Missing-link cultivars: Using fungus-farming ants to solve mysteries of crop domestication

Name of applicant

Jonathan Shik


Associate Professor


University of Copenhagen


DKK 4,996,182



Type of grant

Semper Ardens: Accelerate


The transition from hunting and gathering to sedentary agricultural societies 12,000 years ago was probably the most important event in human history. Today, we take for granted that the grocery store is filled with massive fruits optimized for human tastes. However, the traits that make modern domesticated crops good for humans also make most species unable to survive in the wild without the care of human farmers. Currently, the underlying genomic features that made specific plants good for early pre-domesticated cultivation are mysterious, as the ‘intermediate’ crop varieties are typically lost to history, which constrains our understanding of the genomic adaptations that gave rise to modern crops over thousands of years.


Humans are not the only farmers. A lineage of ants called the ‘attines’ evolved farming societies 60 million years before humans, domesticating fungal food crops they cultivate in monoculture in climate-controlled nests. I propose these ant farmers can provide unique insights into how and why domestication evolves because: 1) they underwent farming transitions like humans towards greater size, productivity, and complexity, 2) key domestication transitions thrive as ‘living fossils’ that enable comparative studies of domestication’s formative steps, and 3) they arose only by natural selection, without culture and technology that can mask evolutionary dynamics in human farming systems. I propose that ant farming systems can provide lessons on crop resiliency as they thrived over millions of years of climate change while the sustainability of human systems is threatened. The cutting-edge research I propose aims to learn these lessons by revealing which genome-evolution mechanisms underlying crop domestication are universal and which are unique to ants. Such insights are fundamental to understanding how the rise of agriculture rapidly transformed human evolution over 12,000 years.


I will use fungus-farming ants as model systems to understand to explore the genomic evolution mechanisms of crop domestication. I will focus on a form of genome duplication that frees redundant gene copies to evolve new functions and is associated with human domesticated plants. I hope to solve a longstanding chicken-egg mystery as we lack transitional plants to test if pre-existing genome duplications enabled domestication or if they evolved as a later result of human cultivation. The ‘missing link’ fungal cultivars of ants provide a unique system to solve this mystery since they exhibit key evolutionary transitions to larger numbers of genome copies coinciding with advances in farming productivity. I will first use cutting edge approaches to sequence the many genomes inside fungal cells and link their individual expression to the farming performance and then use advanced microscopy to trace the flow of individual nutrient molecules through the cultivar to link gene expression and nutritional optimization. The results will: 1) reveal the sequential evolutionary steps that yield more specialized and higher-performing crops, and 2) enable novel tests of functional consequences of ‘missing-link’ polyploidy transitions in living crops.

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