The classical hypothesis proposes that the lack of recombination on sex chromosomes arises due to selection for linkage between a sex-determining locus and sexually antagonistic loci, primarily facilitated by inversions. However, cessation of recombination on sex chromosomes could be attributed also to neutral processes, connected with other chromosome rearrangements or can reflect sex-specific recombination patterns existing already before sex chromosome differentiation. Three Coleonyx gecko species share a complex X1X1X2X2/X1X2Y system of sex chromosomes evolved via a fusion of the Y chromosome with an autosome. We analyzed synaptonemal complexes and sequenced flow-sorted sex chromosomes to investigate the effect of chromosomal rearrangement on recombination and differentiation of these sex chromosomes. The gecko sex chromosomes evolved from syntenic regions that were also co-opted also for sex chromosomes in other reptiles. We showed that in male geckos, recombination is less prevalent in the proximal regions of chromosomes and is even further drastically reduced around the centromere of the neo-Y chromosome. We highlight that pre-existing recombination patterns and Robertsonian fusions can be responsible for the cessation of recombination on sex chromosomes and that such processes can be largely neutral.

Animal Genomics and Bioresource Research Unit Faculty of Science Kasetsart University Bangkok 10900 Thailand

Department of Ecology Faculty of Science Charles University 12844 Prague Czech Republic

Department of Veterinary Medicine Cambridge Resource Centre for Comparative Genomics University of Cambridge Cambridge CB3 0ES UK

Institute of Cytology and Genetics Russian Academy of Sciences Siberian Branch Novosibirsk 630090 Russia

Institute of Environmental and Agricultural Biology University of Tyumen Tyumen 625003 Russia

Institute of Molecular and Cellular Biology Russian Academy of Sciences Siberian Branch Novosibirsk 630090 Russia

Novosibirsk State University Novosibirsk 630090 Russia

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