Lake Victoria
Cichlid fish

Lake Victoria formerly was very rich in fish, including many endemics, but a high percentage of these became extinct since the 1940s. The main group in Lake Victoria is the haplochromine cichlids (Haplochromis sensu lato) with more than 500 species, almost all endemic, and including an estimated 300 that still are undescribed. This is far more species of fish than any other lake in the world, except Lake Malawi. These are the result of a rapid adaptive radiation in the last circa 15,000 years. Their extraordinary diversity and speed of evolution have been the subjects for many scientists studying the forces that drive the richness of life everywhere. The Victoria haplochromines are part of an older group of more than 700 closely related species, also including those of several smaller lakes in the region, notably Kyoga, Edward – George, Albert, and Kivu.

Most of these lakes are relatively shallow (like Victoria) and part of the present-day upper Nile basin. The exception is Lake Kivu, which is part of the present-day Congo River basin, but is believed to have been connected to Lakes Edward and Victoria by rivers until the uplifting of parts of the East African Rift. This deep lake may have functioned as an "evolutionary reservoir" for this haplochromine group in periods where other shallower lakes in the region dried out, as happened to Lake Victoria about 15,000 years ago. In recent history only Lake Kyoga was easily accessible to Victoria cichlids, as further downstream movement by the Victoria Nile (to Lake Albert) is prevented by a series of waterfalls, notably Murchison. In contrast, the Owen Falls (now flooded by a dam) between Victoria and Kyoga were essentially a series of rapids that did not effectively block fish movements between the two lakes.

The Victoria haplochromines are distinctly sexually dimorphic (males relatively brightly colored; females dull), and their ecology is extremely diverse, falling into at least 16 groups, including detritivores, zooplanktivores, insectivores, prawn-eaters, molluscivores and piscivores. As a result of predation by the introduced Nile perch, eutrophication and other changes to the ecosystem, it is estimated that at least 200 species (about 40 percent) of Lake Victoria haplochromines have become extinct, including more than 100 undescribed species. Initially it was feared that this number was even higher, by some estimates 65 percent of the total species, but several species that were feared extinct have been rediscovered after the Nile perch started to decline in the 1990s. Several of the remaining species are seriously threatened and additional extinctions are possible. Some species have survived in nearby small satellite lakes, have survived in refugias among rocks or papyrus sedges (protecting them from the Nile perch), or have adapted to the human-induced changes in the lake itself. Such adaptions include a larger gill area (adaption for oxygen-poor water), changes in the feeding apparatus, changes to the eyes (giving them better sight in turbid water) and smaller head/larger caudal peduncle (allowing faster swimming). The piscivorous (affected by both predation and competition from Nile perch), molluscivorous and insectivorous haplochromines were particularly hard hit with many extinctions. Others have become extinct in their pure form, but survive as hybrids between close relatives (especially among the detritivores). The zooplanktivores have been least affected and in the late 1990s had reached densities similar to, or above, the densities before the drastic declines, although consisting of fewer species and often switching their diet towards macroinvertebrates. Some of the threatened Lake Victoria cichlid species have captive "insurance" populations in zoos, public aquaria and among private aquarists, and a few species are extinct in the wild (only survive in captivity).

Before the mass extinction that has occurred among the lake's cichlids in the last 50 years, about 90 percent of the native fish species in the lake were haplochromines. Disregarding the haplochromines, the only native Victoria cichlids are two critically endangered tilapia, the Singida tilapia or ngege (Oreochromis esculentus) and Victoria tilapia (O. variabilis).

In 1927–1928 Michael Graham conducted the first ever systematic Fisheries Survey of Lake Victoria. In his official report of the expedition, Graham wrote that "The ngege or satu Tilapia esculenta, is the most important food fish of the lake, whether for native or non-native consumption. No other fish equals it in the quality of the flesh. It is convenient size for trade, travels well and is found in much greater numbers than other important fish, such as semutundu (Luganda), Bagrus sp. ". Furthermore, Graham noted that the introduction of the European flax gill net of 5 inch mesh had undoubtedly caused a diminution in the number of ngege in those parts of the Kavirondo Gulf, the northern shore of the lake, the Sesse Islands and Smith's Sound which are conveniently situated close to markets. Survey catches in 1927–28 included several Haplochromis species that are now thought to be extinct, including: Haplochromis flavipinnis, Haplochromis gowersii, Haplochromis longirostris, Haplochromis macrognathus, Haplochromis michaeli, Haplochromis nigrescens, Haplochromis prognathus.

As well as being due to the introduction of Nile Perch, the extinction of cichlids in the genus Haplochromis has also been blamed on the lake's eutrophication. The fertility of tropical waters depends on the rate at which nutrients can be brought into solution. The influent rivers of Lake Victoria provide few nutrients to the lake in relation to its size. Because of this, most of Lake Victoria's nutrients are thought to be locked up in lake-bottom deposits. By itself, this vegetative matter decays slowly. Animal flesh decays considerably faster, however, so the fertility of the lake is dependent on the rate at which these nutrients can be taken up by fish and other organisms. There is little doubt that Haplochromis played an important role in returning detritus and plankton back into solution. With some 80 percent of Haplochromis species feeding off detritus, and equally capable of feeding off one another, they represented a tight, internal recycling system, moving nutrients and biomass both vertically and horizontally through the water column, and even out of the lake via predation by humans and terrestrial animals. The removal of Haplochromis, however, may have contributed to the increasing frequency of algal blooms, which may in turn be responsible for mass fish kills.
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