Craig Barrett, Ph.D.
Our lab focuses on basic questions in plant evolutionary biology, including relationships among plant species, support for those relationships, and how evolutionary forces shape plant diversity. We use genomic data, in combination with morphology, physiology, and ecology to address these questions. Our studies range from the population level to across monocot angiosperms, spanning over 100 million years of evolution, diversification, and extinction.
Primary research foci:
(1) Relationships, support, and genome evolution of monocot angiosperms. The monocots include some of the Earth’s most ecologically important species, many of which are also economically important, forming the major basis for human nutrition (e.g. members of the grass family). Yet, many questions remain with respect to the evolutionary relationships among and within the major groups of monocots. Our work has focused on the ‘commelinid’ monocots, a morphologically and ecologically diverse group containing palms, gingers, grasses, and relatives. Specifically, we are employing genome-scale data to resolve and provide support for relationships among these major groupings, as well as investigating genomic changes such as polyploidy, genome structural variation, and mutational rate changes.
(2) Genome evolution in mycoheterotrophic plants, and their interactions with host fungi. Most plants use energy in the form of sunlight to synthesize sugars, but some plants have forgone this lifestyle and have instead become parasites. Plants such as broomrapes and mistletoes are directly parasitic on host plants, while others have become parasites upon their symbiotic mycorrhizal fungi; these are called ‘mycoheterotrophs.’ A fundamental question we are trying to address is, what happens to the genomes of plants that no longer rely upon photosynthesis? We have chosen mycoheterotrophic orchids to address this question, because there have been more independent transitions to mycoheterotrophy in this family than in any other plant family. Using high-throughput sequencing, we are determining complete plastid (i.e., chloroplast) genomes to assess the consequences of such a radically altered nutritional lifestyle. We are also studying how these plants have evolved to take advantage of their host fungi, from an evolutionary genetic perspective, by sequencing DNA and RNA in both the plants and their fungi.
(3) Integrative species delimitation using multiple sources of data. Determining species boundaries is a critical first step in studies of biodiversity, evolutionary relationships, and conservation. Yet, defining a ‘species’ has been one of the most contentious areas of Biology, and continues to be. Moreover, species may be defined in practice using many different types of information, including morphology, genetics/genomics, ecology, behavior, physiology, and geography. We are working to explore ways of integrating multiple sources of data into single, objective assessments of species boundaries, so that we may improve the accuracy of species delimitation in a holistic sense, and using population-level approaches among various groups of monocots (e.g. orchids, palms) as case studies. Moreover, we focus on groups containing rare or endangered entities, in order to more clearly define species boundaries and population level processes (e.g. genetic diversity, inbreeding, gene flow) to aid in downstream policies for their conservation.
Barrett Lab Website: coming soon.
Selected publications:
Barrett CF, Bacon CD, Antonelli A, Cano A, Hofmann T. 2016 An introduction to plant phylogenomics, with a focus on palms. Botanical Journal of the Linnean Society, special issue on palm biology, Invited review. 182: 234-255.
Barrett CF, Comer J, Leebens-Mack J, Li J, Mayfield-Jones DR, Medina JR, Perez L, Pires JC, Santos C**, Stevenson DW, Zomlefer WB, Davis JI. 2015. Plastid genomes reveal support for deep phylogenetic relationships and extensive rate variation among palms and other commelinid monocots. New Phytologist, 209: 855-870.
Barrett CF, Freudenstein JV, Li J, Mayfield-Jones DR, Perez L, Pires JC, Santos C. 2014. Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms. Molecular Biology and Evolution, 31: 3095-3112.
Barrett CF, Specht CD, Leebens-Mack J, Stevenson DW, Zomlefer WB, Davis JI. 2014. Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales Griseb.)? Annals of Botany, 113: 119-133.
Barrett CF, Davis JI, Leebens-Mack J, Conran JG, Stevenson DW. 2013. Plastid genomes and deep support among the commelinid monocot angiosperms. Cladistics 29: 65-87.
Barrett CF, Davis JI. 2012. The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation. American Journal of Botany, 99: 1513-23.
Barrett CF, Freudenstein JV. 2011. An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid. Molecular Ecology 20: 2771-2786.