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Our research studies the evolution and ecology of plants, using field-based and genomic approaches. Most of our research either tackles the mechanisms driving speciation, or the genetic basis of adaptive trait variation. Such studies can help us understand the evolutionary processes which have given rise to the enormous diversity of flowering plants.
Darwin Tree of Life
We are contributing to the Darwin Tree of Life Project—a visionary initiative to sequence reference genomes for all 60,000 British native eukaryotic organisms. The University of Edinburgh is collaborating with the Royal Botanic Garden Edinburgh to form the Edinburgh Genome Acquisition Laboratory, a hub for collecting and processesing plant samples. Our primary goal is to sample the diverse British bryophyte flora, and in collaboration with the Royal Botanic Gardens Kew, the flowering plants.
The University of Edinburgh group is working with Edinburgh Genomics to sequence representative plant species that have large complex genomes.
Speciation histories in young floras
Recent species radiations can provide fascinating insights into the evolutionary procecsses underlying diversification. Much of our current speciation research is focused on hybrid speciation: a process that has intrigued generations of biologists, including Stebbins and Grant, as it provides a mechanism for the rapid formation of new reproductively isolated taxa. My NERC independent research fellowship is focusing on the origin of novel hybrid taxa in the hemiparasitic plant genus Euphrasia (eyebrights). This group is represented by ~20 species in the UK, with at least 60 recognized hybrid combinations, and 5 species of putative hybrid origin. By studying the genomic composition of the proposed parental taxa and the putative hybrid species Euphrasia vigursii and E. rivularis, I hope to shed light on the role that mating system (selfing vs. outcrossing) and polyploidy (diploid and tetraploid) have on hybrid speciation. This is also the research topic of PhD Student Max Brown, who is studying the origins of British hybrid species. These results will help us understand the repeated outcomes of this important evolutionary process, and improve our knowledge of the formation of recent endemic taxa. You can read more about our Euphrasia research on the dedicated Euphrasia webpage.
One of the greatest challenges in the study of young floras is explaining how new species evolve when they are likely to experience rampant gene flow from congeneric taxa. In my previous work, I showed that strong population genetic structure in conjunction with rapidly evolving reproductive barriers contribute to the exceptional species diversity found in the tropical genus Begonia. Mario Duran (PhD Student) is continuing research on divergence-with-gene flow, in the classic model plant species Antirrhinum. This work, in collaboration with Andrew Hudson, involves RAD sequencing analysis of populations from a recent species radiation in the Sierra Nevada. This is one of a number of collaborative RAD projects ongoing in the lab, such as our long-running work trying to resolve the phylogenetic relationships of the recent rapid radiations of Vireya Rhododendrons in South East Asia (with Valerie Soza, Ben Hall and George Argent).
Genetic basis of adaptive traits
Plants demonstrate a remarkable range of adaptive variation: from growing in some of the harshest environments on earth, to finding remarkable sources of nutrients through parasitism or carnivory. We are using new genomic approaches to find the genes underlying the major adaptive transitions.
Parasitism is a remarkable trait that has involved numerous times independently in different plant groups. In 2015, we were awarded a NERC International Opportunities Fund grant to generate preliminary data on the genetic basis of plant parasitism in the hemiparasitic plant Euphrasia. In collaboration with Claude dePamphilis, Rob Ness, and Galina Gussarova, we have sequenced a draft genome, plastid genomes, and are generating RNA-seq data from plants with and without suitable hosts. This research is aimed to understand the genetic changes associated with the transition to a parasitic lifestyle.
One dramatic yet surprisingly common transition in plants is from perenniality to annuality. In my post-doc with Jannice Friedman in Syracuse University, Upstate New York, I studied the genetic basis of this transition in the common monkey flower Mimulus guttatus. We showed that a major chromosomal inversion maintains this life-history difference across the species range despite high levels of gene flow. These results (see here and here) add to our growing knowledge of the genetic basis of divergence with gene flow.
Shifts in floral form and pollination strategy are perhaps the best-documented of all major evolutionary transitions in plants. Given this, it seems remarkable that a new form of floral dimorphism, termed flexistyly, has been found in the widely cultivated ginger family. PhD Student Surabhi Ranavat is investigating the genetic basis of this unique reproductive strategy, where the style physically moves within a day and thus changes the functional plant gender (read details here).