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

Abstract

Background: The Solanaceae is a plant family of great economic importance. Despite a wealth of phylogenetic work on individual clades and a deep knowledge of particular cultivated species such as tomato and potato, a robust evolutionary framework with a dated molecular phylogeny for the family is still lacking. Here we investigate molecular divergence times for Solanaceae using a densely-sampled species-level phylogeny. We also review the fossil record of the family to derive robust calibration points, and estimate a chronogram using an uncorrelated relaxed molecular clock.

Results: Our densely-sampled phylogeny shows strong support for all previously identified clades of Solanaceae and strongly supported relationships between the major clades, particularly within Solanum. The Tomato clade is shown to be sister to section Petota, and the Regmandra clade is the first branching member of the Potato clade. The minimum age estimates for major splits within the family provided here correspond well with results from previous studies, indicating splits between tomato and potato around 8 Million years ago (Ma) with a 95% highest posterior density (HPD) 7-10 Ma, Solanum and Capsicum c. 19 Ma (95% HPD 17-21), and Solanum and Nicotiana c. 24 Ma (95% HPD 23-26).

Conclusions: Our large time-calibrated phylogeny provides a significant step towards completing a fully sampled species-level phylogeny for Solanaceae, and provides age estimates for the whole family. The chronogram now includes 40% of known species and all but two monotypic genera, and is one of the best sampled angiosperm family phylogenies both in terms of taxon sampling and resolution published thus far. The increased resolution in the chronogram combined with the large increase in species sampling will provide much needed data for the examination of many biological questions using Solanaceae as a model system.

Figure 1

Solanaceae phylogeny. Phylogenetic relationships between major clades of Solanaceae based on a Maximum Likelihood analysis of a 1076 taxon supermatrix (ITS, waxy, ndhF, matK, psbA-trnH, trnS-G, trnL-F) with 10,672 bp of sequence data. Major clades recovered by previous phylogenetic studies [22,43,64] are labelled, as is the M Clade identified for the first time here. Clades with low bootstrap support (60-79%) are shown in pink, while strongly supported clades (boostrap support 80-100%) are in black. A. Major clades of Solanaceae. B. Relationships within Solanum.