Prior hypotheses or regularization allow inference of diversification histories from extant timetrees

Abstract

<jats:title>Abstract</jats:title><jats:p>Phylogenies of extant species are widely used to study past diversification dynamics<jats:sup>1</jats:sup>. The most common approach is to formulate a set of candidate models representing evolutionary hypotheses for how and why speciation and extinction rates in a clade changed over time, and compare those models through their probability to have generated the corresponding empirical tree. Recently, Louca &amp; Pennell<jats:sup>2</jats:sup> reported the existence of an infinite number of ‘congruent’ models with potentially markedly different diversification dynamics, but equal likelihood, for any empirical tree (see also Lambert &amp; Stadler<jats:sup>3</jats:sup>). Here we explore the implications of these results, and conclude that they neither undermine the hypothesis-driven model selection procedure widely used in the field nor show that speciation and extinction dynamics cannot be investigated from extant timetrees using a data-driven procedure.</jats:p>

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

“…A recent study by Morlon et al (2020) presents an alternative point of view that opposes the conclusions in LP. They focus on how a hypothesis-based framework allows us to overcome many of the issues that are raised in LP.…”

“…We are not often interested in determining the precise values of speciation and extinction rate but rather how different diversification scenarios summarised by models containing λ and µ explain patterns in a phylogenetic tree. The criticisms put forward by Morlon et al (2020) will stimulate important discussion about key points that must be considered when using diversification models. We extend this discussion by highlighting several key points that must be considered in addition.…”

“…LP show how results of this approach can be misleading and provide potential solutions to the issues raised by proposing new summary statistics. This publication has provoked a response from the community (Morlon et al, 2020) and stimulated considerable discussion, with some going so far as to suggest that speciation and extinction cannot be estimated using phylogenetic trees (Pagel, 2020). As a result, this study has called into question the meaning of diversification rate estimates generated from any analytical framework.…”

The roles of wing color pattern and geography in the evolution of Neotropical Preponini butterflies

“…(2020) advocated for the kind of hypothesis-driven approach that we adopt here, suggesting that the conclusion that speciation and extinction rates are not identifiable parameters does not apply to all cases. Morlon et al (2020) point out that the fact that there are many congruent diversification models for the same tree topology does not pose a direct challenge to the hypothesis-driven approach used here.…”

Diversification dynamics of hypermetamorphic blister beetles (Meloidae): Are homoplastic host shifts and phoresy key factors of a rushing forward strategy to escape extinction?

“…In recent years, different time-dependent and clade-dependent diversification models have been developed to overcome these issues, some assuming continuous time variation while others model change as discrete time steps (Stadler 2011; Morlon et al 2011; Rabosky et al 2014; May et al 2016; Culshaw et al 2019; Höhna et al 2019). Nevertheless, concerns that these models lack statistical power and can generate an infinite array of undistinguishable diversification histories remain (Louca & Pennell 2020, but see Morlon et al 2020).…”