Open Access Research article

Chasing the hare - Evaluating the phylogenetic utility of a nuclear single copy gene region at and below species level within the species rich group Peperomia (Piperaceae)

Julia Naumann1*, Lars Symmank1, Marie-Stéphanie Samain2, Kai F Müller3, Christoph Neinhuis1, Claude W dePamphilis4 and Stefan Wanke1

Author Affiliations

1 Technische Universität Dresden, Institut für Botanik, D-01062 Dresden, Germany

2 Ghent University, Department of Biology, Research Group Spermatophytes, B-9000 Gent, Belgium

3 University of Münster, Institute for Evolution and Biodiversity, D-48149 Münster, Germany

4 Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA

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BMC Evolutionary Biology 2011, 11:357  doi:10.1186/1471-2148-11-357

Published: 12 December 2011

Additional files

Additional file 1:

Taxa used in the present study. Excel file listing the species used in this study including voucher information and GenBank accession numbers (provided upon final acceptance of manuscript). For detailed information of origin and collection sites see [49].

Format: XLS Size: 36KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 2:

Sequence statistics for the coding and non-coding regions for all markers in this study calculated with SeqState. This table provides information about the general characteristics of the coding, and non-coding parts of the study sequences for different sampling densities.

Format: XLS Size: 18KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 3:

Results from topology tests. Excel file showing Shimodaira-Hasegawa (SH) test results of different topology/dataset combinations. Asterisk indicates a significant rejection (p ≤ 0.05) of the respective combination.

Format: XLS Size: 31KB Download file

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Additional file 4:

Phylogram of agt1 based on a Bayesian inference of full dataset containing cloned sequences. Phylogram from the Bayesian inference of the agt1 data set with relative substitution rates using the GTR+G+I model and posterior probabilities plotted above the branches. Clades are colored according to Figure 3. The applied data set comprises part I and part II of the nuclear gene including all cloned sequences.

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Additional file 5:

Primers used for amplification and sequencing of both the nuclear and chloroplast markers applied in this study. Excel file listing primer sequences of the respective gene region that were used for both PCR and sequencing.

Format: XLS Size: 28KB Download file

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Additional file 6:

Hotspots excluded, due to ambiguous homology assessments. Regions of uncertain sequence homology (hotspots) excluded from the different datasets. Positions are given equivalent to files downloadable from TreeBase.

Format: XLS Size: 30KB Download file

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