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I have a bunch of raster files showing the distribution of different species of mammals, and I would like to obtain the areas where they overlap, the areas in whitch more than one species can be found

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You can use Raster -> Raster Calculator. Using Raster calculator calculate an output raster which is the sum of all individual rasters. Assuming your individual rasters have value of 0 or 1 based of whether species are found or not, the resulting raster will have value > 1 where more than one species are found. You can convert the resulting raster to vector and have polygons representing these areas as well.

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