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The charity said the bodies of puffins, kittiwakes and guillemots had been discovered.
BBC: Hundreds of dead seabirds washed up on East Yorkshire coast
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The islands are home to an estimated 80, 000 breeding pairs of kittiwakes, which build nests on the cliffs to avoid predators.
BBC: Farne Islands no-fly zone to protect kittiwakes
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Scientists examining bird populations on islands such as the Shetlands say the number of kittiwakes has halved in the past five years.
BBC: NEWS | UK | 'Worst' sea bird breeding season
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The Isle of May, which would be included in the area of any ban, is home to 25, 000 pairs of puffins and 4, 000 pairs of kittiwakes.
BBC: Ministers consider sandeel fishing ban
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It was reported that a low-flying jets taking part in training over the Farne Islands on Tuesday led to mass panic among thousands of nesting kittiwakes.
BBC: Kittiwakes nesting on the Farne Islands
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The island is alive with the constant fluttering and cacophony of cawing, flapping and squabbling of more than 70, 000 gannets as well as kittiwakes, Arctic terns, puffins, razorbills and shearwaters.
BBC: Ireland��s outlying islands
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To investigate what impact a forced switch to a low-lipid regime might have on the development of red-legged kittiwakes, the Kitaysky lab designed experiments to explore the effects of various diets.
BBC: NEWS | Science/Nature | Birds hit by climate, diet shift