Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.

Mitchell N, Lewis PO, Lemmon EM, Lemmon AR, Holsinger KE

Date Published: January 20, 2017

DOI: http://dx.doi.org/10.5061/dryad.vj32s

 

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Title README
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Description Description of files contained within this repository
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Title Complete_Sequence_Files
Downloaded 16 times
Description -contains .phy files for all 498 loci and 326 sequences (two alleles per individual) -concatenated.phy contains sequences for all 498 loci together -species-consensus.phy contains concatenated sequence for the species-level consensuses
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Title OnePer_Sequence_Files
Downloaded 10 times
Description -contains .phylip files for all 498 loci and 65 taxa (one sequence per taxon) -T74_Concat_OnePer.phy contains sequences for all 498 loci together
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Title Consensus_Sequence_Files
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Description -contains .phy files for all 498 loci and 65 taxa based on species-leel consensus -consensus.phy contains sequences for all 498 loci together
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Title Reduced_Sequence_Files
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Description -contains .phy files for subset of 354 loci and 60 taxa
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Title Tree_Files
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Description -Astral_Bootstrap.tre newick formatted 100 bootstrap replicates from the COMPLETE ASTRAL-II species analysis -Gene_Trees_Full.tre newick formatted 498 "best" gene trees from RAxML (in ascending order) -Gene_Trees_Reduced.tre newick formatted reduced 354 "best" gene trees form RAxML (in ascending order) -Individual_Trees.tre newick formatted trees based on 326 sequences to check for monophyly -RAxML_Bootstrap.tre -neewick formatted bootstrap replicates from the RAxML species analysis -Species_Trees_Complete.tre newick formatted species trees (ASTRAL-II and SVDquartets) with support values for all 65 taxa, 498 loci (COMPLETE dataset) -Species_Trees_Consensus.tre newick formatted species trees generated using the CONSENSUS dataset -Species_Trees_OnePer.tre newick formatted species trees generated using the ONEPER dataset -Species_Trees_Reduced.tre newick formatted species trees with support values for REDUCED set of 60 taxa, 354 loci -Species_Trees_Schnitzler.tre newick formatted species trees with species and data from Schnitzler et al. included (AUGMENTED dataset) -SVD_bootstrap.tre newick formatted 100 bootstrap replicates from the SVDquartets species analysis
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Title Distances
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Description contains pairwise distances among gene trees, among species trees, and between gene trees (observed, randomly generated, and simulated using COAL)
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Title Internode_Certainty
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Description for all four species trees, contains internode certainty and internode certainty all values from RAxML, along with branch lengths
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Title Locus_Info
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Description matches Table 2 in manuscript, contains information on all loci, including length, parsimony informative sites, and distance to species trees.
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When using this data, please cite the original publication:

Mitchell N, Lewis PO, Lemmon EM, Lemmon AR, Holsinger KE (2017) Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L.. American Journal of Botany 104(1): 102-115. http://dx.doi.org/10.3732/ajb.1600227

Additionally, please cite the Dryad data package:

Mitchell N, Lewis PO, Lemmon EM, Lemmon AR, Holsinger KE (2017) Data from: Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.vj32s
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