Rozprawy doktorskie na temat „Aquatic habitats”

During the 19th and 20th centuries, alterations to the Pecos River in New Mexico and Texas, USA due to anthropogenic activities, including damning and river channelization, vast water extraction for irrigation, as well as pollution of associated habitats, have greatly impacted the fish fauna within the drainage. One of the endemic fish species, the Pecos pupfish (Cyprinodon pecosensis), might be the most affected. Historically abundant and widespread large populations have been disrupted and became a series of small isolated subpopulations that persist at a few highly fragmented habitats restricted to a small area in southern New Mexico. The connectivity among these habitats is extremely low, and can potentially prevent any gene flow among subpopulations, which might eventually result in morphological divergence among subpopulations in face of different ecological conditions. Here I utilized landmark-based Geometric Morphometrics to evaluate body shape variation of the Pecos pupfish at 26 different localities categorized into four general habitat types that each differ greatly in ecological properties. Results from this study suggest that, despite significant sexual dimorphism, body shape morphology of Pecos pupfish varied in response to spatial heterogeneity and it was most intensely influenced by specific localities within habitat types. There were overlaps of the convex hull regions of morphospace among the four habitat types, implying that ecomorphological dynamics of the Pecos pupfish were rather site-specific. Moreover, temporal variation of body morphology was statistically significant but not comparable to body shape variation among different localities. The empirical data collected from this study provides preliminary evidence for phenotypic diversity of Pecos pupfish in varied ecological conditions, which has important implications for the future conservation management of Pecos pupfish diversity and viability. Such implications could be extended to other endemic desert fishes in disrupted habitats.

The Mississippi River is one of the most intensively managed and altered river systems in the world. The alterations to the Mississippi have been largely made to meet navigation demands and mitigate floods. River training has been undertaken using rock structures, commonly referred to as river training structures (RTS), to modify the shape of the river to maintain the Congressional mandated navigation channel dimensions. In addition to maintaining the navigation channel, newer RTS such as chevrons, have been claimed to be designed as an improvement to the previously existing dikes. They are considered to be tools of improving riverine habitat by increasing physical habitat heterogeneity within the highly engineered and consequently uniform river channel. Thus, to evaluate the differences in physical habitat heterogeneity created by the two RTS; a dike and a chevron, this study models and compares the physical aquatic habitats created along the Middle Mississippi River near Grand Tower, Illinois. The hydraulic modelling software HEC-RAS has been used to develop a two-dimensional model of the study area containing the RTS using detailed 2 m- resolution topobathy digital elevation model (DEM), U.S Geologic Survey’s National Land Cover Database (NLCD), an existing one-dimensional model of the Mississippi and hydrologic data from several hydrologic monitoring stations for the years 2008-2016. Depth and velocity grids were extracted from the HEC-RAS model for three different discharge conditions; 0.5 mean annual flow (MAF) with 40% exceedance probability, MAF with 80% exceedance probability and 1.5 MAF with 15% exceedance probability were used to develop and categorize physical habitat distribution maps of the study area using ArcGIS. The modeled physical aquatic habitat patches were assessed at three buffer distances of 30 m, 90 m, and 150 m from the RTS. The area Simpson diversity and Jaccard similarity indices were calculated for the different discharge conditions and associated habitat mosaics. The distribution of physical habitat modeling revealed a variation in the pattern of habitat patches between the dike and chevron. For the chevron dike evaluated in this study, very-slow deep habitat patches are created in the inner portion of the chevron and slow deep patches around the exterior of the structure which extend both up and downstream of the structure. The dike created slow-deep habitat patches along the structure, very-slow deep patches on the riverbank edge and fast- deep patches on the river side edge. Evaluation of physical habitat patch diversity in relation to the distance from the RTS revealed the highest diversity index values were found within the first 30 m buffer and generally decrease with distance away from the structure. Comparison of the Jaccard index values in vicinity of the two evaluated RTS suggest the habitat patch diversity are similar for both structures at 0.5 MAF and 1.5 MAF flow conditions (index value ranging between 0.60-0.87). However, for the MAF flow conditions the Jaccard index suggests there is more physical habitat patch diversity in the vicinity of the chevron relative to the dike. The modeling results suggest both physical habitat patch richness and diversity declines with an increase in discharge. The decline in physical habitat patch richness and diversity with discharge conditions were greater for the dike relative to the chevron, thus while the chevron retains more types of habitat patches with increase in discharge the diversity indices are still higher for the dike. The modeling also suggests both RTS have created and maintain shallow water habitat (SHW) and overwintering habitat patches (OWH) for the flow conditions evaluated in this study. These habitat patches are utilized by fish species at various life stages. Larger area of OWH habitats; 30% of total area by dikes and 35% of total area by chevrons are created in comparison to SWH; 10% by dike and 7% by chevron. The modeling results show that both the dike and chevron evaluated in this study are associated with and likely maintain ecologically relevant habitats and substantially contribute to physical habitat diversity. If the physical characteristics of the RTS investigated here are similar to other dikes and chevrons along the Mississippi River, the results of this study supports the secondary management objective for these structures, increase in physical aquatic habitat patch diversity, is likely being achieved.

Riverine physical habitats and habitat utilization by fish have often been studied independently. Varying flows modify habitat composition and connectivity within a stream but its influence on habitat use is not well understood. This study examined brown trout (Salmo trutta) and bullhead (Cottus gobio) utilization of physical habitats that vary with flow in terms of size and type, persistence or duration, and frequency of change from one state to another, by comparing groundwater-dominated sites on the River Tern (Shropshire) with surface runoff-dominated lowland, riffle-pool sites on the Dowles Brook (Worcestershire). Mesohabitat surveys carried out at two-month intervals on a groundwater-dominated stream and on a surface runoff-influenced stream showed differences in habitat composition and diversity between the two types of rivers. The temporal variability in mesohabitat composition was also shown to differ between the two flow regime types. In the groundwater-influenced stream, mesohabitat composition hardly varied between flows whereas in the flashy stream it varied to a great extent with discharge. Habitat suitability curves for brown trout and bullhead were constructed to predict the potential location of the fish according to flow. The resulting prediction maps were tested in the field during fish surveys using direct underwater observation (snorkelling). Under the groundwater-influenced flow regime brown trout displayed a constant pattern of mesohabitat use over flows. Mesohabitats with non-varying characteristics over flows and with permanent features such as large woody debris, macrophytes or any feature providing shelter and food were favoured. Biological processes, such as hierarchy, life cycle and life stage appeared to play a key role in determining fish habitat use and to a greater extent than physical processes in these streams. Bullhead observations in the flashy river showed that mesohabitat use varied with flow but that some mesohabitats were always favoured in the stream. Pools and glides were the most commonly used mesohabitat, due to their stability over flows and their role as shelter from harsh hydraulic conditions and as food retention zones. The presence of cobbles was also found to be determinant in bullhead choice of habitat. In this flashy environment, physical processes such as flow and depth and velocity conditions appeared to be a more decisive factor in bullhead strategy of habitat use than biological processes. This research shows that: 1. Though differences in habitat use strategies between the two flow regimes can in part be attributed to differing ecology between the species, flow variability affects fish behaviour. 2. A stable flow regime allows biological processes to be the main driving force in determining fishbehaviour and location. A highly variable environment requires fish to develop behaviour strategies in response to variations in hydraulic conditions, such as depth and velocity, which constitute the key factor in determining fish location.

To meet the rising food demands of communities in Accra,Ghana, urban agriculture has been popularized as a way to increase food security and improve nutrition (Donovan et al., 2012). Urban agriculture is defined as "the cultivation of crops at both the subsistence and commercial levels including the keeping of livestock in open spaces in urban areas (Adjaye, n.d.). In Accra, urban agriculture covers 1,091 hectares, employs over one thousand people, and supplies residents with 90% of its vegetables ("Accra Metropolitan", n.d.). Further, 60% of households in Accra participate in backyard farming ("Accra Metropolitan", n.d.). Although urban agriculture provides many benefits for communities in Accra, it has been linked to the creation of suitable habitats for Anopheles gambiae complex larvae. In Accra, a spatio-temporal distribution of An. gambiae complex larvae and larvae habitats has not been established. A larval study in two urban agriculture and two non-urban agriculture sites was conducted in the months of May, July, August, and September 2014. When combined together, 3,807 An. gambiae complex larvae were collected from the urban agriculture sites of Korle Bu and Opeibea over the period of the study. When combining the urban non-agriculture sites of Madina and Ashaiman, 2,484 An. gambiae complex larvae were collected over the same period. The results of this study in Accra show that Korle Bu, an urban agriculture site, was the most productive site, with 2,604 An. gambiae complex larvae collected for the months of May, July, August, and September. July was the most productive month for Korle Bu, with 1,653 An. gambiae complex larvae collected. Further investigations of An. gambiae complex larval habitats are necessary to better understand malaria transmission attributes unique to Accra, Ghana.

The role of mangroves as essential fish habitat has been a focus of extensive research. However, recent evidence has shown that this role should not be evaluated in isolation from surrounding habitats such as seagrass beds and hard-bottom communities. For example, submerged aquatic vegetation (SAV) communities provide potential sources of food and shelter for fish species that may reside in the mangroves, but may also undergo ontogenetic migrations and daily home-range movements into neighboring habitats. The connectivity between the mangrove fish community and the surrounding seascape may be influenced by the level of patchiness, fragmentation, and spatial heterogeneity of adjacent SAV habitats (i.e., SAV seascape structure). The spatial patterns and heterogeneity of SAV seascape structures are driven by internal and external regulatory mechanisms operating at different spatial and temporal scales. In addition, it is likely that many fish species inhabiting the mangrove zones have different home ranges, and foraging and migratory patterns; therefore, different mangrove fish species may respond to seascape heterogeneity at different scales. There are few studies that have assessed the influence and connectivity of benthic habitats adjacent to mangroves for estuarine fish populations at multiple scales. The present research used an exploratory seascape approach in Biscayne Bay (Florida, USA) to evaluate patterns in the patch composition and configuration of SAV communities, and to examine relationships between seascape structural metrics and the abundance, diversity, and distribution of fishes that utilize the adjacent mangrove shoreline as nursery and/or adult habitat. This seascape approach consisted of: a) the multi-scale characterization of the SAV distribution across the seascape with metrics developed in Landscape Ecology, Geographic Information Systems and Remote Sensing; b) multivariate analyses to identify groups with significantly distinct SAV seascape structures within the most heterogeneous scale, and identify possible mechanisms driving the observed SAV seascape structures; and c) an assessment of the mangrove fish community responses to SAV seascape structures. By applying a set of multivariate analyses (e.g., ANOSIM, MDS plots, hierarchical clustering), the buffer within 200 m from shore was identified as the scale with the highest structural heterogeneity. At this scale, two major SAV seascape structures (i.e., areas with similar SAV spatial arrangement and composition) were identified: a fragmented SAV seascape (FSS) structure and a continuous SAV seascape (CSS) structure. Areas with CSS were characterized by large, uniform SAV patches. In contrast, areas with FSS were characterized by a higher density of smaller, more complex SAV patches. Furthermore, the areas with CSS and FSS structures clustered in zones of the bay with distinct salinity properties. The areas with CSS structures were mostly located in zones characterized by high and stable salinity. However, the areas with FSS concentrated in zones that are influenced by freshwater discharges from canals and with low and variable salinity. The responses of fish diversity metrics were not constrained to the scale at which the greatest spatial heterogeneity of SAV seascape structures was observed (i.e., the seascape composition and configuration within 200 m from shore), but was related to SAV seascape characteristics across different scales. The majority of the variability of the fish diversity metrics in the mangrove shoreline was explained by SAV seascape structures within the smaller scales (i.e., 100-400 m from shore), and SAV seascape structures that represented the level of fragmentation and/or the percent of suitable habitat. Different conceptual models were proposed to illustrate and understand the ecological dynamics behind the relationship between the diversity of the mangrove fish community and the structure of the adjacent SAV seascape. In general, the diversity and abundance of fishes is influenced by the type and level of fragmentation of the SAV seascape, which, in turn, influence the proportion of the seascape used for foraging and refuge by fish. In conclusion, this research quantified how the release of large pulses of freshwater into near-shore habitats of coastal lagoons can influence the seascape structure of SAV communities. Namely, freshwater inputs produce fragmentation in otherwise fairly homogeneous SAV meadows. The outcome of this research highlights the importance of seascape characteristics as indicators of ecosystem-level modifications and alterations affecting the spatial distribution, assemblage, and diversity of marine nearshore habitats in coastal regions heavily influenced by human activities. In addition, the results illustrated the cascading effects and synergistic influences of near-shore habitat spatial assemblages on the composition and diversity of estuarine fish communities. Lastly, and very importantly, the relationships established in this project provide quantitative and qualitative information on patterns of species-habitat associations needed for the improved synergistic management and protection of coastal habitats and fisheries resources.

Esta tesis aborda diferentes retos relacionados con la conservación de la biodiversidad acuática en la península ibérica utilizando los macroinvertebrados acuáticos como sistema modelo. Esta información pretende contribuir a un mejor conocimiento de los factores que determinan y amenazan la biodiversidad de macroinvertebrados acuáticos así como proporcionar herramientas útiles para su conservación. Los Capítulos 1 y 2 se centran en la búsqueda y evaluación de posibles sustitutos o indicadores de biodiversidad en ecosistemas acuáticos, mientras que el capítulo 3 está dedicado a testar la eficacia de las redes de áreas protegidas en la representación de la biodiversidad de macroinvertebrados. En el capítulo 4, a partir de nuevos registros de un insecto acuático invasor detectado a lo largo de la península ibérica, se proporcionan mapas globales de distribución potencial considerando que la prevención de invasiones biológicas es la estrategia más efectiva para evitar problemas de conservación y nuevas expansiones. El Capítulo 1 revela que los parques nacionales de montaña en España contienen un porcentaje importante de la biodiversidad ibérica con respecto a las familias de macroinvertebrados. La riqueza de familias de Coleoptera muestra la correlación más alta con los otros grupos taxonómicos y puede ser propuesta como un sustituto/indicador de la biodiversidad de macroinvertebrados en las zonas montañosas bien conservadas. Tal indicador taxonómico podría complementarse con el uso de la riqueza de familias de Odonata en ambientes estancados. El Capítulo 2 presenta una evaluación del funcionamiento de un grupo carismático (aves acuáticas) como sustituto de la biodiversidad de macroinvertebrados en humedales. Los resultados muestran una concordancia limitada entre la composición de la comunidad de aves acuáticas y macroinvertebrados, así como correlación no significativa o negativa entre las métricas de riqueza taxonómica. Ambos grupos muestran diferentes respuestas a gradientes ambientales, y por lo tanto las aves acuáticas se pueden considerar malos indicadores de la biodiversidad acuática en estos ecosistemas. El Capítulo 3 proporciona el primer intento de evaluar la efectividad de las redes de áreas protegidas en la representación de los componentes alfa, beta y gamma de la diversidad tanto taxonómica como funcional de macroinvertebrados a diferentes escalas espaciales. Los resultados muestran un funcionamiento de las áreas protegidas marcadamente diferente en el mantenimiento de la diversidad taxonómica y funcional de macroinverebrados, y apuntan a un sesgo en la representación de determinados hábitats acuáticos dentro de las redes de reservas. Tal desajuste llama a la prudencia en cuanto al uso de cualquier componente de una diversidad como un sustituto para los demás, y hace hincapié en la importancia de adoptar un enfoque integral para la conservación de la biodiversidad en los ecosistemas acuáticos. El último capítulo se centra en Trichocorixa verticalis verticalis (Corixidae, Hemiptera), una de las pocas especies de insectos acuáticos consideradas como exóticas, y para la que se han detectado nuevos registros de poblaciones importantes en numerosos humedales Ramsar en Andalucía (suroeste de España). Los mapas predictivos de distribución potencial obtenidos sugieren que este coríxido puede extenderse mucho más allá de su área de distribución actual y encontrar condiciones habitables en áreas templadas a lo largo de una amplia gama de latitudes. Además, al considerar un escenario climático futuro, el área de idoneidad muestra cambios limitados en comparación con la distribución potencial actual. Los resultados permiten la detección de zonas de contacto entre áreas actualmente colonizadas y áreas potenciales de invasión, así como zonas con alto nivel de idoneidad que coinciden con áreas reconocidas como puntos calientes de biodiversidad a nivel mundial. La combinación de estos resultados entronca con algunos de los retos claves para la conservación de la biodiversidad de macroinvertebrados acuáticos (indicadores de biodiversidad, eficacia de las áreas protegidas y potenciales amenazas a la biodiversidad) y proporciona información útil acerca de temas claves para gestores y biólogos de la conservación.
This thesis addresses different challenges related to the conservation of freshwater biodiversity in the Iberian Peninsula using aquatic macroinvertebrates as a model system. This information will contribute to a better understanding of the determinants that affect and threat aquatic macroinvertebrate biodiversity and, aims to provide insights for use in nature conservation policies. Chapters 1 and 2 focus on the assessment of potential biodiversity surrogates in aquatic ecosystems, while Chapter 3 is dedicated on the effectiveness of protected areas networks in representing freshwater diversity. In Chapter 4, starting from new records of an alien aquatic insect detected in the Iberian Peninsula, global potential distribution maps for this species are produced since the prevention of biological invasions is the most cost-effective way to avoid problems related with nature conservation. Chapter 1 reveals that mountainous national parks in Spain contain a large percentage of the overall Iberian biodiversity with respect to aquatic macroinvertebrates at family level. Coleoptera family richness displays the highest correlation with the other taxonomic groups and remaining richness values and may be used as a macroinvertebrate biodiversity surrogate in well preserved mountainous areas. Such a taxonomic indicator could be complemented by the use of Odonata family richness in case of standing waters. Chapter 2 assesses the performance of a charismatic group (waterbirds) as surrogate of macroinvertebrates biodiversity in wetlands. The results show limited concordance between the community composition of waterbirds and macroinvertebrates, and negligible or negative correlations between the metrics of their taxonomic richness. Contrasting responses to environmental gradients were detected and waterbirds can therefore be considered poor indicators of aquatic biodiversity in these ecosystems. Chapter 3 provides the first attempt at assessing the effectiveness of protected areas in representing alpha, beta and gamma components of taxonomic and functional macroinvertebrate diversity at different spatial scales. The main findings highlight the contrasting performance of reserve systems in the maintenance of taxonomic and functional freshwater diversity, and point to a bias in environmental representation within protected area networks. Importantly, this mismatch means that caution should be exercised when using any one diversity component as a surrogate for others, and emphasizes the importance of adopting an integrative approach to biodiversity conservation in aquatic ecosystems. The last chapter focuses on Trichocorixa verticalis verticalis (Corixidae, Hemiptera), one of the few exclusively aquatic insects that can be considered as an alien species, and for which large populations have been newly recorded in numerous Ramsar wetlands in Andalusia (south-west Spain). The predictive maps obtained of current potential distribution suggest that this corixid may expand well beyond its current range and find inhabitable conditions in temperate areas across a wide range of latitudes. When considering a future climatic scenario, the suitability area showed only limited changes compared with the current potential distribution. The results allow the detection of potential contact zones among currently colonized areas and potential areas of invasion, as well as zones with a high level of suitability overlapping areas recognized as global biodiversity hotspots. These results, taken as a whole, point to some of the main challenges for the conservation of aquatic macroinvertebrate biodiversity (biodiversity surrogates, reserve performance and biodiversity threats) and provide useful information about important topics that concern protected area managers and conservationists.

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Lotic ecosystems are highly complex interacting with acting factors in different spatial and temporal scales. Small forested streams receive direct influence of the surrounding vegetation through the input of organic matter which is the base of the food chain in these ecosystems. I studied the effect of the reduced-impact selective logging on communities of aquatic insects streams to test the hypothesis that communities are affected by their impacts. Despite the metrics used appropriately capture the impact, there were no negative effects on insect communities. However, the results of this study may not be generalizable to other systems because we studied only a fraction of the diversity of Amazonian streams, specifically the insect orders Trichoptera, Plecoptera and Coleoptera. In addition, the absence of the low impact management effects is dependent on the operating system adopted in each enterprise. Another predominant feature in any lotic ecosystem is its directional flow, which consequently affects the distribution of substrates, habitats, and food resources within the streams. I studied the effects of water flow taking it as the main predictor of the selective effect of habitat on the attributes of insect taxa. My hypothesis was confirmed by showing that most rapid flowing streams in Amazon has faunas with morphological and ecological attributes of greater resistance to flow. Environmental factors such as the preference for habitats, dispersive limitation and biotic interactions are among the main mechanisms responsible for structuring communities, and has been widely emphasized in the context of metacommunity theory. A metacommunity is defined as the set of communities in a region which are interconnected by the flow of individuals, which emphasizes the spatial dynamics in structuring the diversity and composition of species in each local community. I tested the effects of environmental factors, spatial filters and biotic interactions in aquatic insects of forested streams of the Amazon, specifically the intraguild segregation and interguild predation effect. My results support the existence of predation effects on the organization of the metacommunity, as evidenced by the exclusive fraction of the predators matrix on prey assemblages of different guilds, and still withstand environmental effects and dispersive limitation in different trophic guilds. The study developed in this thesis help us understand more clearly the effects of the selective logging impacts on aquatic insect communities, assist in understanding about what are the characteristics of the stream habitats filter ecological and morphological attributes of aquatic insects in the Amazon, and advance our understanding of the effects that biotic interactions may have on the structuring streams metacommunities.
Ecossistemas aquáticos lóticos são altamente complexos interagindo com fatores atuando em diferentes escalas espaciais e temporais. Especialmente pequenos riachos florestados recebem a influência direta da vegetação circundante por meio da entrada de matéria orgânica a qual representa a base da cadeia alimentar nestes ecossistemas. Estudei os efeitos do corte manejado de madeira sobre as comunidades de insetos aquáticos de riachos, testando a hipótese de que as comunidades seriam afetadas por estes impactos. Apesar das métricas utilizadas capturarem apropriadamente os impactos, não houveram efeitos negativos sobre nenhum aspecto das comunidades estudadas. Entretanto, os resultados deste estudo não podem ser generalizados considerando que estudamos apenas uma parcela da diversidade dos riachos, especificamente as ordens Trichoptera, Plecoptera e Coleoptera. Além disso, a ausência de efeitos do manejo de baixo impacto é dependente do regime de exploração adotado em cada empreendimento. Outra característica predominante em qualquer ecossistema lótico é seu fluxo direcional da correnteza, que por conseguinte, afeta a distribuição dos substratos, habitats, e de recursos alimentares dentro dos riachos. Estudei os efeitos da velocidade do fluxo tomando-o como o principal preditor do efeito seletivo dos hábitats sobre os atributos das espécies. Minha hipótese foi corroborada, mostrando que riachos de águas mais correntes apresentam faunas com atributos morfológicos e ecológicos de maior resistência a correnteza. Fatores ambientais, como a preferência por habitats, limitação dispersiva e interações bióticas estão entre os principais mecanismos responsáveis pela estruturação de comunidades, e tem sido amplamente enfatizados no contexto da teoria de metacomunidades. Uma metacomunidade é definida como o conjunto de comunidades numa região que são interligadas pelo fluxo de indivíduos, o que enfatiza a importância das dinâmicas espacias estruturando a diversidade e composição de espécies em cada comunidade local e para a diversidade regional. Testei os efeitos de fatores ambientais, filtros espaciais e interações bióticas em insetos aquáticos de riachos florestados da Amazônia, especificamente padrões de segregação intraguildas, como um sinal de competição, e da predação entre guildas, assumindo explicitamente que a abundância e distribuição de predadores devem seguir a disponibilidade das presas consumidas. Meus resultados suportam a existência de efeitos de predação sobre a organização da metacomunidade, como evidenciado pela fração exclusiva da matriz de predadores sobre a comunidade de presas de diferentes guildas, além de suportar efeitos ambientais e limitação dispersiva em diferentes guildas tróficas. Os estudo desenvolvidos na presente tese ajudam a compreender mais claramente como os efeitos dos impactos do corte seletivo de madeira podem afetar comunidades de insetos aquáticos, auxiliam na compreensão de quais são as características dos hábitats selecionando atributos ecológicos e morfológicos de insetos aquáticos na Amazônia, e avançam nossa compreensão dos efeitos que as interações bióticas podem causar sobre a estruturação das metacomunidades de riachos.

Understanding the evolutionary processes underlying extant biodiversity may help us to comprehend why species richness is not equally distributed between clades. One of the main causes to explain the disparity of species richness is the development of key innovations in particular clades, increasing or decreasing their capabilities to occupy new environments, to exploit novel resources or to cope with competition. The present thesis focuses on explaining the macroevolutionary consequences of two of the most common habitat transitions in aquatic environments: between environments with different degree of salinity, and between running and standing waters. Among inhabitants of aquatic environments aquatic Coleoptera are one of the most diverse, with representatives living in all kind of environments, including both running and standing waters and, not infrequently, saline environments. The most speciose aquatic Coleoptera families living in aquatic habitats are Hydrophilidae, Dytiscidae and Hydraenidae, but only the evolution of the ecological transitions of the former have been previously studied under a phylogenetic perspective. In this thesis, we assessed the evolutionary patterns of selected tribes belonging to the other two families. Despite aquatic Coleoptera being a relatively well-studied fauna, we needed to address several systematic modifications that revealed the true evolutionary history of the studied groups, describing a genus and three subgenera of Hygrotini, plus other modifications of both Hygrotini and Ochthebiini taxonomy (Chapters 1 and 3), setting the basis of this thesis. Transitions between environments with different degree of saline waters was addressed for Hygrotini (Dytiscidae family, Chapter 2) and Ochthebiini (Hydraenidae family, Chapter 5). We detected multiple origins of tolerance to saline waters, with a gradual acquisition in almost all cases and only direct transitions to hypersaline waters in fairly isolated clades, mostly associated with coastal rockpools. Moreover, tolerance to hypersaline waters was found to be irreversible, but it did not follow an evolutionary dead-end pattern as lineages exhibiting this trait still maintain their diversification capabilities (as seen in Cobalius subgenus, Chapter 5). Additionally, our results seem to link the origin of lineages exhibiting tolerance to saline waters to periods of global aridification, in accordance with previous studies in Hydrophilidae. Transitions between running and standing waters were studied in Hydroporini (Dytiscidae family, Chapter 6). We unveiled that species living in lotic and lentic habitats display similar diversification patterns, but the habitat preference is affecting the body size of the species, with reduced body sizes in specialized environments (i.e. smaller species in running waters). Finally, the field sampling in saline habitats led to the discovery of a new species for science, described as Ochthebius (Micragasma) minoicus (Chapter 4).
Estudiar los procesos evolutivos que ocasionan la biodiversidad actual puede ayudarnos a comprender mejor como la riqueza de especies está distribuida de forma desigual en diferentes clados. Una de las causas principales para explicar este fenómeno es el desarrollo de innovaciones clave que modifican las capacidades de las especies para sobrevivir en nuevos ambientes, acceder a nuevos recursos, o para lidiar la competencia con otras especies. Esta tesis se focaliza en explicar las consecuencias macroevolutivas de dos de las transiciones de hábitat más comunes en ecosistemas acuáticos: aquellas entre ecosistemas con diferente nivel de salinidad, y aquellas entre ecosistemas de aguas corrientes y aguas estancas. Entre los habitantes de ambientes acuáticos, los escarabajos son uno de los grupos más diversos, con especies capaces de vivir en todo tipo de ambientes, incluyendo aguas corrientes y estancas, y en ocasiones, ambientes salinos. Las familias más diversas de escarabajos acuáticos son Hydrophilidae, Dytiscidae e Hydraenidae, aunque solo la primera ha sido estudiada desde una perspectiva evolutiva. En esta tesis, evaluamos los patrones evolutivos de varias tribus pertenecientes a las otras 2 familias. A pesar de que los escarabajos acuáticos son un grupo bien estudiado en general, ha sido necesario realizar modificaciones en la clasificación de algunos grupos para reflejar su verdadera historia evolutiva, describiendo un nuevo género y tres subgéneros para la tribu Hygrotini. Adicionalmente, se han realizado pequeñas modificaciones tanto en Hygrotini como en Ochthebiini, siendo la base sobre la que se han desarrollado los posteriores estudios filogenéticos de esta tesis. Las transiciones entre ambientes con diferente nivel de salinidad han sido estudiadas para Hygrotini (familia Dytiscidae, Capítulo 2) y Ochthebiini (familia Hydraenidae, Capítulo 5). Se han detectado múltiples orígenes de la tolerancia a la salinidad, adquiriéndose esta característica de forma gradual en la mayoría de los casos. Los casos en los que se han descubierto transiciones directas de ambientes de agua dulce hacia ambientes hipersalinos, son clados aislados en la filogenia y asociados con ambientes de charcas costeros. Además, la tolerancia de aguas hipersalinas ha demostrado ser una característica irreversible, aunque no por ello se trata de un dead-end evolutivo (callejón sin salida), ya que las especies que viven en estos ambientes conservan su capacidad de diversificación, llegando incluso a ser superior a la de otras especies (por ejemplo, el subgénero Cobalius, Capítulo 5). A si mismo, nuestros resultados relacionan el origen de linajes tolerantes a la salinidad con periodos de aridificación a escala global, un patrón que confirma el encontrado en la familia Hydrophilidae. En cuanto a las transiciones entre aguas corrientes y estancas estudiada en Hydroporini (familia Dytiscidae, Capítulo 6), hemos encontrado patrones similares en las especies que viven en ambos ambientes, aunque los análisis sugieren la posibilidad de una mayor tasa de diversificación en ambientes de aguas estancadas. Nuestros resultados han destacado una correlación entre la preferencia del hábitat de las especies con su tamaño corporal, de manera que las especies que se encuentran en ambientes más especializados (en aguas corrientes) son aquellas con menor tamaño. Adicionalmente, se ha demostrado que la transición entre ambientes no es per se un factor que afecta al tamaño corporal de las tesis. Finalmente, gracias a los numerosos trabajos de campo realizados enfocados en los ambientes salinos, se ha podido describir la especie Ochthebius (Micragasma) minoicus (Capítulo 4).

As public awareness of river degradation has grown in recent years, the number of stream restoration activities has increased dramatically. Anthropogenic influences at a range of spatial scales from watershed landuse to riparian vegetation management to local channel morphology can have hierarchical relationships to local (meso- and macro-) in-stream habitat characteristics. This research examined these influences first by examining the influence of complex channel morphology on meso-scale brook trout (Salvelinus fontinalis) habitat in Shenandoah National Park, VA, and then by examining the combined influence of watershed urbanization and riparian vegetation (100-200 m reaches) on stream temperature. Moving beyond one-dimensional (1D) averaged representations of fish habitat, this research explored the distribution of two-dimensional (2D) flow complexity metrics at the meso-habitat scale as explanatory variables for brook trout habitat preferences and as potential metrics to evaluate habitat restoration design. Spatial hydraulic complexity metrics, including area-weighted circulation and kinetic energy gradients, were calculated based on 2D depth averaged modeled velocity distributions in two 100-m reaches on the Staunton River. While there were no statistically significant correlations between kinetic energy gradients or area-weighted circulation and fish density, fish density was positively correlated to the percent of the channel dominated by protruding boulders. The structural complexity of areas with protruding boulders create complex flow patterns suggesting that flow complexity plays an important role in available brook trout habitat preferences at the local scale, although the 2D depth averaged model may not have adequately represented this complexity. The 2D distribution of flow characteristics was then investigated further to quantify areas of flow refugia (low velocity shelters) and the relationship between these areas, traditional measures of habitat quality, and fish biomass. Flow complexity in the vicinity of flow obstructions (in this case, boulders) was investigated further using patch classification and landscape ecology metrics. The relative influence of riparian vegetation on stream temperature (another important habitat characteristic) in urban and nonurban watersheds was investigated in 27 paired forested and nonforested reaches in PA, MD, and DE. Riparian vegetation and watershed-scale urbanization both influence stream temperature, which can have profound impacts on in-stream ecosystems. Generally, increased urbanization and removal of riparian forest influenced maximum stream temperatures resulting in higher maximum summer stream temperatures (up to 1.8°C); however, the influence of riparian forests (at at 100-200 m reach scale) decreased with increasing urbanization. Extreme maximum summer temperatures, which are a concern for aquatic biota, increased in both frequency and duration in urban nonforested reaches relative to forested reaches indicating that the addition of a forested 100-200 m long buffer partially mitigated these temperature extremes even in urban watersheds. Overall, changes to channel morphology and riparian vegetation had measurable local effects on stream habitat (temperature and hydraulic complexity) yet the implications of restoration efforts at the local scale on ecosystem services at a larger (km +) scale requires further study.
Ph. D.

The ecological position of micro-algae at the base of the aquatic food web makes them critical components of aquatic ecosystems. Their short generation time also makes them useful biological indicators because they respond quickly to changes in environmental condition, enabling timely identification and assessment of water quality changes. The inclusion of micro-algae as indicators in water resource regulation and management in South Africa has started recently, their more extensive use in biomonitoring and ecotoxicology programmes for water resource management would contribute to the South African policy if water resource protection. The standard algal growth inhibition assay with the species Pseudokirchneriella subcapitata is currently used for monitoring toxicity of in-stream and industrial wastewater discharges to freshwater micro-algae. The relevance of the data generated by standard toxicity bioassays has been questioned, since micro-algae in particular are extremely variable in their sensitivity to a range of contaminants and these standard species used may not occur in the local aquatic environment. As a result, international regulatory agencies, have recommended algal growth inhibition tests be changed from a single standard species to tests with a number of species. One recommendation, in addition to the use of standard toxicity tests, is the use of species isolated from the local environment which may be more relevant for assessing site specific impacts. This study investigated the value and application of locally isolated South African freshwater micro-algae in toxicity tests for water resource management and was carried out in three phases. The first phase involved isolating micro-algae from South African aquatic resources. Micro-algae suitable for toxicity testing were identified and selected using as set of criteria. Three (Scenedesmus bicaudatus, Chlorella sorokiniana and Chlorella vulgaris) out of eight successfully isolated species satisfied the prescribed selection criteria and these were selected as potential toxicity test species. The second phase focused on refining and adapting the existing algal toxicity test protocol (the algal growth inhibition assay) for use on the locally isolated algal species. The refinement of the test protocol was achieved by exposing the locally isolated species to reference toxicants in order to assess and compare their growth and sensitivity to the toxicants under the prescribed toxicity test conditions with that of the standard toxicity test species (Pseudokirchneriella subcapitata) and a commercial laboratory species (Chlorella protothecoides). During this phase, one of the three local species (Scenedesmus bicaudatus) was eliminated as a potential toxicity test species due to inconsistent growth. The third phase of the study involved assessing the sensitivity of the two remaining species (C. vulgaris and C. sorokiniana) to a range of toxicants (reference toxicants, salts, effluents and a herbicide) and comparing it to that of the standard toxicity test species P. subcapitata and C. protothecoides. The toxicants were selected based on their relative importance in the South African context, as well as the practicality of using these local micro-algae to routinely determine the impact of these toxicants on local aquatic resources. The growth of the four micro-algae was stimulated by the selected effluents. The standard toxicity test species P. subcapitata was ranked the most sensitive and of the four species to two reference toxicants and two inorganic salts. Chlorella sorokiniana was ranked the most sensitive of the three Chlorella species to two reference toxicants and two inorganic salts. The herbicide stimulated the growth of C. vulgaris while inhibiting the growth of the other species. Pseudokirchneriela subcapitata and C. sorokiniana showed high intra-specific variability in growth, which made it difficult to determine the effective concentrations of the herbicide and therefore compare the sensitivity of the species. This varied response of micro-algal species to toxicants may result in the biodiversity shifts in aquatic ecosystems, and also supports the recommendation of using a battery of different species to support more informed decisions in water resource management.

White croaker (Genyonemus lineatus) are a sentinel fish species for contamination due to their direct interaction with contaminated sediments through benthic foraging. White croaker within the Los Angeles and Long Beach Harbor exhibited hierarchical habitat selection: avoiding dredged areas while selecting for areas of high sediment total organic carbon (4.8–8.1%), high polychaete density (406–700 polychaetes/0.1 m²), and small sediment grain size (<23.5 µm). Model results suggest that these fish are moving into shallower waters at night to forage and may refuge more during the day to avoid predation. The predictive model for white croaker habitat use indicated three important areas of use within the LA-LB Harbor: Consolidated Slip, Inner LB Harbor, and Fish Harbor. The areas containing the most preferable habitat to white croaker are also areas of high sediment contamination, and thus are the likely locations where these fish are acquiring contaminants.

Recent advances in methodological and theoretical approaches in fluvial sciences have given rise to increased interest in riverscape perspectives that embrace environmental variability and spatial relationships. These approaches facilitate interdisciplinary understanding of complex fluvial processes that supports conscientious management of river systems. In this context, this dissertation presents the development and application of novel methods to study fluvial structure and eco-hydrogeomorphic relationships. Specifically, the research addresses three main questions: (1) how can UAV-based remote sensing advance the study of fluvial forms and processes? (2) what are the reach-scale geomorphic effects of an extreme flood and to what extent are these changes predictable? and (3) what are the linkages between flood-induced geomorphic change, reach hydraulics, and aquatic habitat? Results based on the case of an extreme flood event on Elbow River, Alberta demonstrate the utility of UAVs to efficiently and accurately measure many aspects of fluvial ecosystem form and function. The combination of high resolution imagery and photogrammetrically derived elevation models provides a powerful way to characterize rivers for a wide range of applications, particularly when combined with numerical flow modeling for a seamless representation of fluvial hydrogeomorphology. Pre- and post-flood UAV surveys documented flood effects with unprecedented detail, showing a largely unpredictable fluvial response characterized by complete channel planform reorganization and widespread bank erosion. These geomorphic changes negatively impacted the study reach in terms of hydraulic diversity and habitat suitability for brown trout and constrain future fluvial adjustment during smaller floods. Overall, the dissertation presents a new way to measure rivers and extract meaningful information and provides an integrative assessment of relationships between geomorphology, hydraulics, and aquatic ecology in a complex, dynamic river system.
Arts, Faculty of
Geography, Department of
Graduate

Physical habitat for instream biota derives from a combination of stream system structural and hydraulic phenomena. Consequently, the quantity and quality of physical habitat is dynamic both over time and in space along the river, laterally, longitudinally and vertically. Its characterization through stream assessment and classification leads to a better understanding of factors that determine and limit habitat extent and quality. This thesis investigates the effects of space and time on nearshore aquatic habitat in the gravel reach of Fraser River, British Columbia by employing a large river, stage-adaptive habitat classification system. The distribution and abundance of habitat are spatially quantified at the reach scale (32 km), and temporally quantified through a period of about 60 years at several adjacent gravel bars (7 km), and at approximately 500 m3 s-1 increments in discharge during the declining limb of the flood hydrograph at two well-developed gravel bars. Of the ten habitat types evaluated, the bar edge habitat type is most abundant by length and number of units. However, its relative importance is reduced when weighted by fish-habitat association characteristics. Preferred habitat types (channel nook, eddy pool and open nook) are frequent and available to aquatic organisms, and most common at well-developed bars and in zones of equilibrium long-term sedimentation. Preferred habitat was at a maximum 30 years ago when major new bars developed and the thalweg shifted, effectively increasing the amount of bar shoreline and nearshore habitat. This increase is due to substantial change in river planform morphology following a 30-year period of large annual floods. However, amounts of habitat did not increase exclusively during periods of higher than average flows, or decrease exclusively during periods of lower than average flows. Instead, habitat abundance response to flow may occur with a two- or three-year lag. Short term changes in stage are critical to amount of preferred habitat. Optimal discharge for maximum preferred habitat vailability is in the range of approximately 2500 m3 s-1 to 4000 m3 s-1, which approximates long term mean flow. As flow increases, the proportion of preferred habitat compared with total bar shoreline decreases. Comparison with the 2006 flow duration curve shows that 15 – 30 % of discharges are optimal for maximum fish density and biomass. These discharges occurred during April 27 to May 17 and July 14 to August 7, 2006.

Habitat heterogeneity is a driving factor for speciation and ecosystem functioning and is well studied in macro-ecology. Yet our understanding of microbial adaptations, and governing processes is incomplete. The here presented thesis aims at giving us a better understanding of patterns in micro-heterogeneity, and microbial adaptations to such heterogeneity with particular focus on surface-dominated, aquatic habitats. The most prominent microbial adaptation to surface associated mode of life is biofilm formation. Biofilms rely heavily on type IV pili. These pili systems are well studied in Bacteria, but largely unknown in Archaea. Therefore, the first part of this thesis focuses on resolving genetic and structural feature of the type IV like aap-pilus of the thermo-acidophilic Sulfolobus acidocaldarius. We found the aap-pilus to be indispensible for biofilm formation, and to be unparalleled in variability of its quaternary structure and cross regulation with other filaments. The second part of this thesis investigates particle colonization in the water column, focusing on diatoms as a model system, allowing an in situ assessment of different stages of particle colonization, and potential particle-specificity of the associated bacterial community. Opposing reports from marine systems, we did not observe diatom-specificity in the associated bacterial community. Instead we found bacterial community subsets, one likely originating from sediment resuspension, and the other being controlled by biofilm-forming populations (e.g. Flexibacter), able to attach to newly formed particle surfaces and subsequently facilitate secondary colonization by other bacteria. Finally, the habitat heterogeneity in top-layers of lake sediments were investigated in experimental microcosms. Cell-specific oxygen consumption rates were determined, to assess microbial activity across different scales. Individual activity rates differed strongly across all investigated scales, likely due to spatially heterogeneous distribution of nutrients with differing quality. Vice versa, the influence of microbial activity on micro-habitat-heterogeneity was investigated. We correlated sediment redox-state with bacterial community composition and populations. Our results indicate that habitat heterogeneity is generally beneficial for microorganism, and greater heterogeneity results in greater bacterial diversity. However, this heterogeneity-diversity relationship is limited and microorganisms actively stabilize their immediate redox environment to a preferred, community-specific, stable state, if cell abundances exceed a minimum threshold.

The Magnuson-Stevens Fishery Conservation and Management Act (MSA; Magnuson-Stevens Fishery Conservation and Management Act. 2014. (16 U.S.C. 1801–1891(d)) mandates that fisheries management councils in the United States prevent adverse, or “more than minimal and not temporary”, fishing effects to essential fish habitat (EFH) to the extent practicable. Councils were left to decide what effects qualified as “minimal” and “temporary”. The lack of explicit definition in the MSA and its accompanying Final Rule has resulted in inconsistent habitat management throughout the country. The EFH mandate was written under an implicit assumption that councils have the scientific information necessary to effectively manage EFH. Basic information is lacking, such as what type of habitat occurs where, and how fishing effects habitat features. Chapter 1 briefly reviews the history of EFH regulation, the consequences of regulatory ambiguities and information gaps, and highlights that high latitude fisheries management can be disproportionately affected by climate variability. Thus, requiring investment in baseline habitat assessment and monitoring and renewed focus on under developed areas of research e.g. Fishing effects and gear-habitat interactions.

Councils have attempting to quantitatively describe fishing effects to EFH through the use of mathematical models. The most recent of which, the Fishing Effects (FE) Model, was used in the North Pacific Fisheries Management Council 2015 EFH Review cycle. The FE Model uses discrete time steps (monthly) and spatially explicit fishing effort and sediment data to calculate an estimated habitat disturbance. The FE Model is calculated in two-dimensions and implicitly assumes that if fishing gear does not contact the seabed, then there is no gear-habitat interaction. Some features stand taller than raised gear (e.g. sea whips, Halipteris willemoesi, in the North Pacific can up to 2m tall) and may interact with fishing gear. The FE Model in two-dimensions does not account for this potential interaction and cannot effectively simulate gear modifications. Chapter 2 proposes an adapted version of the FE Model that accounts for the vertical interactions through the use of discrete height bins. To accurately estimate interactions on and above the seabed, fishing gear has to be recharacterized. To demonstrate this the Bering Sea flatfish trawl was recharacterized by calculating how much of the nominal gear width is present in each height bin. A detailed methodology is provided to allow this method to be applied to any fishing gear. The adapted FE Model can be used to simulate gear modifications, as is shown by simulating two modifications of the flatfish trawl. This chapter will inform the 2020 EFH Review cycle as the FE Model is improved.

Connectivity in aquatic ecosystems is a broad concept that refers to the transfer of both abiotic (i.e. matter and energy) and biotic (organisms) elements through the landscape across a range of spatial and temporal scales. The present study focuses on the patterns of connectivity between populations of aquatic insects in headwater streams. Dispersal, emigration and immigration are the demographic forms of population connectivity, which are largely thought to be by the winged adult stages that spend much of their lives in the riparian zone. These flying adults may disperse laterally and longitudinally to circumvent terrestrial barriers between headwater streams and catchments, thus allowing gene flow between populations in different streams. Riparian vegetation has a potentially strong influence on the survival and success of adult stages through the alteration of the microclimate, habitat structure and potential food sources. Habitat fragmentation caused by forest harvesting can reduce population connectivity by increasing the area of open forest and altering microclimatic conditions, particularly air temperature and humidity. Degradation of adjacent terrestrial habitat through forest harvesting may egatively affect adult dispersal because altered microclimatic conditions may create a barrier to dispersal. For example, the extreme conditions caused by harvesting may exceed tolerance limits of adult aquatic insects. In addition, aquatic insect life history traits may influence the degree to which forest harvesting affects their populations. For example, if a species with a short emergence period emerges during peak summer temperatures, temperatures could be higher in cleared areas compared to forested, thus exceeding the tolerance limit of the species. However, little direct evidence exists on the effects of selective harvesting and the associated changes to the microclimate on adult dispersal and genetic population connectedness.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Griffith School of Environment
Science, Environment, Engineering and Technology
Full Text

Habitats of Chesapeake Bay have been altered due to anthropogenic impacts and climate change. Due to these human disturbances, seagrasses have been extirpated from many areas in lower Chesapeake Bay and persisting beds face future losses as water temperatures continue to rise. Further loss of seagrass habitat will negatively impact juvenile blue crabs (Callinectes sapidus) that use seagrass beds as nursery grounds. Habitat degradation allows for more successful introductions of exotic species, and the communities formed from the mixing of native and exotic species are known as emerging ecosystems. Gracilaria vermiculophylla, an exotic macroalga, may be an emerging nursery habitat for juvenile blue crabs in Chesapeake Bay; however the extent to which the alga is present and used as a nursery by juvenile blue crabs are largely unknown. I investigated algal distribution in the shallow littoral areas of the York River, a subestuary of Chesapeake Bay, over two years (2013 – 2014) and found that G. vermiculophylla presence correlated with salinity and that algal presence and biomass increased with seagrass presence, although biomass was generally low. The alga was present in areas where seagrasses have been lost, and is therefore likely providing nursery habitat in these areas of high megalopal recruitment. Benthic epifaunal communities had lower species richness and were less abundant in G. vermiculophylla relative to seagrass, while benthic infaunal communities had lower species richness but similar abundance in the alga relative to seagrass. Juvenile blue crab densities were similar in the alga and seagrass, although seagrass supported about 3 times as many first and second instar crabs than G. vermiculophylla. Young juvenile blue crabs preferred seagrass, which may be due to epifaunal prey preference, and G. vermiculophylla likely represents a secondary nursery habitat. Juvenile blue crab growth rates of crabs 15 – 50 mm carapace width were similar in the alga, native seagrass, and unvegetated habitat, indicating that growth does not drive ontogenetic shifts in habitat use by larger (20 – 30 mm carapace width) juveniles. Similar growth rates also suggest that G. vermiculophylla performs similarly to seagrass as a nursery habitat in terms of providing resources for growth. Simulations of density-dependent migration of young juvenile blue crabs between habitat types suggest that G. vermiculophylla may mediate continued seagrass loss, at least in part. Together, these results increase our understanding of an emerging Chesapeake Bay ecosystem and the impacts that changes to nursery habitats have on the juvenile component of the blue crab population.

In order to define small and large scale spatial and temporal individual movement patterns of dugongs (Dugong dugon) within the Shark Bay World Heritage Property (SBWHP) a total of 19 dugongs were fitted with remote location recording and transmitting devices. Combined locations from all units totalled over 10,000 locations. This spatial and temporal data was used to define movement patterns of dugongs within Shark Bay as well as areas of high use deemed to be indicative of foraging activity. Platform Transmitting Terminals (PTT?s) using the ARGOS location collection system tracked animals over large temporal scales with 4 animals tracked up to periods of 11 months. Using these instruments it was possible accurately define a previously identified large-scale seasonal movement pattern within the confines of Shark Bay. These four animals showed distinct seasonal home ranges defined by changes in Sea Surface Temperature.