Data from: How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in iguanian lizards

Streicher JW, Schulte JA, Wiens JJ

Date Published: August 10, 2015

DOI: http://dx.doi.org/10.5061/dryad.13t18

 

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Title Table S1
Description Voucher specimens from which tissues were obtained for molecular data. Standard abbreviations are as follows: Louisiana State University Museum of Natural Science, LSU; Yale Peabody Museum, YPM; California Academy of Sciences, CAS; University of Kansas, KU; Museum of Vertebrate Zoology, University of California Berkeley, MVZ; San Diego State University, SDSU; University of Michigan Museum of Zoology, UMMZ. Non-standard abbreviations include the following: APR (Achille P. Raselimanana field series); ATOL (Assembling the Tree of Life voucher series); BPN (Brice P. Noonan field series); JAC (Jonathan A. Campbell field series); JAM (Jimmy A. McGuire field series); JJK (Jason J. Kolbe field series); JPV (John Pablo Valladares field series); LJA (Luciano J. Avila field series); SDZoo (Oliver Ryder, San Diego Zoo); POE (Steve Poe field series); RAN (Ronald A. Nussbaum field series); REE (Richard E. Etheridge field series); RLB (Robert L. Bezy field series); SBH (S. Blair Hedges field series); SDZoo (San Diego Zoo Series); TJS (Thomas J. Sanger field series); TWR (Tod W. Reeder field series), WL (William Lamar), YPM (Yale Peabody Museum). For each newly sequenced sample, a Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) and GenBank numbers are provided.
Download Table_S1_28_July_2015.doc (78.84 Kb)
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Title Table S2
Description Oligonuclotides used for construction of 43 uniquely barcoded adaptors. Index sequences (i.e., barcodes) are bolded.
Download Table_S2_28_July_2015.doc (74.24 Kb)
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Title Figure S1
Description Histograms depicting variation across ultraconserved elements (UCEs) generated for this study. (A–C) The number of segregating sites, (D–F) length in base pairs, and (G–I) number of taxa are reported for all three sampling strategies (16 taxa each with more than 3000 UCEs, 29 taxa each with more than 2000 UCES, and 44 taxa each with more than 120 UCEs) using 50% missing taxa per locus datasets. Note that datasets allowed for up to 50% missing taxa per locus and contained 2,716, 4,319, and 4,789 UCE loci total (16 taxa, 29 taxa, and 44 taxa, respectively).
Download S1_uce_summary.pdf (712.2 Kb)
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Title Figures S2-S37
Description Phylogenetic trees from individual analyses performed in this study.
Download Figs_S2-S37.zip (6.550 Mb)
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Title RAxML_phylip_alignments
Description Zip archive containing the following alignments: Alignment 1: 16 taxa 20% missing taxa dataset analyzed in RAxML. Alignment 2: 16 taxa 30% missing taxa dataset analyzed in RAxML. Alignment 3: 16 taxa 40% missing taxa dataset analyzed in RAxML. Alignment 4: 16 taxa 50% missing taxa dataset analyzed in RAxML. Alignment 5: 16 taxa 60% missing taxa dataset analyzed in RAxML. Alignment 6: 29 taxa 20% missing taxa dataset analyzed in RAxML. Alignment 7: 29 taxa 30% missing taxa dataset analyzed in RAxML. Alignment 8: 29 taxa 40% missing taxa dataset analyzed in RAxML. Alignment 9: 29 taxa 50% missing taxa dataset analyzed in RAxML. Alignment 10: 29 taxa 60% missing taxa dataset analyzed in RAxML. Alignment 11: 44 taxa 20% missing taxa dataset analyzed in RAxML. Alignment 12: 44 taxa 30% missing taxa dataset analyzed in RAxML. Alignment 13: 44 taxa 40% missing taxa dataset analyzed in RAxML. Alignment 14: 44 taxa 50% missing taxa dataset analyzed in RAxML. Alignment 15: 44 taxa 60% missing taxa dataset analyzed in RAxML.
Download RAxML_phylip_alignments.zip (84.60 Mb)
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Title Gene tree set 1
Description 16 taxa 20% missing taxa dataset analyzed in NJst.
Download 16_taxa_0.20_bootstrap_zip.zip (4.396 Mb)
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Title Gene tree set 2
Description 16 taxa 30% missing taxa dataset analyzed in NJst.
Download 16_taxa_0.30_bootstrap_zip.zip (8.185 Mb)
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Title Gene tree set 3
Description 16 taxa 40% missing taxa dataset analyzed in NJst.
Download 16_taxa_0.40_bootstrap_zip.zip (9.217 Mb)
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Title Gene tree set 4
Description 16 taxa 50% missing taxa dataset analyzed in NJst and ASTRAL.
Download 16_taxa_0.50_bootstrap_zip.zip (9.807 Mb)
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Title Gene tree set 5
Description 16 taxa 60% missing taxa dataset analyzed in NJst.
Download 16_taxa_0.60_bootstrap_zip.zip (10.19 Mb)
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Title Gene tree set 6
Description 29 taxa 20% missing taxa dataset analyzed in NJst.
Download 29_taxa_0.20_bootstrap.zip (1.423 Mb)
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Title Gene tree set 7
Description 29 taxa 30% missing taxa dataset analyzed in NJst.
Download 29_taxa_0.30_bootstrap.zip (6.727 Mb)
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Title Gene tree set 8
Description 29 taxa 40% missing taxa dataset analyzed in NJst.
Download 29_taxa_0.40_bootstrap.zip (12.33 Mb)
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Title Gene tree set 9
Description 29 taxa 50% missing taxa dataset analyzed in NJst and ASTRAL.
Download 29_taxa_0.50_bootstrap_zip.zip (14.56 Mb)
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Title Gene tree set 10
Description 29 taxa 60% missing taxa dataset analyzed in NJst.
Download 29_taxa_0.60_bootstrap_zip.zip (15.62 Mb)
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Title Gene tree set 11
Description 44 taxa 20% missing taxa dataset analyzed in NJst.
Download 44_taxa_0.20_bootstrap_zip.zip (21.28 Kb)
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Title Gene tree set 12
Description 44 taxa 30% missing taxa dataset analyzed in NJst.
Download 44_taxa_0.30_bootstrap.zip (408.7 Kb)
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Title Gene tree set 13
Description 44 taxa 40% missing taxa dataset analyzed in NJst.
Download 44_taxa_0.40_bootstrap.zip (4.316 Mb)
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Title Gene tree set 14
Description 44 taxa 50% missing taxa dataset analyzed in NJst and ASTRAL.
Download 44_taxa_0.50_bootstrap.zip (12.24 Mb)
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Title Gene tree set 15
Description 44 taxa 60% missing taxa dataset analyzed in NJst.
Download 44_taxa_0.60_bootstrap.zip (13.72 Mb)
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When using this data, please cite the original publication:

Streicher JW, Schulte JA, Wiens JJ (2016) How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in iguanian lizards. Systematic Biology 65 (1): 128-145. http://dx.doi.org/10.1093/sysbio/syv058

Additionally, please cite the Dryad data package:

Streicher JW, Schulte JA, Wiens JJ (2015) Data from: How should genes and taxa be sampled for phylogenomic analyses with missing data? An empirical study in iguanian lizards. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.13t18
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