Every living species on Earth reproduces with a purpose. For most animals, that purpose is sex, which is not just biologically convenient but evolutionarily essential. When two individuals mate, their genetic material shuffles together, separating bad mutations from good ones, allowing natural selection to act on each gene independently. When we remove this shuffle, theories predict an eventual extinction of the species: harmful mutations pile up, beneficial ones stay unpurged, and eventually the species collapses under the weight of its own accumulating errors.
The Amazon molly — a small, silvery fish found in rivers along the Texas-Mexico border — has been ignoring this prediction for more than 100,000 years.
The molly (Poecilia formosa), as scientists know it, is an all-female species. Every Amazon molly alive today is a clone, descended from a single hybridization event between two other fish species that occurred at least 100,000 years ago near Tampico, Mexico. The fish do require sperm from closely related male species to trigger their egg development. However, they do not incorporate that genetic material into their offspring. Each daughter is a perfect genetic replica of her mother.
A concept known as Muller’s ratchet — named after the geneticist Hermann Muller — predicts that organisms without sexual recombination will steadily accumulate harmful mutations, generation after generation, with no mechanism to clear them. Those mutations pile up, with each copy slightly worse than the last. Computer simulations predicted that the Amazon molly should have gone extinct within fewer than 10,000 years of its origin.
As the team, led by Edward Ricemeyer, a biologist at Ludwig Maximilian University of Munich, notes, the species “has survived far beyond its predicted extinction time.”
But how did it manage to accomplish this feat? A study published in April 2026 in the journal Nature offers a clear answer. By building a detailed genomic portrait of the Amazon molly and tracking the separate genetic contributions of both parent species through time, researchers found that a molecular process called gene conversion has been performing many of the same functions that sex provides in other species.
Ludwig Maximilian University
The emergence of the Amazon molly
At least 100,000 years ago, a female Poecilia mexicana mated with a male Poecilia latipinna, a sailfin molly native to coastal waters farther north. Their offspring founded an entirely new lineage. Every Amazon molly alive today carries two sets of chromosomes: one inherited from P. mexicana, one from P. latipinna. Because the fish reproduces clonally, those two sets have never been reshuffled.
One consequence of this arrangement is that the two halves of a single Amazon molly’s genome have been evolving independently for so long that they now resemble different species more than they resemble each other.
Ricemeyer et al.
To study what 100,000 years of clonal reproduction has done to the Amazon molly’s DNA, Ricemeyer and his colleagues used sequencing technology to assemble the complete genome of the fish, keeping the two parental chromosome sets separate rather than blending them into a composite. They also assembled reference genomes for both parent species and reconstructed the ancestral genomes of all three lineages. This allowed them to track exactly which mutations had accumulated along the asexual lineage and which had been removed.
The sequencing showed that the Amazon molly’s genome has been accumulating mutations faster than those of its sexually reproducing relatives — an effect known as the Meselson effect. The Mexican-derived chromosomes within the fish had diverged from the ancestral state more than the latipinna-derived chromosomes had, suggesting the two halves of the hybrid genome have been mutating at slightly different rates.
Gene conversion at work
The researchers found, contrary to theoretical predictions, that the faster rate of mutation in the asexual fish had not led to a buildup of damaging, function-disrupting changes in genes. When the researchers counted the most damaging categories of mutations — those that disrupt a protein’s structure entirely — they found these were 47 percent less common than neutral mutations in the Amazon molly. The researchers suspected that something was actively removing the most harmful variants from the genome.
That something is gene conversion. Gene conversion is a process in which a cell, while repairing damaged or broken DNA, uses the matching sequence on the opposite chromosome as a template to overwrite a short stretch of one chromosome with the corresponding sequence from the other. In organisms that reproduce sexually, this kind of repair happens routinely during meiosis — the cell division that produces eggs and sperm — and contributes to genetic recombination. In the Amazon, molly gene conversion had been detected in earlier work, but its functional consequences had never been characterized directly.
Across the 19 Amazon molly individuals sampled, gene conversion tracts covered roughly six percent of each fish’s genome on average. Across the entire sample, more than twenty percent of the genome had undergone gene conversion in at least one individual. The tracts cluster near particular repetitive DNA sequences, especially long runs of repeated adenine and thymine bases. The researchers say these repeats may trigger breaks in the DNA strand during copying, which the cell then repairs by copying from the opposite chromosome — inadvertently converting one version of a sequence to match the other.
The team found that more than 195,000 gene conversion events had occurred since the common ancestor of the sampled fish. This process removed harmful mutations far more often than it spread them. There were more than 10 times as many events in which gene conversion reverted a mutated sequence back to the ancestral form as there were events in which a new, derived mutation was fixed in place.
The researchers say this shows that “gene conversion is a powerful mechanism counteracting the expected negative effects of asexual reproduction by facilitating both positive and negative selection.”
By comparing which regions underwent gene conversion with signatures of positive selection in the parent species, the researchers found that sequences favored by natural selection in one parent lineage were preferentially copied into the Amazon molly genome. In effect, the process allows the fish to maintain the most functional version of each genomic region — doing, in a more targeted way, something that resembles what sexual recombination does across the whole genome in ordinary species.
The gene conversion tracts in Amazon mollies are enriched for genes that build the receptors immune cells use to recognise and respond to pathogens. In the immune systems of vertebrates generally, diversity in these receptor genes is critical — the broader the repertoire, the better the immune system’s ability to detect new threats.
Manfred Schartl
“The power of gene conversion to generate recombinant peptide sequences where they are most biologically useful,” researchers say.
When two distantly related species hybridize, some gene variants from one parent do not function well alongside gene variants from the other — a phenomenon called hybrid incompatibility. The researchers found evidence that gene conversion is preferentially active at genomic regions enriched for this kind of conflict, replacing problematic hybrid sequences with more compatible alternatives.
“It remains to be seen whether other long-extant asexual species escape Muller’s ratchet through a similar mechanism,” researchers say.
The researchers say that future studies, particularly those examining gene activity at the level of individual cells, “will be instrumental for better characterizing the specific regulatory impacts of gene conversion and their contribution to organismal phenotype.” The answers, they suggest, could in turn “illuminate adaptive traits that underlie the remarkable success and persistence” of the fish.
