One fish, two fish, 3,000 fish …

Groups of cichlid fishes in East Africa radiated into thousands of species within dazzlingly short periods of time. How did they do it?
A sampling of haplochromine cichlid fish.
A sampling of haplochromine cichlid fish. CREDIT: PHOTOS BY BRIAN GRATWICKE / FLICKR

This article was originally featured on Knowable Magazine.

It was pure serendipity. I had been searching for a suitable pet for my son for months when I spotted a young teenager — let’s call him Matovu — who’d strategically placed himself and several fishbowls near the entrance of one of the many shopping arcades in Uganda’s capital. Speaking in broken English, Matovu told me that the Kampala Capital City Authority frequently detains unlicensed hawkers and confiscates their goods. At this very moment, the coast was clear.

The fishbowls were large, plastics jars nearly a foot high. In each swam half a dozen fry that occasionally nibbled on an aquatic plant anchored by two large pebbles wrapped in plastic and secured with thread. At the base of the jar lay small pieces of broken white and pink quartzite. Matovu wanted 30,000 Ugandan shillings (about US$8) and, reluctant to hang around for fear of the authorities, I paid his price without the usual negotiation.

Matovu said these fishes were ngege, the local Luganda word for tilapia, either the common Nile tilapia (Oreochromis niloticus) like the fish I’d just bought, or the near-threatened Singida tilapia (Oreochromis esculentus). Both belong to a group of fishes called cichlids (pronounced SIH’-klids), which scientists classify in the family Cichlidae. There are as many as 4,000 cichlid species spread across the planet, mainly in tropical and subtropical areas in the Levant, the Americas, India, Iran, Madagascar and sub-Saharan Africa.

And they are remarkable. East Africa is famed for its incredible wildlife such as mountain gorillas and savanna elephants, but for sheer diversity of species not much rivals a subgroup of cichlid fish known as haplochromine cichlids that swim in the waters of Africa’s Great Lakes.

A dazzling diversity of haplochromine cichlid fishes evolved within the African Great Lakes along the East African Rift. Credit: Knowable Magazine

“More than 1,000 species have emerged in these radiations in the past 3 [million] or 4 million years, and more than 500 in Lake Victoria alone within the last 100,000 years or less,” writes Ole Seehausen, an evolutionary ecologist and ichthyologist at the Institute of Ecology and Evolution at the University of Bern, Switzerland, who has been studying haplochromine cichlids for decades. “These are the largest and fastest adaptive radiations known in the animal kingdom, and understanding them will be important for understanding the origin of species diversity in general.”

Scientists define adaptive radiations as the diversification of lineages or tribes into arrays of species with traits that allow them to exploit different environments and resources. Driving the radiations can be environmental changes that make new resources available, or mass extinctions that empty out habitats for creatures to move into. The extinction of the dinosaurs some 66 million years ago created new ecological niches that probably allowed mammals to radiate, for example.

Rapid diversification and speciation is not a trait shared by all members of the family Cichlidae. My son’s pet, for example — grey with a hint of pink and some tiny black spots — is a less flashy cichlid not just in terms of markings but also in terms of its cichlid tribe. But within the haplochromine cichlids that live in Lake Victoria and other lakes nearby, the result of these big radiations has been a dizzying array of species that vary in their habitats, food choice, physical features, male and female coloration, and behavior.

“There is no other group known that matches the haplochromine cichlids of Lake Victoria in the rate of speciation and the species richness,” Seehausen says.

Adaptive radiations have enthralled evolutionary biologists ever since the days of Charles Darwin. Today, researchers in a variety of fields, including evolutionary ecology and genomics, are learning more about the underlying evolutionary processes and ecological mechanisms by which such biological diversity arises, as well as how it is maintained or goes extinct.

Hundreds of species in one lake

Scientists study modern adaptive radiations in cichlids to understand the mechanisms by which such events can occur, with insights for unreachable events in the deep past. During the Cambrian explosion some 540 million years ago, for example, a sudden radiation of complex life, and many of the major animal phyla, began appearing in the fossil record. More recently, birds evolved very rapidly about 65 million years ago as an adaptive radiation.

“It is very difficult to understand today what exactly happened then,” says evolutionary biologist David A. Marques, curator of the vertebrate collection at the Natural History Museum in Basel, Switzerland. In contrast, he says, “recent radiations and genomics allow us to identify the targets of selection and regions in the genome that cause speciation, something that is not feasible in these old, fossilized radiations.”

Within East Africa, adaptive radiations of cichlids exist not only among the Lake Victoria Region Superflock, as it’s called — which includes Victoria and the Western Rift Valley lakes such as Edward, Kivu and Albert — but also in several other East African Rift Valley lakes, including Lake Turkana to the north and Lake Malawi further south.

More than 700 cichlid species have emerged within the superflock, and more than 500 of them in Lake Victoria alone, within the last 15,000 to 16,000 years. Lake Tanganyika has 250 species of cichlids and Lake Malawi has an astonishing 850. Even more remarkable is that these cichlids species occur within overlapping, or even the same, geographical areas.

Cichlids don’t have a monopoly on rapid speciation. Whitefish (Coregonus spp.) in the European Alps and North America also have speciated rapidly. Switzerland alone had an impressive radiation of some 30 species of whitefish in the past 15,000 years.

But none of these creatures evolved more than a handful of species within a single lake, mostly just a single species pair.

Nor are cichlids the only examples of large adaptive radiations. Island fauna such as anole lizards of the Greater Antilles in the Caribbean and surrounding mainlands, the Hawaiian honeycreepers and, of course, Darwin’s finches of the Galápagos have all diversified to take advantage of various niches in their environments.

But it took many millions of years for them to acquire their diversity. In Lake Victoria, haplochromine cichlids evolved into hundreds of species in a mere 15,000 to 16,000 years.

Within the lake, different species have evolved to live in murky water and clear water, the shallows and the depths, to display different colors and courtship behaviors and exploit the full range of foods available to animals. There are cichlids that are carnivores, herbivores and omnivores. There are species that feed on plankton, dead organic matter or other species of fish.

Key to their consumption versatility, scientists think, was a trait all cichlids share: a second set of jaws formed from the fusion of the lower pharyngeal bones into a single, tooth-bearing structure. This allows the fish to double-dip — for instance, having one set of jaws specialized for catching fast-moving prey and one set for powerful, crushing bites.

Researchers believe that the possession of two separate jaws — oral and pharyngeal — has contributed to the rapid radiation of cichlid fishes. One jaw specializes in capturing prey, the other in processing the prey. Credit: Knowable Magazine

The role of hybridization

In recent years, the science of genomics has revolutionized the study of cichlids and helped researchers to piece together events that drove these remarkable adaptive radiations. By comparing the DNA letters of different species, researchers can place species into family trees, estimate when they diverged from each other and when they may have come into contact again, as well as the types of genes that may have been involved in the radiations.

In 2021, for example, investigators reviewed data from genomes of more than 400 cichlid species sampled from several radiations in East African cichlids. The findings, published in the Annual Review of Animal Biosciences, might seem surprising given the fishes’ biological diversity: “The genomes of the various cichlid species are very similar, much more similar than, say, human is to a chimpanzee,” says zoologist and evolutionary biologist Walter Salzburger of the Zoological Institute, University of Basel, Switzerland, and a coauthor of the overview.

East African cichlid fish species vary in the shape of their bodies, jaws, teeth, heads, fins and more, as well as in coloration, patterning and behavior. These differences reflect the niches that given species inhabit. Some may be important in keeping species distinct. Credit: Knowable Magazine

But there could still be significant variation in genes important for adaptive traits, the authors write. For example, a gene that codes for a long-wavelength-sensitive opsin protein, which helps to sense red light, has important variations in Lake Victoria cichlids. Among the differences: Some versions, shifted toward the red, are more suited for seeing in the lake’s murky depths, where some cichlid species live. Others are more suited for life in the clear shallows. The vivid colors of male haplochromines range from neon orange to ultramarine blue to crimson red, along with various multicolor combinations, and the ability of females to sense the males of their own species will be aided by the type of opsin they have.

Where would such diversity originate? Genomic studies have confirmed what researchers had suspected — that hybridization was a major force fueling cichlid radiations. Findings suggest that all the members of the Lake Victoria Region Superflock evolved from a hybrid population between distant species from the Nile and the Congo rivers more than 120,000 years ago. The parent populations had diverged from one another more than 1 million years ago, accumulating genetic differences — for example, the Nile lineage appears to have been the source of the murky-water-adapted opsin and the Congo lineage of the clear-water type.

The coming together of these lineages brought fresh genetic diversity to the resulting hybrid fish, far more rapidly than a slow accumulation of mutations could provide. Mixing and matching of genetic variants produced a “hybrid swarm” of fishes with myriad biological features, fueling rapid radiation into new species adapted to different habitats and lifestyles.

In 2023, the same research team — evolutionary biologist Joana I. Meier, now at the UK’s Wellcome Sanger Institute and the University of Cambridge, with Seehausen, Marques and others — examined the genomes of 464 cichlid species and filled in more details of the history of these Lake Victoria Region Superflock fish. Millennia after the ancestral hybridization, disaster struck. During the Pleistocene, around 20,000 to 16,000 years ago, the waters of Lake Victoria dried up, resulting in widespread collapse of the lake’s cichlid radiation. But genome analysis indicates that at least three lineages must have survived the dry period, perhaps in swamps in the Lake Victorian Basin region.

When the lake refilled with water, roughly 15,000 years ago, these populations merged again through hybridization, yet again passing on variations of genes that mixed and matched to spur the rapid, more recent radiation in Lake Victoria of 500 species.

Repeatedly, the scientists found, cycles of hybridization leading to the fusion of lineages were followed by lineage fission — diversification — throughout the evolutionary history of the Lake Victoria haplochromines. In other words, though we might imagine that the emergence of species requires isolation, isolation would have stopped the process of adaptive radiation. By replenishing genetic variation and permitting successive events of adaptation and speciation, it is hybridization that has kept the diversification momentum going.

The cichlid data to date fit with an increasing appreciation that hybridization is key as an evolutionary force in animals. Hybrid fauna were once seen as rare and therefore unimportant in the evolution of wildlife species. But hybridization in animal species (including humans) may be more common than previously thought — and researchers now see it as a major facilitator of evolution. Recent studies have documented ancient hybridizations in a diverse array of animal taxa, including mammals, birds, fish and insects.

“Only with genomic data were we finally able to prove, with hard evidence, that hybridization has spread adaptive radiations,” Marques says.

Ability to adapt rapidly

Why do some fishes form these adaptive radiations while others do not? Could the ancestors of the Lake Victoria Region Superflock merely have been lucky — arriving early at the newly filled lake and diverging rapidly to fill all the available ecological niches before other fish taxa showed up? Nare Ngoepe, now an evolutionary biology postdoc at the Swiss Federal Institute of Aquatic Science and Technology, with Seehausen and colleagues, recently tested this idea.

The scientists examined 7,623 fish-tooth fossils taken from four sediment cores at Lake Victoria that span the refilling of the lake some 15,000 years ago. They were able to show that all the major taxa of fish now living in the lake arrived simultaneously when the modern lake began to form, and that there was no evidence that the haplochromine cichlids arrived before other aquatic species, or that they did so in greater numbers.

In other words, what the cichlids had that the other fishes lacked seems to be ecological versatility: the ability to rapidly adapt to different diets and different habitats, presumably because of the genetic diversity they got from hybridizations.

The great irony of Lake Victoria’s haplochromine cichlids is that as rapidly as species diversify and evolve, extinction of hundreds of species has occurred in the geological blink of an eye. As many as 200 cichlid species unique to the lake have been lost this past half-century, experts say.

The forces that have led to this are many. The predatory Nile perch introduced into the lake during the 20th century have voraciously consumed scores of cichlid species. Pollution by untreated or partially treated sewage, industrial wastewater and fertilizers since the 1920s has led to nitrogen and phosphorus buildup and to algal growth, decreasing levels of oxygen and increasing turbidity.

“Haplochromine cichlids are highly visual organisms,” says Seehausen. “They use color vision and sophisticated processing of visual signals both for social communication, prey detection, foraging and predator avoidance.” Turbid waters interfere with their choosiness over mates and forage, he explains.

The release of Nile perch into Lake Victoria in the 20th century led to the loss of many cichlid species in the lake. CREDIT: DAIJU AZUMA / WIKIMEDIA COMMONS

Meier, for her part, says she is becoming increasingly concerned about offshore fish farming on the lake, which was implemented to address socioeconomic challenges in the region, providing protein for local people, while allowing dwindling fish stocks time to recover. It “is likely to increase the turbidity of the lake, which will lead to species merging together through hybridization,” she says. While hybridization between more distantly related cichlids has been the life blood of adaptive radiations, hybridization with close relatives can obliterate such variety.

Haplochromine cichlids are also internationally popular ornamental fish species for the aquaria hobby industry, which could pose an added risk to their already dwindling populations in Lake Victoria and elsewhere.

While most captive freshwater fish are bred in captivity, about 10 percent of fish species are sourced from the wild. Such harvesting is open to unsustainable and illegal practices. In addition, the growth of e-commerce and social media has not only increased the popularity of ornamental fish species such as haplochromine cichlids for the international aquaria market but also has made it easier to advertise the sale of live animals.

Matovu’s days of hawking aquarium fish on the pavements of Kampala might be numbered — not by the predatory city council authorities, but by connecting into the global trade of haplochromine cichlids. He already has one foot in the waters of Lake Victoria.

This article originally appeared in Knowable Magazine, an independent journalistic endeavor from Annual Reviews. Sign up for the newsletter.