Research article

Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer

Daniel L Nickrent^{* 1} , Albert Blarer^{* 2} , Yin-Long Qiu³ , Romina Vidal-Russell¹ and Frank E Anderson^{* 4}

¹Department of Plant Biology, Southern Illinois University, Carbondale, IL 62901-6509, USA

²Institute of Systematic Botany, University of Zurich, 8008 Zurich, Switzerland

³Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA

⁴Department of Zoology, Southern Illinois University, Carbondale IL, 62901-6501, USA

author email corresponding author email* Contributed equally

BMC Evolutionary Biology 2004, 4:40doi:10.1186/1471-2148-4-40

Published:	20 October 2004

Abstract

Background

The phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizanthes and Sapria (Rafflesiaceae s. str.) in the angiosperm order Malpighiales and Mitrastema (Mitrastemonaceae) in Ericales. These phylogenetic studies did not, however, sample two additional groups traditionally classified within Rafflesiales (Apodantheaceae and Cytinaceae). Here we provide molecular phylogenetic evidence using DNA sequence data from mitochondrial and nuclear genes for representatives of all genera in Rafflesiales.

Results

Our analyses indicate that the phylogenetic affinities of the large-flowered clade and Mitrastema, ascertained using mitochondrial matR, are congruent with results from nuclear SSU rDNA when these data are analyzed using maximum likelihood and Bayesian methods. The relationship of Cytinaceae to Malvales was recovered in all analyses. Relationships between Apodanthaceae and photosynthetic angiosperms varied depending upon the data partition: Malvales (3-gene), Cucurbitales (matR) or Fabales (atp1). The latter incongruencies suggest that horizontal gene transfer (HGT) may be affecting the mitochondrial gene topologies. The lack of association between Mitrastema and Ericales using atp1 is suggestive of HGT, but greater sampling within eudicots is needed to test this hypothesis further.

Conclusions

Rafflesiales are not monophyletic but composed of three or four independent lineages (families): Rafflesiaceae, Mitrastemonaceae, Apodanthaceae and Cytinaceae. Long-branch attraction appears to be misleading parsimony analyses of nuclear small-subunit rDNA data, but model-based methods (maximum likelihood and Bayesian analyses) recover a topology that is congruent with the mitochondrial matR gene tree, thus providing compelling evidence for organismal relationships. Horizontal gene transfer appears to be influencing only some taxa and some mitochondrial genes, thus indicating that the process is acting at the single gene (not whole genome) level.