River ecosystems integrate all the changes that occur throughout the territory of their basin and for this is why they are among the most threatened and altered ecosystems in the world. This loss of habitat has direct consequences on the organisms inhabiting them. Freshwater fish are the most threatened group of vertebrates on the planet. Therefore, we must prioritize their protection implementing effective management strategies capable to ensure the conservation of riverine habitats and species. Nevertheless, there is a big gap of knowledge involving these ecosystems and biota, hindering their management. This lack of knowledge is especially significant in the Neotropics, where the greatest diversity of freshwater fish of the planet water is found. Unfortunately, these highly biodiverse areas are exposed to great threats that are destroying their habitats. These facts point out the Tropical Andes as a particularly biodiverse but seriously threatened region whose conservation should be prioritized. However, management plans must be based on appropriate ecological studies, providing reliable biological information and guaranteeing the development of appropriate conservation strategies. In the light of this critical knowledge gap, this thesis aims to evaluate the effectiveness of a sampling methodology that aspires to be versatile, inclusive and simple, testing it in different biogeographic contexts. Thus, five river basins (two in the Pyrenees and three in the Tropical Andes) were analyzed conducting electrofishing surveys, collecting aquatic macroinvertebrates, characterizing river habitat and applying environmental quality indices. One of our main goals was to study the freshwater ecological processes and its influence on the distribution of fish communities. Additionally, we evaluated the integrity of river ecosystems, trying to understand the consequences of human impacts on the biota. One of the most common strategies for the protection of ecosystems and species is the creation of protected areas. The Biosphere Reserves aspire to protect biodiversity and promote the sustainable development of the communities inhabiting them. Nevertheless, the scarcity of available biological information and the lack of studies that evaluate the effectiveness of these protected areas may be hindering the successful management and conservation of rivers and fish inside them. Our results point out that, although some Biosphere Reserves are partially fulfilling their protective function, their management strategies should be revised and their action plans adapted to the new available scientific information. Our sampling campaigns provided us with a better understanding of the ecology of poorly known rivers and fish, and the methods proved to reliability to diagnose ecological integrity. Nevertheless, due to time and budged limitations, we could only visit once each of the basins, hindering our interpretation of their complex reality. However, the obtained data allows us to emphasize the urge of prioritizing the protection of the headwaters of the Tropical Andes. They still remain very well preserved, they provide invaluable and irreplaceable ecosystem services and host a large number of fish species endemic to each of the basins. In addition, given the increasing anthropogenic impacts threatening these ecosystems, it is mandatory to delve into ecological studies to understand the natural reference conditions of these rivers, necessary to the appropriate development of management policies and restoration. This urge for knowledge highlights the necessity to continue with exploratory sampling campaigns, aspiring to cover the large knowledge gaps we are facing, and to guarantee the effectivity of the conservation biology. Biodiversity and ecology knowledge are the foundations for protecting nature.
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