Challenges in estimating species age from phylogenetic trees

Abstract

AimSpecies age, the elapsed time since origination, can give an insight into how species longevity might influence eco-evolutionary dynamics and has been hypothesized to influence extinction risk. Traditionally, species ages have been measured in the fossil record. However, recently, numerous studies have attempted to estimate the ages of extant species from the branch lengths of time-calibrated phylogenies. This approach poses problems because phylogenetic trees contain direct information about species identity only at the tips and not along the branches. Here, we show that incomplete taxon sampling, extinction, and different assumptions about speciation modes can significantly alter the relationship between true species age and phylogenetic branch lengths, leading to high error rates. We found that these biases can lead to erroneous interpretations of eco-evolutionary patterns derived from the comparison between phylogenetic age and other traits, such as extinction risk.InnovationFor bifurcating speciation, which is the default assumption in most analyses, we propose a probabilistic approach to improve the estimation of species ages, based on the properties of a birth-death process. We show that our model can reduce the error by one order of magnitude under cases of high extinction and high percentage of unsampled extant species.Main conclusionOur results call for caution in interpreting the relationship between phylogenetic ages and eco-evolutionary traits, as this can lead to biased and erroneous conclusions. We show that, under the assumption of bifurcate, it is possible to obtain better approximations of species age by combining information from branch lengths with the expectations of a birth-death process.