Data from: Resolving rapid radiations within angiosperm families using anchored phylogenomics

Léveillé-Bourret É, Starr JR, Ford BA, Lemmon EM, Lemmon AR

Date Published: May 1, 2017

DOI: http://dx.doi.org/10.5061/dryad.55h30

 

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Title onlineAppendix1--locus_characteristics
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Description Online Appendix 1. Characteristics of loci used in anchored phylogenomics analyses after masking and trimming of alignments. AVE: average value for all loci, MIN: minimum value for all loci, MAX: maximum value for all loci, Locus#: locus identification number, New#: new number assigned to locus for this analysis (necessary because of paralogs), cov: average coverage across all species, ntax: number of taxa possessing the locus, flank%: percentage of total locus length estimated to be in the "flanking region", aveC: average number of copies of locus across species, before orthology filtering, maxC: maximum number of distinct copies of locus, before orthology filtering, len: alignment length, var: number of variable characters, pi: number of parsimony informative characters, GC%: percentage of GC across all non-gapped bases, amb%: percentage of ambiguous bases, miss%: percentage of missing data.
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Title onlineAppendix2--saturationPlot
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Description Online Appendix 2. Saturation plot as calculated in DAMBE, showing GTR distance estimated for the ⅓ fastest-evolving sites in relation to the number of transitions and transversions at these sites. Regression lines (forced through the origin) and slope coefficients are shown. Dashed line indicates slope of 1.
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Title onlineAppendix3--MPtree
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Description Online Appendix 3. Single shortest tree found in PAUP* maximum parsimony searches. Support as MP jackknife, and ACCTRAN branch lengths.
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Title onlineAppendix4--MLtree
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Description Online Appendix 4. Maximum likelihood tree in RAxML searches. Support as ML bootstrap.
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Title P0082_Final_NGS_matrix.nex
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Description Concatenated sequence matrix.
Download P0082_Final_NGS_matrix.nex.zip (1.515 Mb)
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When using this data, please cite the original publication:

Léveillé-Bourret É, Starr JR, Ford BA, Lemmon EM, Lemmon AR (2017) Resolving rapid radiations within angiosperm families using anchored phylogenomics. Systematic Biology, online in advance of print. http://dx.doi.org/10.1093/sysbio/syx050

Additionally, please cite the Dryad data package:

Léveillé-Bourret É, Starr JR, Ford BA, Lemmon EM, Lemmon AR (2017) Data from: Resolving rapid radiations within angiosperm families using anchored phylogenomics. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.55h30
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