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Up to 30,000km (18,600 miles) of wire fences and walls have been built, some in response to 2015's refugee crisis.
Researchers say they can divide threatened species such as deer and bear, as well as increase mortality.
The study points out that many of these "temporary" structures may become permanent and have long-term impacts
"We hypothesise that 9/11 was the main driver, when the risk of terrorism and drug dealers coming in meant that governments were closing their borders to reduce the risk while conservationists were driving for a more open system to allow wildlife to cross," said Dr Matt Hayward from Bangor University, UK
"Certainly, there's a lot of high-profile fences that have been put up in recent times driven by the Syrian and refugee crisis."
The study says that between 25,000 and 30,000km of wire fences and walls surround many countries in Eastern Europe and Central Asia, and they are having significant impacts on species.
However, they also acknowledge there may be times when the construction of fences actually benefits species.
They give the example of the Asiatic Wild Ass, or Khulan, on the Mongolian-Chinese border. A 4,700km fence prevents these animals from wandering into Inner Mongolia where illegal hunting remains a major problem.