Data from: A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: a phylogenomic example from Heuchera (Saxifragaceae)

Folk RA, Mandel JR, Freudenstein JV

Date Published: August 14, 2015

DOI: http://dx.doi.org/10.5061/dryad.4cn66

 

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Title Concatenated low-copy nuclear matrix
Downloaded 13 times
Description Concatenated data matrix of all 277 successfully enriched loci, assembled by BWA and aligned by MAFFT.
Download nuclearmatrix.phy (5.818 Mb)
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Title Concatenated nuclear matrix, exons only
Downloaded 6 times
Description Concatenated nuclear matrix, trimmed of introns.
Download exononlymatrix.phy.txt (1.939 Mb)
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Title Concatenated nuclear matrix, introns only
Downloaded 8 times
Description The concatenated nuclear matrix, with exonic regions deleted. The resultant matrix was shortened to match the exon-only alignment exactly in length, in order to fairly compare phylogenetic signal between the two regions.
Download intrononlyreducedmatrix.phy.txt (1.939 Mb)
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Title Chloroplast genome matrix
Downloaded 7 times
Description Chloroplast genome alignment, assembled by BWA and aligned by MAFFT.
Download chloroplastmatrix.phy (2.542 Mb)
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Title Mitochondrial genome matrix
Downloaded 14 times
Description Mitochondrial genome alignment, assembled in BWA and aligned with Mauve. Tree labels refer to specimen voucher numbers.
Download mitochondrialmatrix.phy (6.740 Mb)
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Title Concatenated nuclear ML tree
Downloaded 4 times
Description Maximum likelihood tree inferred on the concatenated low-copy nuclear data using RAxML. Tree labels refer to specimen voucher numbers.
Download RAxMLnucleartree.tre (769 bytes)
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Title Chloroplast ML tree
Downloaded 3 times
Description Maximum likelihood tree inferred on the chloroplast data using RAxML. Tree labels refer to specimen voucher numbers.
Download RAxMLchloroplasttree.tre (938 bytes)
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Title Mitochondrial ML tree
Downloaded 5 times
Description Maximum likelihood tree inferred on the mitochondrial data using RAxML. Tree labels refer to specimen voucher numbers.
Download RAxMLmitochondrialtree.tre (909 bytes)
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Title Annotated target loci
Downloaded 15 times
Description The 278 loci for which probes were developed, with exonic and intronic regions annotated, in GenBank flatfile format. The loci are numbered in descending order of length, so that "Locus 1" is the longest and "Locus 278" the shortest. One locus was not consistently enriched and was dropped from analyses; this is labeled "Locus 4".
Download AnnotatedTargetLoci.gb (621.8 Kb)
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Title Individual nuclear locus alignments
Downloaded 39 times
Description Individual locus alignments for the 277 successfully enriched loci. Labeling matches other files; hence loci are labeled by descending target length.
Download Alignments.zip (460.1 Kb)
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Title Gene trees
Downloaded 10 times
Description ML gene trees (inferred in RAxML) for each of the 277 enriched loci. The gene trees are unlabeled, but they are in precisely the same order as other files (descending locus length), hence line 1 contains the tree for Locus 1, and line 277 contains the tree for Locus 278 (Locus 4 is again omitted, hence the numbering discrepancy). Gene tree labels refer to specimen voucher numbers.
Download Genetrees.tre (203.5 Kb)
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Title MP-EST tree
Downloaded 5 times
Description Tree inferred in MP-EST; the STAR tree was topologically identical. Branch labels are coalescent branch lengths. Given the lack of infraspecific sampling, it is impossible to estimate tip branch lengths; coalescent programs generally plot these as the maximum possible value (here, 9) but these should be ignored. Internal branch estimates are correct assuming gene tree discord is solely due to the coalescent. Tree labels refer to specimen voucher numbers.
Download MP_EST.tre (282 bytes)
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When using this data, please cite the original publication:

Folk RA, Mandel JR, Freudenstein JV (2015) A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: a phylogenomic example from Heuchera (Saxifragaceae). Applications in Plant Sciences 3(8): 1500039. http://dx.doi.org/10.3732/apps.1500039

Additionally, please cite the Dryad data package:

Folk RA, Mandel JR, Freudenstein JV (2015) Data from: A protocol for targeted enrichment of intron-containing sequence markers for recent radiations: a phylogenomic example from Heuchera (Saxifragaceae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.4cn66
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