From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

Abstract

BackgroundNext-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (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 sequence data.ResultsWe 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.ConclusionsAnalyses of the plastid sequence data recovered a strongly supported framework of relationships for green plants. This framework includes: i) the placement of Zygnematophyceace as sister to land plants (Embryophyta), ii) a clade of extant gymnosperms (Acrogymnospermae) with cycads + Ginkgo sister to remaining extant gymnosperms and with gnetophytes (Gnetophyta) sister to non-Pinaceae conifers (Gnecup trees), and iii) within the monilophyte clade (Monilophyta), Equisetales + Psilotales are sister to Marattiales + leptosporangiate ferns. Our analyses also highlight the challenges of using plastid genome sequences in deep-level phylogenomic analyses, and we provide suggestions for future analyses that will likely incorporate plastid genome sequence data for thousands of species. We particularly emphasize the importance of exploring the effects of different partitioning and character coding strategies.

Montsechia , an ancient aquatic angiosperm

“…Historically, based on molecular data, Ceratophyllum was placed basal to all angiosperms (22). Currently, based on molecular data, Amborella appears to be basal; the position of Ceratophyllum as basal to all eudicots is generally accepted (15,23) but is not strongly supported (16). However, a few analyses (24,25) propose that Ceratophyllum is basal to all angiosperms.…”

“…However, a few analyses (24,25) propose that Ceratophyllum is basal to all angiosperms. In other analyses the Ceratophyllales are placed as sister to the eudicots (15,16,23) or as sister to Chloranthaceae in the analysis including Cretaceous fossils unrelated to Montsechia (26). This difference in placement depends on the backbone used for the analysis.…”

You stay, but I Hop: Host shifting near and far co‐dominated the evolution of Enchenopa treehoppers

“…(2011) and Ruhfel, Gitzendanner, Soltis, Soltis, and Burleigh (2014). We then detangled the subtrees within the two orders with multiple branches: Fagales and Dipsacales.…”

“…To include as much information in the plant phylogeny as possible, we counted the clade rank of host plants by considering all nodes of the order‐level angiosperm tree reconstructed by Ruhfel et al. (2014). Conducting the same analysis by counting the clade rank of host plants in a host‐only phylogeny produced similar results, thus we presented only the results based on the order‐level tree because information on all orders of the angiosperm tree was included.…”

Water from the rock: Ancient aquatic angiosperms flow from the fossil record

“…The following inconsistencies are particularly noteworthy. Analyses of protein-coding gene sequences from chloroplast DNA (cpDNA) data place Amborella as the sister to other angiosperms while placing Ceratophyllum either with Piperales or distant from Piperales, depending on whether different codon positions or amino acid sequences are analyzed (12). Nuclear ribosomal DNA data also are problematic.…”