The spatial and temporal (seasonal and diel) patterns in the hyperbenthic community structure (>500 μm) was investigated in the warm temperate, permanently open Kariega Estuary situated along the south-eastern coastline of South Africa. Spatial and seasonal patterns in the hyperbenthic community structure were assessed monthly at six stations along the length of the estuary over a period of twelve months. Data were collected using a modified hyperbenthic sledge, comprising two super-imposed nets. Physico-chemical data indicate the presence of a constant reverse salinity gradient, with highest salinities measured in the upper reaches and lowest at the mouth of the estuary. Strong seasonal patterns in temperature, dissolved oxygen and total chlorophyll-a (chl-a) concentrations were evident. Total average hyperbenthic densities ranged between 0.04 and 166 ind.m-3 in the lower net and between 0.12 and 225 ind.m-3 in the upper net. Hyperbenthic biomass values ranged between 0.02 and 11.9 mg.dry weight.m-3 in the lower net and between 0.02 and 17.4 mg.dry weight.m-3 in the upper net. A spatial and temporal pattern in total densities was detected with an increase in abundance over the period of September to October 2008 particularly in the middle reaches (Stations 3 and 4). Both the lower and upper nets were numerically dominated by decapods (mainly brachyuran crab zoeae) with the exception of June and July 2008 when mysids (mainly Mesopodopsis wooldridgei) dominated, making up 72.4 ± 58.14% of the total abundance in the lower net. A redundancy analysis (RDA) indicated that 99.2% of the variance in the hyperbenthic community structure could be explained by the first two canonical axes. Axis one, which accounted for 96.8% of the total variation detected in the ordination plot was highly correlated with sedimentary organic content and to a lesser extent the chl-a concentration within the Kariega Estuary. The correlations with the second canonical axis (2.4%) were less obvious, however, salinity and seston concentration were weakly correlated with this axis. Diel variability in the hyperbenthic community structure was assessed during March 2009. Samples were collected during the day and night (n = 6 for each period) using sampling gear described above. Total average hyperbenthic densities during the day (497.9 ± 254.1 ind.m-3) were significantly higher than night-time estimates (129.9 ± 38.5 ind.m-3; p<0.05). There were no significant differences in the average dayand night-time estimates of hyperbenthic biomass (p>0.05). A hierarchical cluster analysis identified two significantly distinct groupings, designated the day and night samples. Results from the SIMPER procedure indicated that the high densities of crab zoeae recorded during the day-time accounted for the majority of the dissimilarity between the day and night groupings (44.7%). In addition, it is apparent that several benthic species, especially from the cumacean and isopod orders, were absent from the hyperbenthos during the day-time and emerged into the water column at night.

Recent emphasis on linkages between essential fish habitat and fish stock productivity has raised concerns about the management of fishing activities such as trawling, which have the potential to impact fish habitat. Knowing specifically where and how intensively trawl effort has occurred over time provides ecologists with the necessary background for habitat impact and recovery studies, and provides fishery managers with an assessment of how habitat conservation objectives are being met. The objectives of this study were to (1) examine the extent to which the 2000 Pacific Fishery Management Council footrope restriction has shifted and reduced trawl fishing effort on Oregon fishing grounds, (2) to relate these changes in distribution to the benthic habitat type over which they occur, and (3) to develop methods for enhancing fine-scale spatial review of targeted fishing effort. Density analysis of available trawl start locations provided a spatial and temporal understanding of how fishing efforts increased and decreased in relation to habitat distribution and fishery management actions between 1995 and 2002. Trawl effort patterns exhibit significant inter-annual variability and patchy distribution. Areas of increased fishing effort were still evident between years, despite an overall decline in trawl tows across the time scale of this study. Tow end point locations for the years 1998-2001 were retrieved from manual logbooks for five reference sites located in the proximity of rock habitat features. Trawl towlines were mapped from start to end point and demonstrated a marked enhancement of fine-scale fishing effort resolution, with increased ability to identify effort shifts over benthic habitat. Distinct spatial shifts in fishing intensity (measured as km towed) away from rock habitat were evident at all reference sites, with an average reduction of 86%. Some slight shifts into surrounding unconsolidated sediments also occurred, indicating effort displacement as well as reduction. Fishing intensity was calculated from commercial trawl and research trawl survey towlines to achieve the most accurate assessment of fishing impacts and potential habitat recovery areas. Research trawling intensity was less than 1% of commercial trawl effort originating from the same sites. A brief comparison of Oregon vessel towlines and California vessel towlines demonstrated similar targeted fishing patterns by both fleets, except at one site. Results indicate that the footrope restriction, in conjunction with associated landing limits, was effective in protecting rocky habitats from trawl fishing impacts. Reference areas were identified where essential fish habitat (EFH) recovery is likely occurring off the coast of Oregon. Substantial regulatory changes continue in this fishery, with trip limits and gear restrictions continuously adjusted. Continued monitoring and review of spatial trawl data would assist in fishery management decision-making and assess conservation objectives for depleted groundfish and associated habitats. Future research should incorporate analysis of catch data and expand the review of trawl towlines for the entire US West coast groundfish fishery. The trawl towline spatial analysis developed in this work is a credible method for reviewing fishing effort at the scale of the fishery and in relation to detailed habitat data. The research presented here provides an example of how an interdisciplinary approach and critical assessment of data can work to resolve marine management challenges. / Graduation date: 2004

Nearshore hypoxia within the Northern California Current (NCC) system is a seasonal phenomenon caused by coastal upwelling and occurs mainly during late-summer and early fall. The effects of low oxygen levels on fish and invertebrate communities, particularly during early-life history stages, however, are poorly known for this area. I investigated the effects of hypoxia on the density, community structure, vertical and horizontal distribution of fish larvae and juveniles, as well as body condition of juveniles, along the central Oregon and Washington coasts during the summers of 2008 - 2011. During this sampling period, bottom dissolved oxygen (DO) values ranged from 0.49 to 9.85 ml l�����, and the number of hypoxic (e.g., < 1.4 ml l�����) stations sampled was low compared to 2002 and 2006 (only 54 sampling stations for the ichthyoplankton study out of 493, and only 12 stations out of 90 for the benthic juvenile study). From the ichthyoplankton study, I found that the overall density of fish larvae increased as bottom-DO values increased; however, the effect on individual species density was limited. Between 44.65 ��N and 46.00 ��N (~Florence, OR ��� Astoria, OR), fish larvae altered their vertical distribution when bottom-DO was low by rising in shallower water layers. From the benthic juvenile study, I found that English sole (Parophrys vetulus), butter sole (Isopsetta isolepis), speckled sanddab (Citharichthys stigmaeus) and Pacific sanddab (Citharichthys sordidus) dominated the catch with annual variation in abundances. Species composition, abundance and length had strong relationships with depth. Species abundance for English sole (< 75 mm), speckled sanddab (<100 mm) and Pacific sanddab also increased with increased bottom-DO. However, the body condition of butter sole (< 75 mm) and of large speckled sanddab (���100 mm) increased with decreased bottom-DO. Overall my research elucidates important patterns of larval and juvenile fish distribution within the NCC during summer. In both studies I have found a limited effect of DO on abundance, distribution and community assemblages. Variables other than DO, such as depth, season and location, dominated the explained variance of the intervening multivariate and univariate analysis. However, due to the paucity of samples during hypoxic events, continued monitoring of nearshore larval and juvenile species over varying hypoxic conditions is necessary for understanding the impact of hypoxia on these communities and subsequent adult populations. / Graduation date: 2013

Rapid Bioassessment Protocols integrate a suite of community, population, and functional metrics, determined from the collection of benthic macroinvertebrates or fish, into a single assessment. This study was conducted in Dallas County Texas, an area located in the blackland prairie eco-region that is semi-arid and densely populated. The objectives of this research were to identify reference streams and propose a set of metrics that are best able to discriminate between differences in community structure due to natural variability from those caused by changes in water quality due to watershed impacts. Using geographic information systems, a total of nine watersheds, each representing a different mix of land uses, were chosen for evaluation. A total of 30 metrics commonly used in RBP protocols were calculated. Efficacy of these metrics to distinguish change was determined using several statistical techniques. Ten metrics were used to classify study area watersheds according to stream quality. Many trends, such as taxa presence along habitat quality gradients, were observed. These gradients coincided with expected responses of stream communities to landscape and habitat variables.