Data from: Earth history and the passerine superradiation

Oliveros CH, Field DJ, Ksepka DT, Barker FK, Aleixo A, Andersen MJ, Alström P, Benz BW, Braun EL, Braun MJ, Bravo GA, Brumfield RT, Chesser RT, Claramunt S, Cracraft J, Cuervo AM, Derryberry EP, Glenn TC, Harvey MG, Hosner PA, Joseph L, Kimball RT, Mack AL, Miskelly CM, Peterson AT, Robbins MB, Sheldon FH, Silveira LF, Smith BT, White ND, Moyle RG, Faircloth BC

Date Published: April 1, 2019

DOI: https://doi.org/10.5061/dryad.2vd01gr

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Title Supplementary File S1
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Description Sampling and sequence data characteristics
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Title Supplementary File S2
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Description Phylogenetic tree files in nexus format from concatenation and coalescent analyses of the entire dataset and subsets of the data matrix.
Download File-S2.trees.tar.gz (138.1 Kb)
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Title Supplementary File S3
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Description Subsampling and trimming strategy for phylogenetic analysis
Download File S3.xlsx (21.14 Kb)
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Title Concatenated alignment
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Description Concatenated alignment of 4,060 UCE loci for 221 individuals in nexus format. Charset definition of each UCE locus included. Each UCE locus aligned with MAFFT, trimmed with Gblocks and contains sequence data for at least 80% of individuals.
Download passerines.concatenated.align.nex.gz (144.1 Mb)
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Title Figure 1 tree file
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Description Figure 1 annotated tree file
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Title RAxML gene trees
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Description Newick file of gene trees estimated using RAxML
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Title Files for dating analyses in BEAST, MCMCTree
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Description Files for dating analyses in BEAST (BEAUTI files and nucleotide data sets) and MCMCTree (control files and calibrated tree file)
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Title BioGeoBEARS files
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Description Input and output files for BioGeoBEARS analyses, including input tree files, geographic area files, dispersal multiplier files, Rdata output files, and output pdf files. BioGeoBEARS scripts are available on Github (https://github.com/carloliveros/passerines); these scripts cannot be hosted on Dryad because of copyright issues.
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Title Data assembly notes
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Description Notes on data assembly with PHYLUCE
Download assembly notes passerines.txt (68.88 Kb)
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Title Unaligned UCE contigs
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Description Unaligned UCE contigs grouped by taxon in fasta format
Download passerines.unaligned.uce.contigs.tar.gz (241.5 Mb)
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Title Diversification analysis files
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Description Files used in diversification analyses in Revbayes and BAMM, including Revbayes and R scripts and summary of parameter estimates in Revbayes
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Title Passerines per locus alignments gbtrimmed 80%
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Description Per locus alignments of UCE sequences aligned with MAFFT and trimmed with Gblocks, each locus containing sequences for at least 80% of 221 taxa.
Download passerines.individual.alignments.gbtrimmed...ar.gz (40.42 Mb)
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Title Passerines per locus alignments untrimmed and unfiltered
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Description Per locus alignments of UCE sequences, no Gblocks trimming, no minimum number of taxa per locus
Download passerines.individual.alignments.untrimmed...ar.gz (50.77 Mb)
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Title Passerines per locus alignments gbtrimmed unfiltered
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Description Per locus alignments of UCE sequences trimmed with Gblocks, no minimum number of taxa per locus.
Download passerines.individual.alignments.gbtrimmed...ar.gz (44.40 Mb)
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When using this data, please cite the original publication:

Oliveros CH, Field DJ, Ksepka DT, Barker FK, Aleixo A, Andersen MJ, Alström P, Benz BW, Braun EL, Braun MJ, Bravo GA, Brumfield RT, Chesser RT, Claramunt S, Cracraft J, Cuervo AM, Derryberry EP, Glenn TC, Harvey MG, Hosner PA, Joseph L, Kimball RT, Mack AL, Miskelly CM, Peterson AT, Robbins MB, Sheldon FH, Silveira LF, Smith BT, White ND, Moyle RG, Faircloth BC (2019) Earth history and the passerine superradiation. Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.1813206116

Additionally, please cite the Dryad data package:

Oliveros CH, Field DJ, Ksepka DT, Barker FK, Aleixo A, Andersen MJ, Alström P, Benz BW, Braun EL, Braun MJ, Bravo GA, Brumfield RT, Chesser RT, Claramunt S, Cracraft J, Cuervo AM, Derryberry EP, Glenn TC, Harvey MG, Hosner PA, Joseph L, Kimball RT, Mack AL, Miskelly CM, Peterson AT, Robbins MB, Sheldon FH, Silveira LF, Smith BT, White ND, Moyle RG, Faircloth BC (2019) Data from: Earth history and the passerine superradiation. Dryad Digital Repository. https://doi.org/10.5061/dryad.2vd01gr
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