Research

Since its origins in the prehistoric times, agriculture have been in constant flux, dispersing around the world, constantly adapting, and benefiting from human improvements and innovations. I have been studying those phenomena in crops using comparative genomics. My current aims are to elucidate how crop dispersals, and new agricultural practices affect natural environment, wild relatives and microbial communities.

Using genomic and metagenomic information from plant historical, archaeological, and living material, we can observe evolution in time and space, and investigate the processes of genomic adaptation, and environmental and microbial associations in plants. I am particularly interested in the evolutionary response of crops and crop wild relatives to new environments and to habitat management. 

Agricultural revolutions depended on adapting plants and animals to new anthropogenic environments to increase food supply and were the cornerstones of the major transitions in human history. The First revolution, better known as ‘Neolithic’, relied on plant and animal domestication worldwide and promoted sedentary lifestyle. The Second and the Third agricultural revolutions intensified food production, and facilitated population and economic growths. The Second revolution took place between the 18-19th century locally in the British Empire. The third revolution, also known as the ‘Green’ revolution took place in Latin America, Africa and Asia in the 20th century, doubling crop production in Asia through the introduction of irrigation, agro-chemicals and elite high-yielding variety monocultures. All three revolutions are hypothesized to have had a huge impact on plant diversity, environment, microbiomes, land use and our dietary habits, however, we known very little about the evolution of interactions among them. To fill those gaps in our knowledge, I propose to take a multilevel view on changes in agriculture ecosystems throughout the Green revolution’s crop population bottleneck and cultivation habitat turnover. The focus of my research is to investigate the direct and indirect interactions of plants with humans, microbiomes, and environment using plant genomics, microbial metagenomics, geochemistry and plant nutrient profiling.  

In the past 10 years a whole new body of genomic research revealed substantial amounts of gene flow between closely related species. Perhaps the most striking case is that of Neanderthals and Denisovans who introgressed with archaic humans. No less important has been the realization that our domesticated crop plants admixed with geographically diverse wild relatives as agriculture expanded from the areas of their origin. In fact, this phenomenon is so prevalent that the vast majority of the scientific community accepted a protracted and multi-origin paradigm of crop domestication. It makes intuitive sense that locally adapted wild species could contribute genetic variants that increase fitness and yield of crop plants in the local environment. Interestingly, the gene flow in the opposite direction, from crop plants to wild relatives, has been less explored. What is the extent of such gene flow? Is it dependent on the intensity of crop cultivation in the region? How many of the wild relative species does it affect and how genetically distant are they? Finally, is there a net gain for the wild relative from such gene flow? Are there any domesticated traits in particular that can contribute to better fitness of wild relatives? Answering those questions is of fundamental importance to i) inform the conservation efforts for crop wild relatives, ii) enhance our understanding of transgene leakage, and iii) help in correct interpretation of crop origins and their domestication.