Nature
Article
Published: 15 April 2020
Extant timetrees are consistent with a myriad of diversification histories
Stilianos Louca & Matthew W. Pennell
Nature (2020)
Figure 1 | Assessing evolutionary histories. Louca and Pennell1 raise questions about a standard approach to estimating past rates of species formation (speciation) and extinction that uses data from a lineage-through-time plot. The number of species in the present depends on how speciation and extinction rates varied over time in the past.
Abstract
Time-calibrated phylogenies of extant species (referred to here as ‘extant timetrees’) are widely used for estimating diversification dynamics1. However, there has been considerable debate surrounding the reliability of these inferences2,3,4,5 and, to date, this critical question remains unresolved. Here we clarify the precise information that can be extracted from extant timetrees under the generalized birth–death model, which underlies most existing methods of estimation. We prove that, for any diversification scenario, there exists an infinite number of alternative diversification scenarios that are equally likely to have generated any given extant timetree. These ‘congruent’ scenarios cannot possibly be distinguished using extant timetrees alone, even in the presence of infinite data. Importantly, congruent diversification scenarios can exhibit markedly different and yet similarly plausible dynamics, which suggests that many previous studies may have over-interpreted phylogenetic evidence. We introduce identifiable and easily interpretable variables that contain all available information about past diversification dynamics, and demonstrate that these can be estimated from extant timetrees. We suggest that measuring and modelling these identifiable variables offers a more robust way to study historical diversification dynamics. Our findings also make it clear that palaeontological data will continue to be crucial for answering some macroevolutionary questions.
Data availability
No new data were generated for this manuscript. All phylogenetic datasets used as examples have previously been published previously, and are cited where appropriate.
Code availability
Computational methods used for this article—including functions for simulating birth–death models, for constructing models within a given congruence class, for calculating the likelihood of a congruence class and for directly fitting congruence classes (either in terms of λp or in terms of rp and ρλo) to extant timetrees—are implemented in the R package castor v.1.5.5, which is available from The Comprehensive R Archive Network at https://cran.r-project.org/package=castor.
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