Major environmental changes can trigger dramatic evolutionary change. Lake Malawi contains an adaptive radiation of more than 800 haplochromine species that have evolved within the last 2–4 million years. Using mitochondrial DNA sequences, we reconstructed temporal changes in effective size of 46 populations from 28 species within the flock. All populations showed expansions within the last million years, but timescales differed substantially. Offshore pelagic species of the genera Diplotaxodon and Rhamphochromis underwent rapid population expansions on average 175,000 and 290,000 years ago, respectively. By contrast, shallow-water benthic-living species underwent rapid population expansions within the last 50,000 years. These results suggest that populations of pelagic taxa persisted through major Pleistocene megadroughts between 160,000 and 90,000 years ago when the lake was smaller, shallower, more saline and turbid. They also suggest that populations of inshore demersal taxa were smaller or absent during these low stands, only expanding when the lake rose towards present levels. Given many shallow-water and benthic-living haplochromine species in Lake Malawi exhibit extreme local endemism, we suggest that many have originated since the last major lake rise. Such new ecological opportunity may have been critical for the evolution of high cichlid species richness that now characterises littoral habitats.
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