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bioRxiv · 10.64898/2026.08.31.748364

Long-range linkage maintained male-specific loci on a young Y chromosome prior to recombination shutdown

Wang, M.·Akhavizadegan, M.·Wang, J.-Y.·Chang, C.-H.·Wei, K. H.-C.
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Abstract

Suppression of recombination on the Y chromosome maintains linkage between male-specific loci and is commonly established by inversions. Here, we describe a young, inversion-free Y chromosome (neo-Y) in Drosophila albomicans with a unique history and paradoxical signature of exchange. Prior to recombination shutdown in males, it repeatedly recombined with the X-linked counterpart (neo-X) but at the same time preserved complete long-range linkage of the chromosome ends. By assembling multiple neo-Ys chromosomes and QTL-mapping, we show that double crossovers maintained linkage between the male-sex determining region at one end to sexually antagonistic alleles and a locus essential for spermatogenesis at the other. We argue that such long-range linkage of distal sex-specific loci disfavors inversions but instead encourages the emergence of achiasmy.

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Wang, M., Akhavizadegan, M., Wang, J.-Y., Chang, C.-H., Wei, K. H.-C.. 2026-09-04. Long-range linkage maintained male-specific loci on a young Y chromosome prior to recombination shutdown. https://doi.org/10.64898/2026.08.31.748364

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