Studying speciation and extinction dynamics from phylogenies: addressing identifiability issues

A lot of what we know about past speciation and extinction dynamics is based on statistically fitting birth-death processes to phylogenies of extant species. Despite their wide use, the reliability of these tools is regularly questioned. It was recently demonstrated that vast 'congruent' sets of alternative diversification histories cannot be distinguished (i.e., are not identifiable) using extant phylogenies alone, reanimating the debate about the limits of phylogenetic diversification analysis. Here, we summarize what we know about the identifiability of the birth- death process and how identifiability issues can be addressed. We conclude that extant phylogenies, when combined with appropriate prior hypotheses and regularization techniques, can still tell us a lot about past diversification dynamics.

Automated summary

The reliability of using birth-death processes to analyze the diversification and extinction dynamics of the past based on phylogenies of extant species is regularly questioned. However, when combined with appropriate prior hypotheses and regularization techniques, extant phylogenies can still provide important information about past diversification dynamics.