10.5061/DRYAD.K1T1F
Ruhfel, Brad R.
Eastern Kentucky University
Gitzendanner, Matthew A.
University of Florida
Soltis, Pamela S.
Florida Museum of Natural History
Soltis, Douglas E.
University of Florida
Burleigh, J. Gordon
University of Florida
Data from: From algae to angiosperms–inferring the phylogeny of green
plants (Viridiplantae) from 360 plastid genomes
Dryad
dataset
2014
Acrogymnospermae
Monilophyta
Lycopodiophyta
composition bias
Precambrian
Chlorophyta
RY-coding
Angiospermae
Embryophyta
Spermatophyta
plastid genome sequences
Viridiplantae
Streptophyta
2014-11-29T00:00:00Z
2014-11-29T00:00:00Z
en
https://doi.org/10.1186/1471-2148-14-23
15785993 bytes
2
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Background: Next-generation sequencing has provided a wealth of plastid
genome sequence data from an increasingly diverse set of green plants
(Viridiplantae). Although these data have been useful for reconstructing
the phylogeny of numerous clades of photosynthetic organisms (e.g., green
algae, angiosperms, and gymnosperms), their utility for inferring
relationships across all green plants is uncertain. Viridiplantae
originated 700-1500 million years ago and may comprise as many as 500,000
species. This clade represents a major source of photosynthetic carbon and
contains an immense diversity of life forms, including some of the
smallest and largest eukaryotes. Here we explore the limits and challenges
of inferring a comprehensive green plant phylogeny from available complete
or nearly complete plastid genome data. Results: We assembled
protein-coding sequence data for 78 genes from 360 diverse green plant
taxa with complete or nearly complete plastid genome sequences available
from GenBank. Phylogenetic analyses of the plastid data recovered
well-supported backbone relationships and strong support for relationships
that were not observed in previous analyses of major subclades within
Viridiplantae. However, there also is evidence of systematic error in some
analyses. In several instances we obtained strongly supported but
conflicting topologies from analyses of nucleotides versus amino acid
characters, and the considerable variation in GC content among lineages
and within single genomes affected the phylogenetic placement of several
taxa. Conclusions: Analyses of the plastid data recovered a strongly
supported framework of relationships for green plants. This includes the
placement of Zygnematophyceace as sister to land plants (Embryophyta) and
a clade of extant gymnosperms (Acrogymnospermae) with cycads + Ginkgo
sister to remaining members and with gnetophytes (Gnetophyta) sister to
non-Pinaceae conifers (Gnecup trees); within the monilophyte clade
(Monilophyta), relationships are strongly supported with Equisetales +
Psilotales sister to Marattiales + leptosporangiate ferns. We also
highlight the challenges of using plastid genome sequences in deep-level
phylogenomic analyses and provide suggestions for future analyses that
will likely incorporate plastid genome data for thousands of species. We
particularly emphasize the importance of exploring the effects of
different partitioning and character coding protocols for the entire data
set as well as subsets of the data.
Alignments and Partition FilesAlignments and partition
filesAlignmentsandPartitionFiles.zipBootstrap Consensus TreesBootstrap
Consensus
TreesBSConsensusTrees.zipMLTreeswBLandBSReadMe_Ruhfeletal_Viridiplantae