Existing networks of nature reserves contain a biased sample of biodiversity. In Patagonia Argentina, most nature reserves focus their protection objectives on a particular ecosystem, geoform or scenic value, and usually are located in inaccessible areas. However, unique species or assemblages could inhabit less protected ecosystems, areas or habitats, which could be threatened depending of management. In this study, we assessed the conservation value of different ecosystem types and areas (fjords) in Isla de los Estados Provincial Reserve (RPIE, Argentina), using birds as study case. We chose three fjords (east, central and west) and five ecosystems types (forests at low and high elevation, open-lands at low and high elevation, and sea coasts). Bird's assemblage richness, density, biomass, trophic level, migratory status, and use of strata per ecosystems and fjords were characterized in 75 points (3 fjords × 5 ecosystems × 5 replicates) and evaluated using ANOVA and multivariate methods. Also, Shannon (H') and Pielou (J) indices were estimated for fjords and ecosystems. Passerine was the most abundant group, being mainly residents, omnivorous and carnivorous-scavenger, and they were observed mainly flying or in the canopy. Assemblage structure and function varied with ecosystem types, with higher richness and biomass in coasts and open-lands than in other ecosystems, but with greater density in forests. Multivariate analyses showed conspicuous groups for forests and coast sampling units, with significant differences among all ecosystem types except between low and high forests. Also, east fjord significantly differed in density and biomass from the others, but west fjord also differed in structure, function and bird assemblage. We conclude that greater conservation value must be assigned to ecosystem types or areas inhabited by threatened species (as open-lands at high elevation) and highest richness and variety of use of strata (as sea coasts). However, bird assemblage patterns have particularities in less valuable ecosystems and areas, which also justify their importance for conservation, or at least, prescriptions of low impact uses and activities in the management planning. Nature reserves are opportunities to preserve endemic species, habitats or areas of special interest, as low latitude or unique isolated landscape communities, and ecosystems underrepresented in the network of local, regional or world protected areas.
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