Sex chromosomes of some closely related species are not homologous, and sex chromosome turnover is often attributed to mechanisms that involve linkage to or recombination arrest around sex-determining loci. We examined sex chromosome turnover and recombination landscapes in African clawed frogs (genus Xenopus) with reduced representation genome sequences from 929 individuals from 19 species. We recovered extensive variation in sex chromosomes, including at least eight nonhomologous sex-associated regions-five newly reported here, with most maintaining female heterogamety, but two independent origins of Y chromosomes. Seven of these regions are found in allopolyploid species in the subgenus Xenopus, and all of these reside in one of their two subgenomes, which highlights functional asymmetry between subgenomes. In three species with chromosome-scale genome assemblies (Xenopus borealis, Xenopus laevis, and Xenopus tropicalis), sex-specific recombination landscapes have similar patterns of sex differences in rates and locations of recombination. Across these Xenopus species, sex-associated regions are significantly nearer chromosome ends than expected by chance, even though this is where the ancestral recombination rate is highest in both sexes before the regions became sex associated. As well, expansions of sex-associated recombination arrest occurred multiple times. New information on sex linkage along with among-species variation in female specificity of the sex-determining gene dm-w argues against a "jumping gene" model, where dm-w moves around the genome. The diversity of sex chromosomes in Xenopus raises questions about the roles of natural and sexual selection, polyploidy, the recombination landscape, and neutral processes in driving sex chromosome turnover in animal groups with mostly heterogametic females.

Centre for Invasion Biology Department of Botany and Zoology Stellenbosch University Stellenbosch 7602 South Africa

Centre for Invasion Biology Institute of Biodiversity Yunnan University in Kunming Yunnan Province China

Department of Biological Sciences The University of Texas at El Paso El Paso TX 79968 USA

Department of Biology Evolutionary Morphology of Vertebrates Ghent University Ghent Belgium

Department of Biology Life Sciences Building Room 328 McMaster University 1280 Main Street West Hamilton ON Canada L8S4K1

Department of Biology University of Antwerp Wilrijk Belgium

Department of Botany and Plant Pathology Oregon State University Cordley Hall 4605 2701 SW Campus Way Corvallis OR 97331 USA

Department of Cell Biology Charles University Viničná 7 Prague 12843 Czech Republic

Department of Zoology National Museum of the Czech Republic Prague Czech Republic

Eugene Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource Marine Biological Laboratory Woods Hole MA USA

Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic

Museum of Vertebrate Zoology University of California Berkeley CA 94720 USA

Naturhistorisches Museum Bern Bern Switzerland

School of Biological Sciences University of Portsmouth Portsmouth UK

UMR 7179 Mécanismes Adaptatifs et Evolution Muséum national d'Histoire naturelle CNRS Paris France

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FISH mapping in Xenopus pygmaeus refines understanding of genomic rearrangements and reveals jumping NORs in African clawed frogs