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Systematic error in seed plant phylogenomics

Affiliation

  • 1 Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand. [email protected]
  • PMID: 22016337
  • PMCID: PMC3237385
  • DOI: 10.1093/gbe/evr105

Free PMC article

Systematic error in seed plant phylogenomics

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Authors

Affiliation

  • 1 Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand. [email protected]
  • PMID: 22016337
  • PMCID: PMC3237385
  • DOI: 10.1093/gbe/evr105

Abstract

Resolving the closest relatives of Gnetales has been an enigmatic problem in seed plant phylogeny. The problem is known to be difficult because of the extent of divergence between this diverse group of gymnosperms and their closest phylogenetic relatives. Here, we investigate the evolutionary properties of conifer chloroplast DNA sequences. To improve taxon sampling of Cupressophyta (non-Pinaceae conifers), we report sequences from three new chloroplast (cp) genomes of Southern Hemisphere conifers. We have applied a site pattern sorting criterion to study compositional heterogeneity, heterotachy, and the fit of conifer chloroplast genome sequences to a general time reversible + G substitution model. We show that non-time reversible properties of aligned sequence positions in the chloroplast genomes of Gnetales mislead phylogenetic reconstruction of these seed plants. When 2,250 of the most varied sites in our concatenated alignment are excluded, phylogenetic analyses favor a close evolutionary relationship between the Gnetales and Pinaceae-the Gnepine hypothesis. Our analytical protocol provides a useful approach for evaluating the robustness of phylogenomic inferences. Our findings highlight the importance of goodness of fit between substitution model and data for understanding seed plant phylogeny.

Figures

( A ) Four major…

( A ) Four major hypotheses for phylogenetic relationships involving Gnetales. ( B…

Bootstrap support in optimal PhyML…

Bootstrap support in optimal PhyML trees for three alternative relationships as intervals of…

Histogram indicating consecutive misfitting site…

Histogram indicating consecutive misfitting site patterns under the ( A ) GTR +…

Plot indicating nucleotide compositional heterogeneity…

Plot indicating nucleotide compositional heterogeneity within intervals sampled from the most varied end…

Relative length of internal branch…

Relative length of internal branch leading to ( A ) Gnetales in a…

( A ) Pearson correlation…

( A ) Pearson correlation analyses. The blue dotted line indicates the Pearson…

Resolving the closest relatives of Gnetales has been an enigmatic problem in seed plant phylogeny. The problem is known to be difficult because of the extent of divergence between this diverse group of gymnosperms and their closest phylogenetic relatives. Here, we investigate the evolutionary proper …