gabriely

• Yedid, Gabriel; Stredwick, Jason; Ofria, Charles A. & Agapow, Paul-Michael (2012). A Comparison of the Effects of Random and Selective Mass Extinctions on Erosion of Evolutionary History in Communities of Digital Organisms. PLOS ONE. 7(5). doi: 10.1371/journal.pone.0037233. Full text in Research Archive Show summary

  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.

• Yedid, Gabriel & Heier, Lise (2012). Effects of Random and Selective Mass Extinction on Community Composition in Communities of Digital Organisms. In Pontarotti, Pierre (Eds.), Evolutionary Biology: Mechanisms and Trends. Springer. ISSN 9783642304248. p. 43–64. doi: 10.1007/978-3-642-30425-5_3. Full text in Research Archive

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• Yedid, Gabriel (2011). Effects of random and selective mass extinction on community composition in communities of digital organisms. Full text in Research Archive
• Yedid, Gabriel (2010). Tree shape "signatures" and erosion of evolutionary history following mass extinction in communities of digital organisms. Full text in Research Archive Show summary

  Over geological time, mass extinctions and recoveries have substantially reshaped the taxonomic composition and ecological profile of biotic communities. The extinction/recovery process is also thought to have important effects on shape parameters of the phylogenetic trees defining ,relationships among clades, such as tree balance[1], and “evolutionary history”, but effects on tree “stemminess”—relative lengths of internal branches—have received less attention. Communities of evolving digital organisms, where phylogenetic relationships may be known with certainty, seem a good way to study effects of extinction and recovery on phylogenetic tree shape. Previous work with digital communities examined how extinction and recovery affect ecological dynamics and expression of a complex trait, but did not address effects on the structure of phylogeny. Here, we use the Avida digital system to investigate changes in tree shape and loss of evolutionary history after two types of mass extinction.

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