The role of clonal interference across genetic backgrounds and environments

The study of adaptation in microorganisms has led to a significant expansion in knowledge at many biological levels, ranging from biochemistry and genetics, to ecology and demography. Experimental evolution, in particular, has been invaluable at elucidating how complex the adaptive dynamics in microbial populations can be. One of the most fundamental characteristics of these dynamics is the distribution of beneficial mutations driving the adaptive process. How often do microorganisms acquire these mutations? And what are their expected effects? These questions have been at the heart of evolutionary biology from the very beginning, and the studies that have tackled these difficult issues have been tremendously enlightening about adaptive processes. However, the increasing awareness of the complexity of the environment where microorganisms live requires constant development of new approaches to answer these fundamental questions about their evolution. Large population sizes lead to increased levels of clonal interference, and thus to a deviation from the expected outcome in classical regimes of periodic selection. Genetic variation within an evolving population, which is now easily detected by sequencing technologies, can create complex interactions between phenotypes. Environments with antagonistic biotic interactions, pose very different selective pressures from the ones experienced when a species grows alone. All these factors influence adaptation in microorganisms and, importantly, drive the pathogenicity traits that create severe clinical and epidemiological problems