A Comparison of the Effects of Random and Selective Mass Extinctions on Erosion of Evolutionary History in Communities of Digital Organisms

The effect of mass extinctions on phylogenetic diversity and branching history of clades remains poorly understood in paleobiology. We examined the phylogenies of communities of digital organisms undergoing open-ended evolution as we subjected them to instantaneous “pulse” extinctions, choosing survivors at random, and to prolonged “press” extinctions involving a period of low resource availability. We measured age of the phylogenetic root and tree stemminess, and evaluated how branching history of the phylogenetic trees was affected by the extinction treatments. We found that strong random (pulse) and strong selective extinction (press) both left clear long-term signatures in root age distribution and tree stemminess, and eroded deep branching history to a greater degree than did weak extinction and control treatments. The widely-used Pybus-Harvey gamma statistic showed a clear short-term response to extinction and recovery, but differences between treatments diminished over time and did not show a long-term signature. The characteristics of post-extinction phylogenies were often affected as much by the recovery interval as by the extinction episode itself

Example phylogenetic trees showing loss of pre-extinction history during and after press episode, from a replicate population that maintained the pre-extinction phylogenetic root.

<p>Node labels are Avida genotype IDs. Branch lengths are scaled in Avida absolute time. a) Immediate pre-extinction tree. Clades highlighted in yellow are lost during press episode; clades highlighted in red survive press episode but are lost during recovery. Clades highlighted in blue are those that comprise the tree in panel c). Organisms in clades D, E, F, G contain same phenotypic profiles as those in clade C (not shown due to space constraints). b) Tree from end of press episode. Clades highlighted in red are lost during recovery. c) Tree from 2000 updates into recovery after press episode (107,000 updates). d) Control tree from 107,000 updates, showing retention of clades that were otherwise lost in the press extinction and recovery.</p

Median age of root of the end-experiment phylogenetic trees, and the median distances (in updates) from the root to the first and second next oldest nodes in the tree, for replicate populations in which the pre-extinction root was retained.

<p>Differences between treatments were tested with a Kruskal-Wallis test, followed by a Tukey-corrected multiple comparison test. Letters in “Multiple comparison grouping” indicates treatments that are NOT significantly different after correction for multiple comparisons.</p

Noncumulative stemminess (NCS) at select time points after the extinction episode.

<p>The y-axis is NCS (plotted on a log₁₀ scale). Data are median NCS values with 25% and 75% interquartiles. a) Replicates where the pre-extinction phylogenetic root was retained over the duration of the recovery period. b) Strong press (blue trace) and strong pulse (orange trace) replicates where the pre-extinction phylogenetic root was lost during either the extinction itself or the recovery period. The black trace is the same as in panel a) (for comparison purposes). Differences between treatments were tested with Kruskal-Wallis tests followed by Tukey-HSD corrected multiple comparison tests. Letters indicate treatments that are NOT significantly different from each other after correction for multiple comparisons, and are colour-coded by treatment. Numbers with each letter indicate the number of replicates used for testing.</p