This is a great question, but unfortunately one that is very difficult to answer. Scientists are able to so readily detect the rate of deforestation in the rainforest, or any land use change, due to technique called remote sensing. This strategy takes advantage of the fact that different surface materials, including different vegetation types (such as a crop of soy and a species diverse forest), interact with light differently and so reflect back different light patterns to a data collecting satellite. Each category of surface material has what is called a spectral signature. However, this technique cannot currently be used for underwater habitats, and therefore it is incredibly challenging to determine the rate at which underwater habitats are disappearing—it is hard to measure on a large scale what you cannot see on a large scale. However, there are several widespread and very alarming trends for ocean habitat that are being measured using alternate methods that cannot be directly compared to the rate of rainforest loss. Three examples include coral bleaching, which is most commonly caused by temperature changes, eutrophication in coastal waters from excess nitrogen from agricultural and urban wastes and acidification of the oceans which will effectively reduce the survival rate of many hard-shelled sea creatures.
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