ABSTRACT
Extinctions, being generally unobservable in the fossil record and in the lifetime of a scientist, are a mystery. Most species that have gone extinct left no trace of their existence. For most species that have lived on Earth, all that remains are their descendants, who themselves have evolved into other forms and perhaps have also gone extinct. Unfortunately, reliably measuring extinction by relying on the relationships among extant taxa and a scant fossil record is problematic, if not impossible (Rabosky 2010). The most widely used birth-death models estimate extinction rates that are close to zero (Nee 2006; Höhna et al. 2011) even though extinction
9.1 Introduction .................................................................................................. 141 9.2 Methods ........................................................................................................ 146 9.3 Results and Discussion ................................................................................. 147 Acknowledgments .................................................................................................. 151 Appendix 9.1 Python Script for Automating the Process of Measuring
the Extinction Index Calculated by the CTNM ............................151 Appendix 9.2 Draft (Not Annotated) R Script
Provided by an Anonymous Reviewer to Calculate the Extinction Index of the CTNM on Simulated Trees with Varying Extinction Rates (0, 0.025, 0.05, 0.1, 0.2, and 0.8) ........154
References .............................................................................................................. 155
rates were more likely to be relatively high (Rosenblum et al. 2012). A lack of a robust measure of extinction is unfortunate because knowledge of the true amount of extinction that has taken place in a clade could be extremely informative (Simpson 1944). Extinction rates could help us better understand speciation and ecological turnover in a clade. Knowing the total number of extinct species in a group can tell us about the total diversity once contained within that clade (He and Hubbell 2011). Past extinction events can even provide relevant information on current ones (Régnier et al. 2015): for example, did past climate change result in a lineage more or less resilient to current levels of change? Are extinction events correlated across groups in space and time?
