Data and Supplementary Files From: Phylogenomics, Biogeography, and a New Family-level Classification of Silversides, Rainbowfishes, and Allies (Teleostei: Atheriniformes)

Data and Supplementary Files From: Phylogenomics, Biogeography, and a New Family-level Classification of Silversides, Rainbowfishes, and Allies (Teleostei: Atheriniformes) Data Phylogenomic_analyses.zip Internal folders are organized by analysis number in Table 1 of the main manuscript. Each folder contains the input data and resulting tree of that analysis. biogeography.zip Contains the R code, input files, and output files for all BioGeoBears analyses. beast.zip Contains the xml and consensus trees for both BEAST configurations, using the concatenated and ASTRAL topologies. gene_alignments.zip Individual gene alignments for all exons, loci added from GenBank, and the loci selected for the dating analysis in BEAST. Supplemental Figures Supplemental Figures S1-31 Figures S1-S19 reference the analyses listed in Table 1 of the main manuscript. Figures S20-S31 show additional BioGeoBears results. 1. S1: Maximum likelihood phylogeny of all nucleotides (Table 1: analysis 1)2. S2: Maximum likelihood phylogeny of G75 nucleotide matrix (Table 1: analysis 2)3. S3: Maximum likelihood phylogeny of G90 nucleotide matrix (Table 1: analysis 3)4. S4: Maximum likelihood phylogeny of all amino acids (Table 1: analysis 4)5. S5: Maximum likelihood phylogeny of G75 amino acid matrix (Table 1: analysis 5)6. S6: Maximum likelihood phylogeny of G90 amino acid matrix (Table 1: analysis 6)7. S7: Maximum likelihood phylogeny of Atherinoidei using all nucleotides with Atherionidae excluded and reduced outgroups (Table 1: analysis 7)8. S8: Maximum likelihood phylogeny of Atherinoidei using all nucleotides with Isonidae excluded and reduced outgroups (Table 1: analysis 8)9. S9: Maximum likelihood phylogeny of Atherinoidei using all nucleotides with Phallostethidae excluded and reduced outgroups (Table 1: analysis 9)10. S10: Maximum likelihood phylogeny of Atherinoidei using all nucleotides with reduced outgroups (Table 1: analysis 10)11. S11: Maximum likelihood phylogeny of Atherinoidei using the G75 matrix with reduced outgroups (Table 1: analysis 11)12. S12: Maximum likelihood phylogeny of Atherinoidei using the G90 matrix with reduced outgroups (Table 1: analysis 12)13. S13: Maximum likelihood phylogeny of Atherinoidei using the G75 matrix with reduced outgroups under the GHOST model (Table 1: analysis 13)14. S14: ASTRAL species tree estimated from all gene trees (Table 1: analysis 14)15. S15: ASTRAL species tree estimated from G75 gene trees (Table 1: analysis 15)16. S16: ASTRAL species tree estimated from G90 gene trees (Table 1: analysis 16)17. S17: ASTRAL species tree of Atherinoidei estimated from all gene trees with reduced outgroups (Table 1: analysis 17)18. S18: ASTRAL species tree of Atherinoidei estimated from G75 gene trees with reduced outgroups (Table 1: analysis 18)19. S19: ASTRAL species tree of Atherinoidei estimated from G90 gene trees with reduced outgroups (Table 1: analysis 19)20. S20: Most likely ancestral states from DEC model on the concatenated Atherinopsidae topology21. S21: Inferred ancestral states as pie charts from the DEC model on the concatenated Atherinopsidae topology22. S22: Most likely ancestral states from DEC model on the MSC Atherinopsidae topology23. S23: Inferred ancestral states as pie charts from DEC model on the MSC Atherinopsidae topology24. S24: Estimated ancestral states for Atherinoidei under the DEC model using the MSC topology25. S25: Estimated ancestral states as pies for Atherinoidei under the DEC model using the MSC topology26. S26: Estimated ancestral states for Atherinoidei under the DEC model using the MSC topology27. S27: Estimated ancestral states as pies for Atherinoidei under the DEC model using the MSC topology28. S28: Estimated ancestral states for Atherinoidei under the DEC model using the concatenated topology29. S29: Estimated ancestral states as pies for Atherinoidei under the DEC model using the concatenated topology30. S30: Estimated ancestral states for Atherinoidei under the DEC model using the concatenated topology31. S31: Estimated ancestral states as pies for Atherinoidei under the DEC model using the concatenated topology