Data from: Convergent regulatory evolution and loss of flight in palaeognathous birds

A core question in evolutionary biology is whether convergent phenotypic evolution is driven by convergent molecular changes in proteins or regulatory regions. We combined phylogenomic, developmental, and epigenomic analysis of 11 new genomes of paleognathous birds, including an extinct moa, to show that convergent evolution of regulatory regions, more so than protein-coding genes, is prevalent among developmental pathways associated with independent losses of flight. A Bayesian analysis of 284,001 conserved noncoding elements, 60,665 of which are corroborated as enhancers by open chromatin states during development, identified 2355 independent accelerations along lineages of flightless paleognaths, with functional consequences for driving gene expression in the developing forelimb. Our results suggest that the genomic landscape associated with morphological convergence in ratites has a substantial shared regulatory component.README_MAINAssemblies and associated code and log files01_assembly.tar.gzGenome annotations and associated files02_annotation.tar.gzHomology calls and associated files03_homology.tar.gzWhole genome alignment and associated files04_whole_genome_alignment.tar.gzPhylogenomic datasets and associated code05_phylogenomics.tar.gzDatasets for protein-coding gene analysis06_protein_coding_datasets.tar.gzScripts and associated files for the analysis of protein-coding genes06_protein_coding_scripts.tar.gzResults from protein-coding analysis06_protein_coding_results.tar.gzScripts and associated files for CNEE analysis07_cnee_scripts.tar.gzDatasets for CNEE analysis07_cnees_datasets.tar.gzResults of PhyloAcc analysis of CNEEs07_cnees_phyloAcc_results.tar.gzParsed CNEE analysis files and output07_cnees_processed.tar.gzData and results from ATAC-seq08_ATACseq.tar.gzAssembly fasta filesAll new assemblies; these are the pre-Genbank versions used for our analysisassemblies.tar.gzConserved element BED filesBED files of conserved elements and CNEEs on both galGal4 and galGal5 coordinatescons_elem_beds.tar.gzEnhancer screen image filesraw images associated with in vivo tests of enhancer functionenhancer_screen_images.zipATAC-seq peak callsATAC-seq peaks called on galGal4 coordinates from a variety of tissues and time points (in chicken)final_consistent_peaks.tar.gzAnnotations in GFF formatgene annotations for each new assembly in GFF3 formatgffs.tar.gzAligned protein sequences (expanded set)Protein alignments from homology groups estimated across birds (including new palaognaths). The expanded set includes additionally sequences from moa and flightless cormorant.HOG_fastas_aligned_filtered_expanded.tar.gzCodon alignments (expanded set)Codon alignments (produced with PRANK) from homology groups estimated across birds (including new palaognaths). The expanded set includes additionally sequences from moa and flightless cormorant.PAML_final_PRANK_fastas_expanded.tar.gzCodon alignmentsCodon alignments (produced with PRANK) from homology groups estimated across birds (including new palaognaths).PAML_final_PRANK_fastas_original.tar.gzAligned protein sequences (expanded set)Protein alignments from homology groups estimated across birds (including new palaognaths).HOG_fastas_aligned_filtered_original.tar.gzProtein FASTA filesFASTA files of annotated proteins from new genomes. One file per genome.protein_fastas.tar.gzSpecies treesSpecies trees in Newick formatspecies_trees.tar.gzTranscript FASTA filesTranscript sequences for newly annotated genomes in FASTA format. One file per species.transcript_fastas.tar.gzFunding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB-135534