Rabosky 2010

Rabosky, D.L. 2010.  Extinction rates should not be estimated from molecular phylogenies.  Evolution.  Early View Date: January 2010.

Hmm weird.  If a paper is accepted in the journal Evolution, it goes through an early viewing thing where you can download the pdf but it is not actually printed in the journal yet, so it doesn't get a volume/issue number yet.

First off, I should state that I enjoyed this paper, mainly because it confirms (using fancy-math) the obvious: that you can't infer extinction rates using phylogenies without fossils.

True, the shape of a tree can be influenced by both the net rate of lineage diversification through time as well as the ratio of the extinction rate to the speciation rate; however, this does not give us license to use living species to provide information on the historical extinction rates.  I mean, if an organism goes extinct without a trace, you really can't know for certain that it existed, right?

One thing that confused me was in the abstract when he states, "molecular phylogenies contain information about the tempo and mode of species diversification through time".  What does he mean by the 'mode'?

In the article, the author shows that when rates vary across the branches of a phylogenetic tree or among clades (as they usually do), estimators that assume rate-constancy among lineages perform poorly (as they should!).  To do this, he first took a number of diversification rates from a set of clades with known extinction rates (an avian families dataset).  He then simulated clade diversity under those rates, and finally estimated the extinction rate for each set of clades.

It is clear from the author's results that among-lineage variation in diversification rates results in messed-up or directionally biased estimates of extinction rate.  He strongly urges that fossils should be used in conjunction with molecular phylogenetic studies to generate a richer perspective on the dynamics of speciation and extinction.  Agreed.