Data from: Phylogenomic systematics of Ostariophysan fishes: ultraconserved elements support the surprising non-monophyly of Characiformes

Chakrabarty P, Faircloth BC, Alda F, Ludt WB, McMahan CD, Near TJ, Dornberg A, Albert JS, Arroyave J, Stiassny MLJ, Sorenson L, Alfaro ME

Date Published: February 27, 2017

DOI: http://dx.doi.org/10.5061/dryad.n9g60

 

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Title alignment-data.tar.gz
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Description Alignment data for concatenated and coalescent-based analyses. Contents in README.
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Title all-contigs-by-taxon.tar.gz
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Description All contigs assembled by Trinity for each taxon in the data set. FASTA format by taxon. Contents in README.
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Title astral.tar.gz
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Description Gene trees and results from coalescent-based (ASTRAL) analyses. Contents in README.
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Title bayesian-analyses.tar.gz
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Description All files (samples, parameter estimates, convergence metrics, etc.) from Bayesian analyses. Contents in README.
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Title fish-uce-1k-probes.tar.gz
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Description Probe set used for UCE enrichment.
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Title ml-analyses.tar.gz
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Description All files (best trees, bootreps) from maximum likelihood analyses. Contents in README.
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Title taxon-set.txt
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Description The taxon set file for use with PHYLUCE.
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Title tip-name-remappings.txt
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Description A text file for PHYLUCE that we used to rename tips in each of the trees to fix taxonomy issues, incorrect spellings, etc.
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Title trees.tar.gz
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Description All trees generated for this manuscript. In newick format. Contents in README.
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Title uce-contigs-by-taxon.tar.gz
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Description All UCE contigs identified for each taxon. FASTA format by taxon. Contents in README.
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Title processing-steps.txt
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Description Text file with step-by-step description of data processing.
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Title TableS1.xlsx
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Description Supplemental Table 1: Number of reads, total number of base pairs sequenced, mean length of adapter- and quality-trimmed reads, 95 CI of trimmed read length, minimum read length, maximum read length, and median length for reads sequenced, by platform, from ostariophysan libraries enriched for UCEs (table also includes outgroup taxa, indicated with an asterisk).
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Title TableS2.xlsx
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Description Supplemental Table 2: Number of contigs assembled, total number of base pairs sequenced, mean contig length, 95 CI of contig length, minimum contig length, maximum contig length, median contig length, and number of contigs > 1 Kb in length from reads sequenced, by platform, from ostariophysan libraries enriched for UCEs (table also includes outgroup taxa, indicated with an asterisk).
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Title TableS3.xlsx
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Description Supplemental Table 3: Number of UCE loci enriched, total number of base pairs in all UCE loci, mean length of UCE loci, 95 CI of UCE locus length, minimum UCE locus length, maximum UCE locus length, median UCE locus length, number of UCE loci having a length > 1 Kb, UCE locus coverage, percentage of reads on-target, and percentage of on-target reads that were unique from reads assembled, by platform, from ostariophysan libraries enriched for UCEs (table also includes outgroup taxa, indicated with an asterisk). We collected Danio rerio UCE data from the danRer7 genome assembly.
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Title Fig_S1.pdf
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Description Supplemental Figure 1: Morphology based ML and Bayesian phylogeny. Support values on every node was (BPP >0.99 and bootstrap support of 100).
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Title Fig_S2.pdf
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Description Supplemental Figure 2: Results from ML analyses of ostariophysans using ultraconserved elements, with 50% complete data coverage, data not partitioned but concatenated.
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Title Fig_S3.pdf
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Description Supplemental Figure 3. Results from Bayesian analyses of ostariophysans using ultraconserved elements, with 50% complete data coverage, partitioned and concatenated.
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Title Fig_S4.pdf
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Description Supplemental Figure 4. Results from ML analyses of ostariophysans using ultraconserved elements, with 50% complete data coverage, partitioned and concatenated.
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Title Fig_S5.pdf
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Description Supplemental Figure 5: Results from ML analyses of ostariophysans using ultraconserved elements, with 75% complete data coverage, not partitioned but concatenated.
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Title Fig_S6.pdf
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Description Supplemental Figure 6: Results from ML and Bayesian analyses of ostariophysans using ultraconserved elements, with 75% complete data coverage, partitioned, and all data concatenated.
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Title Fig_S7.pdf
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Description Supplemental Figure 7: ASTRAL phylogeny of ostariophysans using ultraconserved elements with 50% data coverage, using a coalescent species tree approach. Internodes that were found to potentially be in the anomaly zone are shown with dashed lines (see text).
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Title Fig_S8.pdf
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Description Supplemental Figure 8: Result from a Bayesian analysis using ultraconserved elements (partitioned) and morphology, with 50% complete UCE data coverage.
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Title Fig_S9.pdf
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Description Supplemental Figure 9: Result from a ML analysis using ultraconserved elements (partitioned) and morphology, with 50% complete UCE data coverage.
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Title Fig_S10.pdf
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Description Supplemental Figure 10: Result from a Bayesian analysis using ultraconserved elements (partitioned) and morphology, with 75% complete UCE data coverage.
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Title Fig_S11.pdf
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Description Supplemental Figure 11: Result from a ML analysis using ultraconserved elements (partitioned) and morphology, with 75% complete UCE data coverage.
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When using this data, please cite the original publication:

Chakrabarty P, Faircloth BC, Alda F, Ludt WB, McMahan CD, Near TJ, Dornburg A, Albert JS, Arroyave J, Stiassny ML, Sorenson L, Alfaro ME (2017) Phylogenomic systematics of Ostariophysan fishes: ultraconserved elements support the surprising non-monophyly of Characiformes. Systematic Biology, online in advance of print. http://dx.doi.org/10.1093/sysbio/syx038

Additionally, please cite the Dryad data package:

Chakrabarty P, Faircloth BC, Alda F, Ludt WB, McMahan CD, Near TJ, Dornberg A, Albert JS, Arroyave J, Stiassny MLJ, Sorenson L, Alfaro ME (2017) Data from: Phylogenomic systematics of Ostariophysan fishes: ultraconserved elements support the surprising non-monophyly of Characiformes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.n9g60
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