Rethinking phylogenetic comparative methods

Abstract

As a result of the process of descent with modification, closely related species tend to be similar to one another in a myriad different ways. In statistical terms, this 20 means that traits measured on one species will not be independent of traits measured on others. Since their introduction in the 1980s, phylogenetic comparative methods (PCMs) have been framed as a solution to this problem. In this paper, we argue that this way of thinking about PCMs is deeply misleading. Not only has this sowed widespread confusion in the literature about what PCMs are doing but 25 has led us to develop methods that are susceptible to the very thing we sought to build defenses against -unreplicated evolutionary events. Through three Case Studies, we demonstrate that the susceptibility to singular events indeed a recurring problem in comparative biology that links several seemingly unrelated controversies. In each Case Study we propose a potential solution to the problem. 30While the details of our proposed solutions differ, they share a common theme: unifying hypothesis testing with data-driven approaches (which we term "phylogenetic natural history") to disentangle the impact of singular evolutionary events from that of the factors we are investigating. More broadly, we argue that our field has, at times, been sloppy when weighing evidence in support of causal hypothe-35 ses. We suggest that one way to refine our inferences is to re-imagine phylogenies as probabilistic graphical models; adopting this way of thinking will help clarify precisely what we are testing and what evidence supports our claims.

Tracking temporal shifts in area, biomes, and pollinators in the radiation ofSalvia(sages) across continents: leveraging anchored hybrid enrichment and targeted sequence data

“…We have not explicitly used recent statistical methods for modeling the relationships among character states, speciation rates, and extinction rates on phylogenetic trees (e.g., with BiSSE, MuSSE, GeoSSE, and related phylogenetic comparative models) for an explicit reason. The problem of how to discover plausible histories of singular or near singular events in the context of histories of other characters is a recurring problem in the field of phylogenetic comparative methods that links several seemingly unrelated controversies (Maddison and FitzJohn, ; Uyeda et al., ). Most importantly, the issue of “phylogenetic pseudoreplication” might be inherent with the categorical features examined here in Salvia .…”

“…In the process, these advances have transformed the study of plant diversification from a field of oft‐speculative narrative to a complex discipline that uses sophisticated computational methods to meld, correlate, and interpret results from these disparate fields (e.g., Crisp et al., ; Drummond et al., ; van der Niet and Johnson, ; Beaulieu et al., ; Cornwell et al., ; Givnish et al., , ; Linder et al., ; Zanne et al., ; Uribe‐Convers and Tank, ; Lagomarsino et al., ; Roalson and Roberts, ; Rose et al., ; Spalink et al., , b; Cardillo et al., ; Vamosi et al., ). Additionally, the underlying assumptions and thus interpretation of such correlated findings are now the subject of healthy debate (Maddison and FitzJohn, ; Rabosky and Goldberg, ; Uyeda et al., ).…”

Thirty clues to the exceptional diversification of flowering plants

“…The identified shifts provide information of major diversification changes for angiosperms as a whole at a deep phylogenetic scale. They represent an important starting point to understand major features of angiosperm evolution (Uyeda et al, 2017). The phylogenetic level at which shifts were identified is a function of the used backbone sampling, in which major angiosperm lineages were represented by a small number 355 of placeholders, which convey limited information about species richness distributed among and within angiosperm clades.…”

“…Furthermore, each of these clades includes many intrinsic attributes deployed in a great variety of extrinsic conditions that could potentially be related with increased diversification (Sauquet & Magallón, in review). While this study is not intended 520 to recognize the causal factors underlying angiosperm diversification, it provides a critical framework (Uyeda et al, 2017) by pointing to particular phylogenetic regions to investigate for diversification associated to intrinsic or extrinsic factors (Bouchenak-Khelladi et al, 2015). A further improved understanding of angiosperm radiations, and of the causes that drive them, should necessarily be based on a more precise phylogenetic location of incremental and 525 decremental diversification shifts, derived from a much denser taxonomic sampling, namely species-level phylogenies, and ideally, direct integration of fossil information.…”

Continuous traits and speciation rates: Alternatives to state‐dependent diversification models

“…The use of more sophisticated null models is an important way forward in addressing false positives in SSE methods and in phylogenetic comparative methods generally (Beaulieu & O'Meara, 2016;Uyeda, Zenil-Ferguson, & Pennell, 2017). This approach may be possible with QuaSSE, but implementations are lacking and the computational challenges associated with fitting such models in a QuaSSE framework are expected to be non-trivial.…”