Data from: Explosive diversification of marine fishes at the Cretaceous-Paleogene boundary

Alfaro ME, Faircloth BC, Harrington RC, Sorenson L, Friedman M, Thacker CE, Oliveros CH, Černý D, Near TJ

Date Published: March 12, 2018

DOI: https://doi.org/10.5061/dryad.085dd

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Title 1-All-Assembled-Contigs.tar
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Description All contigs assembled from target-enriched sequence data. Also be sure to see NCBI BioProject PRJNA348720 and NCBI Targeted Locus Study database KALI00000000-KAPX00000000.
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Title 2-Assembled-Contigs-That-Are-UCEs.tar
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Description Of the assembled contigs in 1-All-Assembled-Contigs.tar.gz, these are the loci, for each species, that are targeted UCE loci.
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Title 3-All-Alignments-Untrimmed.tar
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Description These are all alignments generated as part of this manuscript. Manuscripts in this archive are UNTRIMMED (we used TRIMMED alignments in the manuscript - see 4-95p-Trimmed-Alignments.tar.gz and 5-75p-Trimmed-Alignments.tar.gz for those).
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Title 4-95p-Trimmed-Alignments.tar
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Description These are the trimmed alignments used in analyses of the 95% complete (95p) data set.
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Title 5-75p-Trimmed-Alignments.tar
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Description These are the trimmed alignments used in analyses of the 75% complete (75p) data set.
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Title 6-95p-Concatenated-Alignment-For-Analysis.tar
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Description Contains the concatenated loci from the 95% (95p) complete data set.
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Title 7-75p-Concatenated-Alignment-For-Analysis.tar
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Description Contains the concatenated loci from the 75% (75p) complete data set.
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Title 8-75p-Concatenated-RAxML-Analyses.tar
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Description RAxML Analysis files for the 75% (75p) complete data set. Includes unpartitioned, partitioned, and RY-coded analyses.
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Title 9-95p-Concatenated-ExaBayes-Analyses.tar
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Description ExaBayes analysis files for the 95% (95p) complete data set. Includes unpartitioned and partitioned analyses.
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Title 10-75p-Concatenated-ExaBayes-Analyses.tar
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Description ExaBayes analysis files for the 75% (75p) complete data set. Includes unpartitioned and partitioned analyses.
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Title 11-75p-Astral-Analyses.tar
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Description Astral analysis files for the 75% (75p) complete data set.
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Title 12-All-Phylo-Trees.tar
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Description All phylogenetic trees from this manuscript, in a variety of formats.
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Title 13-95p-Rate-Based-Partition-For-PAML.tar
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Description Files used for rate-based partitioned of the 95% complete (95p) concatenated data, prior to analysis using PAML.
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Title 14-PAML-Inputs.tar
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Description Input files (alignments, guide trees, control files) for all PAML dating analyses (baseml and mcmctree).
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Title 15-Dated-Tree.tar
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Description The dated tree resulting from mcmctree analysis.
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Title 16-Dating-Figures-Inputs.tar
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Description Tabular (CSV) output from mcmctree analyses that form the basis of Figures 5, S7, and S8, along with a description of steps used in R to plot the figures.
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Title README-Data-Processing-Analysis-Steps
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Description A description of the steps used to assemble the data, prepare them for phylogenetic analysis, and run analyses.
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Title README-Tree-Figure-Formatting-for-Supplement
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Description A description of the steps used to format trees for the Supplement (specifically, Figures S1-S5).
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Title fish-uce-1k-probes.MyBaits.UCE-Acanthomorphs.1Kv1.fasta
Downloaded 5 times
Description Design file for Acanthomorph baits. Also available as bait set from Arbor Biosciences (UCE-Acanthomorphs 1Kv1). Additionally same as bait set design file used in https://doi.org/10.5061/dryad.9pg8d.
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When using this data, please cite the original publication:

Alfaro ME, Faircloth BC, Harrington RC, Sorenson L, Friedman M, Thacker CE, Oliveros CH, Černý D, Near TJ (2018) Explosive diversification of marine fishes at the Cretaceous-Paleogene boundary. Nature Ecology & Evolution 2(4): 688–696. https://doi.org/10.1038/s41559-018-0494-6

Additionally, please cite the Dryad data package:

Alfaro ME, Faircloth BC, Harrington RC, Sorenson L, Friedman M, Thacker CE, Oliveros CH, Černý D, Near TJ (2018) Data from: Explosive diversification of marine fishes at the Cretaceous-Paleogene boundary. Dryad Digital Repository. https://doi.org/10.5061/dryad.085dd
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