DOI: 10.5061/dryad.4tb10
title: Data from: Trans-species variation in Dmrt1 is associated with sex determination in four European tree-frog species

description: Empirical studies on the relative roles of occasional XY recombination
 versus sex-chromosome turnover in preventing sex-chromosome
 differentiation may shed light on the evolutionary forces acting on
 sex-determination systems. Signatures of XY recombination are difficult to
 distinguish from those of homologous transitions (i.e., transitions in
 sex-determination systems that keep sex-chromosome identity): both models
 predict X and Y alleles at sex-linked genes to cluster by species.
 However, the XY-recombination model specifically predicts the reverse
 pattern (clustering by gametologs) for those genes that are directly
 involved in sex determination. Hence, the latter model can only be
 validated by identification of an ancestral sex-determining region (SDR)
 with trans-species polymorphism associated to sex. Here we combine a
 candidate-gene approach with a genome scan to identify a small SDR shared
 by four species of a monophyletic clade of European tree frogs. This SDR
 encompasses at least the N-terminal part of Dmrt1 and immediate upstream
 sequences. Our findings provide definitive evidence that sex-chromosome
 homomorphy in this clade results only from XY recombination, and take an
 important step towards the identification of the sex-determining locus.
 Moreover, the sex-diagnostic markers we identify will enable research on
 environmental sex reversal in a wider range of frog species.
description: Hyla GBS genotypes in
 gzip-compressed VCF formatThe VCF file contains
 genotypes for 4 male and 4 female frogs of 4 species, H. arborea, H.
 intermedia, H. orientalis, and H. molleri. H. arborea sample names begin
 with "Ha", H. intermedia with "Hi", H. orientalis with
 "Ho", and H. molleri with "Hm". Samples with names
 containing "F" are female, samples with names containing
 "M" are male. Genotyping-by-sequencing libraries were
 constructed with restriction enzymes EcoRI and MseI, with a selective
 nucleotide on the MseI PCR primer. Single-end Illumina reads were aligned
 to a low-coverage draft genome of H. arborea, and SNPs called with
 SAMtools. Raw genotypes were filtered based on genotype quality, missing
 data, and minor allele frequency.HylaDmrt1.variants.vcf.gzHyla Dmrt1 exon 1 phased alignmentAlignment of Dmrt1 exon 1 and upstream sequences of five Hyla species. Phased X and Y haplotypes were determined with PHASE software. All sites containing indel variation within or between species were removed. All sequences ending in "X" or "Y" could be assigned to the X or Y chromosome. See readme file for key to sample names.dmrt1ex1PHASE.fasHyla Dmrt1 exon 3 phased alignmentAlignment of Dmrt1 exon 3 and adjacent partial intron sequences of five Hyla species. Phased X and Y haplotypes were determined with PHASE software. All sites containing indel variation within or between species were removed. All sequences ending in "X" or "Y" could be assigned to the X or Y chromosome. See readme file for key to sample names.Dmrt1Ex3PHASE.fasHyla Kank1 intron 10 phased alignmentAlignment of Kank1 intron 10 sequences of five Hyla species. Phased X and Y haplotypes were determined with PHASE software. All sites containing indel variation within or between species were removed. All sequences ending in "X" or "Y" could be assigned to the X or Y chromosome. See readme file for key to sample names.kank1intron10.PHASE.fas