Why extinction estimates from extant phylogenies are so often zero

Time-calibrated phylogenies of extant species (extant timetrees'') are widely used to estimate historical speciation and extinction rates by fitting stochastic birth-death models.(1) These approaches have long been controversial, as many phylogenetic studies report zero extinction in many taxa, contradicting the high extinction rates seen in the fossil record and the fact that the majority of species ever to have existed are now extinct.(2-9) To date, the causes of this discrepancy remain unresolved. Here, we provide a novel and simple explanation for these zero-inflated'' extinction estimates, based on the recent discovery that there exist many alternative congruent'' diversification scenarios that cannot be distinguished based solely on extant timetrees.(10) Due to such congruencies, estimation methods tend to converge to some scenario congruent to (i.e., statistically indistinguishable from) the true diversification scenario, but not necessarily to the true diversification scenario itself. This congruent scenario may exhibit negative extinction rates, a biologically meaningless but mathematically feasible situation, in which case estimators will tend to stick to the boundary of zero extinction. Based on this explanation, we make multiple testable predictions, which we confirmusing analyses of simulated trees and 121 empirical trees. In contrast to other proposed mechanisms for erroneous extinction rate estimates,(5,11-14) our proposed mechanism specifically explains the zero inflation of previous extinction rate estimates in the absence of detectable model violations, even for large trees. Not only do our results likely resolve a long-standing mystery in phylogenetics, they demonstrate that model congruencies can have severe consequences in practice.

Automated summary

Time-calibrated phylogenies of extant species are commonly used in estimating historical speciation and extinction rates, but controversy exists due to zero inflation in extinction estimates. A novel explanation is provided based on the discovery of alternative congruent diversification scenarios, which may result in estimators converging to scenarios with negative extinction rates. This mechanism explains the zero inflation of extinction rate estimates without detectable model violations, potentially resolving a long-standing mystery in phylogenetics.