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

Additional files

Additional File 1:

MP strict consensus tree from mitochondrial matR Strict consensus of 200,000+ trees obtained from maximum parsimony (unconstrained MP) analysis of the 77-taxon mitochondrial matR matrix. Bootstrap percentages are shown above the lines. Rafflesiales taxa are shown in bold italics.

Format: EPS Size: 8.4MB Download file

Additional File 2:

Strict consensus MP tree from mitochondrial atp1 Strict consensus of 328 trees resulting from a MP analysis of the 71-taxon mitochondrial atp1 matrix. Rafflesiales taxa are shown in bold italics. Bootstrap percentages are given above the branches.

Format: EPS Size: 8.5MB Download file

Additional File 3:

Majority rule consensus BI tree from 3-gene data set Majority rule consensus of 20,000 trees (10 million generations, 5 million burn-in) resulting from Bayesian analysis of the 77-taxon nuclear 3-gene matrix. Clades with Bayesian posterior probabilities are indicated above the clades. Rafflesiales taxa are shown in bold italics.

Format: EPS Size: 9.1MB Download file

Additional File 4:

Strict consensus constrained MP tree from nuclear SSU rDNA Strict consensus of 6 trees resulting from the constrained MP analysis of the 77-taxon nuclear SSU rDNA matrix. Rafflesiales taxa are shown in bold italics. Bootstrap percentages are given above selected nodes (Rafflesiales).

Format: EPS Size: 7.7MB Download file

Additional File 5:

Taxa used in this study MS Excel file giving taxon names and GenBank numbers for all genes used.

Format: XLS Size: 58KB Download file

This file can be viewed with: Microsoft Excel Viewer