This Dryad package contains data used in: "Comparative analysis suggests that polyploidy does not decelerate diversification in fish" by Shing H. Zhan, Lior Glick, Costas S. Tsigenopoulos, Sarah P. Otto, and Itay Mayrose 1) The folder, 'data', contains sequence data and chromosome number data for the fish groups examined, each with its own folder. a) 'Acipenseridae' b) 'Botiidae' c) 'Cyprininae' d) 'Salmoniformes' Each of the above folders contains 2 sub-folders: 'current' and 'rabosky'. 1.1) File extensions in 'current': *.bisse - ploidy level estimates used as input to BiSSE analysis *.fac - per-taxon chromosome number data in FASTA-like format *.mb_in - commands used to run MrBayes analysis *.mb_trees - MrBayes trees in Newick format *.mb_tree.pruned.con.newick - 50% majority-rule consensus tree summarizing outgroup-pruned MrBayes trees *.mb_tree.shuffled.pruned - randomly shuffled outgroup-pruned MrBayes trees used for BiSSE analysis *_parsed.aln - MUSCLE alignment of sequence data in FASTA format *_parsed.fa - sequence data in FASTA format *_parsed.modeltest - results of jModelTest on MUSCLE alignment *_parsed.nxs - MUSCLE alignment of sequence data in NEXUS format 1.1.1) 'Acipenseridae' contains 'partitions', which holds per-locus *.aln, *.fa, and *.modeltest files. 1.1.2) 'Cyprininae' contains 'partitions', which holds sequence data for each major lineage within Cyprininae. 1.2) File extensions in 'rabosky': *.bisse - ploidy level estimates used as input to BiSSE analysis *.fac - per-taxon chromosome number data in FASTA-like format (only for Cyprininae) *.tree - subtree extracted from the time-calibrated megaphylogeny published by Rabosky et al. (2013; available at doi:10.5061/dryad.j4802) 2) A text file 'TableS2_Cyprininae_data.txt' is a tab-delimited version of Table S2 found in the Supplementary Materials document.