1) Taxon sampling
Lamiales sampling:
To place Lamiaceae within Lamiales, we will conduct plastome sequencing for 96 taxa, representing the following families: Acanthaceae, Bignoniaceae, Byblidaceae, Lentibulariaceae, Linderniaceae, Martyniaceae, Mazaceae, Orobanchaceae, Paulowniaceae, Pedaliaceae, Phrymaceae, Rehmanniaceae, Schlegeliaceae, Scrophulariaceae (sensu strico), Stilbaceae, Thomandersiaceae, and Verbenaceae. Sampling will be guided by results from our unpublished data, Schäferhoff et al. (2010), McDade et al. (2012), Olmstead (2012), and Refulio-Rodriguez & Olmstead (2014).
Lamiaceae sampling:
We plan to sample ~1000 species of Lamiaceae, representing approximately 14% of currently recognized species diversity. Our sampling strategy is designed to encompass all ~236 genera of Lamiaceae and roughly equal proportions of the total species diversity within each subfamily.
2) Sequencing and Assembly
We will follow workflows and protocols for capture and sequencing of plastomes developed by the Soltis lab at the University of Florida (e.g., Godden et al. 2012, 2013; Stull et al. 2013).
Assembly of NGS data will proceed following the workflow recommendations of Godden et al. (2012), approaches we have used successfully in the past (e.g., Stull et al. 2013).
3) Divergence Time Analyses
For estimation of divergence times we will employ penalized likelihood (Sanderson 2002) as implemented in treePL (Smith & O’Meara 2012) and Bayesian methods using BEAST v 1.8.0 (Drummond & Rambaut 2007).
Including the Lamiaceae within a broader phylogeny of Lamiales allows the implementation of several well-documented fossils as calibration points. Bignoniaceae have a rich fossil history (e.g., Reid & Chandler 1926; Brown 1962; Muller 1981; Wilf 1997; Manchester 1994; Pigg & Wehr 2002) that extends to the Paleocene. Likewise, Acanthaceae fossils have been reported from the Oligocene and Eocene (reviewed in Tripp & McDade 2014). and Oleaceae fossils are known from the middle Eocene (Call & Dilcher 1992; Meyer & Manchester 1997; Manchester 1994; Greenwood et al. 2005; Wang et al. 2010) and will provide minimum age constraints near the root of our phylogeny.