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The high mountains have retained a noticeable degree of wilderness even in the most populated regions of the planet. This is the reason why many nature reserves have been established in these landscapes. Currently, climate change and long-range transport of contaminants are affecting those protected areas, and thus conservation priorities may be challenged by these new pressures. In fact, many high mountains hold a legacy of on-site past human activities (e.g., pasturing, forestry, mining), which in some areas may partially persist, even increase, whereas in others are substituted by new uses (e.g., tourism, mountain sport). Therefore, high mountain nature reserves face a challenging future. The conservation goals have to be revised. Former alternative paradigms respectively based on the preservation of wilderness or a traditional cultural landscape will be insufficient. Indeed, global change provides new goals for the high mountain conservation areas as suitable places where to study the nature’s response in the absence of, or combined with, other local pressures. Different branches of sciences may contribute to inform about the changes; however, conservation is ultimately a societal endeavour and thus their goals must be linked to the social demand for a fair society in a sustainable planet. As an added-value to this task, the high mountains hold a large amount of symbolism.

High mountain ecosystems present features that determine their conservation: isolation, harsh environmental conditions and steep gradients. The vulnerability of ecological systems to disruptive agents can be addressed by considering exposure to these agents and the sensitivity of the system. Conservation management usually offsets trade-offs of resources allocated to minimise exposure with strategies designed to reduce sensitivity. Although exposure to human action may be reduced in high mountains by isolation, this effect is offset by disruptive agents operating at global or regional scales, such as pollution and climate change. In the long term, climate change can be expected to have a strong impact on alpine habitats, as the dispersal of their native species is severely constrained. Alternatively, high mountains may provide refuges for threatened species currently populating lower altitudes. When reducing exposure is not a feasible strategy, the alternative is to reduce sensitivity, which in high mountains would focus on improving connectivity, preserving habitat quality and controlling antagonistic interactions such as grazing. Lowering vulnerability to climate change requires interventions in various contributing drivers. Cost-effective models make help to optimise the outcome of different goals subject to trade-offs, and they can also be useful for allocating alternative actions over time. The application of ecological trade-off concepts helps to frame conservation from a functional perspective. This approach should also take into account the fact that the functional properties of ecological entities are multifactorial and interactive. This concept is recognised in ecosystem services that present negative correlations—trade-offs—as well as positive ones—synergies.

The biogeography of alpine and arctic–alpine species is complex, much more complex than thought until relatively recently. Alpine species survived glacial periods mostly within refugia in close proximity to the mountains where they are found today. One mountain range can be colonised from several glacial refugia, while one refugium can be the source of colonisation of more than one mountain range. The zonal distributions in the glacial cold steppes are only of importance for arctic–alpine species. Their arctic ranges normally derive from there, while the southern mountains were colonised from there or from near-mountain refugia as in the cases of the alpine species.

During the last two decades, the archaeological research carried out in the Pyrenees challenged the traditional images of the past in this mountain area. The archaeological sequence of the range goes back and sites like Balma Margineda, treated until recently as an exception, now are seen as part of more global process. Actual data suggest that main valleys of the Pyrenean frequented by humans at the end of the last glacial period, with sites slightly over 1000 o.s.l. After the Younger Dryas, the human presence ascended to alpine and subalpine areas, in accordance with current archaeological data. The Neolisitation process was early in some hillsides, with intense remains of farming and pastoralism in many sites from dated in the second half of the 6th millennia cal BC. Human settlements like Coro Tracito, Els Trocs and El Sardo confirm the full introduction of agrarian activity in the central part of the Pyrenees between 5300 and 4600 cal BC. After 3500/3300 cal BC the indices oh sheepherding rises to alpine areas, with an abrupt increase of known archaeological sites in alpine areas, above the current timberline. This phenomena, as well as the signs of anthropic disturbance of the alpine environment in sedimentary sequences, suggests a more stable and ubiquitous human presence, probably largely associated with the development of mobile herding practices.

Proper management of the perceived value of any geographic space requires the capacity to interpret research results from spatial, temporal, and environmental points of view, applying the principles of environmental geohistory. Basic concepts such as baseline, threshold, or resilience are discussed from a long-term ecological perspective, with examples that explain the dynamics of fir forests as well as the changes in agricultural cover. Studying the changes in the altitudinal limit of the forest and surveying the wetlands dynamics on the southern slopes of the central Catalan Pyrenees have been shown to be effective tools to develop appropriate management tasks. The arguments presented are useful to enrich the public debate over management policies for natural protected spaces in high-mountain areas.

The drivers and patterns of drought-related forest dieback are not as well understood in mountain conifer forests. Most studies have obviated the role of historical use as a predisposing factor of forest dieback. Here I focus on the recent silver-fir () dieback observed since the 1980s in the Aragón Pyrenees (NE Spain) as study case. I argue that such dieback was predisposed by past historical logging and incited by warming-induced drought. I analyzed environmental, structural and tree-ring data from 32 sites with contrasting degrees of dieback at the tree and stand levels. I found that a peak in late-summer water deficit observed in 1985 caused a severe growth reduction in 1986, resulting in subsequent crown defoliation, dieback and increased mortality. Dieback was more severe and widespread in western low-elevation mixed forests dominated by smaller trees with low growth rates. These marginal sites receive less late-summer rainfall, which is a key climatic variable controlling silver-fir growth, than eastern sites. Declining sites showed more frequent growth releases induced by historical logging than non-declining sites. Silver-fir growth is becoming more dependent on climatic conditions of previous September, which may be connected with changing modes of atmospheric variability affecting Iberian climate. Historical logging and warming-induced drought stress during late summer are the most likely predisposing and inciting factors driving silver-fir dieback, respectively. A sustainable management of mountain forests shaped by past historical use requires changing their current structure and composition to make them more resilient to climate warming.

Microorganisms are fundamental components to maintain the ecological integrity of any ecosystem. Microscopic organisms have been, however, mostly excluded in conservation studies and microbiology has been developed as a scientific discipline lacking a natural history background. The detailed genetic studies carried out in the Aigüestortes i Estany de Sant Maurici National Park and recent works in the mostly scarce literature, show that the mostly oligotrophic and highly diluted waters in high mountain lakes hold a larger microbial phylogenetic uniqueness than expected and are reservoirs of large evolutionary potential, providing an overall natural history perspective for alpine archaea, bacteria, fungi and protists. Microbes arise as an important part of the biological richness of these environments that should be considered as a fundamental component of the natural heritage. Microbial ecologists are now closer than ever to deal with conservation biology concepts such as biological richness, extinction, biotic interactions, and ecosystems management. First insights emerge for establishing the microbial tolerance to different environmental conditions, for estimating which is the potentiality of survival and dispersal abilities in the different species, and for highlighting how the underappreciated microbiota will respond to stresses and disturbances brought by the global change. Warming and eutrophication may jeopardise the most idiosyncratic microbial populations that have found in these (ultra)oligotrophic and diluted systems the most appropriate conditions to thrive. Environmental managers and lawyers, citizen, and stakeholders, in general, have now access to scientifically informed advice for the unseen microbial life in the unexpectedly rich high mountain microbial ecosystems.

High mountain lakes are originally fishless, although many have had introductions of non-native fish species, predominantly trout, and recently also minnows introduced by fishermen that use them as live bait. The extent of these introductions is general and substantial often involving many lakes over mountain ranges. Predation on native fauna by introduced fish involves profound ecological changes since fish occupy a higher trophic level that was previously inexistent. Fish predation produces a drastic reduction or elimination of autochthonous animal groups, such as amphibians and large macroinvertebrates in the littoral, and crustaceans in the plankton. These strong effects raise concerns for the conservation of high mountain lakes. In terms of individual species, those adapted to live in larger lakes have suffered a higher decrease in the size of their metapopulation. This ecological problem is discussed from a European perspective providing examples from two study areas: the Pyrenees and the Western Italian Alps. Species-specific studies are urgently needed to evaluate the conservation status of the more impacted species, together with conservation measures at continental and regional scales, through regulation, and at local scale, through restoration actions, aimed to stop further invasive species expansions and to restore the present situation. At different high mountain areas of the world, there have been restoration projects aiming to return lakes to their native fish-free status. In these areas autochthonous species that disappeared with the introduction of fish are progressively recovering their initial distribution when nearby fish-free lakes and ponds are available.

Mountain grasslands are generally rich in soil organic C, but the typical high spatial variability of mountain environments, together with the different management systems, makes their soil C content particularly variable. Socio-economic changes of the past decades have caused a progressive abandonment of the traditional use for grazing of some areas, while grazing pressure at easily accessible grasslands have increased. Here, we analyse the effect of these land-use changes on the factors regulating the soil C accumulation and stocks. Overgrazing generally leads to a reduction above- and below-ground litter inputs and a decrease in soil C stocks, affecting some soil physicochemical and biological properties. Additionally, the labile C inputs coming from animal faeces may accelerate the mineralisation of organic matter. Grazing abandonment causes a reduction of aboveground productivity, but the lack of consumption causes a short-term accumulation of organic matter. Its effect on belowground biomass and productivity is less clear. At longer term, grazing abandonment causes a change in the plant community composition, having the shrub encroachment the strongest effect on C storage. The low biochemical quality of shrub litter delays its decomposition and allows higher organic matter accumulation in the topsoil. But the effect of shrub proliferation at the deeper soil is less clear. The low root turnover of shrubs compared to grasses may reduce the C inputs to the soil. But, at the same time, the reduction of the root exudates may also reduce the microbial activity and the organic matter mineralisation.

Large carnivores are keystone species in the ecosystems where they inhabit. Their loss may provoke an imbalance at several levels of the ecosystem. Conservation strategies for existing populations of large carnivores and restoration programmes of disappeared populations can help at maintaining the ecosystem balance and foster the perception links of humans with nature. The case of the restoration of the brown bear population in the Pyrenees during the last 20 years is a successful example of conservation measures carried out to assure the coexistence between this species and the local society, which economy is based on extensive livestock, beekeeping and tourism. In this chapter, I describe the role of large carnivores in mountain ecosystems and the context and development of the of the brown bear in the Catalan Pyrenees as an example of the challenges of large carnivore conservation in a rural context but a high influence from nearby urban areas.