LMU computational biologist helps uncover how the Amazon molly maintains a healthy genome without sexual reproduction

The Amazon molly is a remarkable species: all individuals are female and reproduce clonally. Although females must mate with males of related species to trigger reproduction, the male’s DNA is not incorporated into the offspring. Because of this unusual reproductive strategy, evolutionary theory predicts that harmful mutations should gradually accumulate in the genome over time, eventually threatening the species’ survival. Yet the Amazon molly has persisted for thousands of generations—raising the question of how its genome remains healthy.
Researchers from an international team led by Dr. Edward Ricemeyer, a computational biologist in the Chair of Animal Systems Genomics at LMU’s Faculty of Veterinary Medicine, have now uncovered how this unusual fish species avoids the genetic deterioration expected in organisms that reproduce without sex.
The findings, published in the journal Nature, reveal that the Amazon molly (Poecilia formosa) maintains its genome through a genetic mechanism called gene conversion, which helps remove harmful mutations even in the absence of recombination.

Gene conversion allows natural selection to keep working
In sexually reproducing species, recombination during reproduction helps separate harmful mutations from beneficial ones so that natural selection can remove damaging variants. In a clonal species like the Amazon molly, this mechanism is largely absent.
Using high-quality genome sequences from multiple individuals, the researchers searched for signatures of mutation accumulation and the evolutionary forces acting on the genome.
Instead of the expected genetic decay, they discovered widespread evidence of gene conversion, a process in which one DNA sequence is copied over another similar sequence. This process can replace damaged versions of genes with intact copies.
“Gene conversion can effectively overwrite harmful mutations with healthy copies of the same gene,” explains Ricemeyer. “That means natural selection can still remove damaging mutations, even in a lineage that reproduces clonally.”

A genome that behaves more like a sexual species
The team’s analyses suggest that gene conversion allows beneficial variants to spread and harmful mutations to be purged from the population, helping maintain overall genome integrity.
“This was surprising because the standard expectation is that clonal genomes should gradually deteriorate,” says Ricemeyer. “Instead, we see evidence that this species has a mechanism that keeps the genome remarkably functional.”
The findings suggest that the Amazon molly retains some of the evolutionary benefits normally associated with sexual reproduction, despite reproducing clonally.
“This fish seems to have the best of both worlds — the genetic health that normally comes from sexual reproduction while not needing a male’s DNA to reproduce,” says senior author Professor Wesley Warren from the University of Missouri Graduate School.

Insights into one of evolution’s biggest questions
Beyond explaining the long-term success of the Amazon molly, the research sheds light on a fundamental question in evolutionary biology: why organisms that can only reproduce asexually, although relatively rare, are more widespread than previously thought.
“Our results show that evolution may have more ways to maintain genome health than previously recognized,” says Ricemeyer. “Studying unusual systems like the Amazon molly helps us understand the basic forces shaping genomes across the tree of life.”
The study was led by Ricemeyer (LMU and University of Missouri) and Dr. Nathan Schaefer (University of California, San Francisco), with senior authors Professor Manfred Schartl (University of Würzburg) and Professor Wesley C. Warren (University of Missouri), and involved collaborators from multiple institutions.