Research
My research interests encompass the profound impacts of whole genome duplication and the convergent evolution of complex traits in vascular plants. These processes underpin the extraordinary diversity of life on Earth and are essential to our understanding of evolutionary biology.
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Currently, my work is centered on the convergent evolution of Crassulacean Acid Metabolism (CAM). As a postdoctoral researcher in the Heyduk lab I am investigating the evolutionary origins of CAM in Yucca, utilizing an integrative multi-omics approach to examine changes in gene regulation, protein abundance, and rewiring of metabolic networks associated with the shift from C3 to CAM. Ultimately I hope to apply what I learn in Yucca to aquatic CAM plants in Isoetes and beyond.
Convergent origins of CAM photosynthesis
If convergently evolved traits are likened to natural replicates in the experiment that is evolution, CAM plants are metaphorical laboratories. While most efforts including some of my current research focus on the evolution of CAM in arid environments, I am particularly fascinated by its utility to aquatic plants. I am interested in integrating genomic resources with time-course data that combines gene expression and metabolite abundance to synthesize a detailed explanation of the molecular mechanisms driving the transition from C3 to CAM in vascular plants. I believe that the evolutionary and ecological distinctness of the genus Isoetes provides a vital counterpoint to similar studies in terrestrial angiosperms. My prior research has already shown that CAM in Isoetes is virtually indistinguishable from that in dry-adapted plants despite occupying nearly opposite niches and being separated by hundreds of millions of years of evolution. By comparing nature's replicates, I hope to gain valuable insights into mechanisms of adaptation, the constraints of evolution, and the selective pressures driving it all onward through time.
Neo-polyploid speciation in Isoetes
Allopolyploidy is an important source of species diversity and a primary contributor to genetic novelty across the plant tree of life. However, recurrent formation of polyploid lineages and subsequent gene flow complicate taxonomic circumscription and hinder conservation efforts in hybrid and polyploid species complexes. Additionally, the importance of extant polyploid lineages has been at times called into question. The high frequency of neo-polyploid lineages relative to ancient ones suggests that the vast majority of recent polyploids may constitute evolutionary “dead-ends.”
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The lycophyte genus Isoetes is known for frequent hybridization and high rates of polyploidy making it an ideal system to investigate the formation and short-term evolutionary trajectory of polyploid lineages relative to their diploid progenitors. My research utlizes ddRADseq and whole chloroplast sequencing to unravel reticulate polyploid species complexes in Isoetes. My recent findings in the I. appalachiana species complex demonstrates that allopolyploid 'species' in Isoetes are in fact the product of multiple independent origins. The resulting lineages appear to be genetically isolated with little to no gene flow being conclusively found between geographically distant populations. Our research informs both evolutionary biology and conservation, suggesting a "diploids first" approach that prioritizes the preservation the processes that drive recurrent formation of polyploids.
A reticulogram showing just some of the natural hybrids associated with a single North American species, Isoetes engelmannii.
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Isoetes appalachiana from the type locality at Tipton Reservoir in central Pennsylvania.
Circos plot of intra-genomic synteny retained for over 100 million years in the Alsophila spinulosa genome. Each line represents a collinear block of at least four genes.
Circos plot of inter-genomic synteny retained for over 300 million years between Diphasiastrum complanatum and Huperzia asiatica. Each line represents a collinear block of at least four genes.
Ancient WGD and diploidization in seed-free vascular plants
Ancient whole genome duplication (WGD) is ubiquitous among land plants and casts a long shadow across their evolutionary history. Following WGD, plants undergo a subsequent process known as diploidization to restore diploid patterns of inheritance and expression. In angiosperms, diploidization is characterized by extensive and often rapid changes to gene content, gene order, chromatin organization, and chromosome structure. However, due to a historical lack of genomic resources this process is not well understood in pteridophytes. The homosporous ferns and lycophytes are notorious for their large genomes and astronomical chromosome numbers. This has in turn led researchers to suggest that this process of genomic reorganization following WGD might proceed very differently in some spore-bearing plants than in their "seedy" cousins.
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During my dissertation research, I had the opportunity to conduct a thorough analysis of some the first high quality genome assemblies generated for homosporous ferns and lycophytes. Within their genomes I found incredible amounts of intragenomic synteny preserved from WGDs occuring over 100 million years ago. Even more surprisingly, I found a great deal of intergenomic synteny preserved between homosporous lycophytes Huperzia asiatica and Diphasiastrum digitatum despite over 300 million years of divergence and multiple independent WGD events. Taken together, our results seem to suggest that genomic rearrangement proceeds much slower in some homosporous vascular plants compared to heterosporous lineages. Though we have yet to identify the precise mechanism for this genome-wide deceleration, our investigation into diploidization within seed-free vascular plants offers a compelling contrast to analogous research in angiosperms.
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The first step to advancing our knowledge regarding the mechanisms of WGD and diploidization in seed-free free plants is generating highly complete genome assemblies across the fern and lycophyte phylogenies. This dream is finally becoming a reality as long-read sequencing technology and chromatin conformation capture put ever larger genomes within our grasp. By comparing content, position, and order of genes and pseudogenes we can begin to reconstruct the history of genomic rearrangement in the homosporous pteridophytes. Transcriptomics and phylogenomics can give us information on the fate of duplicated genes allowing us to probe for evidence of selection, expression bias, and neo/sub-functionalization. Finally, the rise of pan-genomics in other lineages has demonstrated a great deal of diversity in the genome structure of closely related angiosperms. As sequencing technology continues to advance it will be fascinating to find if this pattern extends to their seed-free relatives.
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