Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers.

@article{Bowe2000PhylogenyOS,
  title={Phylogeny of seed plants based on all three genomic compartments: extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers.},
  author={L M Bowe and G. Coat and Claude W. dePamphilis},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  year={2000},
  volume={97 8},
  pages={
          4092-7
        }
}
  • L. Bowe, G. Coat, C. dePamphilis
  • Published 11 April 2000
  • Biology
  • Proceedings of the National Academy of Sciences of the United States of America
Efforts to resolve Darwin's "abominable mystery"-the origin of angiosperms-have led to the conclusion that Gnetales and various fossil groups are sister to angiosperms, forming the "anthophytes." Morphological homologies, however, are difficult to interpret, and molecular data have not provided clear resolution of relationships among major groups of seed plants. We introduce two sequence data sets from slowly evolving mitochondrial genes, cox1 and atpA, which unambiguously reject the anthophyte… 

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Phylogeny of Basal Angiosperms: Analyses of Five Genes from Three Genomes1
TLDR
The standard most parsimonious trees search, taxon deletion analyses, and constraint analyses in combination with Kishino‐Hasegawa tests provided a rigorous analytical perspective for identifying Amborella, Nymphaeales, and Illiciales‐Trimeniaceae‐Austrobaileya (ANITA) as the basalmost lineages of extant angiosperms.
Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants.
TLDR
Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants, and phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions.
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