Homoplasy Increases Phylogenetic Structure

@article{Klersj1999HomoplasyIP,
  title={Homoplasy Increases Phylogenetic Structure},
  author={Mari K{\"a}lersj{\"o} and Victor A. Albert and James S Farris},
  journal={Cladistics},
  year={1999},
  volume={15}
}
According to currently accepted theories, rapidly evolving nucleotide sites are phylogenetically less informative than more slowly evolving ones, especially for recognizing more ancient groupings. For this reason third codon positions are often regarded as less reliable than first and second positions as indicators of phylogeny. Analysis of the largest nucleotide matrix treated to date—2538 rbc L sequences covering all major lineages of green plants—shows the opposite: although rapidly evolving… 
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