Nitrogen-fixing symbioses, particularly in the form of root nodules, are major drivers in many terrestrial ecosystems. Remarkably, these evolutionary strategies are concentrated in one small branch of the plant tree of life, traditionally thought to be due to an underlying "predisposition" that enabled multiple subsequent origins of plant-microbe symbioses (increasingly genomic evidence is suggesting the possibility of a single origin followed by dozens of losses). Commonalities and differences among multiple origins of the nodule organ, assessed at multiple levels from genes to ecology, will be highly relevant to crop improvement in non-fixing lineages.
Given the presence of multiple evolutionary transitions, and high diversity across phylogenetic and phenotypic axes, this clade is an exemplar for elucidating the mechanisms behind symbiotic strategies. I am using previously developed approaches (below) and newly assembled trait and phylogenomic datasets to investigate the evolutionary context that led to global dominance and species richness of this clade. This research is supported by UF seed funding and a recently funded Department of Energy grant focused on massive phylogenomic approaches to elucidating and engineering symbioses.
Niche biology in the Saxifragales
The Saxifragales are an ancient, relatively isolated clade of angiosperms associated with the Rosids and Vitales, whose heterogeneous composition is one of the great surprises of plant molecular systematics. In comparison with other clades at this level, it is relatively modest in size but exhibits a vast diversity of habitats. For instance, in this group one finds desert succulents closely related to aquatic weeds, or forest dwellers near alpine cushion plants. I am using this clade as a test case for new ideas in integrating niche modeling and phylogenetics to examine historical habitat transitions.
Part of this work involves some methods development in the field of phyloclimatic modeling. Another important element is the use of collections; I have sequenced hundreds of specimens, including collections made over a century ago. This part of my work was funded as part of the first cohort of collections postdocs in the NSF PRFB program. Undergraduate students have played a major role in data collection for this project.
Deep hybridization in Heuchera
Heuchera has frequently been cited as a model for chloroplast capture, but recently developed sequencing technologies and coalescent methods have allowed me to return to this system with a high-resolution and probabilistically rigorous approach using hundreds of thousands of basepairs from all three plant genomic compartments. This work has revealed deep phylogenetic incongruence involving Heuchera and two closely related genera, as well as numerous instances within the genus. The chloroplast and mitochondrial phylogenies are inconsistent with gene tree distributions generated assuming the coalescent, suggesting that incomplete lineage sorting is a poor explanation for this phylogenetic incongruence. This work was part of my dissertation and was funded by the NSF DDIG program.
I am currently working on applying ancestral reconstruction of niche space in this system in order to evaluate how historical range dynamics could drive gene flow among lineages that are currently allopatric, particularly under Pleistocene cooling scenarios. Another area of continued work is improved taxon sampling; we are beginning to approach completion on this front. This work was funded by the NSF PRFB program.
Sky island diversification
Discontinuous habitats create unique population pressures for organisms, creating numerous persistent barriers to gene flow and therefore opportunities for speciation events. Oceanic islands and "sky islands" – archipelago-like montane systems of the western U.S. – are typical examples of this scenario. Many have argued that these principles apply to other habitat types that are less often recognized, such as caves. I have performed joint molecular and morphological species delimitation in the Heuchera parviflora complex with the aim of elucidating an island-like system comprising rockhouses of the eastern U.S. These cave-like habitats are found in dissected plateau regions across a number of divergent substrate types – principally sandstone, dolomite, and quartzite – correlating with lineages that we have recognized as taxonomic species or varieties.
I am currently finishing some new work with an undergraduate on the Heuchera longiflora system, also in the eastern U.S. In this instance, calcareous outcrops instead of rockhouses are the discontinuous substrates that appear to have driven island-like diversification in this system. This work, supported by an NSF REU, underlines the continued existence of under-appreciated biodiversity even in parts of the world that some might think well-explored.