Research article
Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae
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* Corresponding author: Bengt Oxelman bengt.oxelman@dpes.gu.se
1 Department of Biology, University of Virginia, Charlottesville, VA, USA
2 Department of Plant and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
3 Department of Systematic Biology, EBC, Uppsala University, Uppsala, Sweden
BMC Evolutionary Biology 2009, 9:260 doi:10.1186/1471-2148-9-260
Published: 31 October 2009Additional files
Additional file 1:
Estimated divergence times (in millions of years) from three different dating methods. [See Additional file 2 for definitions of node names].
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Additional file 2:
Names for internal nodes. The labels to the right of each node correspond to the names used in Additional files 1, 3, and 4.
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Additional file 3:
Detailed data on dN, dS, RN, RS and associated error for each gene and concatenated dataset (all species). Each row corresponds to a phylogenetic branch defined by its basal node and derived node/tip. RN and RS values are in terms of SSB. Approximated standard errors (SEs) are provided for RN and RS. Note that SE approximations are undefined and reported as 0 for any absolute rate estimate of 0. This table does not include atp9 because it was not sequenced in all species. [See Additional file 2 for definitions of node names].
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Additional file 4:
Detailed data on dN, dS, RN, RS and associated error for each gene and concatenated dataset (atp9 subset). Same setup as Additional file 2. Only the 61 species for which atp9 was sequenced are included, so that data for atp9 and the concatenation of all four mitochondrial genes could be presented. [See Additional file 2 for definitions of node names].
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Additional file 5:
Maximum likelihood trees for each of the 4 mitochondrial genes (generated without topological constraint). Parsimony bootstrap values are noted to the left of the corresponding node. Only values > 0.5 are shown. Branch lengths are in terms of substitutions per site.
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Additional file 6:
Maximum likelihood tree for matK dataset. Branch lengths are in terms of substitutions per site.
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Additional file 7:
BEAST analysis of matK dataset with unconstrained topology. Time scale is in millions of years. Posterior support is shown to the right of each node.
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Additional file 8:
Sequences and references for PCR primers. Nucleotide sequences (5' to 3') of primers used for PCR amplification and DNA sequencing.
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Additional file 9:
GenBank accession numbers for all sequences. Accession numbers in bold are not from the voucher listed in Table 1.
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Additional file 10:
Table S3. Alignments for each gene in FASTA format.
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