Data from: Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes)

Betancur-R. R, Li C, Munroe TA, Ballesteros JA, Ortí G

Date Published: May 31, 2013

DOI: http://dx.doi.org/10.5061/dryad.dj31p

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title FIG_SUPP_1_DNA_AA
Downloaded 103 times
Description Supplementary Figure 1. RAxML tree estimated with the DNA-AA data set (214 taxa, 7428 sites). Nodal numbers indicate support values (≥ 75%), estimated with the rapid bootstrapping algorithm in RAxML.
Download FIG_SUPP_1_DNA_AA.pdf (239.3 Kb)
Details View File Details
Title FIG_SUP_2_Subset_trees
Downloaded 63 times
Description Supplementary Figure 2. Four representative multi-locus phylogenies based on the subset. Color branches represent flatfish lineages (cyan, Pleuronectoidei; orange, Psettodoidei).
Download FIG_SUP_2_Subset_trees.pdf (1.517 Mb)
Details View File Details
Title Supplementary_Table_1
Downloaded 110 times
Description Supplementary Table 1. Material examined and GenBank Accession numbers.
Download Supplementary_Table_1.xlsx (51.78 Kb)
Details View File Details
Title Supplementary_Table_2
Downloaded 106 times
Description Supplementary Table 2. Primers used and optimized PCR conditions.
Download Supplementary_Table_2.pdf (87.66 Kb)
Details View File Details
Title Supplementary_Table_3
Downloaded 67 times
Description Supplementary Table 3. Characterization of molecular markers, variation, distribution of present/missing sequences and taxa, and GenBank accession numbers (see also Supplementary Table 1).
Download Supplementary_Table_3.pdf (88.87 Kb)
Details View File Details
Title ALL_TAXA_20_GENES
Downloaded 105 times
Description Nexus dataset with the complete alignment (214 taxa and 20 gene fragments; 19461 sites). The alignment file is fully annotated for gene partitions, including the batch command in PAUP* to export individual gene files .
Download ALL_TAXA_20_GENES.nex (4.175 Mb)
Details View File Details
Title SUBSET_18_GENES
Downloaded 52 times
Description Nexus alignment file for the subset (37 taxa and 18 gene fragments; 17616 sites; no missing data). The alignment file is fully annotated for gene partitions, including the batch command in PAUP* to export individual gene files.
Download SUBSET_18_GENES.nex (655.1 Kb)
Details View File Details
Title Supplementary Table4
Downloaded 64 times
Description Likelihood (ln) scores for gene trees and AU test P values comparing gene tree topologies estimated with RAxML against the concatenation topology (from Fig. 3, pruned to only include taxa in the subset), calculated under homogeneous (RAxML) and non-homogeneous (nhPhyML) optimization. The nhPhyML model used unlimited base equilibrium frequencies. Values in bold highlight cases in which the concatenation topology resulted in either better or non-significantly worse likelihood scores.
Download Supplementary_Table4.docx (126.4 Kb)
Details View File Details

When using this data, please cite the original publication:

Betancur-R R, Li C, Munroe TA, Ballesteros JA, Ortí G (2013) Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes). Systematic Biology 62(5): 763-785. http://dx.doi.org/10.1093/sysbio/syt039

Additionally, please cite the Dryad data package:

Betancur-R. R, Li C, Munroe TA, Ballesteros JA, Ortí G (2013) Data from: Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.dj31p
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: