Author: VD

Evolution and the Fish of Lake Victoria

Richard Dawkins loves the cichlid fish of Lake Victoria. In his 2024 book The Genetic Book of the Dead, he calls the lake a “cichlid factory” and marvels at what evolution accomplished there. Four hundred species, he tells us, all descended from perhaps two founder lineages, all evolved in the brief time since the lake last refilled—somewhere between 12,400 and 100,000 years depending on how you count. “The Cichlids of Lake Victoria show how fast evolution can proceed when it dons its running shoes,” he writes. He means this as a compliment to natural selection. Look what it can do when conditions are right!

Dawkins even provides a back-of-the-envelope calculation to reassure us that 100,000 years is plenty of time. He works out that you’d need roughly 800 generations between speciation events to produce 400 species. Cichlids mature in about two years, so 800 generations is 1,600 years. Comfortable margin. He then invokes a calculation by the botanist Ledyard Stebbins showing that even very weak selection—so weak you couldn’t measure it in the field—could turn a mouse into an elephant in 20,000 generations. If a mouse can become an elephant in 20,000 generations, surely a cichlid can become a slightly different cichlid in 800? “I conclude that 100,000 years is a comfortably long time in Cichlid evolution,” Dawkins writes, “easily enough time for an ancestral species to diversify into 400 separate species. That’s fortunate, because it happened!”

Well, it certainly happened. But whether natural selection did it is another question—one Dawkins never actually addresses.

You see, Dawkins asks how many speciation events can fit into 100,000 years. That’s the wrong question. Speciation events are just population splits. Two groups of fish stop interbreeding. That part is easy. Fish get trapped in separate ponds during a drought, the lake refills, and now you have two populations that don’t mix. Dawkins describes exactly this process, and he’s right that it doesn’t take long.

But population splits don’t make species different. They just make them separate. For the populations to become genetically distinct—to accumulate the DNA differences that distinguish one species from another—something has to change in their genomes. Mutations have to arise and spread through each population until they’re fixed: everyone in population A has the new variant, everyone in population B either has a different variant or keeps the original. That process is called fixation, and it’s the actual genetic work of divergence.

The question Dawkins should have asked is: how many fixations does cichlid diversification require, and can natural selection accomplish that many in the available time?

Let’s work it out, back-of-the-envelope style, just as Dawkins likes to do.

When geneticists compare cichlid species from Lake Victoria, they find the genomes differ by roughly 0.1 to 0.2 percent. That sounds tiny, and it is—these are very close relatives, as you’d expect from such a recent radiation. But cichlid genomes are about a billion base pairs long. A tenth of a percent of a billion is a million. Call it 750,000 to be conservative. That’s how many positions in the genome are fixed for different variants in different species.

Now, how many fixations can natural selection actually accomplish in the time available?

The fastest fixation rate ever directly observed comes from the famous Long-Term Evolution Experiment with E. coli bacteria—Richard Lenski’s project that’s been running since 1988. Under strong selection in laboratory conditions, beneficial mutations fix at a rate of about one per 1,600 generations. That’s bacteria, mind you—asexual organisms that reproduce every half hour, with no messy complications from sex or overlapping generations. For sexual organisms like fish, fixation is almost certainly slower. But let’s be generous and grant cichlids the bacterial rate.

One hundred thousand years at two years per generation gives us 50,000 generations. Divide by 1,600 generations per fixation and you get 31 achievable fixations. Let’s round up to 50 to be sporting.

Fifty fixations achievable. Seven hundred fifty thousand required.

The shortfall is 15,000-fold.

If we use the more recent date for the lake—12,400 years, which Dawkins mentions but sets aside—the situation gets worse. That’s only about 6,000 generations, yielding perhaps 3 to 5 achievable fixations. Against 750,000 required.

The shortfall is now over 100,000-fold.

Here’s the peculiar thing. Dawkins chose the Lake Victoria cichlids precisely because they evolved so fast. They’re his showpiece, his proof that natural selection can really motor when it needs to. “Think of it as an upper bound,” he says.

But that speed is exactly the problem. Fast diversification means short timescales. Short timescales mean few generations. Few generations mean few fixations achievable. The very feature Dawkins celebrates—the blistering pace of cichlid evolution—is what makes the math impossible.

His mouse-to-elephant calculation doesn’t help. Stebbins was asking a different question: how long for selection to shift a population from one body size to another? That’s about the rate of phenotypic change. MITTENS asks about the amount of genetic change—how many individual mutations must be fixed to account for the observed DNA differences between species. The rate of change can be fast while the throughput remains limited. You can sprint, but you can’t sprint to the moon.

Dawkins’s running shoes turn out to be missing their soles. And their shoelaces.

None of this means the cichlids didn’t diversify. They obviously did, since the fish are right there in the lake, four hundred species of them, different colors, different shapes, different diets, different behaviors. The fossils, (such as they are) the history, and the DNA all confirm a rapid radiation. That happened.

What the math shows is that natural selection, working through the fixation of beneficial mutations, cannot have done the genetic heavy lifting. Not in 100,000 years. Not in a million. The mechanism Dawkins invokes to explain the cichlid factory cannot actually run the factory.

So what did? That’s not a question I can answer here. But I can say what the answer is not. It’s not the process Dawkins describes so charmingly in The Genetic Book of the Dead. The back-of-the-envelope calculation he should have done—the one about fixations rather than speciations—shows that his explanation fails by five orders of magnitude.

One hundred thousand times short.

That’s quite a gap. You don’t close a gap like that by adjusting your assumptions or finding a more generous estimate of generation time. You close it by admitting that something is fundamentally wrong with your model.

Dawkins tells us the Lake Victoria cichlids show “how fast evolution can proceed when it dons its running shoes.” He’s right about the speed. He’s absolutely wrong about the shoes. Natural selection can’t run that fast. Nothing that works by fixing mutations one at a time, or even a thousand at a time, can run that fast.

The cichlids did something. But whatever they did, it wasn’t what Dawkins thinks.

And speaking of the cichlid fish, as it happens, the scientific enthusiasm for them means we can demonstrate the extent to which it is mathematically impossible for natural selection to account for their observed differences. For, you see, we recently extended our study of MITTENS from the great apes to a wide range of species, including the cichlid fish.

From “The Universal Failure of Fixation: MITTENS Applied Across the Tree of Life”:

Lake Victoria Cichlids: The Lake Victoria cichlid radiation is perhaps the most famous example of explosive speciation. Over 500 species arose in approximately 15,000 years from a small founding population following a desiccation event around 14,700 years ago (Brawand et al. 2014). At 1.5 years per generation, this provides only 10,000 generations. Even with d = 0.85, achievable fixations = (10,000 × 0.85) / 1,600 = 5.

Interspecific nucleotide divergence averages 0.15% over a 1 Gb genome, requiring approximately 750,000 fixations to differentiate species. Shortfall: 750,000 / 5 = 141,500×.

This is a devastating result. The radiation celebrated as evolution’s greatest achievement fails MITTENS by 141,000-fold. Five fixations achievable; three-quarters of a million required.

The math does not work. Again.

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That’s not taxonomically correct, as neither chimpanzees nor bonobos are, strictly speaking, monkeys. But why resist a perfectly good alliteration considering how flexible the biologists have gotten to be where speciation is concerned, right?

Anyhow, one of the obvious and more shortsighted objections to MITTENS is that its formal presentation focused solely on the human-chimpanzee divergence, although literally from the moment of its origins its claims have been all-encompassing with regards to all genetic divergences between all species. I simply hadn’t gotten around to digging up the genomic evidence required to empirically anchor the math and the logic involved. One has to start somewhere, after all, and complaining that an initial test of a hypothesis is not all-inclusive is not a reasonable objection.

But now that PZ and TFG are both out, I can take some time to fill in the blanks and explore a few interesting lines of possibility, and to hunt down the various escape routes that the increasingly desperate IFLSists are attempting to find. So, I downloaded several gigabytes of data from the Great ape genome diversity program at the University of Vienna, crunched the numbers, and can now demonstrate that the expected shortfall in the fixation capacity definitely applies to the chimp-bonobo divergence as well as two intra-chimpanzee divergences.

As before, this is an approach with assumptions favorable to the post-Darwinian New Modern Synthesis, as we went with the traditional 20 years for a chimpanzee generation rather than the most recent calculation of 22 years. However, we also discovered an anomaly which is reflected in the title “The Pan Paradox: MITTENS Applied to Chimpanzee Subspecies Divergence”, because in addition to supporting MITTENS, the evidence also directly contradicts neutral theory.

The MITTENS framework (Mathematical Impossibility of The Theory of Evolution by Natural Selection) demonstrated a 220,000-fold shortfall in the fixation capacity required to explain human-chimpanzee divergence. A natural objection holds that this represents a special case—perhaps the human-chimp comparison uniquely violates the model’s assumptions. We test this objection by applying MITTENS to divergence within the genus Pan: the split between bonobos and chimpanzees, and the subsequent radiation of chimpanzee subspecies. Using genomic data from the Kuhlwilm et al. (2025) Great Ape Genome Diversity Panel comprising 67 wild Pan individuals, we identify 1,811,881 fixed differences between subspecies and calculate achievable fixations given published divergence times and effective population sizes. Using 20-year generations (shorter generations favor the standard model) and the empirically-derived Selective Turnover Coefficient d = 0.86 for wild chimpanzees, the bonobo-chimpanzee split (930,000 years, 40,000 effective generations) permits a maximum of 25 fixations—a shortfall of at least 13,000-fold against the observed fixed differences. Subspecies divergences show comparable failures: Western versus Central chimpanzees (460,000 years) fail by ~7,500-fold; Central versus Eastern (200,000 years) fail by ~3,600-fold.

You can read the whole paper here if you like. I’ve also added a link on the left sidebar to provide regular access to my open repository of science papers for those who are interested since I seldom talk about most of them here, or anywhere else, for that matter.

And we’re back with a vengeance. Thanks to everyone who has bought the book, and especially to those who have read and reviewed it. Hopefully we’ll be 1 and 2 in Biology before long.

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