Evolutionary genomics of host-use in bifurcating demes of RNA virus Φ6.

BMC Evol Biol. 2012 Aug 22;12(1):153.
Year of Publication: 
Turner, P.E., R.C. McBride, S. Duffy, R. Montville, L.S. Wang, Y.W. Yang, S.J. Lee, J. Kim.

Viruses are exceedingly diverse in their evolved strategies to manipulate hosts for viral replication. However, despite these differences, most virus populations will occasionally experience two commonly-encountered challenges: growth in variable host environments, and growth under fluctuating population sizes. We used the segmented RNA bacteriophage Φ6 as a model for studying the evolutionary genomics of virus adaptation in the face of host switches and parametrically varying population sizes. To do so, we created a bifurcating deme structure that reflected lineage splitting in natural populations, allowing us to test whether phylogenetic algorithms could accurately resolve this ‘known phylogeny’. The resulting tree yielded 32 clones at the tips and internal nodes; these strains were fully sequenced and measured for phenotypic changes in selected traits (fitness on original and novel hosts).