The study found that in North America, all of the largest terrestrial predators have been in decline during the past 200 years while the ranges of 60 percent of mesopredators, or smaller predators, have expanded.
The problem is global, growing and severe, scientists say, with few solutions in sight.
For instance, in parts of Sub-Saharan Africa, lion and leopard numbers have been decimated, allowing a surge in the mesopredator population next down the line, baboons.
In some cases children are now being kept home from school to guard family gardens from brazen packs of crop-raiding baboons.
"This issue is very complex, and a lot of the consequences are not known," said William Ripple, professor of forest ecosystems and society at Oregon State University (OSU).
"But there's evidence that the explosion of mesopredator populations is very severe and has both ecological and economic repercussions."
In case after case around the world, the researchers said, primary predators such as wolves, lions or sharks have been dramatically reduced if not eliminated, usually on purpose and sometimes by forces such as habitat disruption and hunting.
Many times this has been viewed positively by humans, fearful of personal attack, loss of livestock or other concerns.
But the new picture that's emerging is a range of problems, including ecosystem and economic disruption that may dwarf any problems presented by the original primary predators.
"I 've done a lot of work on wildlife in Africa, and people everywhere are asking some of the same questions, what do we do?" said Clinton Epps, assistant professor at OSU who is studying the interactions between humans and wildlife, according to an OSU release.
Elimination of wolves is often favoured by ranchers, for instance, who fear attacks on their livestock. However, that has led to a huge surge in the number of coyotes, a "mesopredator" once kept in check by the wolves.
The problems are not confined to terrestrial ecosystems. Sharks, for instance, are in serious decline due to overfishing.
Primary or apex predators can actually benefit prey populations by suppressing smaller predators, and failure to consider this mechanism has triggered collapses of entire ecosystems.
These findings were published in the October edition of Bioscience.
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