DOI: 10.5061/dryad.450qq
title: Data from: Some limitations of public sequence data for phylogenetic inference (in plants)

description: The GenBank database contains essentially all of the nucleotide sequence
 data generated for published molecular systematic studies, but for the
 majority of taxa these data remain sparse. GenBank has value for
 phylogenetic methods that leverage data–mining and rapidly improving
 computational methods, but the limits imposed by the sparse structure of
 the data are not well understood. Here we present a tree representing
 13,093 land plant genera—an estimated 80% of extant plant diversity—to
 illustrate the potential of public sequence data for broad phylogenetic
 inference in plants, and we explore the limits to inference imposed by the
 structure of these data using theoretical foundations from phylogenetic
 data decisiveness. We find that despite very high levels of missing data
 (over 96%), the present data retain the potential to inform over 86.3% of
 all possible phylogenetic relationships. Most of these relationships,
 however, are informed by small amounts of data—approximately half are
 informed by fewer than four loci, and more than 99% are informed by fewer
 than fifteen. We also apply an information theoretic measure of branch
 support to assess the strength of phylogenetic signal in the data,
 revealing many poorly supported branches concentrated near the tips of the
 tree, where data are sparse and the limiting effects of this sparseness
 are stronger. We argue that limits to phylogenetic inference and signal
 imposed by low data coverage may pose significant challenges for
 comprehensive phylogenetic inference at the species level. Computational
 requirements provide additional limits for large reconstructions, but
 these may be overcome by methodological advances, whereas insufficient
 data coverage can only be remedied by additional sampling effort. We
 conclude that public databases have exceptional value for modern
 systematics and evolutionary biology, and that a continued emphasis on
 expanding taxonomic and genomic coverage will play a critical role in
 developing these resources to their full potential.
description: Streptophytina_by_genus_alignment.phyA phylip-format alignment file for use with the program RAxML, containing nucleotide sequence data extracted from GenBank for all available land plant genera. The partition file "Streptophytina_by_genus_partitions.part.reduced" should be used in conjunction with this one.Streptophytina_by_genus_partitions.partA RAxML partition file to be used with the alignment file "Streptophytina_by_genus_partitions.alignment.reduced".RAxML_bestTree.generic_treeThe maximum likelihood tree topology found using the alignment file "Streptophytina_by_genus_partitions.alignment.reduced" and the partition file "Streptophytina_by_genus_partitions.part.reduced" using the parameters described in the PLoS One publication. The tree has been rooted manually.generic.ultrametricAn ultrametric chronogram generated using the program treePL and the maximum likelihood topology, as described in the PLoS One manuscript text.scriptsPython (and some other) scripts used to create figures, automate analyses, and perform other tasks related to the generation of the results as well as the manuscript itself. These are explained further internally using comments, and also discussed in the PLoS One publication.code.zipgeneric_tree_datedA configuration file for treePL used to generate the "generic.ultrametric.tre" file.Supplemental tree figuresA collection of figures showing branches on generic phylogeny for which each locus contains decisive data. This Appendix is a PDF file. View its table of contents to browse the contained figures by locus name.File_S1.pdf