Molecular Mechanisms of Cellular Evolution

  1. The Role of Chance and Necessity in Evolution

This project asks whether adaptive pathways are inherently deterministic, dominated by internal or external controlling or limiting processes, or highly contingent upon chance events such that very different evolutionary outcomes may arise from identical initial conditions. Little is currently known about how prior evolutionary history shapes future evolutionary trajectories, or a lineage’s capacity to produce adaptive variation. Our approach is to systematically investigate how prior history affects the evolution of modern organisms. We individually engineer modern bacterial genomes with a series of inferred ancient genetic sequences (that produce what we refer to as Lazarus proteins) and then experimentally evolve the ancient-modern hybrid bacteria in the laboratory to examine how the ancient genes and modern genome adapt to each other. The work draws upon tools from a variety of disciplines such as paleogenetics, synthetic biology, experimental evolution, whole-genome sequencing as well as proteomics, and demonstrates a new approach with which to probe historical pathways of evolution, as well as to connect genotype and phenotype. (We are currently hiring for work in this area, please see Opportunities).

Screen Shot 2015-11-22 at 5.28.37 PM

Our paper on experimental evolution of bacteria harboring an ancient ribosomal protein:

2.   Evolutionary Relationship Between Essential Genes and Genomes

The main goal of this project is to develop a molecular framework to delineate the underpinnings of lateral gene transfer and provide molecular insights into the constraints of adaptation between foreign genes and host genomes. It was suggested that a foreign gene that is transferred to a genome is initially deleterious, yet may persist if its function is fine-tuned through compensatory mutations that improve its function in the new host. Further, the phylogenetic distance between the donor and recipient genome was assigned as one of the main determinants of this tuning. Here our primary aim is to test this idea and identify the link between the phylogenetic distance among a host genome and an alien gene. Our second aim is to assess how much going back in the phylogenetic time will affect an organism’s survival in comparison to transferring genes from currently existing homologs.

Read our BioRxiv preprint relevant to this study:

More on what we do.