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Sex chromosome divergence has been documented across phylogenetically diverse species, with amphibians typically having cytologically nondiverged ("homomorphic") sex chromosomes. With an aim of further characterizing sex chromosome divergence of an amphibian, we used "RAD-tags" and Sanger sequencing to examine sex specificity and heterozygosity in the Western clawed frog Silurana tropicalis (also known as Xenopus tropicalis). Our findings based on approximately 20 million genotype calls and approximately 200 polymerase chain reaction-amplified regions across multiple male and female genomes failed to identify a substantially sized genomic region with genotypic hallmarks of sex chromosome divergence, including in regions known to be tightly linked to the sex-determining region. We also found that expression and molecular evolution of genes linked to the sex-determining region did not differ substantially from genes in other parts of the genome. This suggests that the pseudoautosomal region, where recombination occurs, comprises a large portion of the sex chromosomes of S. tropicalis. These results may in part explain why African clawed frogs have such a high incidence of polyploidization, shed light on why amphibians have a high rate of sex chromosome turnover, and raise questions about why homomorphic sex chromosomes are so prevalent in amphibians.
Fig. 1.—. Genotypic scenarios for sex-linked regions. Expectations for heterozygosity depend on which sex is heterogametic and the region of the sex chromosome (pseudoautosomal region vs. sex-determining region). Female heterogamy is potentially associated with female-biased heterozygosity (Scenario 1a), male-only heterozygosity (Scenario 2a), or female-only homozygosity with no male genotypes (Scenario 3c). Corresponding scenarios (Scenarios 1b, 2b, and 3b) apply to the opposite sex for male heterogamy.
Fig. 2.—. Phylogenetic analysis of mitochondrial DNA sequences suggest that the “golden” strain used by Olmstead et al. (2010) and samples used in this study (8 for RAD tag analysis and 27 others for PCR assays) originate from Nigeria. Nodes with ≥95% posterior probability are indicated with a black circle. Species names, including those undescribed, follow Evans et al. (2004). Abbreviated country names include the Republic of the Congo (R. Congo), the Democratic Republic of the Congo (DRC), and Equatorial Guinea (EG). The scale bar refers to the number of substitutions per site, gray areas on the map indicate the distribution of tropical forest in West Africa, and the dotted line indicates the approximate distribution of Silurana tropicalis inferred by Tinsley et al. (1996).
Fig. 3.—. Average nucleotide diversity per site (π) in 500,000-bp windows is similar in males (blue) and females (red) throughout much of the Silurana tropicalis genome. Plots are labeled with numbers referring to scaffolds 1–10, which collectively comprise approximately 75% of the genome. A gray bar on scaffold/chromosome 7 indicates the petite arm based on the linkage map of Wells et al. (2011), which carries the sex-determining region in the S. tropicalis golden strain (Olmstead et al. 2010).
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