Microbial and Viral Evolution

Coordinators: Santiago Elena, Michael Lassig, Luca Peliti, Paul Sniegowski

Scientific Advisors: Matthew Kane

The program will bring together theorists and experimentalists to discuss the forefront of research in a rapidly moving field of evolutionary biology: the evolution of bacteria, archaea, and viruses. This topic offers a particularly promising interplay between theory and experiment. The evolution of these systems can be followed in laboratory experiments and, by massive sequencing, be traced at the level of entire populations. The proposed program will link these topics with epidemiology and the dynamics of host-pathogen interaction and of immune systems, on the one hand, and with fundamental ecological issues about the organisms that drive the Earth’s global elemental cycles on the other. It will thus contribute to connecting the scientific communities of these fields. On the theoretical side, it will address the challenge of understanding molecular evolution as a dynamical process governed by multiple interactions: linkage in a genome, fitness effects and spatiotemporal structure of a population. Particular care will be taken to provide timely introductory tutorials to make theoretical and applied topics of the program accessible to a cross-disciplinary audience of scientists with backgrounds in physics, biology, and public health.

The program consists of seminars by the participants and additional invited speakers, fostering in-depth discussion and collaborations in a relaxed interdisciplinary environment. KITP invites applications from interested scientists ranging from a few weeks to the duration of the program. Some level of financial support will be available to invitees, the amount depending both on the needs of the participants and the availability of funds.

This program builds on a series of successful previous activities, which enjoyed enthusiastic response from participants, including Population Genetics and Genomics (2008), Evolution of Molecular Networks (2007), Bio-Molecular networks (2003), and Statistical Physics of Biological Information (2001).

This program will cover the following topics:

  • Microbial evolution and phylogenetics
  • Population genetics I: selection, linkage and gene transfer
  • Regulatory evolution in prokaryotes
  • Evolution of host-pathogen and symbiotic interactions
  • Human microbiome, immune interaction, immune dynamics
  • Viral evolution: Exploration, discovery and experimentation
  • Population genetics II: ecology, selection and game theory
  • Topical week on influenza/emerging viruses
  • Epidemiology and ecology of diseases
  • Population genetics III: spatio-temporal models