10.5061/DRYAD.62F0R
Rothfels, Carl J.
University of British Columbia
University of California, Berkeley
Li, Fay-Wei
Duke University
Sigel, Erin M.
Smithsonian Institution
Huiet, Layne
Duke University
Larsson, Anders
Uppsala University
Burge, Dylan O.
California Academy of Sciences
Ruhsam, Markus
Royal Botanic Garden Edinburgh
Deyholos, Michael
University of British Columbia
Soltis, Douglas E.
University of Florida
Stewart Jr., C. Neal
Shaw, Shane W.
Orleans, Vermont 05860 USA
Pokorny, Lisa
Real Jardín Botánico
Chen, Tao
Chinese Academy of Sciences
dePamphilis, Claude
DeGironimo, Lisa
The Bronx Defenders
Chen, Li
Beijing Genomics Institute
Wei, Xiaofeng
Beijing Genomics Institute
Sun, Xiao
Beijing Genomics Institute
Korall, Petra
Uppsala University
Stevenson, Dennis W.
The Bronx Defenders
Graham, Sean W.
University of British Columbia
Wong, Gane Ka-Shu
Pryer, Kathleen M.
Duke University
Stewart, C. Neal
University of Tennessee at Knoxville
Wong, Gane K-S.
University of Alberta
de Pamphilis, Claude
Pennsylvania State University
Data from: The evolutionary history of ferns inferred from 25 low-copy
nuclear genes
Dryad
dataset
2016
Polypodiopsida
DET1
nexus
TPLATE
pgiC
HEMERA
GClev
COP9
Hsp40
newick
tree file
IBR3
Polypodiidae
Equisetum
transducin
z-test
Marattiales
Sequin
Codon models
Python
Psilotales
MCD1
model selection
t-test
bootstrap support
Pteridophyta
Cryptochrome
SQD1
GenBank
IGPD
monilophytes
DUF1077
voucher table
Ferns
ApPEFP
NDUFS6
SEF
Ophioglossales
gapCp
divergence time dating
low-copy nuclear gene
fern chronogram
2016-06-24T00:00:00Z
2016-06-24T00:00:00Z
en
https://doi.org/10.3732/ajb.1500089
193617138 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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.