This figure illustrates how much variability exists in each site of the genomes of an entire evolving population.
At each point along the X-axis, we look at the genetic sequence of every organism in the population (3600 organisms total) at each site (Y-axis). Each line is colored from conserved (cold) to variable (hot) based on how many sequences have the same instruction at that line. The graph is colored according to the entropy of each site.
Repeating this for succesive points in time (along the X-axis),
we can visualize sites fixating (hot becoming cold) as sites that encode
something useful are selected
for. There are also transitions where cold sites become hot; these
occur when the organisms evolve to become more efficient, thereby taking
fewer lines to do the same thing. One further point of interest is the
apparent hitchiking event shown by all hot lines cooling down and warming
back up when a few lines become fixed. When an adaptation occurs, the
new strain sweeps across the population forcing all the others to
extinction, but slowly mutations cause any unslected lines to warm back
up as variant strains emerge.
Fitness, measured as the replication rate of the organisms, plotted as a function of time gives a further view of adaptation.
The cooling transitions seen in the figure above almost invariably
correspond to an increase in fitness, corroborating the idea that the
cooling events are caused by adaptive events.
