Potential survival of some, but not all, diversification methods

Abstract

Models have long been used for understanding changing diversification patterns over time. The rediscovery that models with very different rates through time can fit a phylogeny equally well has led to great concern about the use of these models. We share and add to these concerns: even with time heterogeneous models without these issues, the distribution of the data means that estimates will be very uncertain. However, we argue that congruence issues such as this also occur in models as basic as Brownian motion and coin flipping. Taxon-heterogeneous models such as many SSE models appear not to have this particular issue.

A flexible method for estimating tip diversification rates across a range of speciation and extinction scenarios

“…From a mathematical standpoint, there is an advantage in using tip rates because it is at the tips where the certainty around the probability of being in a particular rate class is the highest (O’Meara & Beaulieu, 2021). The certainty around these probabilities decreases as one moves towards the root of the tree, and so the ability to point out changes in rate classes also decreases.…”

“…The certainty around these probabilities decreases as one moves towards the root of the tree, and so the ability to point out changes in rate classes also decreases. Of course, the model does use information from the whole phylogenetic tree in the calculations of tip-rates, but as one moves towards the present in the tree, the more information is available to reconstruct those rates and thus we are more likely to be certain about the probabilities of being in different rate categories (see O’Meara & Beaulieu, 2021).…”

“…Note too that MiSSE is still a model of tree and character states like other SSE models, and so the topology matters to assign tips to the correct (hidden) states. Because it uses data from the topology as well as branch lengths, MiSSE likelihood can distinguish between trees that have the same lineage through time plot, but different topologies (O'Meara & Beaulieu, 2021). Also note that, contrary to previous SSE models, transition rates (q) among rate classes are always set equal.…”

“…While it is true that phylogenies are often used to address problems beyond their capabilities (Losos, 2011; Cooper et al, 2016; Uyeda et al, 2018), there is still a considerable amount of information that extant-only phylogenies can provide about the diversification process (Helmstetter et al, 2021; Morlon et al, 2022). For instance, O’Meara and Beaulieu (2021) demonstrated that state-dependent speciation and extinction (SSE) models can identify different likelihoods for the generating parameters of trees with different topologies but identical lineage through time plots. However, they also discuss how the uncertainty around parameter estimates increases as one moves from tip to root in the tree, due to the decreasing amount of information in ancestral rate reconstructions (O’Meara and Beaulieu, 2021).…”

“…For instance, O’Meara and Beaulieu (2021) demonstrated that state-dependent speciation and extinction (SSE) models can identify different likelihoods for the generating parameters of trees with different topologies but identical lineage through time plots. However, they also discuss how the uncertainty around parameter estimates increases as one moves from tip to root in the tree, due to the decreasing amount of information in ancestral rate reconstructions (O’Meara and Beaulieu, 2021).…”