Projects and collaborations


Unveiling the fitness landscape leading to a key viral innovation

Roy Kishony and I are developing high throughput techniques to reveal the fitness landscape underlying lambda evolution to exploit a novel receptor.  We expect to build landscapes on the order of >10^7 genotypes.  With this approach, we will be able to identify higher order epistatic interactions and test how ecological interactions affect the architecture of the landscape.

Postdoc Jenna Gailey and graduate student Alita Burmeister are leading the way with the first round of experiments on the architecture of lambda's fitness landscape.

Revealing the first principals of biophysics underlying fitness landscapes

William Cramer and I are studying the biochemistry and structural biology of the interactions between mutant lambda J proteins and LamB (native receptor) and OmpF (novel receptor). Characteristics of these interaction determine epistasis and the form of the fitness landscape.

Sympatric speciation of lambda

A former undergraduate assistant Devin Dobias and I observed the sympatric speciation of lambda in the lab and are developing the system to test theory on ecological speciation.  

Evolution of E. coli-lambda interactions

Joshua Weitz and I have a long-running collaboration on how different nonrandom structures form in bacterial-phage interaction networks.  To study this, we preform meta analyses, coevolution experiments, and sample natural microbial communities.

Biophysics of Lambda resistance and its costs

Robert Beardmore and I study lamB (Lambda receptor) mutations and their effects on resistance, pleiotropic costs, their biophysical causes, and effects on coexistence.  To do this, we combine experiments with protein models, morphometric analyses, and population genetic simulations.

The role of recombination with junk DNA and adaptation of viruses. 

Jeff Barrick and I observed Lambda recombine with a relict prophage gene trapped in E. coli's genome.  A former undergraduate Ryan Quick and I are studying whether the recombination provided beneficial variation. 

Evolution along the parasite-mutualist continuum 

Luis Zaman is heading a project on the evolution of Lambda's relationship with its host, from providing a benefit for E. coli to causing its lysis. 

Past collaborators:
Richard Lenski, Jeffrey Barrick, Nelson Hairston Jr., Stephen Ellner, Laura Jones, Takehito YoshidaRees Kassen, Sijmen Schoustra, Frances Pick, Anurag Agrawal, Dominique Schneider, Ellinor Michel, Pete McIntyre

Past working groups and projects
DARPA FunBio Project

NESCent Working Group: Mathematical Models, Microbes & Evolutionary Diversification

NYANZA Project

side note

.Fitness landscape, large network

Example of a large fitness landscape described as a network of genotypes.  Lambda's path from ancestral function (blue) to new function (green).

Coevolutionary landscape

This figure was published in Science, it demonstrates the relationship between physical qualities of the host, ie. receptors, and the architecture of viral fitness landscapes.  Also, how coevolution changes the architectures of fitness landscapes and can open new paths.

interaction matrix

Large interaction matrix of coevolved  lambda and E. coli.

LamB Deformations

Figure describing how deformations in lambda's receptor confer resistance to the phage.