The genome is typically regarded as an instruction manual for building an organism. However, the majority of DNA in every plant and animal cell derives from the activity of transposable elements (TEs) or “jumping genes.” These entities exploit the cell’s replication machinery to self-copy and reinsert into new chromosomal locations. TEs have long been recognized as evolutionary agents in the (minimal) sense of behaving like genomic parasites: they initiate and control their own replication in ways that benefit their populations, sometimes at the expense of the host organism.
Our project is distinctive in regarding TEs also as ecological agents. This involves identifying specific features of a genome (e.g. chromosome structure, gene density, methylation patterns) that impact the abundance, distribution, and diversity of TE populations. Put differently, our project regards individual TEs as if they were organisms residing within an intra-cellular ecosystem. By identifying a variety of niches and ecological interactions within genomes, this new perspective will transcend the simplistic dichotomy between functional versus “junk” DNA. It will also shed light on otherwise perplexing questions about variability in genome size, such as why the genome of an onion is five times larger than that of a human.
This project will generate 15-20 articles clarifying foundational concepts and applying ecological methods to genomic data. Our project includes interdisciplinary training for two postdocs and several graduate student researchers. We will also host two “hothouse” workshops on genome-level ecology, where early career researchers from different disciplines collaborate on small projects. The primary outcome of this project will be the establishment of genome-level ecology as a novel and exciting discipline. By harnessing insights and methods from the science of ecology we will shed new light on the structure and function of DNA.
