The mint family (Lamiaceae) is among the most diverse and economically important families of flowering plants, with many species used in traditional medicines or serving as important sources of timber, culinary herbs and spices, and essential oils. The extreme morphological complexity of the Lamiaceae, combined with the large number of species spanning diverse habitats, presents many taxonomic, or classification, problems; it is often difficult to distinguish closely related species. Numerous molecular studies have been published recently to help revise classifications?studies that reconstruct phylogenetic (genealogical) relationships among species using information from the genetic code (DNA). However, these analyses regularly yield patterns of unresolved relationships, and standard approaches used to resolve phylogenies, such as the reasonable addition of species and genes into the analyses, have been largely ineffective. The proposed research uses Lamiaceae as a case study to evaluate new, alternative approaches for resolving difficult phylogenetic problems and explores the limits of how evolutionary relationships can be efficiently and cost-effectively reconstructed for large groups of organisms. These approaches involve large-scale DNA (or genome) sequencing and new computational methods for phylogenetic inference. The research represents a necessary step towards resolving difficult phylogenetic problems in Lamiaceae and will help move mint systematics ?out of the bushes and into the trees??that is, to resolve clear evolutionary trees from the current unresolved ?bush? patterns.
The proposed research is at the forefront of systematic biology, combing field botany with recent advances in computational biology and molecular genetics, and it has the potential to demonstrate the efficacy of new, cross-disciplinary approaches to resolving difficult phylogenetic problems that can be applied to other problematic groups of plants and animals. The results of this study will: produce the first chloroplast genomes for Lamiaceae; contribute insights into the evolutionary history and biogeography of North American mint groups; and provide an essential framework for a much-needed taxonomic revision. Moreover, because this study requires field exploration and population sampling, it will facilitate the discovery and recognition of new mint species or important sources of genetic diversity that may warrant protection by government agencies or conservation organizations.
The mint family (Lamiaceae) is the sixth-largest flowering plant family (>7,000 species) and is of major ecological, economical, and cultural importance worldwide. Mint species are found virtually everywhere and, collectively, they exhibit a remarkably diverse range of growth forms and life histories (e.g. annual herbs to long-lived trees), ecological niche preferences (e.g. submerged aquatics to salt-tolerant desert plants), and physical attributes (e.g. simple to complex flower traits and chemistry). For these reasons, mints are a biologically interesting study group; they offer an exciting opportunity to investigate how a major plant group evolved and established in new habitats around the globe. However, these types of investigations require a comprehensive understanding of how mint species are related to each other, and reconstructing their relationships from DNA evidence has proven intractable in recent decades. The primary goals of our NSF-sponsored research were to help remedy this situation and to facilitate future research with best practices recommendations—more specifically, our goals were to design, develop, and test new, alternative approaches to reconstructing species relationships from large-scale DNA datasets in order to propose effective solutions to this complex problem. First, we published a detailed review of newly available ‘next-generation’ molecular laboratory techniques and DNA sequencing technologies, and we recommended efficient and economical research workflows to guide researchers through the complex process of identifying and acquiring large-scale data for evolutionary studies. We also collaborated to develop a new research tool (MarkerMiner 1.0) that identifies useful single-copy nuclear gene sets from flowering plant transcriptomes (i.e. sets of expressed genes from a plant’s genetic code or "genome"). Lastly, we tested our recommended workflows and tools as part of two independent test cases. For the first test case, we evaluated the utility of large-scale chloroplast DNA datasets in reconstructing mint relationships. We captured and sequenced whole chloroplast genomes from 96 closely related mint species (Hedeoma and allied mints from the southwestern USA and Mexico) and used these data to infer species relationships. Despite use of over 128 kilobase pairs of DNA sequence data, relationships were not fully reconstructed among the sampled mint species; large-scale chloroplast DNA datasets appear impractical for investigations of closely related mint species. For the second test case, we evaluated the utility of large-scale DNA data sets from the nuclear genome in reconstructing relationships in Lamiales—an inclusive group that includes mints and 24 other closely related families. We used our new tool, MarkerMiner 1.0 and processed transcriptome data for 77 species from Lamiales (including 19 mint species) generated by the One Thousand Plants (oneKP.com) project. The tool identified 1,993 new, single-copy nuclear genes for Lamiales, and we randomly selected 85 of these genes to infer species relationships. Our study produced the first hypothesis of family-level relationships in Lamiales based on nuclear DNA sequences, and most relationships were strongly supported. Workflows for capture of single-copy nuclear genes offer promising potential for future studies of Lamiaceae and Lamiales. This project provided research training for Mr. Grant Godden, a Ph.D. student in the Department of Biology and the Florida Museum of Natural History at the University of Florida. Mr. Godden in turn provided mentored research training to a visiting undergraduate student from Brazil and contributed, along with PI Soltis, to summer workshops for high school students and teachers sponsored by UF’s Center for Precollegiate Education and Training with content developed by members of the PI’s lab.
