Amplification of noncoding chloroplast DNA for phylogenetic studies in lycophytes and monilophytes with a comparative example of relative phylogenetic utility from Ophioglossaceae.

@article{Small2005AmplificationON,
  title={Amplification of noncoding chloroplast DNA for phylogenetic studies in lycophytes and monilophytes with a comparative example of relative phylogenetic utility from Ophioglossaceae.},
  author={Randall L. Small and Edgar B. Lickey and Joey Shaw and Warren D. Hauk},
  journal={Molecular phylogenetics and evolution},
  year={2005},
  volume={36 3},
  pages={
          509-22
        }
}

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References

SHOWING 1-10 OF 70 REFERENCES
Evaluation of atpB nucleotide sequences for phylogenetic studies of ferns and other pteridophytes.
  • P. Wolf
  • Biology
    American journal of botany
  • 1997
TLDR
The demonstrated utility of atpB suggests that sequences from this gene should play a role in phylogenetic analyses that incorporate data from chloroplast genes, nuclear genes, morphology, and fossil data.
Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae).
TLDR
A refined hypothesis of species phylogeny of section Paeonia was proposed by considering the discordance between the nuclear and cpDNA phylogenies to be results of hybrid speciation followed by inheritance of cpDNA of one parent and fixation of ITS sequences of another parent.
Phylogenetic analysis of Asplenium subgenus Ceterach (Pteridophyta: Aspleniaceae) based on plastid and nuclear ribosomal ITS DNA sequences.
TLDR
The maternally inherited plastid sequences support the hypothesis that Asplenium subgenus Ceterach is polyphyletic, and biparentally inherited nrITS sequencessupport the allopolyploid status of A. aureum, A. lolegnamense, and A. punjabense.
Phylogenetic relationships of ferns deduced from rbcL gene sequence
TLDR
Part of the large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) gene (rbcL) was sequenced from three fern species, and the closest relative to Botrypus among the three species was Osmunda, which did not support the hypothesis that the Ophioglossaceae are linked to the progymnosperm-seed plant lineage.
Phylogenetics of seed plants : An analysis of nucleotide sequences from the plastid gene rbcL
TLDR
Two exploratory parsimony analyses of DNA sequences from 475 and 499 species of seed plants, respectively, representing all major taxonomic groups indicate that rbcL sequence variation contains historical evidence appropriate for phylogenetic analysis at this taxonomic level of sampling.
rbcL gene sequences provide evidence for the evolutionary lineages of leptosporangiate ferns.
TLDR
To compare competing classifications, DNA sequences of a chloroplast gene were obtained and phylogenetic trees were inferred by the neighbor-joining and the parsimony methods that provided insights concerning major general evolutionary trends in the leptosporangiate ferns.
Systematics of the Ant-Fern Genus Lecanopteris (Polypodiaceae): Testing Phylogenetic Hypotheses with DNA Sequences
TLDR
DNA sequences of the rbcL gene and the trnL-F non-coding region were obtained to test hypotheses of evolutionary history for Lecanopteris and related taxa and low levels of infrageneric sequence divergence between morphologically distinct species suggest a relaxation of selective pressure on morphology.
Phylogenetic relationships in Selaginellaceae based on RBCL sequences.
TLDR
A phylogenetic framework is developed for the clubmoss family Selaginellaceae based on maximum parsimony analyses of molecular data that provides support for monophyly of subgenera Selaginella and Tetragonostachys and indicates a large number of new groupings not previously recognized on morphological grounds.
...
...