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Open Access Highly Accessed Research article

A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree

Tiina Särkinen12*, Lynn Bohs3, Richard G Olmstead4 and Sandra Knapp1

Author Affiliations

1 Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK

2 Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK

3 Department of Biology, University of Utah, 257 S 1400 E, Salt Lake City, UT 84112, USA

4 Department of Biology, University of Washington, Seattle, WA 98195, USA

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BMC Evolutionary Biology 2013, 13:214  doi:10.1186/1471-2148-13-214

Published: 30 September 2013

Additional files

Additional file 1:

Solanaceae fossil record. Details of all records of Solanaceae with full references to primary sources.

Format: DOCX Size: 33KB Download file

Open Data

Additional file 2:

Solanaceae time-calibrated phylogeny with tips. A detailed dated phylogeny of Solanaceae showing mean node ages and 95% confidence intervals for all nodes. Posterior probability branch support values are indicated in branch colours, where red refers to nodes with < 80% support. Major clades are indicated, and studies which include more detailed phylogenies of the particular groups are indicated on the left. These studies should be referred to as primary phylogenetic sources for the particular clades with more up-to-date details of species-level relationships because the individual studies used more markers and discuss specific issues relevant at such low taxonomic levels, including polyploidy, hybridisation, and gene tree – species tree incongruences.

Format: TIFF Size: 7MB Download file

Open Data

Additiona file 3:

Solanaceae time-calibrated phylogeny. Dated molecular phylogeny of the Solanaceae based on the supermatrix calibrated using fossil data. Major clades are shown with their associated ages and 95% confidence intervals. Thick branches indicate highly supported clades with > 0.9 posterior probability. Clade size is proportional to the number of species sampled in each clade. Associated floral and fruit forms are shown on the right. A more detailed view of this phylogeny is shown in Additional file 2.

Format: ZIP Size: 6.9MB Download file

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Additional file 4:

New sequence data. Voucher data and GenBank numbers for sequences newly generated as part of the study.

Format: DOCX Size: 18KB Download file

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Additional file 5:

New sequence data. Details of sequences downloaded from GenBank which appeared clearly misidentified or potentially contaminated sequences based on BLAST searches and their position in our preliminary Maximum Likelihood phylogenies.

Format: DOCX Size: 14KB Download file

Open Data

Additional file 6:

Supermatrix sequence alignment file (RAxML input). Final supermatrix alignment file in phylip format used as input for the Maximum Likelihood phylogeny estimation in RAxML.

Format: TXT Size: 11MB Download file

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Additional file 7:

Supermatrix partitions (RAxML input). Details of the partitioning scheme used in the supermatrix for the Maximum Likelihood analysis in RAxML.

Format: TXT Size: 1KB Download file

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Additional file 8:

Supermatrix excluded regions (RAxML input). Details of the excluded regions within the supermatrix alignment file in RAxML.

Format: TXT Size: 1KB Download file

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Additional file 9:

BEAST xml input file. Input file used for Bayesian relaxed molecular clock dating analysis in BEAST.

Format: XML Size: 9.3MB Download file

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Additional file 10:

PATHd8 input file. Input file used for local clock model dating analysis in PATHd8.

Format: TXT Size: 72KB Download file

Open Data