Phylogenomics and Coalescent Analyses Resolve Extant Seed Plant Relationships

@article{Xi2013PhylogenomicsAC,
  title={Phylogenomics and Coalescent Analyses Resolve Extant Seed Plant Relationships},
  author={Zhenxiang Xi and Joshua S. Rest and Charles C. Davis},
  journal={PLoS ONE},
  year={2013},
  volume={8}
}
The extant seed plants include more than 260,000 species that belong to five main lineages: angiosperms, conifers, cycads, Ginkgo, and gnetophytes. Despite tremendous effort using molecular data, phylogenetic relationships among these five lineages remain uncertain. Here, we provide the first broad coalescent-based species tree estimation of seed plants using genome-scale nuclear and plastid data By incorporating 305 nuclear genes and 47 plastid genes from 14 species, we identify that i) extant… 

Figures and Tables from this paper

Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms
TLDR
This study generated a consistent and well-resolved phylogeny of seed plants, which places Gnetales as sister to Pinaceae and thus supports the Gnepine hypothesis, and finds that G netales and angiosperms have similar molecular evolutionary rates, which are much higher than those of other gymnosperms.
Phylogeny and Divergence Times of Gymnosperms Inferred from Single-Copy Nuclear Genes
TLDR
This study uses LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera and strongly supports cycads as the basal-most lineage of Gymnosperms rather than sister to Ginkgoaceae.
Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants
TLDR
This study identified single-copy genes in a broad collection of seed plants and used these to infer phylogenetic relationships between major seed plant taxa, and phylogenetic trees from concatenated alignments without 3rd codon positions and amino acid alignments under the CAT + GTR model support gnetophytes as a sister group to Pinaceae.
Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies.
TLDR
A broad coalescent-based species tree estimation of 45 seed plants is provided and it is suggested that the Amborella alone placement inferred using concatenation methods is likely misled by fast-evolving sites, which appear to be more robust to elevated substitution rates.
Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants
TLDR
The results suggest that angiosperms and gymnosperms differ considerably in their rates of molecular evolution per unit time, with gymnosperm rates being, on average, seven times lower than angiosperm species.
Evolution and biogeography of gymnosperms.
From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
TLDR
The limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data are explored and the importance of exploring the effects of different partitioning and character coding strategies is emphasized.
The dynamic history of gymnosperm plastomes: Insights from structural characterization, comparative analysis, phylogenomics, and time divergence
TLDR
It was found that plastome size, structure, and gene order were highly variable in the five gymnosperm groups, of which Parasitaxus usta (Vieill.) de Laub.
The Cycas genome and the early evolution of seed plants
TLDR
The 10.5-Gb reference genome of Cycas panzhihuaensis is reported, complemented by the transcriptomes of 339 cycad species, finding evidence for an ancient whole-genome duplication in the common ancestor of extant gymnosperms.
...
...

References

SHOWING 1-10 OF 96 REFERENCES
Phylogeny of seed plants based on evidence from eight genes.
TLDR
A data set of four plastid genes, three mitochondrial genes, and one nuclear gene for 19 exemplars representing the five groups of living seed plants revealed a gymnosperm clade that is sister to angiosperms and the preferred topology based on the LR test is that Gnetales are sister to Pseudotsuga.
Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers.
TLDR
The Gnetales may be viewed as extremely divergent conifers, and the many morphological similarities between angiosperms and G netales arose independently.
Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes
TLDR
Comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of substitution than chloropleft genes, are informative phylogenetic markers, and are particularly suitable for resolving deep relationships.
Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers.
TLDR
The molecular phylogeny strongly conflicts with current interpretations of seed plant morphology, and implies that many similarities between gnetophytes and angiosperms were independently derived, whereas other characters could emerge as synapomorphies for an expanded conifer group including Gnetales.
The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes
TLDR
This study demonstrates that Amboreella, Nymphaeales and Illiciales-Trimeniaceae-Austrobaileya represent the first stage of angiosperm evolution, with Amborella being sister to all other angiosperms, and shows that Gnetales are related to the conifers and are not sister to the angios perms, thus refuting the Anthophyte Hypothesis.
A Nonflowering Land Plant Phylogeny Inferred from Nucleotide Sequences of Seven Chloroplast, Mitochondrial, and Nuclear Genes
TLDR
Most of the relationships among all major lineages of nonflowering land plants are supported by bootstrap values of 75% or higher, except those among basal monilophyte lineages and among some gymnosperm lineages, probably because of extinctions.
Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences.
To study the evolutionary relationships among the four living gymnosperm orders and the interfamilial relationships in each order, a set of 65 nuclear 18S rRNA sequences from ferns, gymnosperms, and
Systematic Error in Seed Plant Phylogenomics
TLDR
It is shown that non-time reversible properties of aligned sequence positions in the chloroplast genomes of Gnetales mislead phylogenetic reconstruction of these seed plants, highlighting the importance of goodness of fit between substitution model and data for understanding seed plant phylogeny.
The deepest divergences in land plants inferred from phylogenomic evidence
TLDR
It is shown here that densely sampled taxon trees built with multiple genes provide an indispensable test of taxon-sparse trees inferred from genome sequences.
Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data.
TLDR
It is likely that improved sampling of gymnosperm diversity in nucleotide data sets will help alleviate some of the analytical issues encountered in the estimation of seed plant phylogeny, providing a more definitive test of morphological trees.
...
...