, X2 = 37.7, p = 0.00087), indicating that seals may assess their competition based on underwater vocalization displays and adopt individual strategies for attracting females during breeding season based on social status. Individual mating strategies may include defending underwater territories, using scramble tactics, and developing social alliances. (PDF contains 105 pages)

Population structure, long-term connectivity, and effective size of mutton snapper (Lutjanus analis) in the Caribbean Sea and Florida Keys

Genetic structure and average long-term connectivity and effective size of mutton snapper (Lutjanus analis) sampled from offshore localities in the U.S. Caribbean and the Florida Keys were assessed by using nuclear-encoded microsatellites and a fragment of mitochondrial DNA. No significant differences in allele, genotype (microsatellites), or haplotype (mtDNA) distributions were detected; tests of selective neutrality (mtDNA) were nonsignificant after Bonferroni correction. Heuristic estimates of average long-term rate of migration (proportion of migrant individuals/generation) between geographically adjacent localities varied from 0.0033 to 0.0054, indicating that local subpopulations could respond independently of environmental perturbations. Estimates of average longterm effective population sizes varied from 341 to 1066 and differed significantly among several of the localities. These results indicate that over time larval drift and interregional adult movement may not be sufficient to maintain population sustainability across the region and that there may be different demographic stocks at some of the localities studied. The estimate of long-term effective population size at the locality offshore of St. Croix was below the minimum threshold size considered necessary to maintain the equilibrium between the loss of adaptive genetic variance from genetic drift and its replacement by mutation. Genetic variability in mutton snapper likely is maintained at the intraregional level by aggregate spawning and random mating of local populations. This feature is perhaps ironic in that aggregate spawning also renders mutton snapper especially vulnerable to overexploitation.

Growth variation and stock structure in North Pacific albacore

Working paper NPALB/87/21 submitted to the 10th North Pacific Albacore Workshop. Paper reports the results of ongoing research on validated age and growth models and the elucidation of stock structure for the North Pacific albacore. (Document pdf contains 22 pages)

Extreme events and ecological forecasting

Almost all extreme events lasting less than several weeks that significantly impact ecosystems are weather related. This review examines the response of estuarine systems to intense short-term perturbations caused by major weather events such as hurricanes. Current knowledge concerning these effects is limited to relatively few studies where hurricanes and storms impacted estuaries with established environmental monitoring programs. Freshwater inputs associated with these storms were found to initially result in increased primary productivity. When hydrographic conditions are favorable, bacterial consumption of organic matter produced by the phytoplankton blooms and deposited during the initial runoff event can contribute to significant oxygen deficits during subsequent warmer periods. Salinity stress and habitat destruction associated with freshwater inputs, as well as anoxia, adversely affect benthic populations and fish. In contrast, mobile invertebrate species such as shrimp, which have a short life cycle and the ability to migrate during the runoff event, initially benefit from the increased primary productivity and decreased abundance of fish predators. Events studied so far indicate that estuaries rebound in one to three years following major short-term perturbations. However, repeated storm events without sufficient recovery time may cause a fundamental shift in ecosystem structure (Scavia et al. 2002). This is a scenario consistent with the predicted increase in hurricanes for the east coast of the United States. More work on the response of individual species to these stresses is needed so management of commercial resources can be adjusted to allow sufficient recovery time for affected populations.

Kurzinformation zum EU - Projekt: "Mechanisms influencing long term trends in reproductive success and recruitment of Baltic cod : implications for fisheries management"

In July 1994 an internationally coordinated and EU financed multidisciplinary research project about Baltic cod recruitment was started. The primary goals are to identify and describe dominant biotic and abiotic processes affecting the developmental success of early stages and the maturation of cod in the Central Baltic, to incorporate these processes into recruitment models in order to enhance prediction of future stock fluctuations due to environmental pertubations, species interactions and fisheries management directives as a prerequisite for an integrated fish stock assessment in the Central Baltic and to evaluate the feasibility and possible effects of stock enhancement programs on stock and recruitment and providing the biological basis for assessing their economic value.

The application of methods of ecosystem analysis to the evaluation of water quality

Guided by experience and the theoretical development of hydrobiology, it can be considered that the main aim of water quality control should be the establishment of the rates of the self-purification process of water bodies which are capable of maintaining communities in a state of dynamic balance without changing the integrity of the ecosystem. Hence, general approaches in the elaboration of methods for hydrobiological control are based on the following principles: a. the balance of matter and energy in water bodies; b. the integrity of the ecosystem structure and of its separate components at all levels. Ecosystem analysis makes possible a revelation of the whole totality of factors which determine the anthropogenic evolution of a water body. This is necessary for the study of long-term changes in water bodies. The principles of ecosystem analysis of water bodies, together with the creation of their mathematical models, are important because, in future, with the transition of water demanding production into closed cycles of water supply, changes in water bodies will arise in the main through the influence of 'diffuse' pollution (from the atmosphere, with utilisation in transport etc.).

Structural dynamic eutrophication models

This article discusses problems of modelling the seasonal succession of algal species in lakes and reservoirs, and the adaptive selection of certain groups of algae in response to changes in the inputs and relative concentrations of nutrients and other environmental variables. A new generation of quantitative models is being developed which attempts to translate some important biological properties of species (survival, variation, inheritance, reproductive rates and population growth) into predictions about the survival of the fittest, where ”fitness” is measured or estimated in thermodynamic terms. The concept of ”exergy” and its calculation is explored to examine maximal exergy as a measure of fitness in ecosystems, and its use for calculating changes in species composition by means of structural dynamic models. These models accomodate short-term changes in parameters that affect the adaptive responses (species selection) of algae.

Otolith morphometrics and population structure of Pacific sardine (Sardinops sagax) along the west coast of North America

The broad distribution of Pacific sardine (Sardinops sagax) along the Pacif ic coast of North America makes it difficult for fisheries managers to identify regional stocks of this dominant small pelagic species. An investigation of morphometric characteristics of otoliths of Pacific sardine across most of their range revealed regional differences in populations. In a survey of over 2000 otoliths, all ages (with an emphasis on age-1 recruits) were compared. Principal components analysis, multivariate analysis of variance, and a novel method derived from regression and residuals calculations, termed perimeter-weight profiles (PWPs), revealed otolith similarities and differences. The results of the different approaches to statistical comparisons did not always agree. Sardine otoliths from Mexican waters were generally lighter and more lobate than those from U.S. and Canadian populations. Age-1 otoliths from northern California in 2006–07 tended to be heavier and smoother than those from other areas, including year-class cohorts from southern California. Comparisons of age-groups and year-classes of northern California otoliths with the use of the PWP models indicated signif icant trends in year-to-year patterns. In conjunction with other established indices of population structure, otolith PWPs are a useful tool for identifying local and regional stocks of Pacific sardine and may help distinguish populations of other fish species as well.

Use of SARIMA models to assess data-poor fisheries: a case study with a sciaenid fishery off Portugal

Research on assessment and monitoring methods has primarily focused on fisheries with long multivariate data sets. Less research exists on methods applicable to data-poor fisheries with univariate data sets with a small sample size. In this study, we examine the capabilities of seasonal autoregressive integrated moving average (SARIMA) models to fit, forecast, and monitor the landings of such data-poor fisheries. We use a European fishery on meagre (Sciaenidae: Argyrosomus regius), where only a short time series of landings was available to model (n=60 months), as our case-study. We show that despite the limited sample size, a SARIMA model could be found that adequately fitted and forecasted the time series of meagre landings (12-month forecasts; mean error: 3.5 tons (t); annual absolute percentage error: 15.4%). We derive model-based prediction intervals and show how they can be used to detect problematic situations in the fishery. Our results indicate that over the course of one year the meagre landings remained within the prediction limits of the model and therefore indicated no need for urgent management intervention. We discuss the information that SARIMA model structure conveys on the meagre lifecycle and fishery, the methodological requirements of SARIMA forecasting of data-poor fisheries landings, and the capabilities SARIMA models present within current efforts to monitor the world’s data-poorest resources.

Seasonal variability in ichthyoplankton abundance and assemblage composition in the northern Gulf of Mexico off Alabama

Multiyear ichthyoplankton surveys used to monitor larval fish seasonality, abundance, and assemblage structure can provide early indicators of regional ecosystem changes. Numerous ichthyoplankton surveys have been conducted in the northern Gulf of Mexico, but few have had high levels of temporal resolution and sample replication. In this study, ichthyoplankton samples were collected monthly (October 2004–October 2006) at a single station off the coast of Alabama as part of a long-term biological survey. Four seasonal periods were identified from observed and historic water temperatures, including a relatively long (June–October) “summer” period (water temperature >26°C). Fish egg abundance, total larval abundance, and larval taxonomic diversity were significantly related to water temperature (but not salinity), with peaks in the spring, spring–summer, and summer periods, respectively. Larvae collected during the survey represented 58 different families, of which engraulids, sciaenids, carangids, and clupeids were the most prominent. The most abundant taxa collected were unidentified engraulids (50%), sand seatrout (Cynoscion arenarius, 7.5%), Atlantic bumper (Chloroscombrus chrysurus, 5.4%), Atlantic croaker (Micropogonias undulatus, 4.4%), Gulf menhaden (Brevoortia patronus, 3.8%), and unidentified gobiids (3.6%). Larval concentrations for dominant taxa were highly variable between years, but the timing of seasonal occurrence for these taxa was relatively consistent. Documented increases in sea surface temperature on the Alabama shelf may have various implications for larval fish dynamics, as indicated by the presence of tropical larval forms (e.g., fistularids, labrids, scarids, and acanthurids) in our ichthyoplankton collections and in recent juvenile surveys of Alabama and northern Gulf of Mexico seagrass habitats.

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.

Periodic autoregressive moving average models for the analysis of streamflow [abstract]

EXTRACT (SEE PDF FOR FULL ABSTRACT): Streamflow values show definite seasonal patterns in their month-to-month correlation structure. The structure also seems to vary as a function of the type of stream (coastal versus mountain or humid versus arid region). The standard autoregressive moving average (ARMA) time series model is incapable of reproducing this correlation structure. ... A periodic ARMA time series model is one in which an ARMA model is fitted to each month or season but the parameters of the model are constrained to be periodic according to a Fourier series. This constraint greatly reduces the number of parameters but still leaves the flexibility for matching the seasonally varying correlograms.

Meteorological and hydrologic studies in the Alaskan Arctic in support of long-term ecological research

Long-term hydrologic studies in the Arctic simply do not exist. Although the Arctic has been identified as an area that is extremely sensitive to climate change, continuous scientific research has been limited to the past seven years. Earlier research was spotty, of short duration, and directed at only one or two hydrologic elements. Immediate future research needs to encompass all the major hydrologic elements, including winter processes, and needs to address the problem of scaling from small to larger areas in hydrologic models. Also, an international program of cooperation between northern countries is needed to build a greater scientific base for monitoring and identifying potential changes wrought by the climate.