Why hybridizing darters use three different sex chromosomes

Whole-genome sequencing and the association analyses showed that all three species use an XY system, as humans do. Males carry one copy each of two different sex chromosomes, but the chromosomes serving the X and Y roles differ by species:

• Orangethroat darters: chromosome 9.
• Rainbow darters: chromosome 23.
• A third hybridizing species, E. radiosum: chromosome 22.

Across the darter family tree, those roles have repeatedly moved onto different chromosomes. Researchers call this process sex chromosome turnover. Scientists have rarely documented turnover this rapid across a large, closely related group, especially one that interbreeds as freely as darters do.

The team’s analyses suggest the turnovers occurred while the species remained geographically isolated. By the time their ranges overlapped again, their sex-determining systems had already diverged enough to create mismatches in hybrid offspring.

Takeaway: Different sex chromosomes can stop formerly isolated lineages from collapsing back into one species when they meet again.

Why do chromosomes and mitochondria disagree?

The newly identified sex-chromosome regions also resisted gene flow, meaning the transfer of DNA between species through interbreeding. Those regions contained nuclear genes whose protein products physically interact with proteins encoded by mitochondrial genes.

Mitochondria are the cell’s energy-producing machinery and inherit their DNA only from the mother. A hybrid can therefore receive a mitochondrial genome from one species alongside mismatched nuclear genes from the other. The resulting protein partners may not fit together properly and could disrupt cellular metabolism.

Moran said scientists have long considered mitonuclear incompatibilities—mismatches between mitochondrial and nuclear systems—and sex-linked incompatibilities separately. They have rarely examined how the two problems interact.

Near sex-determining regions, recombination, the exchange and reshuffling of DNA during reproduction, remains low. Moran said: “Because we found a lot of these mitochondrial-associated nuclear genes near sex-determining regions that have low recombination, they can’t coevolve with the mitochondrial genome as easily. That could favor the sex chromosome switching over to a different spot to restore recombination.”

Researchers describe the turnover as an evolutionary “escape hatch.” Moving a sex chromosome can restore DNA reshuffling and ease a mitochondrial conflict, but it can also generate new incompatibilities between the species.

Takeaway: Relocating a sex chromosome may relieve one genetic conflict while creating another barrier to interbreeding.

What comes next?

Darters rank among North America’s most diverse vertebrate groups, yet scientists still know little about their sex chromosomes at the genomic level. Radcliffe plans to map those chromosomes across many more species as part of her doctoral dissertation.

She also hopes eventually to use CRISPR, a gene-editing tool, to identify the exact genes responsible for flipping the sex switch. Radcliffe said understanding how species evolve and diverge can help researchers maintain diversification and prevent species loss.

The current study combines laboratory crosses with genome comparisons, so its evidence supports a plausible barrier rather than identifying every causal gene. The researchers still need to determine how widely the mechanism operates and which genes make the chromosomes incompatible.

Wynne V. Radcliffe and colleagues published “Support for a role of sex chromosome turnover and mitonuclear conflict in reproductive isolation in darters” in Nature Communications in 2026. The paper’s DOI is 10.1038/s41467-026-78756-7.

For darters, reproductive isolation can emerge without a complete halt to interbreeding, through offspring that inherit mismatched genetic systems.