Currently, little is known about the demographics of the Oncorhynchus mykiss irideus, or steelhead trout, populations in San Luis Obispo County. Specifically, demographic information including length, age, and condition when first leaving a watershed for the open ocean is lacking. This thesis takes a closer look at a biological and environmental data collected by the California Department of Fish and Game Central Coast Steelhead and Coho Salmon project under the direction of Associate Biologist Jennifer Nelson. The main goal of this thesis is to analyze demographic and habitat data from the steelhead populations of two northern San Luis Obispo county coastal streams, San Simeon and Santa Rosa Creeks. Habitat mapping surveys were conducted on each stream in order to identify suitable habitat for various steelhead life stages. The data generated from the habitat mapping surveys was compared between the two creeks over the two different survey years (1993 and 2005). The results of these surveys showed that habitat types have changed on San Simeon Creek between survey years while Santa Rosa Creek appeared to remain the same. Biological inventory methods were conducted on the populations of O. m. irideus in San Simeon and Santa Rosa Creeks during the years of 1993 and 2005. There were very few observations of steelhead moving downstream on both survey creeks in 1993. During the 2005 out-migrant trapping season, the data revealed that non-smolting fish are moving downstream in the watershed in addition to smolting fish. There is evidence that age 1+ and 2+ fish make up the majority of downstream migrants. Older, larger fish tend to migrate downstream earlier in the trapping season. Fork length – weight relationships are not significant between steelhead sampled from out-migrant traps, while those sampled throughout the watersheds by means of electrofishing were different between creeks. Percent frequency distribution of electrofished steelhead reveal that steelhead sampled in 2005 have a similar distribution of total lengths between creeks, where as those sampled in 1993 have a slightly different distribution from each other. Further analysis of steelhead scales sampled from the populations on San Simeon and Santa Rosa Creeks in 2005 gave greater insight into the growth of these fish. In most cases, steelhead from Santa Rosa Creek have greater growth increments and higher circuli counts per annuli than those surveyed from San Simeon Creek. The majority of scale samples analyzed showed growth since the last annuli mark suggesting an increase in growth over the winter months. The average number of circuli to the first annuli is significantly different between watersheds, as is the relationship between fork length and scale radius. Analyzing steelhead demographics is important to understanding the life history pattern of steelhead in the South Central California Coast Distinct Population Segment (DPS). Surveys that monitor environmental conditions and habitat help to identify potential limiting factors and risks to steelhead populations. The results of this thesis present such data in hopes to promote continued research and efficient management practices of steelhead trout populations in San Luis Obispo County.

Virtually all marine conservation planning and management models in place or proposed have in common the need for improved scientific rigour in identifying and characterising the marine habitats encompassed. An emerging central theme in the last few years has been the concept of representativeness, or representative systems of Marine Protected Areas (MPAs). The habitat classification and mapping needed to incorporate considerations of representativeness into MPA planning must logically be carried out at the same scale at which management occurs. Management of highly protected areas occurs almost exclusively at local scales or finer, independent of the reservation model or philosophy employed. Moreton Bay, on Australia’s east coast, was selected for studies at the local scale to map and classify macrobenthic habitats. In a site scale (1 km) trial for the major habitat classification study, remote underwater videography was used to map and characterise an unusual assemblage of epibenthic invertebrates on soft sediments. The assemblage included congregations of the comatulid crinoid Zygometra cf. Z. microdiscus (Bell) at densities up to 0.88 individuals.m-2, comparable to those found in coral reef habitats. There was no correlation between the distribution of this species and commonly used abiotic surrogates depth (6 – 18 m), sediment composition and residual current. This site scale trial is the first quantitative assessment of crinoid density and distribution in shallow water soft-sediment environments. The high densities found are significant in terms of the generally accepted picture of shallow-water crinoids as essentially reefal fauna. The findings highlight the conservation benefits of an inclusive approach to marine habitat survey and mapping. Assemblages such as the one described, although they may be of scientific and ecological significance, would have been overlooked by common approaches to marine conservation planning which emphasise highly productive or aesthetically appealing habitats. Most habitat mapping studies rely solely or in part on abiotic surrogates for patterns of biodiversity. The utility of abiotic variables in predicting biological distributions at the local scale (10 km) was tested. Habitat classifications of the same set of 41 sites based on 6 abiotic variables and abundances of 89 taxa and bioturbation indicators were compared using correlation, regression and ordination analyses. The concepts of false homogeneity and false heterogeneity were defined to describe types of errors associated with using abiotic surrogates to construct habitat maps. The best prediction by abiotic surrogates explained less than 30% of the pattern of biological similarity. Errors of false homogeneity were between 20 and 62%, depending on the methods of estimation. Predictive capability of abiotic surrogates at the taxon level was poor, with only 6% of taxon / surrogate correlations significant. These results have implications for the widespread use of abiotic surrogates in marine habitat mapping to plan for, or assess, representation in Marine Protected Areas. Abiotic factors did not discriminate sufficiently between different soft bottom communities to be a reliable basis for mapping. Habitat mapping for the design of Marine Protected Areas is critically affected by the scale of the source information. The relationship between biological similarity of macrobenthos and the distance between sites was investigated at both site and local scales, and for separate biotic groups. There was a significant negative correlation between similarity and distance, in that sites further apart were less similar than sites close together. The relationship, although significant, was quite weak at the site scale. Rank correlograms showed that similarity was high at scales of 10 km or less, and declined markedly with increasing distance. There was evidence of patchiness in the distributions of some biotic groups, especially seagrass and anthozoans, at scales less than 16 km. In other biotic groups there was an essentially monotonic decline in similarity with distance. The spatial agglomeration approach to habitat mapping was valid in the study area. Site spacing of less than 10 km was necessary to capture important components of biological similarity. Site spacing of less than 2.5 km did not appear to be warranted. Macrobenthic habitat types were classified and mapped at 78 sites spaced 5 km apart. The area mapped was about 2,400 km2 and extended from estuarine shallow subtidal waters to offshore areas to the 50 m isobath. Nine habitat types were recognised, with only one on hard substrate. The habitat mapping characterised several habitat types not previously described in the area and located deepwater algal and soft coral reefs not previously reported. Seagrass beds were encountered in several locations where their occurrence was either unknown or had not previously been quantified. The representation of the derived habitat types within an existing marine protected area was assessed. Only two habitat types were represented in highly protected zones, with less than 3% of each included The study represents the most spatially comprehensive survey of epibenthos undertaken in Moreton Bay, with over 40,000 m2 surveyed. Derived habitat maps provide a robust basis for inclusion of representative examples of all habitat types in marine protected area planning in and adjacent to Moreton Bay. The utility of video data to conduct a low-cost habitat survey over a comparatively large area was also demonstrated. The method used has potentially wide application for the survey and design of marine protected areas.

The Coastal and Marine Ecological Classification Standard (CMECS) provides a comprehensive framework of common terminology for organizing physical, chemical, biological, and geological information about marine ecosystems. Federally endorsed as a dynamic content standard, all federally funded data must be compliant by 2018; however, applying CMECS to deep sea datasets and underwater video have not been extensively examined. The presented research demonstrates the extent to which CMECS can be applied to deep sea benthic habitats, assesses the feasibility of applying CMECS to remotely operated vehicle (ROV) video data in near-real-time, and establishes best practices for mapping environmental aspects and observed deep sea habitats as viewed by the ROV’s forwardacing camera. All data were collected during 2014 in the Northern Gulf of Mexico by the National Oceanic and Atmospheric Administration’s (NOAA) ROV Deep Discoverer and ship Okeanos Explorer.

AbstractThe mapping of habitats is the first step that is done in policies that target theenvironment, as well as in spatial planning and management. The biodiversityplans are always centered around habitats. Therefore, constant monitoring ofthese delicate species in terms of health, changes, and extinction is a must inbiodiversity plans. Human activities are constantly growing, resulting in theextinction of land and marine habitats. Land habitats are being destroyed using airpollution and the cutting of forests. At the same time, marine habitats are beingdestroyed due to acidification of ocean waters and waste materials from theindustries and pollution. The author has focused on aquatic habitats in thisdissertation, mainly coral reefs. An estimate of 27% of coral reef ecosystems havebeen destroyed, and a further 30% are at risk of being damaged in the comingyears. Coral reefs occupy 1% of the ocean floor, and yet they provide a home to30% of marine organisms. To analyze the health of these aquatic habitats, theyneed to be assessed through habitat mapping. Habitat mapping shows thegeographic distribution of different habitats within a particular area. Marinehabitats are typically mapped using camera imagery. The quality of underwaterimages suffers from the characteristics of the marine environment. This results inblurry images or containing particles that cover many parts of an image. Toovercome this, underwater image enhancement algorithms are used to preprocessimages beforehand. Now, there are many underwater image enhancementalgorithms that target different characteristics of the marine environment, butthere is no consensus among researchers about a single underwater technique thatcan be used for any marine dataset. In this dissertation, multiple experiments onvarious popular image enhancement techniques (seven) were conducted and usedto reach a decision about a single underwater approach for all datasets. Thedatasets include EILAT, EILAT2, RSMAS, and MLC08. Also, two state-of-the-artdeep convolutional neural networks for habitat mapping, i.e., DenseNet andMobileNet tested. Maximum results from the combination of Contrast LimitedAdaptive Histogram Equalization (CLAHE) achieved as underwater imageenhancement technique and DenseNet as deep convolutional network. / Not applicable

As all of Sweden's hydropower is to be re-examined within a 20-year period, methods are needed to carry out ecological investigations of dammed waterways. The first aim of this thesis is to evaluate whether methods for salmon and trout habitat mapping take all relevant indicators into account. In addition, the report aims to investigate which factors affect the results of habitat mapping based on hydraulic simulation and to investigate whether this method can be made more efficient through the use of simpler models, drone images and calculations. The work began with a literature study. A model was then built over a dammed stretch where mapping through hydraulic simulation was carried out. A mapping was then carried out on another stretch of stream based on a simpler model, drone images and shadow calculations, in parallel with a field mapping. The results of the literature study showed that the mapping methods capture the physical indicators well and indirectly link to certain chemical and ecological indicators. The method could be improved by including the water's nitrogen content and pH in the assessment.Important factors in habitat estimation with hydraulic simulation are the flow and the accuracy of the terrain model, as well as how the result is produced. The result from mapping with a simpler hydraulic model showed large deviations from the results obtained in the field, with respect above all to depth and width. Drone imagery for substrate assessment works well in shallow and clear water bodies. Shadow calculations based on how they were applied in this work to habitat mapping have not given satisfactory results, why the method needs to be developed. / Då all Sveriges vattenkraft ska omprövas inom en 20-årsperiod behövs metoder för att genomföra ekologiska utredningar av uppdämda vattendrag. Det första syftet med detta examensarbete är att utvärdera om metoder för lax- och öringhabitatkartering tar hänsyn till alla relevanta indikatorer. Därutöver syftar rapporten till att undersöka vilka faktorer som påverkar resultatet vid habitatkartering utifrån hydraulisk simulering och att undersöka om denna metod kan effektiviseras genom användning av enklare modeller, drönarbilder och beräkningar. Arbetet inleddes med en litteraturstudie. Därpå byggdes en modell upp över en indämd sträcka där kartering genom hydraulisk simulering genomfördes. En kartering genomfördes sedan på en annan strömsträcka utifrån en enklare modell, drönarbilder och skuggberäkningar, parallellt med en fältkartering. Litteraturstudiens resultat visade på att karteringsmetoderna väl fångar upp de fysikaliska indikatorerna och indirekt kopplar till vissa kemiska och ekologiska indikatorer. Metoden skulle kunna förbättras genom att ta in vattnets kvävehalt och pH i bedömningen. Viktiga faktorer vid habitatskattning med hydraulisk simulering är flödet och terrängmodellens noggrannhet, samt klassningen för vad som anses som goda habitat. Resultatet från kartering med en enklare hydraulisk modell visar på stora avvikelser mot resultaten inhämtade i fält, med avseende på framför allt djup och bredd. Drönarbilder för substratbedömning fungerar väl vid grunda och klara vattendrag. Skuggberäkningar utifrån hur de i detta arbete applicerats på habitatkartering har inte gett tillfredställande resultat, varför metoden behöver utvecklas.

Remote sensing studies based on satellite and aerial imagery have improved our understanding of the morphology and distribution of several shallow reefs along the Red Sea Arabian coast and of the benthic assemblages associated to them (Bruckner et al., 2011; Bruckner et al., 2012; Rowlands et al., 2016). However, data concerning the deeper benthic assemblages' composition and spatial distribution in the central Red Sea are still missing. Using high-resolution acoustic technology and an underwater remotely operated vehicle (ROV), we aim to map, describe, and classify the reefs found in Thuwal's coastal area, filling the information gap by producing the first benthic habitat map of this area and making progress towards the evaluation of shallow and upper mesophotic benthic resources in the Saudi Arabian Red Sea. High-resolution acoustic data was collected using a multibeam echosounder system, which generated a bathymetric model. Based on this, the seafloor features were classified into 12 morphotypes following a visual assessment. Based on the morphotypes classification, 28 sites were visually selected for ground-truthing data acquisition and characterization of the substrate and benthic assemblages using a remotely operated vehicle equipped with an ultra-short baseline (USBL) positioning system. With the information obtained from the bathymetry data and the ROV video transects, a Top-Down approach in which we analyzed, categorized, and classified the data was used to create Thuwal's reefs benthic habitat map in which 23 different benthic habitat types were identified. This research uncovered previously poorly studied reef morphologies in the Red Sea and their associated benthic assemblages. Moreover, this work will help improve the understanding of the spatial distribution of benthic communities located on Thuwal's reefs, giving a baseline with the potential to provide fundamental information that can be used for mapping, management, conservation, and future research at other Red Sea reef sites in Saudi Arabia.

Using a towed underwater video camera system, benthic habitats were classified along transects in a popular offshore fishing area on the West Florida Shelf (WFS) known as “The Elbow.” Additionally, high resolution multibeam bathymetry and co-registered backscatter data were collected for the entire study area. Using these data, full coverage geologic and biotic habitat maps were developed using both unsupervised and supervised statistical classification methodologies. The unsupervised methodology used was k-means clustering, and the supervised methodology used a random forest algorithm. The two methods produced broadly similar results; however, the supervised methodology outperformed the unsupervised methodology. The results of the supervised classification demonstrated “substantial agreement” (κ>0.6) between observations and predictions for both geologic and biotic habitat, while the results of the unsupervised classification demonstrated “moderate agreement” (κ>0.4) between observations and predictions for both geologic and biotic habitat. Comparisons were made with the previously existing map for this area created by Florida Fish and Wildlife Conservation Commission’s Fish and Wildlife Research Institute (FWC-FWRI). Some features are distinguishable in both maps, but the FWC-FWRI map shows a greater extent of low relief hard bottom features than was predicted in our habitat maps. The areas predicted as low relief hard-bottom by FWC-FWRI often coincide with areas of higher uncertainty in the supervised map of geologic habitat from this study, but even when compared with ground-truth points from the towed video rather than predictions, the low relief hard bottom in FWC-FWRI’s map still corresponds to what was identified as sand in the video 73% of the time. The higher uncertainty might be a result of the presence of mixed habitats, differing morphology of hard-bottom, or the presence of sand intermixed with gravel or debris. More ground-truth samples should be taken in these areas to increase the confidence of these classifications and resolve discrepancies between the two maps. Data from the towed video system were also used to assess differences in fish communities among habitat types and to calculate habitat-specific densities for each taxa. Fish communities were found to significantly differ between soft and hard bottom habitats as well as among the hard-bottom habitats with different vertical relief (flat hard-bottom vs more steeply sloping areas). Additionally, significant differences were found between the fish communities in habitats with attached fauna such as sponges and gorgonians, and areas without attached fauna; however, attached fauna require rock to attach to and the rock habitats rarely lacked attached fauna, so this difference may just reflect the difference between fish communities in sand and rock habitats without the consideration of vertical relief. Moreover, the species driving the differences in the fish communities were identified. Fish were more likely to be present and assemblages were more species rich in more complex habitats (rockier, higher relief, presence of attached fauna). Habitat specific densities were calculated for each species, and general trends are discussed. Lastly the habitat-specific densities were extrapolated to the total area of habitat type (sand vs rock) as predicted by the supervised geologic habitat map. There is predicted to be approximately 111,000 fish (95% CI [67015, 169405]) within the study area based on this method, with ~47,000 (~43%) predicted to be within the sand habitat and ~64,000 (~57%) in the rock habitat. This demonstrates the potential of offshore rocky reefs as “critical habitats” for demersal fish in the offshore environment as rock accounts for just 4% of the study area but is expected to contain over half of the total abundance. The value of sand habitats is also shown, as due to their large area they are able to contribute substantially to the total number of fish despite sustaining comparatively low densities.

Coral reef habitats are being threatened by global warming, natural disasters and the increased pressure of the global population. These habitats are in urgent need of efficient monitoring and management programs to sustain their biological, economic and cultural values for the global community. Habitats maps, describing the extent, composition and the condition of the benthos in time and space, form a valuable information source for scientists and managers to answer their management questions. Adequate and accurate habitat maps are needed and can be provided by a range of mapping approaches, which are based on integration of field and remotely sensed image data sets. Scientists, technicians and managers lack knowledge on the cost effectiveness and procedures for calibrating and validating mapping approaches that integratef field data and remote sensing imagery, for use in various coral reef and seagrass environments. This knowledge is required to adequately design, apply and assess operational mapping approaches and their maps. Hence, the aim of this study is to improve habitat mapping capabilities by integrating low cost remote sensing approaches and field-calibration and -validation methods for a range of coral reef and seagrass environments. To achieve this aim, commonly used habitat mapping approaches that integrated field-calibration and -validation methods with remote sensing image based processing techniques were studied, in different coral reef and seagrass environments in Fiji and Australia. These environments varied in: water clarity, water depth, benthic composition, spatial complexity of benthic features, and remoteness. The study had three objectives: (1) to evaluate the accuracy, cost and perceived relevance of eight commonly used benthic cover mapping approaches for three different coral reef environments. (2) Conduct a cost-benefit comparison of two field survey methods for calibrating and validating maps of coral reef benthos derived from high-spatial resolution satellite images in three different coral reef environments. (3) Identify considerations for comparing the thematic accuracy of multi-use image based habitat maps in various coral reef and seagrass environments. A scientific assessment and an evaluation of the relevance for managers, was conducted on eight commonly used habitat mapping approaches for three different coral reef environments. This analysis revealed a preference for a mapping approach based on supervised classification of Quickbird imagery integrated with basic field data. This approach produced an accurate map within a short time with low cost in that suited the user’s purpose. Additionally, the results indicated that user preference in selecting a suitable map was affected by: variations in environmental complexity; map purpose, and resource management requirements. To assess the variation in performance of methods for calibration and validation for coral reef benthic community maps, derived from high-spatial resolution satellite images, a comparison was conducted between spot check and georeferenced photo-transect based mapping approaches. The assessment found that the transect based method was a robust procedure which could be used in a range of coral reef environments to map the benthic communities accurately. In contrast, the spot check method is a fast and low cost approach suitable to map benthic communities which have lower spatial complexity. However, the spot check approach provides robust results, if it is applied in a standardised manner, providing a description of selected homogenous areas with georeferenced benthic cover photos. Considerations for comparing the thematic accuracy of multi-use image based habitat maps in various coral reef and seagrass environments were assessed. This included a review of 80 scientific publications on coral reef and seagrass habitat mapping, which revealed a lack of knowledge and reporting in regards to the assessment of the thematic map accuracy. These publications commonly used thematic accuracy measures and factors controlling their variation were then determined for various habitat mapping approaches for different coral reefs and seagrass environments. Assessment of these measures found that variations in accuracy levels were not only a result of actual differences in map accuracy, but were also due to: spatial complexity of benthic features present in the study area; distribution of the calibration and validation samples relative to each other, and the level of detail provided by these samples. Two main outcomes resulted from this dissertation. The first was the development of a robust mapping approach based on georeferenced photo-transect method integrated with high spatial resolution imagery, which is able to accurately map a variety of coral reef and seagrass habitats. The second outcome is an increase in capacity for coral reef and seagrass habitat mapping by scientists and managers. This increase is accomplished by providing knowledge on various habitat mapping approaches in regards to their: cost/time, accuracy and user relevance; performance of calibration and validation field methods; and performance of accuracy measures, when applied in a range of coral reef and seagrass environments. The findings and outcomes from this dissertation will significantly contribute to management of coral reef and seagrass environments by enabling scientists and managers to choose appropriate combinations of: field and image data sources; processing approaches, and validation methods for habitat mapping in these environments.

This thesis concerns with implementation of the Habitats Directive into Czech legislation. It deals with the change in quality of habitats and European habitat types. It also considers potential impact of special areas of conservation on this change in the South Bohemian Region. In the intersections of segments from the layer of habitat mapping and the updated layer, the data from these layers that describe quality were compared. From the reports under Article 17 submitted by the Czech Republic, information about future prospects and structure and function change in those habitat types was obtained. Negative change in quality was found in habitats, while the change in habitat types was mostly positive or none. This difference is a reflection of distinct methodologies.

Remote sensing has transformed coral reef science in the last decades. It is now possible to audit reef health and geomorphology at global scale and very high spatial resolution. This work utilizes the vast and no-cost archive of imagery housed within Google Earth (GE). GE was used to interrogate the morphometric properties (size, shape, complexity, etc) of the components that combine to yield a reef environment (reef structures, sediment sheets, and so forth). The data populated a morphometric database for reefs globally that are partitioned by their architecture. The database has been investigated using information theory. The aim of the work is to identify whether motifs of carbonate platforms within these reef types are predictable on the basis of environmental parameters. The results are relevant to assess depositional patterns to develop rules for predicting how facies are distributed in modern systems and ancient reservoirs.