Two New Fern Chloroplasts and Decelerated Evolution Linked to the Long Generation Time in Tree Ferns

@article{Zhong2014TwoNF,
  title={Two New Fern Chloroplasts and Decelerated Evolution Linked to the Long Generation Time in Tree Ferns},
  author={Bojian Zhong and Richard Fong and Lesley J. Collins and Patricia A. McLenachan and David Penny},
  journal={Genome Biology and Evolution},
  year={2014},
  volume={6},
  pages={1166 - 1173}
}
We report the chloroplast genomes of a tree fern (Dicksonia squarrosa) and a “fern ally” (Tmesipteris elongata), and show that the phylogeny of early land plants is basically as expected, and the estimates of divergence time are largely unaffected after removing the fastest evolving sites. The tree fern shows the major reduction in the rate of evolution, and there has been a major slowdown in the rate of mutation in both families of tree ferns. We suggest that this is related to a generation… 
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References

SHOWING 1-10 OF 73 REFERENCES
Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants
TLDR
It is shown that there are three monophyletic groups of extant vascular plants: (1) lycophytes, (2) seed plants and (3) a clade including equisetophytes (horsetails, psilotophytes) and all eusporangiate and leptosporangiates ferns.
Overcoming deep roots, fast rates, and short internodes to resolve the ancient rapid radiation of eupolypod II ferns.
TLDR
Among the significant phylogenetic results is the near-complete support along the eupolypod II backbone, the demonstrated paraphyly of Woodsiaceae as currently circumscribed, and the well-supported placement of the enigmatic genera Homalosorus, Diplaziopsis, and Woodsia.
The evolutionary root of flowering plants.
TLDR
It is shown that support for Amborella as the sole representative of the most basal angiosperm lineage is founded on sequence site patterns poorly described by time-reversible substitution models, and indicates that aquatic and herbaceous species dominate the earliest extant lineage of flowering plants.
Utility of a large, multigene plastid data set in inferring higher-order relationships in ferns and relatives (monilophytes).
TLDR
The utility of this plastid-based data set in corroborating relationships found in previous studies, improving support, and resolving uncertainties in monilophyte phylogeny is supported.
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.
Rates of Molecular Evolution Are Linked to Life History in Flowering Plants
TLDR
Exceptionally large phylogenies of five major angiosperm clades demonstrate that rates of molecular evolution are consistently low in trees and shrubs, with relatively long generation times, as compared with related herbaceous plants, which generally have shorter generation times.
Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae)
TLDR
It is suggested that removal of misleading signal in phylogenomic datasets can result not only in increased resolution for poorly supported nodes, but may serve as a tool for identifying erroneous yet highly supported topologies.
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.
Origin of land plants using the multispecies coalescent model.
Rate heterogeneity among lineages of tracheophytes: Integration of molecular and fossil data and evidence for molecular living fossils
TLDR
This study minimize the potential error caused by inaccurate topology and uncertain calibration times by using a well-supported tree, multiple genes, and multiple well-substantiated dates to explore the correspondence between the fossil record and molecular-based age estimates for major clades of tracheophytes.
...
...