Pulled Diversification Rates, Lineages-Through-Time Plots, and Modern Macroevolutionary Modeling

• Published in: Systematic biology Vol. 71; no. 3; pp. 758 - 773
• Main Authors: Helmstetter, Andrew J, Glemin, Sylvain, Käfer, Jos, Zenil-Ferguson, Rosana, Sauquet, Hervé, de Boer, Hugo, Dagallier, Léo-Paul M J, Mazet, Nathan, Reboud, Eliette L, Couvreur, Thomas L P, Condamine, Fabien L
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 19.04.2022; Oxford University Press (OUP)
• Subjects: Biodiversity; Biodiversity and Ecology; Biological Evolution; Environmental Sciences; Genetic Speciation; Phylogeny; Point of View; Time
• ISSN: 1063-5157; 1076-836X; 1076-836X
• DOI: 10.1093/sysbio/syab083

Abstract Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth–death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticized such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here, we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations, we illustrate the characteristics of newly proposed “pulled rates” and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modeling, but they in no way suggest we should abandon diversification modeling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methods, but by acknowledging them we can better target our joint efforts as a scientific community. [Birth–death models; extinction; phylogenetics; speciation.]