Project Abstract: Sex determination occurs across animal species, but most of our knowledge about the mechanisms of sex determination comes from only a handful of bilaterian taxa. This limits our ability to infer the evolutionary history of sex determination within animals. In this study, we generated a linkage map of the genome of the colonial cnidarian Hydractinia symbiolongicarpus and used this map to determine that this species has an XX/XY sex determination system. We delineate the pseudoautosomal and non-recombining regions of the Y chromosome and show that the latter encodes a number of genes with male gonad-specific expression. These findings establish Hydractinia as a tractable non-bilaterian model system for the study of sex determination. This archive contains supplemental data files for "XY sex determination in a cnidarian" by Chen et. al. The manuscript will be submitted to bioRxiv. 160429_CRATOS_HKM5MBCXX.lane1.12268798.read1.DOWNSAMPLE_0.2.fq.gz: Illumina reads for paternal genome downsampled with seqtk. 160429_CRATOS_HKM5MBCXX.lane1.12268798.read2.DOWNSAMPLE_0.2.fq.gz: Illumina reads for paternal genome downsampled with seqtk. rawvariants.90f1.vcf.gz: Raw genotypes for all 90 offspring and the two parents, called by GATK HaplotypeCaller GATKBP-passed.vcf.gz: Genotypes quality filtered according to GATK best practices and custom critera. GATKBP-passed.femaleHet.abxabRemoved.vcf.gz: Genotypes suitable for mapping the maternal genome with a pseudo-testcross strategy. GATKBP-passed.maleHet.abxabRemoved.vcf.gz: Genotypes suitable for mapping the paternal genome with a pseudo-testcross strategy.