New research blames rising temperatures over the last century as the key cause of decline in one of the world’s most important fisheries.
Lake Tanganyika is Africa’s oldest lake and its fish are a critical part of the diet of neighbouring countries.
But catches have declined markedly in recent decades as commercial fleets have expanded.
However this new study says that climate warming and not overfishing is the real cause of the problem.
Estimated to be the world’s second-largest freshwater lake, Tanganyika is an important resource for the countries that border it: Burundi, the Democratic Republic of Congo, Tanzania and Zambia.
As well fish from the lake providing up to 60% of the animal protein consumed in the region, it is also an important biodiversity hotspot.
But there have been growing concerns about the impact of overfishing, land use change and changes in climate on this key ecosystem.
In an attempt to understand what’s happening, researchers have examined samples of sediment from the bottom of the lake.
The chemical analysis of the cores and the fossils found there indicate that fish numbers have been dropping in parallel with a rise in global temperatures.
The scientists say that in tropical lakes a warming of the waters reduce the mixing between the oxygenated top layer and the nutrient-rich layer at the bottom.
This increasing stratification of the waters means fewer nutrients get to top, meaning less algae which means less food for fish.
The authors conclude that sustained warming is associated with reduction in mixing in the lake, stagnation of algal production, and significant shrinking of the habitat of the lake’s key bottom dwellers, such as molluscs and crustaceans.
"Our idea was to look at the fish fossil record and to see when that decline actually started," said Prof Andrew Cohen from the University of Arizona,
"If it happened before the start of the industrial fishing in the 1950s, you’d have strong evidence that the decline is not simply driven by this fishing activity and that’s exactly what we found."
The scientists don’t discount the impact of fishing over the past six decades. They recognise that there has been a significant increase in the 1990s as refugees from numerous regional conflicts poured into the areas around the lake.
"Fishing in the lake is a Wild West activity, there are nominal controls but no teeth," said Prof Cohen.
"Given the current trends of warming, the lake stratification will get stronger and the productivity will continue to be affected by that. The people in charge of these decisions need to be thinking about alternative livelihoods for people in the region."
Other researchers are alarmed about the future of the lake. One said: "We are sleepwalking into a disaster."
Others point to the fact that the in Europe and North America, a warming climate is increasing production in lakes. But the tropics are very different.
"In tropical regions, the increased stratification is doing the reverse, at least in some lakes," said Prof John Smol from Queen’s University in Kingston, Canada.
"Decreasing algal production means that the base of the food chain is being affected - and this can cascade though the food chain up to fish and organisms - like humans - who depend on these resources."
Besides the threat to food supplies and jobs, the impact of warming on the biodiversity of Lake Tanganyika is of great scientific concern as well. Prof Cohen argues that we should think of the lake as being as significant as some of the world’s key hotspots.
"Think about the Galapagos, and how iconic they are, Lake Tanganyika has probably 50 times more endemic species and nobody knows about it," he said.
"It’s coming to bite us in terms of really impacting livelihoods for people around the lake, and the fact they have so many unsettled people in the region.
"These social and environmental trends are converging and I would say it’s a really urgent issue to be aware of and start doing something about."
The research has been published in the Proceedings of the National Academy of Sciences journal.