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Emergence and stabilization of a neo-Y chromosome in nematode species with rare males

Brice Letcher, Lewis Stevens, Nathanaëlle Saclier, Andrew Hsiao, Manuela Kieninger, Eva Wenger, Caroline Launay, Mark Blaxter, and Marie Delattre (2026)

Molecular Biology and Evolution, 43(8):msag177.

How do sex chromosomes evolve in the transition to asexuality? So far, species that depart from canonical sexual reproduction—for example, parthenogens with rare sex or species where the paternal genome is set aside—have been found to carry either no sex chromosomes or sex chromosomes but no male-specific sex chromosome (i.e. no Y). Here we reveal that, in Mesorhabditis nematodes, a new Y chromosome evolved once, from sexual ancestors, in species that have transitioned into an unconventional mode of reproduction called autopseudogamy. In this reproductive system, females produce clonal females plus rare (∼10\%) males that are needed for fertilization but that do not contribute to the female genome. Analyzing the Y chromosomes of two autopseudogamous species, we found high levels of degeneration, most likely due to loss of recombination, and two additional conserved features: (i) they accumulated male-beneficial genes, and (ii) they display a strong fertilization drive, in that mainly Y-bearing sperm fertilize female oocytes. Both features are likely evolutionarily favorable in the context of autopseudogamy. Our results suggest that male-specific chromosomes can still be maintained in systems with rare, and possibly “genetically useless,” males.

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