Comparison of echogram measurements against data expectations and assumptions for distinguishing seafloor substrates

Defining types of seafloor substrate and relating them to the distribution of fish and invertebrates is an important but difficult goal. An examination of the processing steps of a commercial acoustics analyzing software program, as well as the data values produced by the proprietary first echo measurements, revealed potential benef its and drawbacks for distinguishing acoustically distinct seafloor substrates. The positive aspects were convenient processing steps such as gain adjustment, accurate bottom picking, ease of bad data exclusion, and the ability to average across successive pings in order to increase the signal-to-noise ratio. A noteworthy drawback with the processing was the potential for accidental inclusion of a second echo as if it were part of the first echo. Detailed examination of the echogram measurements quantified the amount of collinearity, revealed the lack of standardization (subtraction of mean, division by standard deviation) before principal components analysis (PCA), and showed correlations of individual echogram measurements with depth and seafloor slope. Despite the facility of the software, these previously unknown processing pitfalls and echogram measurement characteristics may have created data artifacts that generated user-derived substrate classifications, rather than actual seafloor substrate types.

Age- or length-based methods of growth estimation. What drives the choice?

Based upon a global comparison of over 400 fisheries, the Principal Components Analysis (PCA) methodology was used to identify factors affecting the choice of growth estimation methods. Of the six factors examined, the growth rate (K) and asymptotic length (L8) explained most of the variations. Financial resources, i.e., Gross National Product (GNP), and latitude were also important factors.

The zonation of soft-bottom sediments in Gorgan Bay (Caspian Sea) using macrobenthos as indicator of ecological health

In this study, in order to assess the ecological health status and zoning of soft bottom of Gorgan Bay, the spatial and temporal distribution of macrofauna and their relationship with environmental stress were investigated. Sediment samples were collected using a Van Veen grab at 22 sampling points, seasonally during 2012-2013. The averages (±SD) of the percentages of sand, silt, clay and TOM (Total Organic Matter) in the sediment samples were determined (44.4± 15, 53.4 ± 14, and 2.2 ±2.2 and 7.2% ± 1.6, respectively). Our results showed that mean (range) of Al, As, Cu, Fe, Ni, Pb and Zn in the sediment samples were 1.2 % (0.4-2.1), 4.8 (2.5- 10.3) ppm, 10.5 (4.4-16.9) ppm, 1 (0.4 – 1.6) % , 13.6 (6.2-21.5) ppm, 9.1 (4.7-12.9) ppm and 23.9 (3.1-39.4) ppm, respectively. In spring, both Al and Ni were higher than the guideline level. In the event that arsenic was exceeds the guidelines in summer. In this study, 14 species of macrofauna from 12 families were identified. Polychaeta with 3 species was the most dominant group in terms of abundance. The four most abundant taxa making up 85% of all specimens (Streblospio gynobranchiata, Tubificidae, Hediste versicolor and Abra segmentum). The western area were characterized by the higher species diversity (H', 1.94). So Gorgan Bay presents transitional macrobenthic assemblages that are spatially distributed along substrate gradients .The mean of Shannon index, BENTIX, BO2A, AMBI and M-AMBI in the bay was 1.3, 2.2, 0.4, 3.2 and 0.65 respectively. According to the results of these indices, ecological status of the western part of the bay assessed better than the other parts. According to the results of the nmMDS (non-metric Multidimensional Scaling), PCA (Principal Components Analysis), the map of distribution of heavy metals and the map of the ecological status , it seems Gorgan Bay is divided into two separate zones (the eastern and the western parts).M-AMBI finaly introduced reliable index for assessing the ecological status of the Bay.

Assessing the sustainability of brackish water aquaculture systems in the Phillipines. Working Paper 1: A typology of brackish-water pond aquaculture systems in the Philippines

Aquaculture in the Philippines is a long-standing activity but has witnessed relatively recent, rapid, technical change with the introduction of hatchery technology and commercial feed-mills changing the production possibilities for a fishpond operator. We are confronted with a diversity of aquaculture practices in the coastal areas of the Philippines, with new technologies being incorporated into more traditional systems. As a first step to understanding the sector, we therefore present a typology of farming systems with the motivation of generating domains (farm “types”) over which we can compare performance on a number of indicators. Our typology, restricted to brackish-water pond systems, is constructed using multivariate methods (principal components analysis, cluster analysis). Eight variables are used relating to the management of the farm across all the major factors of production. A stratified net sample of 136 observations provides the data for the analysis, from a farm-level survey carried out between January and June 2003 in the two main brackish-water production regions in the Philippines. We define five farm types from this analysis. In later work we will show how the use of this typology can be used for comparative study of economic, social and ecological performance at the farm-level. [PDF contains 42 pages]

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.

Regional and seasonal patterns of epipelagic fish assemblages from the central California Current

The coastal Pacific Ocean off northern and central California encompasses the strongest seasonal upwelling zone in the California Current ecosystem. Headlands and bays here generate complex circulation features and confer unusual oceanographic complexity. We sampled the coastal epipelagic fish community of this region with a surface trawl in the summer and fall of 2000–05 to assess patterns of spatial and temporal community structure. Fifty-three species of fish were captured in 218 hauls at 34 fixed stations, with clupeiform species dominating. To examine spatial patterns, samples were grouped by location relative to a prominent headland at Point Reyes and the resulting two regions, north coast and Gulf of the Farallones, were plotted by using nonmetric multidimensional scaling. Seasonal and interannual patterns were also examined, and representative species were identified for each distinct community. Seven oceanographic variables measured concurrently with trawling were plotted by principal components analysis and tested for correlation with biotic patterns. We found significant differences in community structure by region, year, and season, but no interaction among main effects. Significant differences in oceanographic conditions mirrored the biotic patterns, and a match between biotic and hydrographic structure was detected. Dissimilarity between assemblages was mostly the result of differences in abundance and frequency of occurrence of about twelve common species. Community patterns were best described by a subset of hydrographic variables, including water depth, distance from shore, and any one of several correlated variables associated with upwelling intensity. Rather than discrete communities with clear borders and distinct member species, we found gradients in community structure and identified stations with similar fish communities by region and by proximity to features such as the San Francisco Bay.

An objective classification of climatic regions in the Pacific and Indian oceans

We have applied a number of objective statistical techniques to define homogeneous climatic regions for the Pacific Ocean, using COADS (Woodruff et al 1987) monthly sea surface temperature (SST) for 1950-1989 as the key variable. The basic data comprised all global 4°x4° latitude/longitude boxes with enough data available to yield reliable long-term means of monthly mean SST. An R-mode principal components analysis of these data, following a technique first used by Stidd (1967), yields information about harmonics of the annual cycles of SST. We used the spatial coefficients (one for each 4-degree box and eigenvector) as input to a K-means cluster analysis to classify the gridbox SST data into 34 global regions, in which 20 comprise the Pacific and Indian oceans. Seasonal time series were then produced for each of these regions. For comparison purposes, the variance spectrum of each regional anomaly time series was calculated. Most of the significant spectral peaks occur near the biennial (2.1-2.2 years) and ENSO (~3-6 years) time scales in the tropical regions. Decadal scale fluctuations are important in the mid-latitude ocean regions.

Deep-sea benthic footprint of the Deepwater Horizon blowout

The Deepwater Horizon (DWH) accident in the northern Gulf of Mexico occurred on April 20, 2010 at a water depth of 1525 meters, and a deep-sea plume was detected within one month. Oil contacted and persisted in parts of the bottom of the deep-sea in the Gulf of Mexico. As part of the response to the accident, monitoring cruises were deployed in fall 2010 to measure potential impacts on the two main soft-bottom benthic invertebrate groups: macrofauna and meiofauna. Sediment was collected using a multicorer so that samples for chemical, physical and biological analyses could be taken simultaneously and analyzed using multivariate methods. The footprint of the oil spill was identified by creating a new variable with principal components analysis where the first factor was indicative of the oil spill impacts and this new variable mapped in a geographic information system to identify the area of the oil spill footprint. The most severe relative reduction of faunal abundance and diversity extended to 3 km from the wellhead in all directions covering an area about 24 km2. Moderate impacts were observed up to 17 km towards the southwest and 8.5 km towards the northeast of the wellhead, covering an area 148 km2. Benthic effects were correlated to total petroleum hydrocarbon, polycyclic aromatic hydrocarbons and barium concentrations, and distance to the wellhead; but not distance to hydrocarbon seeps. Thus, benthic effects are more likely due to the oil spill, and not natural hydrocarbon seepage. Recovery rates in the deep sea are likely to be slow, on the order of decades or longer.

The zooplankton population structure and their trend of variations in the southern of Caspian Sea (Iranian waters)

Caspian Sea has gone under a lot of changes due to human influences and the unwanted presence of a ctenophora Menomiopsis leidyi which has greatly changed the structure of planktons in the last recent years. Therefore, this study was carried out in order to determine these changes in the zooplankton community. the Sampling was done in 8 transacts in Astara, Anzali, Sefidrood, Tonekaboun, Noushahr, Babolsar, Amirabad and Bandar Torkaman coastal waters at 5 different depths including 5, 10, 20, 50 and 100 m. Sampling was carried out in four seasons of spring, summer, autumn and winter during 2008, 2009 and 2010 on board of R/V Gilan. Altogether, 12 species of zooplankton were identified in 2008, 22 species in 2009 and 14 species in 2010. The zooplankton included four groups: copepoda (4 species), cladocera (8species), rotatoria (10 species) and protozoa (2 species).The increase of diversity in 2009 was due to cladocera and rotatoria groups. The abundance of zooplankton in the spring was 5074 + 7807 ind/m3 more than other season in 2008. The abundance of copepoda in the summer reached the highest value of 3332 ind/m3 and since autumn the abundance gradually decreases and in the winter reached to the lowest value. The most abundance of cladocera was 797 ind/m3 in winter and decreased in summer and autumn. The abundance of rotatoria was 2189 ind/m3 in winter. rotifera and copepoda consisted the main population of Zooplanktons in the winter. The results of 2009 and 2010 showed that the abundance of zooplankton in winter was 2.6 fold of autumn, 1.6 fold of summer and 1.1 fold (1/9 fold in 2010)of spring. After increasing increased of temperature, phytoplankton, and zooplankton in summer, M.leidyi increased too. In the autumn M. leidyi reached to the highest rate and decreased zooplankton. The maximum population of zooplankton was in the layer 0-20 m and in the layer more than 20 meters, the abundance of zooplankton decreased very much. In 216 2008, 2009 and 2010, the abundance of zooplankton was 87, 77 and 77 percent in the layer 0-20 m respectively. In this study, the thermocline was observed in the layer 10 – 20 meters in the spring, that formed a thin layer but in the summer it was in the layer 20 to 50 meters. Temperature decreased between 11 to 15 oC in this layer. The variation of temperature between surfaces to bottom was 10 to 13 oC in spring, 19 to 21 in summer, about 9 oC in autumn and maximum 3 oC in winter. The most biomass of zooplankton was in the west. The biomass of zooplankton in central west and east of Southern of Caspian Sea was 54 %, 22 % and 24 % respectively in 2008, in 2009 was 48%, 33% and 20% respectively and in 2010 was 54 %, 29 % and 16 % respectively .The biomass decreased from west to east. The model of zooplankton designed by principal component analysis (PCA)and linear regression for Southern of Caspian Sea.

Investigation on biodiversity and population structure of Penaeus sernisulcatus [sic] in northern waters of Persian Gulf

Green tiger prawn, Penaeus sentisulcatus is one of the commercial species of Persian Gulf, which is distributed from north to Strait of I Iormoze. Concerning its role in fisheries economic, various research projects on stock assessment, biology and aquaculture has been conducted. This research is targeted the identification of various populations of green tiger prawn in northern waters of Persian Gulf. The area has been divided to five regions from north to south named; Bahrakan, Boushehr, Tangestan, Motaaf and Strait of Hormoz. In each region, numbers of sampling stations trawled, and live shrimp species carried in containers equipped with air pump, to coastal laboratories in Boushehr and Bandar Abbass Fisheries Research Centers. Biometeric, morphometeric and merestic measures for 45 factars done, and peices of muscles, eye and ovary tissues dissected, and stored in liquid nitrogen. Protein extraction, and polyacrylamid gel electrophoresis by SDS-PAGE technique for tissues samples conducted. Data of 45 morphometeric and merestic characteristics analyzed by principal component analysis (PCA), and clustering analysis methods. The results of analysis showed that, the populations of Bahrakan and Mota.af regions are differentiated, while population of Boushehr and Tangestan regions were mixed, and named as a single population. The analysis of electrophoretic data also confirmed this result, and showed a distinct population in Strait of Hormoz. Therefore, this research illustrated four distinct populations for P. semisulcatus in northern area of Persian Gulf, named Bahrakan (north of Boushehr), Boushehr and Tangesta.n (adjacent), Motaaf and it's south, and Strait of Hormoz. Study of morphometeric characteristics of carapace factors, genital organs, antenna and life cycle of samples of different regions resulting identification of a subspecies, which is named Penaeus seinisuleatus persicus.

Preparation of environmental monitoring plan pattern for surface water quality in Iran (Case study: Gharehsou River)

Using water quality management programs is a necessary and inevitable way for preservation and sustainable use of water resources. One of the important issues in determining the quality of water in rivers is designing effective quality control networks, so that the measured quality variables in these stations are, as far as possible, indicative of overall changes in water quality. One of the methods to achieve this goal is increasing the number of quality monitoring stations and sampling instances. Since this will dramatically increase the annual cost of monitoring, deciding on which stations and parameters are the most important ones, along with increasing the instances of sampling, in a way that shows maximum change in the system under study can affect the future decision-making processes for optimizing the efficacy of extant monitoring network, removing or adding new stations or parameters and decreasing or increasing sampling instances. This end, the efficiency of multivariate statistical procedures was studied in this thesis. Multivariate statistical procedure, with regard to its features, can be used as a practical and useful method in recognizing and analyzing rivers’ pollution and consequently in understanding, reasoning, controlling, and correct decision-making in water quality management. This research was carried out using multivariate statistical techniques for analyzing the quality of water and monitoring the variables affecting its quality in Gharasou river, in Ardabil province in northwest of Iran. During a year, 28 physical and chemical parameters were sampled in 11 stations. The results of these measurements were analyzed by multivariate procedures such as: Cluster Analysis (CA), Principal Component Analysis (PCA), Factor Analysis (FA), and Discriminant Analysis (DA). Based on the findings from cluster analysis, principal component analysis, and factor analysis the stations were divided into three groups of highly polluted (HP), moderately polluted (MP), and less polluted (LP) stations Thus, this study illustrates the usefulness of multivariate statistical techniques for analysis and interpretation of complex data sets, and in water quality assessment, identification of pollution sources/factors and understanding spatial variations in water quality for effective river water quality management. This study also shows the effectiveness of these techniques for getting better information about the water quality and design of monitoring network for effective management of water resources. Therefore, based on the results, Gharasou river water quality monitoring program was developed and presented.