Data from: Trans-species variation in Dmrt1 is associated with sex determination in four European tree-frog species

Brelsford A, Dufresnes C, Perrin N

Date Published: February 17, 2016

DOI: http://dx.doi.org/10.5061/dryad.4tb10

 

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Title Hyla GBS genotypes in gzip-compressed VCF format
Downloaded 1 time
Description The 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.
Download HylaDmrt1.variants.vcf.gz (4.507 Mb)
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Title Hyla Dmrt1 exon 1 phased alignment
Downloaded 2 times
Description Alignment 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.
Download README.txt (335 bytes)
Download dmrt1ex1PHASE.fas (14.86 Kb)
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Title Hyla Dmrt1 exon 3 phased alignment
Downloaded 1 time
Description Alignment 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.
Download README.txt (364 bytes)
Download Dmrt1Ex3PHASE.fas (24.44 Kb)
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Title Hyla Kank1 intron 10 phased alignment
Description Alignment 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.
Download README.txt (363 bytes)
Download kank1intron10.PHASE.fas (21.80 Kb)
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When using this data, please cite the original publication:

Brelsford A, Dufresnes C, Perrin N (2016) Trans-species variation in Dmrt1 is associated with sex determination in four European tree-frog species. Evolution 70(4): 840–847. http://dx.doi.org/10.1111/evo.12891

Additionally, please cite the Dryad data package:

Brelsford A, Dufresnes C, Perrin N (2016) Data from: Trans-species variation in Dmrt1 is associated with sex determination in four European tree-frog species. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.4tb10
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