Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions

@article{Cox2014ConflictingPF,
  title={Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions},
  author={Cymon J. Cox and Blaise Li and Peter G. Foster and T Martin Embley and Peter Civ{\'a}ň},
  journal={Systematic Biology},
  year={2014},
  volume={63},
  pages={272 - 279}
}
Plants are the primary producers of the terrestrial ecosystems that dominate much of the natural environment. Occurring approximately 480 Ma (Sanderson 2003; Kenrick et al. 2012), the evolutionary transition of plants from an aquatic to a terrestrial environment was accompanied by several major developmental innovations. The freshwater charophyte ancestors of land plants have a haplobiontic life cycle with a single haploid multicellular stage, whereas land plants, which include the bryophytes… 

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References

SHOWING 1-10 OF 61 REFERENCES
Evolution of the life cycle in land plants
TLDR
Seed plants have the best developed sexual reproduction system that can be matched only by mammals among eukaryotes, and Hornworts and lycophytes represent critical extant transitional groups in the change from the gametophyte to the sporophyte as the independent free‐living generation.
Origin of land plants: Do conjugating green algae hold the key?
TLDR
A large data set of nuclear-encoded genes from 40 green plant taxa including 21 embryophytes and six streptophyte algae is used to investigate the phylogenetic relationships of streptophical algal lineages, and phylogenetic analyses indicate that either the Zygnematales or a clade consisting of the Zyghmatales and the Coleochaetales are the sister group to embryophyts.
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.
Presence of three mycorrhizal genes in the common ancestor of land plants suggests a key role of mycorrhizas in the colonization of land by plants.
TLDR
The results indicate that the mycorrhizal genes were present in the common ancestor of land plants, and that their functions were largely conserved during land plant evolution.
Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages
TLDR
Results from this study demonstrate resolution among the four monilophytes lineages, albeit with moderate support; and posit a clade consisting of Equisetaceae and Psilotaceae that is sister to the "true ferns," including Marattiaceae.
Fragments of the earliest land plants
TLDR
These fossils provide direct evidence for the nature of the spore-producing plants and confirm that the earliest spores developed in large numbers within sporangia, providing strong evidence that they are the fossilized remains of bona fide land plants.
Establishing a time-scale for plant evolution.
TLDR
A post-Jurassic origin of angiosperms and a post-Cambrian origin of land plants are rejected, and it is suggested that the establishment of the major embryophyte lineages occurred at a much slower tempo than suggested in most previous studies.
The Closest Living Relatives of Land Plants
TLDR
A four-gene phylogenetic analysis supports the hypothesis that the land plants are placed phylogenetically within the Charophyta, identifies the Charales (stoneworts) as the closest living relatives of plants, and shows the Coleochaetales as sister to this Charales/land plant assemblage.
Walkabout on the long branches of plant evolution.
  • J. Bowman
  • Biology
    Current opinion in plant biology
  • 2013
...
...