Data from: Phylogenetic signal detection from an ancient rapid radiation: effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae

Straub SCK, Moore MJ, Soltis PS, Soltis DE, Liston A, Livshultz T

Date Published: August 27, 2014

DOI: http://dx.doi.org/10.5061/dryad.ff749

 

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Title Read me first, translation key for taxon names in files
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Title Starting alignment of 13 plastomes
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Description Starting alignment of 13 plastomes (including partial Anodendron plastome), 145,064 base pairs long, Phylip format.
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Title Starting alignment of 12 plastomes
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Description Starting alignment of 12 plastomes (excluding partial Anodendron plastome) 144,864 base pairs long, created from the 145,064 alignment by 1) deletion of Anodendron plastome and 2) deletion of all gap and all “N” characters, Phylip format.
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Title RaxML partition file for 13 plastome, 145,064 base pair, alignment from Partition Finder analysis.
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Title RaxML partition file for 12 plastome, 144,864 base pair alignment from Partition Finder analysis.
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Title RaxML exclude file for 13 plastome, 145,064 base pair alignment; 1075 segments excluded based on GBLOCKS analysis.
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Title RaxML exclude file for 12 plastome, 144,864 base pair alignment; 1065 segments excluded based on GBLOCKS analysis.
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Title RaxML input matrix “Allsites_alltaxa”
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Description Anodendron included; 125,369 aligned base pairs, undetermined and ambiguously aligned sites identified by GBLOCKS removed; Phylip format.
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Title RaxML partition file for matrix “Allsites_alltaxa”
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Description Anodendron included, 125,369 aligned base pairs, undetermined and ambiguously aligned sites identified by GBLOCKS removed.
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Title Maximum likelihood bootstrap tree for matrix “Allsites_alltaxa” analyzed with linked branch lengths.
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Title Maximum likelihood bootstrap tree for matrix “Allsites_alltaxa” analyzed with unlinked branch lengths.
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Title Most parsimonious tree for matrix “Allsites_alltaxa”, Winclada tree file.
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Title Maximum likelihood bootstrap tree for matrix “Allsites_alltaxa” with Rhabdadenia excluded, linked branch lengths.
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Title Maximum likelihood bootstrap tree for matrix “Allsites_alltaxa” with Rhabdadenia excluded, unlinked branch lengths.
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Title Most parsimonious trees for matrix “Allsites_alltaxa” with Rhabdadenia excluded, Winclada tree file.
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Title Maximum likelihood bootstrap tree for matrix “Allsites_alltaxa” with Periploca excluded, linked branch lengths.
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Title Maximum likelihood bootstrap tree for matrix “Allsites_alltaxa” with Periploca excluded, unlinked branch lengths.
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Title Most parsimonious trees for matrix “Allsites_alltaxa” with Periploca excluded, Winclada format.
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Title RaxML input matrix “Allsites_noAno”
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Description RaxML input matrix “Allsites_noAno”, Anodendron excluded, 126,430 aligned base pairs, undetermined and ambiguously aligned sites identified by GBLOCKS removed, Phylip format.
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Title RaxML partition file for matrix “Allsites_noAno”, Anodendron excluded, 126,430 aligned base pairs, undetermined and ambiguously aligned sites identified by GBLOCKS removed.
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Title Maximum likelihood bootstrap tree for matrix “Allsites_noAno” analyzed with linked branch lengths.
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Title Maximum likelihood bootstrap tree for matrix “Allsites_noAno” analyzed with unlinked branch lengths.
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Title Most parsimonious trees for matrix “Allsites_noAno”, Winclada format.
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Download 126430_names.tre (518 bytes)
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Title Maximum likelihood bootstrap tree for matrix “Allsites_noAno” with Rhabdadenia excluded, branch lengths linked.
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Title Maximum likelihood bootstrap tree for matrix “Allsites_noAno” with Rhabdadenia excluded, branch lengths unlinked.
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Title Most parsimonious trees for matrix “Allsites_noAno” with Rhabdadenia excluded, Winclada format.
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Title Maximum likelihood bootstrap tree for matrix “Allsites_noAno” with Periploca excluded, branch lengths linked.
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Title Maximum likelihood bootstrap tree for matrix “Allsites_noAno” with Periploca excluded, branch lengths unlinked.
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Title Most parsimonious trees for matrix “Allsites_noAno” with Periploca excluded, Winclada format.
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Title RaxML input matrix “>3.4_excluded”
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Description RaxML input matrix “>3.4_excluded”, Anodendron excluded, created from matrix “Allsites_noAno” by exclusion of sites with AIR rates > 3.4, 125,871 base pairs retained, 559 base pairs excluded, Phylip format.
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Title RaxML exclusion file, sites excluded from “Allsites_noAno” to create matrix “>3.4_excluded”.
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Title Maximum likelihood bootstrap tree for matrix “>3.4_excluded” analyzed with linked branch lengths.
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Title Maximum likelihood bootstrap tree for matrix “>3.4_excluded” analyzed with unlinked branch lengths.
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Title Most parsimonious trees for matrix “>3.4_excluded”
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Title RaxML input matrix “>3.3_excluded”
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Description RaxML input matrix “>3.3_excluded”, Anodendron excluded, created from matrix “Allsites_noAno” by exclusion of sites with AIR rates > 3.3, 125,487 base pairs retained, 943 base pairs excluded, Phylip format.
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Title RaxML exclusion file, sites excluded from “Allsites_noAno” to create matrix “>3.3_excluded”.
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Title Maximum likelihood bootstrap tree for matrix “>3.3_excluded” analyzed with linked branch lengths.
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Title Maximum likelihood bootstrap tree for matrix “>3.3_excluded” analyzed with unlinked branch lengths.
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Title Most parsimonious trees for matrix “>3.3_excluded”
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Title RaxML input matrix “>3.0_excluded”
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Description RaxML input matrix “>3.0_excluded”, Anodendron excluded, created from matrix Allsites_noAno (4b) by exclusion of sites with AIR rates > 3.0, 123,995 base pairs retained, 2,435 base pairs excluded.
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Title RaxML exclusion file, sites excluded from “Allsites_noAno” to create matrix “>3.0_excluded”.
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Title Maximum likelihood bootstrap tree for matrix “>3.0_excluded” analyzed with linked branch lengths.
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Title Maximum likelihood bootstrap tree for matrix “>3.0_excluded” analyzed with unlinked branch lengths
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Title Most parsimonious trees for matrix “>3.0_excluded”, Winclada tree file format
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Title RaxML partition file for matrix “>3.4_excluded”
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Title RaxML partition file for matrix “>3.3_excluded”
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Title RaxML partition file for matrix “>3.0_excluded”
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Title RaxML input matrix, inverse exclusion matrix for matrix “>3.4_excluded”, includes only 559 sites with AIR rate >3.4, analyzed without partitions
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Title Maximum likelihood bootstrap tree for inverse exclusion matrix for matrix “>3.4_excluded”
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Title RaxML input matrix, inverse exclusion matrix for matrix “>3.3_excluded”, includes only 943 sites with AIR rate >3.3
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Title Maximum likelihood bootstrap tree for inverse exclusion matrix for matrix “>3.3_excluded”
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Title RaxML input matrix, inverse exclusion matrix for matrix “>3.0_excluded”, includes only 2,435 sites with AIR rate >3.0
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Title Maximum likelihood bootstrap tree for inverse exclusion matrix for matrix “>3.0_excluded”
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Title RaxML input tree file of 105 topologies for SH test of matrix “Allsites_alltaxa”.
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Title Result of SH test on matrix “Allsites_alltaxa” with linked branch lengths.
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Description tab delimited text file
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Title Result of SH test on matrix “Allsites_alltaxa” with unlinked branch lengths.
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Description tab delimited text file.
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Title Alternative topologies (105) for SH test of matrices “Allsites_noAno”, “>3.4_excluded”, “>3.3_excluded”, “>3.0_excluded”.
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Description tab delimited text file.
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Title Result of SH test on matrix “Allsites_noAno” with linked branch lengths.
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Title Result of SH test on matrix “Allsites_noAno” with unlinked branch lengths.
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Title Result of SH test on matrix “>3.4_excluded” with linked branch lengths.
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Download SH_linked_AIR559excl_3.4_7tr.txt (13.22 Kb)
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Title Result of SH test on matrix “>3.4_excluded” with unlinked branch lengths.
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Download SH_unlinked_AIR559excl_3.4_7tr.txt (13.22 Kb)
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Title Result of SH test on matrix “>3.3_excluded” with linked branch lengths.
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Description Tab delimited text file.
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Title Result of SH test on matrix “>3.3_excluded” with unlinked branch lengths.
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Title Result of SH test on matrix “>3.0_excluded” with linked branch lengths.
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Description tab delimited text file.
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Title Result of SH test on matrix “>3.0_excluded” with unlinked branch lengths.
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Title AIR analysis output, based on 7 trees
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Description AIR analysis output, average rates for each site in matrix “Allsites_noAno” for 7 trees with p>0.05 from SH test of “Allsites_noAno” with linked branch lengths. Tab delimited text file.
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Title AIR analysis output, based on 12 trees
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Description AIR analysis output, average rates for each site in matrix “Allsites_noAno” for 12 trees with p>0.05 from SH test of “Allsites_noAno” with unlinked branch lengths. Tab delimited text file.
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Title Sites removed by GBLOCKS and AIR sorted by genomic feature
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Description Genomic features associated with sites excluded from the alignment of 12 full plastomes by GBLOCKS to produce matrix Allsites_noAno and by AIR to produce matrix >3.0_excluded, data for Figure 4. Tab delimited text file.
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Title Morphological character matrix: pollen aggregation.
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Title Anodendron oblongifolium partial plastome assembly
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Description fasta file
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When using this data, please cite the original publication:

Straub SCK, Moore MJ, Soltis PS, Soltis DE, Liston A, Livshultz T (2014) Phylogenetic signal detection from an ancient rapid radiation: effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae. Molecular Phylogenetics and Evolution 80: 169-185. http://dx.doi.org/10.1016/j.ympev.2014.07.020

Additionally, please cite the Dryad data package:

Straub SCK, Moore MJ, Soltis PS, Soltis DE, Liston A, Livshultz T (2014) Data from: Phylogenetic signal detection from an ancient rapid radiation: effects of noise reduction, long-branch attraction, and model selection in crown clade Apocynaceae. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.ff749
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