DOI: 10.5061/dryad.62f0r
title: Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes

description: Premise of the study: Understanding fern (monilophyte) phylogeny and its
 evolutionary timescale is critical for broad investigations of the
 evolution of land plants, and for providing the point of comparison
 necessary for studying the evolution of the fern sister group, seed
 plants. Molecular phylogenetic investigations have revolutionized our
 understanding of fern phylogeny, however, to date, these studies have
 relied almost exclusively on plastid data. Methods: Here we take a curated
 phylogenomics approach to infer the first broad fern phylogeny from
 multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12
 outgroup species) with focused character sampling (25 loci comprising
 35877 bp), along with rigorous alignment, orthology inference and model
 selection. Key results: Our phylogeny corroborates some earlier inferences
 and provides novel insights; in particular, we find strong support for
 Equisetales as sister to the rest of ferns, Marattiales as sister to
 leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods.
 Our divergence-time analyses reveal that divergences among the extant fern
 orders all occurred prior to ∼200 MYA. Finally, our species-tree
 inferences are congruent with analyses of concatenated data, but generally
 with lower support. Those cases where species-tree support values are
 higher than expected involve relationships that have been supported by
 smaller plastid datasets, suggesting that deep coalescence may be reducing
 support from the concatenated nuclear data. Conclusions: Our study
 demonstrates the utility of a curated phylogenomics approach to inferring
 fern phylogeny, and highlights the need to consider underlying data
 characteristics, along with data quantity, in phylogenetic studies.
description: MrBayes_configAndResultsNexus datafile (alignment), MrBayes commands, and resulting parameter and tree log files.alignments_andTrees_v5Nexus files (alignments) for each locus, with their corresponding maximum likelihood tree.add_genbankNums_toVouchertablePython script to extract the genBank numbers from the list supplied by NCBI (in response to a sequin submission) and format them into an accession-by-locus table.add_node_numbers_to_treePython script to print a version of an input phylogeny with the nodes annotated with their node number. (So that, e.g., the nodes can be matched to their divergence time estimates, etc.)append_metadata_tofasta_forSequinA python script that goes through a single-locus alignment and matches each taxon in that alignment with the corresponding metadata, which it adds in a Sequin block to the alignment file. For automating the production of Sequin submission to GenBank in cases where there are many loci, each with different combinations of taxa.nexusToNewickPython script to convert a bunch of tree files from nexus to newick format.summarizing_supportR script to summarize support values across analyses. Computes average node support, does t- and z-tests to examine whether average support differs across analyses/whether support for particular nodes differs.