Detecting phylodiversity-dependent diversification with a general phylogenetic inference framework

Diversity-dependent diversification models have been extensively used to study the effect of ecological limits and feedback of community structure on species diversification processes, such as speciation and extinction. Current diversity-dependent diversification models characterise ecological limits by carrying capacities for species richness. Such ecological limits have been justified by niche filling arguments: as species diversity increases, the number of available niches for diversification decreases. However, as species diversify they may diverge from one another phenotypically, which may open new niches for new species. Alternatively, this phenotypic divergence may not affect the species diversification process or even inhibit further diversification. Hence, it seems natural to explore the consequences of phylogenetic diversity-dependent (or phylodiversity-dependent) diversification. Current likelihood methods for estimating diversity-dependent diversification parameters cannot be used for this, as phylodiversity is continuously changing as time progresses and species form and become extinct. Here, we present a new method based on Monte Carlo Expectation-Maximization (MCEM), designed to perform statistical inference on a general class of species diversification models and implemented in the R package emphasis. We use the method to fit phylodiversity-dependent diversification models to 14 phylogenies, and compare the results to the fit of a richness-dependent diversification model. We find that in a number of phylogenies, phylogenetic divergence indeed spurs speciation even though species richness reduces it. Not only do we thus shine a new light on diversity-dependent diversification, we also argue that our inference framework can handle a large class of diversification models for which currently no inference method exists.

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