Rosa Rubicondior: Refuting Creationism - How New Genetic Information Can Arise Rapidly, Naturally

A small selection of Lake Malawi cichlids

How ‘supergenes’ help fish evolve into new species | University of Cambridge

Creationists like William A. Dembski constantly reassure their fellow believers that new genetic information cannot arise naturally and therefore requires divine intervention. This claim depends on a misrepresentation of the laws of thermodynamics and a deliberate confusion of information with energy. It is clung to despite the obvious and overwhelming evidence to the contrary, with the same tenacity that creationists bring to their insistence that evolution either does not happen at all or, if it does, must somehow have occurred at an impossibly rapid rate after the Flood to produce such enormous variation within their invented ‘kinds’ from just a single surviving pair.

So now we have yet more contrary evidence for creationists to ignore, this time in the form of an explanation for how the cichlid fishes of Lake Malawi in East Africa were able to evolve into more than 800 species in a fraction of the time it took humans and chimpanzees to diverge from a common ancestor. Readers of this blog with long memories may recall that, back in 2012, I described these fish as a particularly powerful argument against creationism.

The fact of this rapid adaptive radiation, taking place on a timescale that could be independently verified, was already indisputable. What we lacked at the time was a clear understanding of the underlying mechanism that made it possible. That gap has now been filled by researchers from the Universities of Cambridge and Antwerp, who have shown that the source of this new genetic information lies in genetic inversions, where an entire section of DNA is inserted in reverse orientation. They have recently published their findings in the journal Science.

During the normal process of meiosis, in which reproductive cells are formed, crossing-over reshuffles genes to produce new combinations in offspring. But when a segment of DNA has been inverted, that section cannot take part properly in the crossing-over process. As a result, the genes within it remain linked together as an intact block, forming what geneticists call a ‘supergene’. These supergenes can then be inherited largely unchanged across generations. The effect is to create barriers to hybridisation much more quickly than would otherwise be possible, effectively isolating a new gene pool within the wider population and allowing new species to evolve far more rapidly than usual, instead of having novel gene combinations continually diluted by interbreeding across the whole population.

Why we know the Lake Malawi cichlid radiation was exceptionally rapid. Lake Malawi’s cichlids are not just diverse; they are diverse on a timescale so short that even evolutionary biologists regard them as one of the most spectacular known examples of rapid vertebrate adaptive radiation. Depending on how species are counted, the lake contains well over 500 and probably more than 800 cichlid species, all descended from a comparatively recent common ancestral stock. [1]

The reason we know this radiation was especially fast is that several independent lines of evidence converge on the same conclusion. Geological and palaeoenvironmental work on Lake Malawi shows that the major phase of diversification is associated with the lake’s deep-water history over roughly the last 800,000 years. In evolutionary terms, that is an extraordinarily short period in which to generate hundreds of species occupying a wide range of ecological niches. [2]

Genomics confirms just how recent this diversification was. Whole-genome comparisons show that many of these supposedly separate species are genetically astonishingly similar, with average sequence divergence between species pairs of only about 0.1–0.25%. In fact, the differences between species overlap with the amount of variation found within species, and about 82% of heterozygous sites are shared between them. That is exactly what we would expect if many lineages split so recently and so quickly that there has not yet been time for deep genome-wide differences to accumulate. [1]

Their family tree tells the same story. Instead of deep, neatly separated branches, Malawi cichlids show the genetic signature of rapid branching, ongoing gene flow, and incomplete lineage sorting — all classic signs of a radiation that happened quickly enough for much ancestral variation to remain shared among descendant species. [1]

So the evidence is not simply that Lake Malawi has many cichlid species. It is that hundreds of species, with striking differences in body shape, feeding strategy, colouration and habitat use, evolved in a geologically brief window and left behind precisely the genomic pattern expected from rapid, recent diversification. That is why these fishes have become one of the textbook examples of evolution happening fast enough to be measured, dated and explained. [1]

How the researchers arrived at this discovery is explained in a University of Cambridge news item.

How ‘supergenes’ help fish evolve into new species
Researchers have found that chunks of ‘flipped’ DNA can help fish quickly adapt to new habitats and evolve into new species, acting as evolutionary ‘superchargers’.
Why are there so many different kinds of animals and plants on Earth? One of biology’s big questions is how new species arise and how nature’s incredible diversity came to be.

Cichlid fish from Lake Malawi in East Africa offer a clue. In this single lake, over 800 different species have evolved from a common ancestor in a fraction of the time it took for humans and chimpanzees to evolve from their common ancestor.

What’s even more remarkable is that the diversification of cichlids happened all in the same body of water. Some of these fish became large predators, others adapted to eat algae, sift through sand, or feed on plankton. Each species found its own ecological niche.

Now, researchers from the Universities of Cambridge and Antwerp have determined how this evolution may have happened so quickly. Their results are reported in the journal Science.

The researchers looked at the DNA of over 1,300 cichlids to see if there’s something special about their genes that might explain this rapid evolution.

“We discovered that, in some species, large chunks of DNA on five chromosomes are flipped – a type of mutation called a chromosomal inversion.

Hennes Svardal, senior author
Evolutionary Ecology Group
Department of Biology
University of Antwerp
Antwerp, Belgium.

Normally, when animals reproduce, their DNA gets reshuffled in a process called recombination – mixing the genetic material from both parents. But this mixing is blocked within a chromosomal inversion. This means that gene combinations within the inversion are passed down intact without mixing, generation after generation, keeping useful adaptations together and speeding up evolution.

It’s sort of like a toolbox where all the most useful tools are stuck together, preserving winning genetic combinations that help fish adapt to different environments.

L. Moritz Blumer, first author
Department of Genetics
University of Cambridge Cambridge, UK.

These preserved sets of genes are sometimes called ‘supergenes. In Malawi cichlids, the supergenes seem to play several important roles. Although cichlid species can still interbreed, the inversions help keep species separate by preventing their genes from blending too much. This is especially useful in parts of the lake where fish live side by side – like in open sandy areas where there’s no physical separation between habitats.

The genes inside these supergenes often control traits that are key for survival and reproduction – such as vision, hearing, and behaviour. For example, fish living deep in the lake (down to 200 meters) need different visual abilities than those near the surface, require different food, and need to survive at higher pressures. Their supergenes help maintain those special adaptations.

When different cichlid species interbred, entire inversions can be passed between them – bringing along key survival traits, like adaptations to specific environments, speeding up the process of evolution.

L. Moritz Blumer.

The inversions also frequently act as sex chromosomes, helping determine whether a fish becomes male or female. Since sex chromosomes can influence how new species form, this opens new questions about how evolution works.

While our study focused on cichlids, chromosomal inversions aren’t unique to them. They’re also found in many other animals — including humans — and are increasingly seen as a key factor in evolution and biodiversity.

Professor Richard Durbin, senior co-author
Department of Genetics
University of Cambridge Cambridge, UK.

We have been studying the process of speciation for a long time. Now, by understanding how these supergenes evolve and spread, we’re getting closer to answering one of science’s big questions: how life on Earth becomes so rich and varied.

Hennes Svardal.

Publication:
L. M. Blumer et al.
Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid radiation.
Science 388, eadr9961 (2025). DOI:10.1126/science.adr9961

Structured Abstract

INTRODUCTION
Ecological speciation is responsible for much of the biodiversity on our planet. Despite its fundamental importance, this process, in which new species emerge through evolutionary adaptation to distinct ecological niches, is still not fully understood. Intriguing case studies are adaptive radiations, bursts of ecological speciation that give rise to large numbers of diverse species over timescales that are short compared with the fixation time for new genetic variants. Genome sequencing studies increasingly point towards the importance of hybridization and cross-species gene flow in producing the diversity needed for ecological speciation and adaptive radiation. However, a major conundrum is the role of meiotic recombination in this process. On the one hand, recombination can create new, beneficial combinations of genetic alleles. On the other, it breaks down co-adapted allelic combinations, impeding speciation.

RATIONALE
Chromosomal inversions, stretches of DNA that are flipped in their orientation, provide a potential solution to the conflicting roles of recombination in ecological speciation. This is because inversions show suppressed recombination with the original chromosomal orientation, enabling them to lock together adaptive combinations of alleles in so-called “supergenes.” Inversions have been found to be important in ecological adaptation and speciation in many groups of organisms, but so far, there has been little evidence for their significance in adaptive radiations. To address this gap, we systematically investigated the presence and role of inversions across the lake Malawi cichlid fish adaptive radiation, the largest recent vertebrate radiation.

RESULTS
The genomes of 1375 Malawi cichlids from 240 species revealed the presence of multiple chromosomal inversions. The five largest of these segregate within the diverse and species-rich benthic subradiation, with a strong association between inversion states and habitat depth. Phylogenetic tracking of inversion states revealed a hybrid origin of the benthic clade, along with several introgression events transporting inversions and other genetic material between lineages within and outside of the radiation. Inversion haplotypes showed strong signals of adaptive evolution, including being enriched for sensory functions, behavior, and reproduction. For three chromosomes, the re-introgression of haplotypes of the ancestral orientation into benthic lineages coincides with an apparent Y chromosome–like role of this haplotype in the sex determination of some benthic species but not others.

CONCLUSION
The spread of chromosome-scale inversions in Malawi cichlids coincided with the phenotypic and ecological diversification of benthic species across habitats, with evidence for a role of inversion haplotypes in ecological adaptation. The additional transient sex linkage of introgressed inversion-region haplotypes points to an interplay of sex-linked and natural selection in shaping the evolution of inversion haplotypes and the diversification of cichlids.

Five large chromosomal inversions contribute to the diversification of Malawi cichlids.
Inversions established in the diverse benthic subradiation. Inversion-region haplotypes were exchanged through hybridization of lineages within and outside of the Malawi radiation and contribute to ecological and habitat divergence, sensory adaptation, and sex determination.

Abstract Chromosomal inversions can contribute to adaptive speciation by linking coadapted alleles. By querying 1375 genomes of the species-rich Malawi cichlid fish radiation, we discovered five large inversions segregating in the benthic subradiation that each suppress recombination over more than half a chromosome. Two inversions were transferred from deepwater pelagic Diplotaxodon through admixture, whereas the others established early in the deep benthic clade. Introgression of haplotypes from lineages inside and outside the Malawi radiation coincided with bursts of species diversification. Inversions show evidence for transient sex linkage, and a notable excess of protein changing substitutions points toward selection on neurosensory, physiological, and reproductive genes. These results indicate that repeated interplay between depth adaptation and sex-specific selection on large inversions has been central to the evolution of this iconic system.

L. M. Blumer et al.
Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid radiation.
Science 388, eadr9961 (2025). DOI:10.1126/science.adr9961

© 2025 American Association for the Advancement of Science.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

Lake Malawi’s cichlids are not just diverse; they are diverse on a timescale so short that even evolutionary biologists regard them as one of the most spectacular known examples of rapid vertebrate adaptive radiation. Depending on how species are counted, the lake contains well over 500 and probably more than 800 cichlid species, all descended from a comparatively recent common ancestral stock.

The reason we know this radiation was especially fast is that several independent lines of evidence converge on the same conclusion. Geological and palaeoenvironmental work on Lake Malawi shows that the major phase of diversification is associated with the lake’s deep-water history over roughly the last 800,000 years. In evolutionary terms, that is an extraordinarily short period in which to generate hundreds of species occupying a wide range of ecological niches.

Genomics confirms just how recent this diversification was. Whole-genome comparisons show that many of these supposedly separate species are genetically astonishingly similar, with average sequence divergence between species pairs of only about 0.1–0.25%. In fact, the differences between species overlap with the amount of variation found within species, and about 82% of heterozygous sites are shared between them. That is exactly what we would expect if many lineages split so recently and so quickly that there has not yet been time for deep genome-wide differences to accumulate.

Their family tree tells the same story. Instead of deep, neatly separated branches, Malawi cichlids show the genetic signature of rapid branching, ongoing gene flow, and incomplete lineage sorting — all classic signs of a radiation that happened quickly enough for much ancestral variation to remain shared among descendant species.

So the evidence is not simply that Lake Malawi has many cichlid species. It is that hundreds of species, with striking differences in body shape, feeding strategy, colouration and habitat use, evolved in a geologically brief window and left behind precisely the genomic pattern expected from rapid, recent diversification. That is why these fishes have become one of the textbook examples of evolution happening fast enough to be measured, dated and explained. Certainly — here is a more forceful side-panel version aimed squarely at Dembski’s claim: Discovery Institute Fellow, William A. Dembski’s argument depends on the assertion that biologically useful new genetic information cannot arise by natural processes and therefore must be inserted by an intelligent designer. The Lake Malawi cichlids are a direct empirical refutation of that claim. In a single lake, a recent common ancestor gave rise to hundreds of species — probably more than 800 — occupying a remarkable range of ecological niches, making this one of the most extensive recent vertebrate adaptive radiations known.

What makes this especially awkward for ID creationists is that researchers have now identified a natural mechanism that helps explain how this happened so quickly. By analysing more than 1,300 cichlid genomes, researchers found large chromosomal inversions — sections of DNA flipped into reverse orientation — on five chromosomes. These inversions suppress recombination across large regions, preserving successful combinations of genes as inherited blocks, or “supergenes”. In other words, ordinary mutation and inheritance can generate new, heritable genomic arrangements with functional evolutionary consequences. No designer is required to step in and add anything by magic.

This matters because Dembski and similar creationists often play a semantic trick: they talk as though “new information” must mean the miraculous insertion of entirely novel material from outside the system. But in real genetics, evolution often works by reorganising, preserving, combining and differentially filtering existing variation in ways that create genuinely new adaptive outcomes. In the Malawi cichlids, these inversions helped maintain co-adapted sets of genes involved in traits such as vision, physiology, behaviour and reproduction, while also helping keep species distinct even when they could still interbreed. That is exactly the sort of naturally arising functional genomic novelty Dembski claims cannot happen.

The wider genomic evidence shows just how rapidly all this occurred. Whole-genome comparisons found that many Lake Malawi cichlid species are still genetically extremely similar overall, with average sequence divergence between species pairs of only about 0.1–0.25%, and with roughly 82% of heterozygous sites shared between species. Yet despite this shallow overall divergence, they have already split into a huge array of ecologically and anatomically distinct species. That is what rapid natural diversification looks like in the real world: not a designer injecting “information”, but known evolutionary mechanisms generating adaptive novelty and reproductive separation faster than creationist dogma says should be possible.

So the problem for Dembski is not merely that the Malawi cichlids evolved rapidly. It is that they did so by exactly the sort of natural genetic processes he insists are incapable of producing functional evolutionary innovation. The evidence shows the opposite: genomes can generate new adaptive architectures naturally, selection can preserve them, and new species can result — all without the slightest hint of supernatural intervention.

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