Some 500 species of cichlid fish dart through the turbid yellowish waters of East Africa’s Lake Victoria; little insectivores fin over the pebbles near shore, while larger predatory species cruise deeper water. Although the oceans are the evocative epicenters of fish biodiversity worldwide, freshwater streams, rivers, and lakes like Victoria actually hold just as much fish diversity. Of the roughly 30,000 known fish species, about half live in freshwater (1). The longstanding question is why.
The explosive adaptive radiation of cichlids—such as the colorful male and drab female of the species Lithochromis rufus native to Lake Victoria—could help explain the comparable diversity of freshwater and saltwater fishes. Image credit: Florian Moser (photographer).
Most biologists expect the vast oceans to be more diverse—as a general rule, larger areas tend to contain more species (2). With some 97% of Earth’s water volume locked up in the sea, and just 0.0093% in habitable freshwater, the even split of fish species richness between marine and freshwater environments seems paradoxical—and indeed, has been labeled the “freshwater fish paradox.” Ichthyologists working in the 1970s first theorized that freshwater fish might evolve faster, driving up their relative diversity, because they live in geographically fragmented tributaries with more opportunities for evolution by isolation than in continuous seas (3, 4).
But new research by evolutionary biologist Elizabeth Miller, now a postdoc at the University of Oklahoma in Norman, and others suggests there’s more nuance to the story. Rates of fish evolution in salt and freshwater may not be so different after all. Some species, most prominently the fast-evolving cichlids, may account for the perceived discrepancy.
Getting to the bottom of the freshwater fish paradox could shed light on a much larger question in evolutionary biology: Why does species richness vary between different habitats in the first place? Across all macroscopic organisms, about 80% of species are terrestrial, 15% are marine, and 5% are freshwater (5). Understanding what’s going on in fish could help illuminate more general mechanisms at work in other animals globally on land and sea.
Marine fish communities, such as this one in the Galapagos Islands featuring the Ember parrotfish, Scarus rubroviolaceus, are famous for their diversity. But researchers have long been unsure as to why freshwater fishes are just as species rich as ocean fishes. Image credit: Ricardo Betancur (photographer).
The Paradox That Isn’t
The freshwater fish paradox seems to contradict a core ecological principle known as the species–area relationship: The bigger the area, the more species you should count. Naturalists first made this observation in the 18th century, for instance documenting that larger islands indeed had more species than smaller ones (6, 7). Technically, it’s not a true paradox— patterns of species richness don’t contradict theory necessarily. “Nobody has ever suggested a single type of species–area relationship across all habitats,” says University of Oxford, UK, biogeographer Robert Whittaker. Oceans and rivers have different relationships; the type of habitat matters, not just the sheer size of the ecosystem in question.
The paradox label may not be quite right, but the pattern is perplexing. Studies of the so-called paradox are trying to explain this unusual pattern of species richness, explains ichthyologist Peter Wainwright at the University of California, Davis. “The real question there,” he says, is “what exactly is the history of fishes in these two habitats?” Angelfishes and butterflyfishes waft through saltwater reefs, while cichlids swirl in freshwater African rift lakes, each as a result of their own evolutionary histories.
In 2012, evolutionary ecologist John J. Wiens at the University of Arizona in Tucson coauthored one of the first studies tackling the apparent paradox (8). He tested whether freshwater fish species had diversified faster than saltwater groups, one possible explanation for the higher freshwater diversity per unit area. The study began with a phylogenetic tree of 97 ray-finned fish families, representing 22 clades —the majority of fish diversity—based on differences in one gene from 124 different fish species. For every clade, Wiens and co-authors calculated diversification rates—speciation rate minus extinction rate—using an estimator that is similar to taking the logarithm of the number of species, divided by the age of the clade. Hence, a young clade with many species would have a high diversification rate, while an old clade with only a few species would have a low rate. Each of the 22 clades had either freshwater species, saltwater species, or a mix of freshwater and saltwater species.
It turned out that freshwater and saltwater clades had similar diversification rates. A closer look at the phylogenetic tree pointed to a possible reason: Two of the largest, most diverse fish clades—the predominantly freshwater Ostariophysi and the predominantly saltwater Percomorpha—were roughly the same age, about 150 million years old, and diversifying at similar rates.
Although that work was state-of-the-art at the time, says fish evolutionary biologist Ricardo Betancur at the University of Oklahoma in Norman, studies since 2012 have used denser phylogenies, including thousands more species and many more genes, and updated statistical tools to make new inferences about fish evolution. Yet there is still no consensus. Some newer studies even suggest that marine lineages diversified faster than freshwater groups; others come to the exact opposite conclusion (9, 10).
Fishing for Answers
“We’re in a big mess of macroevolutionary results,” says evolutionary biologist Daniel Rabosky at the University of Michigan in Ann Arbor. Trying to make inferences from imperfect data is one major reason why. Diversification is speciation minus extinction. And although speciation rates are simple to calculate, based on the length and branching of a phylogenetic tree, extinction rates are harder in part because the fossil record doesn’t preserve the vast majority of fish species, and in part because phylogenetic trees don’t preserve any extinct species. It’s unclear when past groups died out.
Nevertheless, existing diversification studies do attempt to estimate extinction rates, sometimes arbitrarily, Rabosky says. “It’s taken us a decade to figure out just how nonrobust those estimates of extinction are, and I don’t trust any of it,” he says.
To explain patterns of fish species richness while avoiding the pitfalls of extinction calculations, Rabosky authored a 2020 study analyzing the most robust fish tree of life to date. As part of a large collaboration, he and coauthors originally published the tree in 2018, based on 11,638 fish species, 27 genes, and dated using 130 fossil calibrations. However, in 2020, Rabosky limited the scope of his analysis to recent speciation rates in the last 50 million years, where confidence in the data is highest (11, 12). He knew that bursts of rapid species formation often accompany transitions to new habitats. If fish arose in the oceans but then invaded freshwater multiple times, perhaps they’d gone through bursts of speciation that explain the relatively high diversity of freshwater fish per unit area today.
Rabosky used a model based on habitat data and known relationships between fish lineages to scan the phylogeny for large groups of extant freshwater fish in which all ancestors are marine. It identified the time point in the tree when those freshwater lineages diverged from their marine ancestors then compared speciation rates in those groups before and after the transition to freshwater. Unexpectedly, there was no evidence for a general trend of rapid speciation after colonizing new habitats. However, two huge groups did speciate faster upon entering freshwater: the cichlids and the Otophysi (minnows, catfishes, piranhas, and a number of other groups), which together represent about 80% of freshwater fish diversity. Perhaps something about these exceptional clades could help explain patterns of freshwater species richness.
Evolutionary biologist Ole Seehausen calls Neochromis simotes “one of the most amazing species in the radiation.” The fish has highly adapted mouthparts—rows of densely spaced and movably implanted teeth—that enable grazing algae on the rocks in the rapids of the Nile, just after that river leaves Lake Victoria. The roughly 20 species in the Neochromis genus are all endemic to the lake, arising in the last 15,000 years. Image Credit: Ole Seehausen (University of Bern, Bern, Switzerland).
Moving the Needle
When Elizabeth Miller read Rabosky’s 2020 work, a lightbulb went on. The cichlids in Lake Victoria are the fastest cases of adaptive radiation known in the animal world (see Box). They all descend from several distantly related species that came together and formed a hybrid population in the region in the last 150,000 years. Indeed, in Lake Victoria, 500 new species evolved in just the last 15,000 years (13). Miller realized that when cichlids had been lumped in with other freshwater fish in past analyses, the cichlids’ light speed diversification rates have skewed the results, making it appear that freshwater fish in general evolve faster than marine ones.
Miller herself had found elevated diversification rates for freshwater members of the bony fish clade Percomorpha in a 2018 study (14). She repeated her analysis in a 2021 article, this time excluding cichlids. Sure enough, diversification rates for the remaining freshwater and saltwater groups roughly matched (15). Probing deeper, Miller classified the remaining fishes as lake, river, or marine species and compared their diversification rates across habitats. She found that lake fish species in general do have higher diversification rates than river or marine species. Lakes seem to be crucibles of exceptionally fast evolution, of which the cichlids are perhaps the most extreme example, she says. Researchers aren’t yet sure why, but it’s possible that when lakes periodically fill, early colonists are released from predation or competition, so they’re free to quickly diversify into available niches. Looking ahead, future ecological fieldwork will need to test whether fish really do experience less competition in lakes, she says. Another possibility is that fish have more stratified niches by depth in lakes and so can avoid competition by diving deeper, compared with typically shallower rivers.
But the rapid diversification of lake fish species only tells part of the story, as lake fishes are a minority of freshwater groups. Cichlids, for example, total only about 2,500 of the 15,000 freshwater species (16). Even without them, marine and freshwater habitats would be similarly diverse. The vast majority of freshwater fish species evolved in rivers. When Miller looked to river fish in her 2021 analysis, she found diversification rates comparable with those of marine groups. Miller also found that the major fish groups in rivers and oceans have been diversifying at similar rates on average for much of their history, roughly the last 100 million years. She also repeated her analysis but calculated more-reliable speciation rates and, reassuringly, found the same trends.
The latest findings hint that, more than anything else, the so-called paradox is driven by the age of certain fish groups and how long they’ve been diversifying at similar rates, as Wiens suggested in 2012. Miller, who worked with him on her PhD, found in her latest work that modern marine and riverine fish species, in particular, have been accumulating diversity at comparable rates for 100 million years. Although her study is not the first to offer an explanation based on similar ages and similar diversification rates, that explanation was largely overlooked in the last decade in favor of the focus on contrasting diversification rates, Miller notes.
Since the earliest days of the so-called paradox, ichthyologists have hypothesized that fish must diversify faster in freshwater because freshwater systems are so fragmented compared with the oceans. Fish populations separated into isolated pockets this way would in theory have more opportunities for diversification. Miller’s findings suggest that 100 million years is long enough; faster speciation, she writes, is not necessary to explain high richness in freshwater. These latest studies suggest that “there [are] a lot of ways to end up with a lot of species,” Miller says. Rapid evolution in lakes is one way. Slower and steadier evolution in rivers and oceans is another. Clearly, fish species do not obey the same rules across habitats.
Taken together, these findings suggest that perhaps evolutionary biologists should revisit the way they think about differences in species richness across habitats. There is a long tradition of efforts to explain biodiversity gradients globally, not just for fish but for terrestrial, marine, and freshwater animals and plants. Biologists and ecologists typically invoke different rates of speciation and diversification to explain differences in species richness at large. Maybe the lesson from fish, Miller points out, is that the answer doesn’t have to be different rates of speciation and extinction at all. The contribution of outliers could be masking the actual history of evolution in many groups.
Cichlid Secrets
Cichlids speciate incredibly fast; recent work is offering good clues as to how they do it. The answer seems to be unusual genetic flexibility, according to a 2020 study by evolutionary biologist Ole Seehausen at the University of Bern, in Switzerland. Seehausen and his colleagues analyzed 100 Lake Victoria cichlid genomes, sampling species across habitats and niches. Using DNA extracted from the preserved pectoral fins of each fish, the researchers compared and contrasted the genomes of cichlids from different dietary groups and habitats (17).
They found hundreds of distinct DNA regions strongly tied to different ecological niches and scattered across 22 chromosomes. “We think that’s the key to make hundreds of species and not just two or three,” Seehausen says. When the fish hybridize, they can rearrange these modular genes, “almost like Lego bricks,” he says, to build many possible combinations suited, for example, to a rocky inshore fish that feeds on insects, or one that eats the same bugs but lives in weedy lake grass.
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