Bias and conflict in phylogenetic inference of myco-heterotrophic plants: a case study in Thismiaceae

V. Merckx, F.T. Bakker, K. Huysmans, B.F. Smets

Research output: Contribution to journalArticleAcademicpeer-review

43 Citations (Scopus)

Abstract

Due to morphological reduction and absence of amplifiable plastid genes, the identification of photosynthetic relatives of heterotrophic plants is problematic. Although nuclear and mitochondrial gene sequences may offer a welcome alternative source of phylogenetic markers, the presence of rate heterogeneity in these genes may introduce bias/systematic error in phylogenetic analyses. We examine the phylogenetic position of Thismiaceae based on nuclear 18S rDNA and mitochondrial atpA DNA sequence data, as well as using parsimony, likelihood and Bayesian inference methods. Significant differences in evolutionary rates of these genes between closely related taxa lead to conflicting results: while parsimony analyses of 18S rDNA and combined data strongly support the monophyly of Thismiaceae, Bayesian inference, with and without a relaxed molecular clock, as well as the Swofford-Olsen-Waddell-Hillis (SOWH) test confidently reject this hypothesis. We show that rate heterogeneity in our data leads to long-branch attraction artifacts in parsimony analysis. However, using model-based inference methods the question of whether Thismiaceae are monophyletic remains elusive. On the one hand maximum likelihood nonparametric bootstrapping and parametric hypothesis tests fail to support a paraphyletic Thismiaceae, on the other hand Bayesian inference methods (both without and with a relaxed clock) significantly reject a monophyletic Thismiaceae. These results show that an adequate sampling, the use of rate homogeneous data, and the application of different inference methods are important factors for developing phylogenetic hypotheses of myco-heterotrophic plants
Original languageEnglish
Pages (from-to)64-77
JournalCladistics-The International Journal of the Willi Hennig Society
Volume25
Issue number1
DOIs
Publication statusPublished - 2009

Keywords

  • long-branch attraction
  • 18s rdna sequences
  • parasitic plants
  • nucleotide substitution
  • flowering plants
  • tree selection
  • molecular-data
  • gene-transfer
  • data sets
  • burmanniaceae

Fingerprint Dive into the research topics of 'Bias and conflict in phylogenetic inference of myco-heterotrophic plants: a case study in Thismiaceae'. Together they form a unique fingerprint.

Cite this