In south-eastern Madagascar, patches of forest that were once cut down to make way for farms are slowly naturally regenerating after being left to lie fallow. But recovering a native forest needs more than just gaining tree cover. The animals that once lived in these forests also need to make their way back so that the forest can function the way it used to. When these native animals try to return, however, they often find that the forest has been taken over by invasive species they’ve never encountered before. Read more: Invasive rats are changing fish behaviour on coral reefs – new study I am part of a group of interdisciplinary biologists from Canadian, American and British universities who are working with students from the University of Antananarivo in Madagascar to study how forests there regenerate. For the past two years, we’ve studied the forest in and around Ranomafana National Park, in south-eastern Madagascar. This park is home to 12 species of the country’s famous lemurs.Our aim was to find out how birds, mammals and plants recover (or not) when forests are left to regenerate naturally, but we also found some unexpected results.We found that native small mammals, such as brown mouse lemurs (Microcebus rufus), tanala tufted-tail rats (Eliurus tanala) and greater long-tailed shrew tenrecs (Microgale principula), were rare in recovering forests. Instead, we found that black rats (Rattus rattus) were the most common small mammal even in forests that had been recovering for more than 50 years. Black rats are the most widespread invasive alien mammal worldwide, and have ecologically wreaked havoc in many island and tropical ecosystems. They evolved in south-east Asia, but have made their way across the world, as unintentional cargo in land and maritime trade. Read more: The endangered species list: counting lemurs in Madagascar We also found that forest areas with many black rats had fewer native species, while sites with fewer black rats had more native species, regardless of how long the forest had been regenerating. This pattern was inverted in mature forests within Ranomafana National Park.For example, about 90% of the small mammals in protected forests were native species. But in regenerating forests, almost 80% of the small mammals were invasive. This may suggest that invasive rats struggle to establish themselves in intact old-growth forests but can dominate forests that are still recovering, preventing native species from returning. Read more: Tourist visits to Madagascar help conserve some forests, but others suffer: study suggests what to do Our findings question the belief that regenerating the vegetation of a native forest will automatically ensure that the whole ecosystem recovers. Instead, our research suggests that forest regeneration alone is not enough to help small mammal communities recover if and when invasive rat populations are left to flourish.Mouse lemurs vs. invasive ratsWe could not know which species had been there before the forest was cut down since these sites were not sampled many years ago. But we looked at 25 plots in the forest, comparing five (the control sites) in the protected part of the forest with 20 outside the protected area. Read more: Climate change is threatening Madagascar’s famous forests – our study shows how serious it is We set up folding traps at each site for six consecutive nights every three months for one year. These traps close when an animal enters, capturing it without hurting it. We identified every individual animal captured, and measured and released them back to the same area.To understand how invasive rats affect individual native species, we needed enough observations of each species to make reliable statistical tests. However, most native species were caught too rarely to provide statistically reliable results. Only brown mouse lemurs were found often enough for us to confidently analyse how their numbers changed as invasive rat numbers increased. Mouse lemurs play a key role in rainforest regeneration, as they eat fruits and defecate their seeds in degraded sites, helping the seeds to sprout. Unfortunately, they are also an endangered species, mostly because of human destruction of their habitat. While we did not find a direct effect of black rat abundance on brown mouse lemur abundance, we did find a negative effect on their weight. The greater the number of invasive rats we found at a site, the skinnier mouse lemurs would get. This could indicate that mouse lemurs are competing with invasive rats for food resources, and losing, which could negatively affect their health and long-term survival. Read more: Coral reefs are at risk from rats that have invaded nearby islands Another interesting finding was that mouse lemurs may be able to coexist with rats, provided rat numbers remained low. We estimated that finding no more than 3.3 black rats per 100 trap nights indicates a rat population low enough not to affect mouse lemurs.This calculation is useful because it gives conservation managers a practical target. Our results suggest that if rat numbers can be kept below this level, brown mouse lemurs may be able to coexist alongside them. However, we still don’t know whether the same is true for other native species.What needs to happen nextWhile invasive black rats are a clear threat to native species, eradicating them without endangering native species would be hard to achieve. Poisoned pellets have successfully been used to eradicate black rats in other island ecosystems where they had no native small mammals. But many native birds also consumed the poison and died.Trapping is a safer way of removing black rats. Our identified threshold can be used as an early benchmark for when intervention is warranted, at least for brown mouse lemurs. But it would be impossible to set up enough traps across huge forests to control their population. However, traps can be placed in human settlements. This could both help curtail the spread of black rats in forests and reduce their negative effects on human populations.The only thing we can be certain of is that protecting old-growth forests is vital for native species to thrive in the long term.Sabine Cudney-Valenzuela works for the University of California, Berkeley, and she receives funding from the National Science Foundation.