Supplementary Data for the manuscript "Male sterility in Drosophila mojavensis × D. arizonae hybrids is not caused by gene movements in the Y chromosome" (T. Vanderlinde et al.)

This Figshare record contains all data and scripts associated with our investigation of Y chromosome gene content in Drosophila arizonae, D. mojavensis, and related species. The files here support the findings described in our manuscript, where we explored the hypothesis that an essential male fertility gene might have moved from the Y chromosome to an autosome in the D. arizonae lineage.1. Annotation and Alignment of GI18320 OrthologsFile: G18320_repletagrp_cds6.fastaAnnotated coding sequences (CDS) of the GI18320 ortholog in D. navojoa, D. adrichi, D. buzzatii, and D. repleta. These species provide a comparative framework increasingly distant from our focal species D. arizonae and D. mojavensis.File: GI18320_repletagrp_cds8_aln.fasAlignment of the above CDS, with poorly aligned regions removed. Two gaps were introduced in the D. mojavensis autosomal pseudogene to correct the reading frame.2. HyPhy Analysis ScriptFile: GI18320_v11.bfImplements dN/dS estimation and hypothesis testing using HyPhy (Kosakovsky Pond et al. 2005; Windows version 2.2.4). The best-fitting substitution model (HKY85, coded as 010010) was automatically selected by HyPhy.3. Corrected Reference TranscriptomesWe provide four corrected reference transcriptomes for each species—D. mojavensis, D. arizonae, D. navojoa, and D. virilis:Files:moj_all_cds_corrected.fastaari_all_cds_corrected.fastanav_all_cds_corrected.fastavir_all_cds_corrected.fastaThese transcriptomes had all sequences corresponding to the 14 annotated Y-linked genes removed using cd-hit-est-2d (Li and Godzik 2006). The correctly annotated Y-linked genes were then reintroduced, and RSEM was run to quantify expression.4. Y-linked SequencesFile: Y-linkedgenes_CDS_moj_ari_navIncludes the Y-linked sequences for D. mojavensis, D. arizonae, and D. navojoa, used to confirm the presence or copy number of these genes across species.5. YGS resultsWe provide the results generated by the YGS (Y-chromosome Genome Scan) procedure for each of the three focal species:moj_YGS_output.txtnavojoa_YGS_output.txtari_YGS_output.txtThese datasets and scripts enable the replication of our analyses on Y-linked genes, their copy numbers, and their evolutionary dynamics in the D. repleta species group. For additional details on methodology, please refer to the Methods section of our manuscript.