Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification

Citation

Pannetier T, Martinez C, Bunnefeld L & Etienne RS (2021) Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification. Evolution, 75 (1), pp. 25-38. https://doi.org/10.1111/evo.14124

Abstract
One of the primary goals of macroevolutionary biology has been to explain general trends in long‐term diversity patterns, including whether such patterns correspond to an upscaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity‐dependent (DD) diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time dependence without diversity dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time‐dependent, but diversity‐independent model that matches the expected diversity through time of a DD model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity dependence. We advocate that tests encompassing additional data, for example, traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.

Keywords
Birth‐death models; diversity dependence; macroevolution; maximum likelihood; simulations; time dependence

Journal
Evolution: Volume 75, Issue 1

• Published version