Phylogenetic estimation of diversity-dependent biogeographic rates using deep learning

Abstract

Abstract Ecological theory predicts that local species richness can influence biogeographic rates of speciation, extinction, and dispersal. For instance, increasing the number of competing species within a region may cause local speciation and dispersal rates to decrease but local extinction rates to increase, inducing a carrying capacity for local species richness. In this article, we introduce a fully generative, event-based phylogenetic diversification model, called DDGeoSSE, that allows diversity-dependent effects of local species richness to modulate biogeographic rates of diversification and range evolution. DDGeoSSE can accommodate and test a variety of alternative diversification scenarios that involve positive, negative, and neutral interactions among sympatric species for speciation, extinction, and dispersal. We derive mathematical and statistical properties of biogeographic outcomes generated by this model, such as the carrying capacity for a clade at equilibrium, which we validate through simulation. Because diversity-dependent phylogenetic models typically do not have tractable likelihood functions, we use deep learning with phyddle to perform parameter inference and model selection. Separately applying DDGeoSSE to Caribbean Anolis lizards and cloud forest-dwelling Viburnum plants, we find evidence that local species richness plays a significant role in shaping diversification dynamics for both clades.

The authors' abstract, as published at the source. Systematic Biology, 2026 · DOI ↗