Data from: Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting

Alda F, Tagliacollo VA, Bernt MJ, Waltz BT, Ludt WB, Faircloth BC, Alfaro ME, Albert JS, Chakrabarty P

Date Published: December 28, 2018

DOI: https://doi.org/10.5061/dryad.k57430s.2

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Title Online Appendix 1
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Description Extended Methods section including: DNA Extraction and Library Preparation, and Target Enrichment and Sequencing of UCEs.
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Title Online Appendix 2
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Description Extended Methods section including: Assembly and Alignment of Sequence Capture Data.
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Title gymno_full_dataset_min75_complete
Downloaded 2 times
Description Individual UCE loci alignments that are common to at least 75% of taxa in the full dataset of Gymnotiformes (966 loci, 47 taxa). Codes for individual names in README.
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Title gymno_reduced_dataset_min75_complete
Description Individual UCE loci alignments that are common to at least 75% of taxa in the reduced dataset of Gymnotiformes (1472 loci, 11 taxa). Name codes in README.txt.
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Title gymno_reduced_dataset_100_complete
Downloaded 1 time
Description Individual UCE loci alignments that are common to 100% of taxa in the reduced dataset of Gymnotiformes (368 loci, 11 taxa). Codes for individual names in README.
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Title gymno_full_dataset_min75_concatenated.nex
Downloaded 1 time
Description Concatenated matrix of UCE loci in common to at least 75% of taxa in the Gymnotiformes full dataset. Code names in README.txt.
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Title gymno_reduced_dataset_min75_concatenated
Downloaded 3 times
Description Concatenated matrix of UCE loci in common to at least 75% of taxa in the Gymnotiformes reduced dataset. Code names in README.txt.
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Title gymno_reduced_dataset_100_concatenated
Downloaded 1 time
Description Concatenated matrix of UCE loci in common to at least 100% of taxa in the Gymnotiformes reduced dataset. Code names in README.txt.
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Title Aldaetal_SystBio_SupplMat
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Description Supplementary Tables S1-S4, and Supplementary Figures S1-S16.
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Title all_gene_trees
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Description All gene trees (best and bootstrapped) inferred in RAxML for each individual UCE locus for the full and reduced taxon sets. Contents in README.
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Title pruned_gene_trees
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Description All gene trees (best and bootstrapped) inferred in RAxML for all the filtered datasets. Contents in README.
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When using this data, please cite the original publication:

Alda F, Tagliacollo VA, Bernt MJ, Waltz BT, Ludt WB, Faircloth BC, Alfaro ME, Albert JS, Chakrabarty P (2018) Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting. Systematic Biology, online in advance of print. https://doi.org/10.1093/sysbio/syy085

Additionally, please cite the Dryad data package:

Alda F, Tagliacollo VA, Bernt MJ, Waltz BT, Ludt WB, Faircloth BC, Alfaro ME, Albert JS, Chakrabarty P (2018) Data from: Resolving deep nodes in an ancient radiation of neotropical fishes in the presence of conflicting signals from incomplete lineage sorting. Dryad Digital Repository. https://doi.org/10.5061/dryad.k57430s.2
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