INNER WORKINGS

Reeling in answers to the “freshwater paradox” INNER WORKINGS Amy McDermott, Science Writer

Some 500 species of fish dart through the turbid and freshwater environments seems paradoxical—and in- yellowish waters of East Africa’s Lake Victoria; little insec- deed, has been labeled the “ paradox.” tivores fin over the pebbles near shore, while larger Ichthyologists working in the 1970s first theorized that predatory species cruise deeper water. Although the freshwater fish might evolve faster, driving up their rela- oceans are the evocative epicenters of fish biodiversity tive diversity, because they live in geographically frag- worldwide, freshwater streams, rivers, and lakes like mented tributaries with more opportunities for evolution Victoria actually hold just as much fish diversity. Of by isolation than in continuous seas (3, 4). the roughly 30,000 known fish species, about half live But new research by evolutionary biologist Eliz- in freshwater (1). The longstanding question is why. abeth Miller, now a postdoc at the University of Most biologists expect the vast oceans to be more Oklahoma in Norman, and others suggests there’s diverse—as a general rule, larger areas tend to contain more nuance to the story. Rates of fish evolution in more species (2). With some 97% of Earth’swatervolume salt and freshwater may not be so different after all. locked up in the sea, and just 0.0093% in habitable fresh- Some species, most prominently the fast-evolving water, the even split of fish species richness between marine , may account for the perceived discrepancy.

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 . Image credit: Florian Moser (photographer).

Published under the PNAS license. Published September 1, 2021.

PNAS 2021 Vol. 118 No. 36 e2113780118 https://doi.org/10.1073/pnas.2113780118 | 1of4 Downloaded by guest on September 29, 2021 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 sug- gested a single type of species–area relationship across all habitats,” says University of Oxford, UK, biogeogra- pher 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 Marine fish communities, such as this one in the Galapagos Islands featuring the waft through saltwater reefs, while cichlids swirl in Scarus rubroviolaceus Ember , , are famous for their diversity. But freshwater African rift lakes, each as a result of their researchers have long been unsure as to why freshwater fishes are just as species rich as ocean fishes. Image credit: Ricardo Betancur (photographer). own evolutionary histories. In 2012, evolutionary ecologist John J. Wiens at Getting to the bottom of the freshwater fish par- the University of Arizona in Tucson coauthored one of adox could shed light on a much larger question in the first studies tackling the apparent paradox (8). He tested whether freshwater fish species had diversified evolutionary biology: Why does species richness vary faster than saltwater groups, one possible explanation between different habitats in the first place? Across all for the higher freshwater diversity per unit area. The macroscopic organisms, about 80% of species are study began with a phylogenetic tree of 97 ray-finned terrestrial, 15% are marine, and 5% are freshwater (5). fish families, representing 22 —the majority of Understanding what’s going on in fish could help illu- fish diversity—based on differences in one gene from minate more general mechanisms at work in other an- 124 different fish species. For every , Wiens and imals globally on land and sea. co-authors calculated diversification rates—speciation rate minus extinction rate—using an estimator that is ’ The Paradox That Isn t similar to taking the logarithm of the number of spe- The freshwater fish paradox seems to contradict a core cies, divided by the age of the clade. Hence, a young – ecological principle known as the species area relationship: clade with many species would have a high diversifi- cation rate, while an old clade with only a few species would have a low rate. Each of the 22 clades had ei- ther 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). Evolutionary biologist Ole Seehausen calls Neochromis simotes “one of the most amazing species in the radiation.” The fish has highly adapted mouthparts—rows of for Answers densely spaced and movably implanted teeth—that enable grazing algae on the “We’re in a big mess of macroevolutionary results,” 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 says evolutionary biologist Daniel Rabosky at the years. Image Credit: Ole Seehausen (University of Bern, Bern, Switzerland). University of Michigan in Ann Arbor. Trying to make

2of4 | PNAS McDermott https://doi.org/10.1073/pnas.2113780118 Inner Workings: Reeling in answers to the “freshwater fish paradox” Downloaded by guest on September 29, 2021 inferences from imperfect data is one major reason fastest cases of adaptive radiation known in the why. Diversification is speciation minus extinction. world (see Box). They all descend from several dis- And although speciation rates are simple to calculate, tantly related species that came together and formed based on the length and branching of a phylogenetic a hybrid population in the region in the last 150,000 tree, extinction rates are harder in part because the years. Indeed, in Lake Victoria, 500 new species fossil record doesn’t preserve the vast majority of fish evolved in just the last 15,000 years (13). Miller real- species, and in part because phylogenetic trees don’t ized that when cichlids had been lumped in with other preserve any extinct species. It’s unclear when past freshwater fish in past analyses, the cichlids’ light groups died out. speed diversification rates have skewed the results, Nevertheless, existing diversification studies do making it appear that freshwater fish in general evolve attempt to estimate extinction rates, sometimes arbi- faster than marine ones. trarily, Rabosky says. “It’s taken us a decade to figure Miller herself had found elevated diversification out just how nonrobust those estimates of extinction rates for freshwater members of the bony fish clade are, and I don’t trust any of it,” he says. Percomorpha in a 2018 study (14). She repeated her To explain patterns of fish species richness while analysis in a 2021 article, this time excluding cichlids. avoiding the pitfalls of extinction calculations, Rabosky Sure enough, diversification rates for the remaining authored a 2020 study analyzing the most robust fish freshwater and saltwater groups roughly matched (15). tree of life to date. As part of a large collaboration, he Probing deeper, Miller classified the remaining fishes and coauthors originally published the tree in 2018, as lake, river, or marine species and compared their based on 11,638 fish species, 27 genes, and dated diversification rates across habitats. She found that using 130 fossil calibrations. However, in 2020, Rabosky lake fish species in general do have higher diversifi- limited the scope of his analysis to recent speciation cation rates than river or marine species. Lakes seem rates in the last 50 million years, where confidence in to be crucibles of exceptionally fast evolution, of the data is highest (11, 12). He knew that bursts of rapid which the cichlids are perhaps the most extreme ex- species formation often accompany transitions to new ample, she says. Researchers aren’t yet sure why, but habitats. If fish arose in the oceans but then invaded it’s possible that when lakes periodically fill, early freshwater multiple times, perhaps they’d gone through colonists are released from predation or competition, bursts of speciation that explain the relatively high di- so they’re free to quickly diversify into available versity of freshwater fish per unit area today. niches. Looking ahead, future ecological fieldwork will Rabosky used a model based on habitat data and need to test whether fish really do experience less known relationships between fish lineages to scan the competition in lakes, she says. Another possibility is phylogeny for large groups of extant freshwater fish in that fish have more stratified niches by depth in lakes which all ancestors are marine. It identified the time and so can avoid competition by diving deeper, point in the tree when those freshwater lineages di- compared with typically shallower rivers. verged from their marine ancestors then compared But the rapid diversification of lake fish species speciation rates in those groups before and after the only tells part of the story, as lake fishes are a minority transition to freshwater. Unexpectedly, there was no of freshwater groups. Cichlids, for example, total only evidence for a general trend of rapid speciation after about 2,500 of the 15,000 freshwater species (16). colonizing new habitats. However, two huge groups Even without them, marine and freshwater habitats did speciate faster upon entering freshwater: the would be similarly diverse. The vast majority of fresh- cichlids and the Otophysi (minnows, catfishes, pira- water fish species evolved in rivers. When Miller nhas, and a number of other groups), which together looked to river fish in her 2021 analysis, she found represent about 80% of freshwater fish diversity. Per- diversification rates comparable with those of marine haps something about these exceptional clades could groups. Miller also found that the major fish groups in help explain patterns of freshwater species richness. rivers and oceans have been diversifying at similar rates on average for much of their history, roughly the Moving the Needle last 100 million years. She also repeated her analysis When Elizabeth Miller read Rabosky’s 2020 work, a but calculated more-reliable speciation rates and, re- lightbulb went on. The cichlids in Lake Victoria are the assuringly, found the same trends.

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.

McDermott PNAS | 3of4 Inner Workings: Reeling in answers to the “freshwater fish paradox” https://doi.org/10.1073/pnas.2113780118 Downloaded by guest on September 29, 2021 The latest findings hint that, more than anything not necessary to explain high richness in freshwater. else, the so-called paradox is driven by the age of These latest studies suggest that “there [are] a lot of certain fish groups and how long they’ve been diver- waystoendupwithalotofspecies,” Miller says. sifying at similar rates, as Wiens suggested in 2012. Rapid evolution in lakes is one way. Slower and Miller, who worked with him on her PhD, found in her steadier evolution in rivers and oceans is another. latest work that modern marine and riverine fish spe- Clearly, fish species do not obey the same rules cies, in particular, have been accumulating diversity at across habitats. comparable rates for 100 million years. Although her Taken together, these findings suggest that per- study is not the first to offer an explanation based on haps evolutionary biologists should revisit the way similar ages and similar diversification rates, that ex- they think about differences in species richness across planation was largely overlooked in the last decade in habitats. There is a long tradition of efforts to explain favor of the focus on contrasting diversification rates, biodiversity gradients globally, not just for fish but for Miller notes. terrestrial, marine, and freshwater and plants. Since the earliest days of the so-called paradox, Biologists and ecologists typically invoke different ichthyologists have hypothesized that fish must di- rates of speciation and diversification to explain versify faster in freshwater because freshwater systems differences in species richness at large. Maybe the are so fragmented compared with the oceans. Fish lesson from fish, Miller points out, is that the answer populations separated into isolated pockets this way doesn’t have to be different rates of speciation would in theory have more opportunities for diversi- and extinction at all. The contribution of outliers fication. Miller’s findings suggest that 100 million could be masking the actual history of evolution in years is long enough; faster speciation, she writes, is many groups.

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