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Open Access Highly Access Research article

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

Daniel L Nickrent1*†, Albert Blarer2†, Yin-Long Qiu3, Romina Vidal-Russell1 and Frank E Anderson4†

Author Affiliations

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

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

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

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

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BMC Evolutionary Biology 2004, 4:40 doi: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: 8.2MB Download file

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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: 8.3MB Download file

Open Data

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: 8.9MB Download file

Open Data

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: 7.5MB Download file

Open Data

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

Open Data