The Amazon molly is an evolutionary enigma: an all-female fish that reproduces by cloning itself. Because it doesn’t mix its DNA with a mate’s, Darwinian logic holds that harmful mutations should pile up over time, eventually driving the species extinct.
Yet the molly (Poecilia formosa) has stubbornly refused to follow that script. That seems to be because the fish’s genome repeatedly rewrites itself, researchers report March 11 in Nature. It uses a copy-and-paste DNA repair mechanism called gene conversion, in which small stretches of genetic code are copied from one chromosome to another. These genetic handoffs can erase unfavorable mutations and sometimes spread beneficial ones, allowing natural selection to keep operating.
“It’s pushing back against this accumulation of mutations,” says Wes Warren, a comparative genomicist at the University of Missouri in Columbia.
The results provide the first evidence that gene conversion can counteract mutation buildup in an asexual vertebrate — that is, one whose offspring are essentially genetic copies, or clones, of the parent.
“If these patterns hold broadly, it suggests we may need to treat DNA repair and gene conversion as part of the toolkit shaping the evolutionary fate of clonal species,” says Waldir Miron Berbel-Filho, an evolutionary biologist at the University of West Florida in Pensacola who was not involved in the research but wrote an accompanying commentary in the same issue of Nature.
The Amazon molly has thrived for more than 100,000 years in warm rivers and lagoons along the Mexico-Texas border. Although still reliant on males from closely related species to trigger egg development, females propagate themselves clonally with little sign of genetic decay.
Warren and his colleagues first published a version of the fish’s genome in 2018. But, owing to limitations of DNA sequencing technologies available at the time, they could not say how exactly the genome kept its mutations in check.
The team needed newer sequencing tools that could cleanly separate the fish’s paired chromosomes, each of which came from a different ancestral species that mated long ago to produce the first of this unusual hybrid lineage. Such tools make it possible to study mutations in much finer detail and to pinpoint hidden processes shaping the genome over time.
Once that technology became available, Warren and his colleagues took another look. Now, the researchers could clearly see telltale patterns of gene conversion occurring across the genome, echoing results others have seen in simpler organisms, including rotifers, water fleas, mites and flatworms.
By generating new pockets of genetic variation, the process “gives natural selection something to act on,” says computational biologist Edward Ricemeyer from the Ludwig Maximilian University of Munich.
Gene conversion doesn’t just scrub away harmful mutations and fix advantageous variants, though. The chromosome changeovers also appear to iron out genetic mismatches that can give rise to hybrid incompatibility, a situation in which genes inherited from two different parental species do not work well together.
The mechanism is not a perfect substitute for sex. The molly still accumulates mutations faster than a sexually reproducing species would. And the process cannot generate the flood of new gene combinations produced by sexual reproduction.
Still, the findings suggest that the fate of asexual species may not be quite as bleak as once thought — and could prompt scientists to refine their thinking about the evolutionary logic behind sex, notes Anne-Marie Dion-Côté, an evolutionary geneticist at the Université de Moncton in New Brunswick, Canada, who was not involved in the study.
“It really forces us to think outside of the box and outside of the textbooks,” she says.
