Strength and tempo of selection revealed in viral gene genealogies

July 25, 2011

I just had a paper published online in BMC Evolutionary Biology. I've hosted a compiled PDF with all the figures inline, while their production office gets the official version together.

This was a fun project. It's essentially showing how the basic models of selection in population genetics play out in detailed phylogenies, where the passage of time is clearly evident. I think a visual / phylogenetic approach really helps to understand the processes at work. In this case, rather than describing an allele that reaches 100% frequency, the process of fixation describes a lineage that outcompetes its contemporaries and comes to be the progenitor of the entire future population. A fundamental finding in population genetics is that selection reduces effective population size, that is when there is heritable variation for fitness, then the patterns of ancestry connecting individuals will resemble a smaller population. Essentially, only a few fitter individuals have a chance of contributing their genetic legacy to the future population. This paper explores the effects of selection on phylogeny shape, with particular attention to uncovering selective dynamics through time.

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