Dataset from: Rapid radiation of ant parasitic butterflies during the Miocene aridification of Africa

Description of the files: 2_PHASED_ALIGNMENTS: Individual phased alignments used as input to produce gene trees in IQ-TREE. In fasta format.-- 3_UNPHASED_ALIGNMENTS: Individual alignments used to produce the full ML tree. In fasta format.-- 4_CONCATENATED_ALIGNMENT: The full concatenated alignment i...

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Detalles Bibliográficos
Autores: Espeland, Marianne, Chazot, Nicolas, Condamine, Fabien L., Lemmon, Alan R., Moriarty Lemmon, Emily, Pringle, Ernest, Heath, Alan, Collins, Steve C., Tiren, Wilson, Mutiso, Martha, Lees, David C., Fisher, Stewart, Murphy, Raymond, Woodhall, Stephen, Tropek, Robert, Baker, Christopher C. M., Ahlborn, Svenja S., Cockburn, Kevin, Dobson, Jeremy, Bouyer, Thierry, Kaliszewska, Zofia A., Talavera, Gerard, Vila, Roger, Gardiner, Alan J., Williams, Mark, Martins, Dino J., Sáfián, Szabolcs, Edge, David A., Pierce, Naomi E.
Tipo de recurso: conjunto de datos
Fecha de publicación:2023
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/347503
Acceso en línea:http://hdl.handle.net/10261/347503
Access Level:acceso abierto
Palabra clave:Butterfly-ant interactions
Lepidochrysops
Lycaenidae
Myrmecophagy
Phytopredation
Descripción
Sumario:Description of the files: 2_PHASED_ALIGNMENTS: Individual phased alignments used as input to produce gene trees in IQ-TREE. In fasta format.-- 3_UNPHASED_ALIGNMENTS: Individual alignments used to produce the full ML tree. In fasta format.-- 4_CONCATENATED_ALIGNMENT: The full concatenated alignment in phylip format and a .nex file with the models and partition scheme.-- 5_DATING: Concatenated reduced alignment in phylip format and the fixed input tree in Newick format used for dating. Taxon names were renamed since MCMCtree cannot handle taxon names longer than 49 characters. The file Rename.txt can be used to rename files back to the original names using sed: sed -f Rename.txt file > renamed_file. Convergence_plots.pdf contains plots of the mean age and upper and lower 95% highest posterior density (HPD) credibility intervals of two and two MCMCtree runs against each other to assure convergence of MCMC chains.-- 6_GENETREES: Genetrees used for input in ASTRAL. In Newick format.-- 7_FINAL_TREES: The ASTRAL species tree (Fig. S2), full ML tree (Fig. S1) and reduced, dated ML tree (Fig. 1, Fig. S4), with only on specimen included per species. The dated tree is in nexus format, and the others in Newick format.

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