Phylogenetic Depth vs Time

This figure illustrates the number of organisms (from a population of 3600) that occupy a particular depth in a "genotypic family tree" rooted back at the ancestor genotype, which was used to see the experiment. The graph displays the course of an experiment with time progressing on the X axis, and the phylogenetic depth (i.e., the number of mutations that have ocured to produce the current genomtypes from the ancestor) is represented on the y axis. The color scale indicates the number of organisms in the population at each distance.

We construct the phylogenetic tree by noting every time a mutation occurs that generates a new genotype. This produces a tree analagous to a geneological tree recording your family's history, except the units are genotypes (strains) instead of individuals.

Every generation we produce a histogram of the number of organisms at each level in the tree. By placing these histograms edge to edge and viewing their heights as colors from above (instead of the side view normally used to visualize histograms), we can see a one dimensional view of the population's search through different genotypes as it adapts.

Characteristics to note:

• Punctuation: When a new, more fit genotype comes into existence through mutation, there is a peak in the distribution as that genotype and it's close relatives take over the population.
• Diversification: After an adaptive event (visible as punctuation), the distribution speads out as more and more genotypes are tried out. Many of these new genotypes neutral (have nearly the same fitness), so more of genotype space is explored.
• Leap-Frogging: Occasionally, two distinct genotypes with beneficial mutations are found at nearly the same time. The first to be found starts to form a punctuation event, but the second (if it is better than the first) takes over before the first has a chance to fix. Near update 2000 and again near update 8000 are good examples of this effect.
• Hyper-mutatiors: Just barely visibile (because of our color choice) are small flamelike spikes. These are lineages of genotypes that mutate almost every generation, and therefore traverse phylogenetic distance very quickly. Since mutation rates are the same for the entire populaton, these organisms achieve their hyper-muator status by copying themselves incorrectly. The last major transition in this figure is actually caused by a hyper-mutator lineage that finds a fitness advantage and converts itself back to a normal mutation rate.