The tiny Amazon molly (Poecilia formosa) has always fascinated researchers because, according to the rules of evolution, it shouldn't have survived as a species, let alone thrive as a species for over 100,000 years. Using advanced genetic mapping and comparison techniques to track how the Amazon molly's DNA has changed over time, a new study set out to uncover the genetic secrets behind this apparent rebellion against evolutionary theory.

The molly undergoes asexual reproduction and gives live birth to its young, which are its clones, because the species is made up entirely of females—much like the all-female Amazonian warriors of Greek mythology, from whom it gets its name, not the Amazon Basin (where it doesn't live).

As per Muller's ratchet, a standard evolutionary theory, they should have gone extinct because clonal organisms accumulate harmful mutations over time due to a lack of genetic diversity.

The genetic evidence from this study, published in Nature, shows that the Amazon molly picks up mutations faster than its sexual relatives, yet somehow avoids the expected genetic decay—the secret behind this surprising act of resilience is gene conversion. This process purges harmful mutations by spotting damaged genes, "copying" a healthy version of the same gene from another part of the fish's own DNA, and "pasting" it over the faulty region to overwrite the mistake.

Accidental origin of the species

The Amazon molly didn't slowly evolve into a new species, it was the result of a 100,000-year-old accident. A long time ago, near Tampico, Mexico, a female Poecilia mexicana mated with a male Poecilia latipinna and created the hybrid—the Amazon molly. Every fish of that species alive today traces its lineage back to that single cross.

Unlike hybrid animals like a liger or mule, which are sterile and cannot reproduce, the Amazon molly is fully capable of reproducing asexually. Inside the mother's ovaries are specialized cells that undergo a modified version of meiosis—a type of cell division in sexually reproducing organisms—where the pairing up of chromosomes from two parents and swapping genetic information before dividing doesn't occur.

Instead, the mother produces eggs that already contain a full, double set of DNA that develops into new fish that are genetically identical to the mother. This form of cloning is called apomixis.

For a long time, scientists believed sexual reproduction was essential for long-term survival because it shuffles genes, removing harmful mutations and combining beneficial ones. The Amazon molly, however, gets the same advantages without ever mating.

Previous studies hinted at its high genetic diversity and signs of gene conversion, but detailed, haplotype-resolved genomic data were still missing.

Clues hidden in the genetic code

In this study, the researchers filled in this knowledge gap by creating a highly detailed and complete map of the entire genetic code for the Amazon molly and its two parent species using advanced long-read sequencing technology.

The researchers combined Hi-C and trio-binning to unravel the Amazon molly's genome. While Hi-C showed how DNA folds into chromosomes, trio-binning separated the two parental DNA sets, letting them study each lineage independently.

They found widespread presence of gene conversion, which supports two different pathways to reverse or correct unwanted genetic mutations: adaptive, or positive, selection, which promotes beneficial genetic mutations that enhance an organism's fitness, and second is purifying, or negative, selection, which helps reduce the presence of harmful genetic variations within a population.

The team also observed a higher rate of genetic repairs happening near DNA that carry crucial biological instructions, such as immunity or cell signaling.

Another fascinating detail revealed by the genome map was that out of the two sets of DNA present in the Amazon molly, one from each ancestral parent, is that the P. mexicana half of the fish's DNA is mutating and changing faster than the P. latipinna half, with changes mirroring those happening to the original species in the wild.

The study sheds light on long-debated questions about the evolutionary costs of asexual reproduction and establishes gene conversion as a powerful mechanism for effectively offsetting the negative effects. The findings give rise to a new question for future studies to explore: Do other long-lived asexual species avoid Muller's ratchet through the same process or is there something completely different at play?