title: Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments.
abstract: Microbial evolution experiments enable us to watch adaptation in real time, and to quantify the repeatability and predictability of evolution by comparing identical replicate populations. Further, we can resurrect ancestral types to examine changes over evolutionary time. Until recently, experimental evolution has been limited to measuring phenotypic changes, or to tracking a few genetic markers over time. However, recent advances in sequencing technology now make it possible to extensively sequence clones or whole-population samples from microbial evolution experiments. Here, we review recent work exploiting these techniques to understand the genomic basis of evolutionary change in experimental systems. We first focus on studies that analyze the dynamics of genome evolution in microbial systems. We then survey work that uses observations of sequence evolution to infer aspects of the underlying fitness landscape, concentrating on the epistatic interactions between mutations and the constraints these interactions impose on adaptation.
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, United States; Department of Physics, Harvard University, Cambridge, MA 02138, United States; FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, United States.
authors.forename: Elizabeth R
authors.initials: ER
authors.lastname: Jerison
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, United States; Department of Physics, Harvard University, Cambridge, MA 02138, United States; FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, United States. Electronic address: mmdesai@fas.harvard.edu.
authors.forename: Michael M
authors.initials: MM
authors.lastname: Desai
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D005075:Biological Evolution; D004843:Epistasis, Genetic / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics*; D019143:Evolution, Molecular; D056084:Genetic Fitness; D016680:Genome, Bacterial / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D008957:Models, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D012641:Selection, Genetic