How do horizontal processes like DNA transfer and organellogenesis arise from ecological interactions and create new ones, and how does this affect evolutionary outcomes across communities?
Disentangling the “web”
My goal for this lab is to be more question-driven than system-focused. The “tree of life” is a generally bifurcating scheme for understanding descent and ancestry of extant taxa. Much of the data within genomes is transferred vertically from parent to offspring, but sometimes nucleic acids incorporate horizontally, within a generation, into new genomes and may be subsequently passed down vertically (if permitted by selection or drift). This creates a tree of life that appears web-like at finer resolution. The transfers that build this web can range from bits of non-coding DNA to whole operons and chromosomes to organisms themselves (that become organelles). What DNA gets moved around in nature is largely dependent on transfer mechanism, however, not a lot of work has been done to understand the breadth and variety of these mechanisms or to build programs and pipelines that discern between them when doing studies of horizontal transfer. Nucleic acids can move horizontally between individual genomes within the same population or across domains. All transfer events are preceded by a broader context that puts two (or more) organisms (or nucleic acid-containing entities) in direct (or indirect) contact, but to date, that context is largely ignored. There is so much we can learn from studying horizontal processes in new and creative ways, such as:
What is the background level of DNA transfer across the biosphere?
What drives horizontal transfer? Is more DNA transferred under certain environmental conditions or during periods of change? Between organisms with particular community roles? By certain mechanisms?
How can we use the genome-to-genome connections created by DNA transfer to learn more about organismal interactions and extrapolate past and present ecology?
How can we build better tools to measure rates of both coding and non-coding DNA transfers? (AI/ML people, get in touch! We’re writing a grant proposal on this right now.)
How random is the process of DNA transfer and can we model the predictable parts that arise from different transfer mechanisms and environmental changes that induce them?
To contradict my own text, there are some systems that are important to focus on when studying horizontal processes and attempting to “disentangle the web of life”. We work in all domains of life here but protists are of particular importance. They are under-studied, under-surveyed, and under-appreciated. (So is eukaryotic HGT…) By looking at eukaryote genomes that retain fewer DNA transfers than prokaryotes, it becomes possible to study the contexts and fates of individual transfer events. Protists also only exist because of the primary endosymbiotic event that created the mitochondrion (a horizontal process), and they include algae that acquired photosynthesis via primary and serial endosymbioses. The more we can learn from horizontal processes that occur on different scales, the more we can understand ecological and evolutionary drivers of major transitions. Read about three active projects below that address gaps in our knowledge of horizontal processes and please reach out to get involved in one or more of these areas!
“Ecological HGT” project
Horizontal gene transfer (HGT) creates genetic variation in populations across all domains of life, however, most studies of HGT focus on individual transfers and the functional information derived therefrom. This is useful but does not consider DNA transfer more broadly, i.e., non-gene transfers, donor-recipient dynamics, or trends and background levels of transfer that may help infer ecological information. Ecological interactions put organisms in positions to exchange more DNA, DNA transfer can lead to lifestyle transitions, and these changes create new ecological interactions. By adapting and developing new bioinformatic tools and running long-term experiments in the lab, we aim to build better ways to detect DNA transfers in metagenomic data to uncover community-level trends and mechanistic information.
SEM image taken by J. Van Etten and J. Burns
Major evolutionary transitions: Paulinella projects
The photosynthetic Paulinella lineage repesents the ONLY acquisition of photosyntheis via primary endosymbisois outside of the event that created Archaeplastida and led to the advent of all other photosynthetic eukaryotes on Earth. Whereas the Archaeplastida lineage arose >2 billion years ago, Paulinella’s photosynthetic organelle originated only ~100 million years ago, allowing us to witness the process of primary endosymbiosis “in action”. Using comparative genomics and experimental approaches, we aim to better characterize both the nuclear and organellar (‘chromatophore’) genomes to better understand major evolutionary and ecological transitions, and why some taxa can acquire organelles while others cannot. We are currently sequencing a novel photosynthetic Paulinella species and have many future projects planned for this organism that range from genetic engineering to biophysics to population genomics.
Protist biodiversity projects
Most species on the planet remain unknown. An ongoing goal for this research program is to continue finding and describing novel microbial species (including rare and low abundance taxa) using microscopy, high throughput techniques, and alignment-free phylogenomics. Our existing specialty is in algae/protists (current active projects on Paulinella [above] and glaucophytes [ask me about this]), but we are interested in any and all novel or unculturable taxa from all domains of life. Discovering new species typically involves applying one of two contrasting philosophies: (i) targeted exploration, systematically surveying a predetermined environment in a hypothesis-driven manner, or (ii) understanding algal/protist morphology and behavior, making educated guesses on where to look in a discovery-based approach. In this lab, we are working to unite both frameworks to optimize the potential for discovery and characterization of new organisms. We are interested in working with researchers and hobbyists who have a passion for looking at weird stuff under the microscope and contributing to or leading projects that grow from these findings.