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National Academy of Sciences, Proceedings of the National Academy of Sciences, 52(117), p. 33396-33403, 2020

DOI: 10.1073/pnas.2006511117

figshare, 2020

DOI: 10.6084/m9.figshare.13000100.v1

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Evolutionary determinism and convergence associated with water-column transitions in marine fishes

Journal article published in 2020 by Melissa Rincon-Sandoval ORCID, Emanuell Duarte-Ribeiro ORCID, Aaron M. Davis ORCID, Aintzane Santaquiteria ORCID, Lily C. Hughes ORCID, Carole C. Baldwin ORCID, Luisángely Soto-Torres ORCID, Arturo Acero P. ORCID, H. J. Walker ORCID, Kent E. Carpenter ORCID, Marcus Sheaves ORCID, Guillermo Ortí ORCID, Dahiana Arcila ORCID, Ricardo Betancur-R.
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Usage NotesAlignments- Lutjanidae_Expanded_duplicates.phy: Concatenated nucleotide alignment – 1,115 exon alignments, 132 species, 474,132 nucleotide sites.- Lutjanidae_Expanded.phy: Concatenated nucleotide alignment – 1,115 exon alignments, 110 species, 474,132 nucleotide sites.- Lutjanidae_Reduced.phy: Concatenated nucleotide alignment – 1,047 exon alignments, 103 species, 448,410 nucleotide sites.TreeFiles- Lutjanidae_Expanded_BestTrees: 28 expanded best trees inferred with RAxML and ASTRAL-II.- Lutjanidae_Expanded_Calibrated_Trees_NoOutgroup: 28 Lutjanidae-only calibrated trees inferred with MCMCTree.- Lutjanidae_Calibrated_Trees_Outgroup: 28 Haemulidae-Lutjanidae expanded calibrated trees, 2 Haemulidae-Lutjanidae reduced calibrated trees inferred with MCMCTree.ScriptsScripts and input data used for macroevolutionary analyses. Note that some of the R_codes file codes are adaptations of the original scripts provided by packages developers (See references). Includes the Threshold model, mvMORPH, Wheatsheaf, convevol, HiSSE, StereoMorph, L1OU, SURFACE, BioGeoBEARS.Additionally, three sub-folders are included: - BioGeoBEARS: input data for 3 and 6 areas (areas_allowed, code_areas, dispersal_multipliers, time periods)- MCMCTreeFiles: files for running divergence time estimation in MCMCTree.- StereoMorph: files for running StereoMorph R code.