Conservation managers worldwide are increasingly faced with the challenges of managing and protecting fragmented landscapes, largely as a consequence of human activities. Over recent decades, ecological theory has made a significant contribution to the development of landscape-scale conservation and practice. However, recommendations accounting for what is practically achievable in the modern-day landscape are currently lacking, while criteria for conservation planning and prioritisation continue to neglect the role of habitat networks at the required spatial scale for the long-term persistence of biodiversity. In this thesis, I test and apply ideas surrounding the complexities of managing and conserving species in a landscape context, using a suite of bird species endemic to papyrus (Cyperus papyrus) swamps in East and Central Africa as a model system. In the face of large-scale habitat loss and degradation, practical measures that account for the fragmented nature of this system, the needs of multiple specialist species, and the reliance on this habitat by local people, are urgently required. I first review the concepts originating from reserve design theory to provide a decision-making framework for those involved in landscape-scale conservation amid 21st century challenges to biodiversity, highlighting the key principles to be considered for informed choices to be made. Second, I show that the needs of local people can be compatible with conservation planning in the tropics, and may play an important part in maintaining habitat quality for species residing in historically disturbed landscapes. Third, I develop a novel framework to make an explicit link between metapopulation dynamics and conservation planning. Despite differences in the patch-level dynamics of individual species, areas of habitat where populations of multiple species are resistant to extinction, and resilient because of high chances of (re)colonization can be identified, highlighting where resources could be invested to ensure species have the capacity to respond to future change. Finally, I simulate the metapopulation dynamics of the papyrus-endemic birds to demonstrate that the optimal conservation strategy for the long-term persistence of all species residing in a network depends on the characteristics of individual species, and the total area that can be protected. Overall, this thesis develops and tests the ecological theory used in spatial conservation planning, emphasising the importance of habitat disturbance and interspecific ecological differences for the effective management of habitat networks. The results increase the evidence base for the conservation of wetland birds in Africa, as well as for species residing in fragmented landscapes more generally.

Complex biogenic habitats created by large canopy-forming macroalgae on intertidal and shallow subtidal rocky reefs worldwide are increasingly affected by degraded environmental conditions at local scales and global climate-driven changes. A better understanding of the mechanisms underlying the impacts of complex suites of anthropogenic stressors on algal forests is essential for the conservation and restoration of these habitats and of their ecological, economic and social values. This thesis tests physical and biological mechanisms underlying the impacts of different forms of natural and human-related disturbance on macroalgal assemblages dominated by fucoid canopies along the east coast of the South Island of New Zealand. A field removal experiment was initially set up to test assemblage responses to mechanical perturbations of increasing severity, simulating the impacts of disturbance agents affecting intertidal habitats such as storms and human trampling. Different combinations of assemblage components (i.e., canopy, mid-canopy and basal layer) were selectively removed, from the thinning of the canopy to the destruction of the entire assemblage. The recovery of the canopy-forming fucoids Hormosira banksii and Cystophora torulosa was affected by the intensity of the disturbance. For both species, even a 50% thinning had impacts lasting at least eighteen months, and recovery trajectories were longer following more intense perturbations. Independently of assemblage diversity and composition at different sites and shore heights, the recovery of the canopy relied entirely on the increase in abundance of these dominant fucoids in response to disturbance, indicating that functional redundancy is limited in this system. Minor understory fucoids, which could have provided functional replacement for the dominant habitat formers, had reduced rates of growth or recruitment when the overlying canopy was disturbed. I then used a combination of field and laboratory experiments to test the impacts of physical and biotic stress sources on the dominant fucoids H. banksii and C. torulosa. The large fucoid Durvillaea antarctica was also included in one of the laboratory investigations. I assessed how altered physical and biotic conditions affect these important habitat formers, both separately and in combination. Physical stressors included increased sedimentation, nutrient enrichment and warmer water temperatures. Biotic stress originated from interspecific competition with turfs of articulated coralline algae and ephemeral, fast-growing green and brown algae. Sediment deposition severely reduced the survival and growth of recently settled H. banksii, C. torulosa and D. antarctica germlings in laboratory experiments. In the field, the recruitment of H. banksii on unoccupied substrates was significantly higher than in treatments in which sediments or mats of turf-forming coralline algae covered the substrate. This shows that sediment deposition and space pre-emption by algal turfs can synergistically affect the development of fucoid beds. Further impacts of sediment accumulation in the benthic environment were investigated using in situ and laboratory photorespirometry techniques to assess the contribution of coralline algae to assemblage net primary productivity (NPP), both in the presence and absence of sediment. The NPP of articulated corallines was reduced by sediment. Sediment accumulation among the thalli limited the access of the corallines to the light and induced photoinhibitive mechanisms. In the absence of sediment, however, coralline algae enhanced the NPP of assemblages with a fucoid canopy, showing the importance of synergistic interactions among the components of multi-layered assemblages in optimizing light use. Nutrient enrichment had a less pervasive influence on the dominant fucoids H. banksii and C. torulosa than sedimentation. In laboratory experiments, nutrients stimulated the growth of H. banksii and C. torulosa germlings. However, negative impacts of high nutrient levels were observed for the early life stages of D. antarctica. The abundance of opportunistic, fast-growing algae rapidly increased in response to nutrient enrichment both in the laboratory and in the field. Impacts of ephemeral species on fucoid early life stages were only evident in laboratory contexts, where green algae of the genus Ulva impaired both the settlement of H. banksii zygotes and the growth of its germlings. Fucoid recruitment in the field was not affected by increased covers of ephemeral algae caused by enhanced nutrient regimes, indicating that H. banksii and C. torulosa may be resistant to short-term (one year) nutrient pollution. In the laboratory, increased temperatures within the range predicted for the end of the 21st century caused increased mortality in the H. banksii, C. torulosa and D. antarctica germlings. In a separate experiment, a combination of warmer water temperatures and nutrient enrichment enhanced the growth of ephemeral green algae. These results suggest that opposite responses to altered climate conditions may contribute to shifts from complex biogenic habitats dominated by macroalgal canopies to simplified systems monopolized by a limited number of stress-tolerant species. This research contributes to a clearer mechanistic understanding of biotic and physical mechanisms shaping the structure of coastal marine hard bottom communities under increasingly stressful conditions worldwide. These findings may provide insights for other studies investigating the complex mosaic of challenges facing marine coastal ecosystems.

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The historical range of the Indus River dolphin has declined by 80% since the 19th century and has been fragmented into 17 river sections by construction of irrigation barrages. Dolphin sighting and interview surveys showed that river dolphins persist in six river sections, have been extirpated from ten, and are of unknown status in the remaining section. Logistic regression and survival modelling showed that low dry season river discharge was the primary factor responsible for the Indus dolphins range decline. Abundance of the three largest Indus dolphin subpopulations was estimated using tandem vessel-based direct counts, corrected for missed animals using conditional likelihood capture-recapture models. The entire subspecies was estimated to number between 1550-1750 in 2006. Dolphin encounter rates within the Guddu-Sukkur subpopulation (10.35/km) were the highest reported for any river dolphin and direct counts suggest that this subpopulation may have been increasing in abundance since the 1970s when hunting was banned. The dry season habitat selection of Indus dolphins was explored using Generalised Linear Models of dolphin distribution and abundance in relation to river geomorphology, and channel geometry in cross-section. Channel cross-sectional area was shown to be the most important factor determining dolphin presence. Indus dolphins avoided channels with small cross-sectional area <700m2, presumably due to the risk of entrapment and reduced foraging opportunities. The phylogenetics of Indus and Ganges River dolphins was explored using Mitochondrial control region sequences. Genetic diversity was low, and all 20 Indus River dolphin samples were identical. There were no haplotypes shared by Indus and Ganges River dolphins, phylogenetic trees demonstrated reciprocal monophyletic separation and Bayesian modelling suggested that the two dolphin populations diverged approximately 0.66 million years ago. Declining river flows threaten Indus dolphins especially at the upstream end of their range, and it is important to determine how much water is required to sustain a dolphin population through the dry season. Fisheries interactions are an increasing problem that will be best addressed through localised, community-based conservation activities.

RESUMEN Los peces nativos son indicadores de la salud de los ecosistemas acuáticos, y se han convertido en un elemento de calidad clave para evaluar el estado ecológico de los ríos. La comprensión de los factores que afectan a las especies nativas de peces es importante para la gestión y conservación de los ecosistemas acuáticos. El objetivo general de esta tesis es analizar las relaciones entre variables biológicas y de hábitat (incluyendo la conectividad) a través de una variedad de escalas espaciales en los ríos Mediterráneos, con el desarrollo de herramientas de modelación para apoyar la toma de decisiones en la restauración de ríos. Esta tesis se compone de cuatro artículos. El primero tiene como objetivos modelar la relación entre un conjunto de variables ambientales y la riqueza de especies nativas (NFSR), y evaluar la eficacia de potenciales acciones de restauración para mejorar la NFSR en la cuenca del río Júcar. Para ello se aplicó un enfoque de modelación de red neuronal artificial (ANN), utilizando en la fase de entrenamiento el algoritmo Levenberg-Marquardt. Se aplicó el método de las derivadas parciales para determinar la importancia relativa de las variables ambientales. Según los resultados, el modelo de ANN combina variables que describen la calidad de ribera, la calidad del agua y el hábitat físico, y ayudó a identificar los principales factores que condicionan el patrón de distribución de la NFSR en los ríos Mediterráneos. En la segunda parte del estudio, el modelo fue utilizado para evaluar la eficacia de dos acciones de restauración en el río Júcar: la eliminación de dos azudes abandonados, con el consiguiente incremento de la proporción de corrientes. Estas simulaciones indican que la riqueza aumenta con el incremento de la longitud libre de barreras artificiales y la proporción del mesohabitat de corriente, y demostró la utilidad de las ANN como una poderosa herramienta para apoyar la toma de decisiones en el manejo y restauración ecológica de los ríos Mediterráneos. El segundo artículo tiene como objetivo determinar la importancia relativa de los dos principales factores que controlan la reducción de la riqueza de peces (NFSR), es decir, las interacciones entre las especies acuáticas, variables del hábitat (incluyendo la conectividad fluvial) y biológicas (incluidas las especies invasoras) en los ríos Júcar, Cabriel y Turia. Con este fin, tres modelos de ANN fueron analizados: el primero fue construido solamente con variables biológicas, el segundo se construyó únicamente con variables de hábitat y el tercero con la combinación de estos dos grupos de variables. Los resultados muestran que las variables de hábitat son los ¿drivers¿ más importantes para la distribución de NFSR, y demuestran la importancia ecológica de los modelos desarrollados. Los resultados de este estudio destacan la necesidad de proponer medidas de mitigación relacionadas con la mejora del hábitat (incluyendo la variabilidad de caudales en el río) como medida para conservar y restaurar los ríos Mediterráneos. El tercer artículo busca comparar la fiabilidad y relevancia ecológica de dos modelos predictivos de NFSR, basados en redes neuronales artificiales (ANN) y random forests (RF). La relevancia de las variables seleccionadas por cada modelo se evaluó a partir del conocimiento ecológico y apoyado por otras investigaciones. Los dos modelos fueron desarrollados utilizando validación cruzada k-fold y su desempeño fue evaluado a través de tres índices: el coeficiente de determinación (R2 ), el error cuadrático medio (MSE) y el coeficiente de determinación ajustado (R2 adj). Según los resultados, RF obtuvo el mejor desempeño en entrenamiento. Pero, el procedimiento de validación cruzada reveló que ambas técnicas generaron resultados similares (R2 = 68% para RF y R2 = 66% para ANN). La comparación de diferentes métodos de machine learning es muy útil para el análisis crítico de los resultados obtenidos a través de los modelos. El cuarto artículo tiene como objetivo evaluar la capacidad de las ANN para identificar los factores que afectan a la densidad y la presencia/ausencia de Luciobarbus guiraonis en la demarcación hidrográfica del Júcar. Se utilizó una red neuronal artificial multicapa de tipo feedforward (ANN) para representar relaciones no lineales entre descriptores de L. guiraonis con variables biológicas y de hábitat. El poder predictivo de los modelos se evaluó con base en el índice Kappa (k), la proporción de casos correctamente clasificados (CCI) y el área bajo la curva (AUC) característica operativa del receptor (ROC). La presencia/ausencia de L. guiraonis fue bien predicha por el modelo ANN (CCI = 87%, AUC = 0.85 y k = 0.66). La predicción de la densidad fue moderada (CCI = 62%, AUC = 0.71 y k = 0.43). Las variables más importantes que describen la presencia/ausencia fueron: radiación solar, área de drenaje y la proporción de especies exóticas de peces con un peso relativo del 27.8%, 24.53% y 13.60% respectivamente. En el modelo de densidad, las variables más importantes fueron el coeficiente de variación de los caudales medios anuales con una importancia relativa del 50.5% y la proporción de especies exóticas de peces con el 24.4%. Los modelos proporcionan información importante acerca de la relación de L. guiraonis con variables bióticas y de hábitat, este nuevo conocimiento podría utilizarse para apoyar futuros estudios y para contribuir en la toma de decisiones para la conservación y manejo de especies en los en los ríos Júcar, Cabriel y Turia. / Olaya Marín, EJ. (2013). Ecological models at fish community and species level to support effective river restoration [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/28853 / TESIS