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Updated: Jun 19, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Trait-mediated speciation and human-driven extinctions in proboscideans revealed by unsupervised Bayesian neural
Torsten Hauffe1, Juan L Cantalapiedra2,3,4, Daniele Silvestro1,5
1Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland.
None:
Species life-history traits, paleoenvironment, and biotic interactions likely influence speciation and extinction rates, affecting species richness over time. Birth-death models inferring the impact of these factors typically assume monotonic relationships between single predictors and rates, limiting our ability to assess more complex effects and their relative importance and interaction. We introduce a Bayesian birth-death model using unsupervised neural networks to explore multifactorial and nonlinear effects on speciation and extinction rates using fossil data. It infers lineage- and time-specific rates and disentangles predictor effects and importance through explainable artificial intelligence techniques. Analysis of the proboscidean fossil record revealed speciation rates shaped by dietary flexibility and biogeographic events. The emergence of modern humans escalated extinction rates, causing recent diversity decline, while regional climate had a lesser impact. Our model paves the way for an improved understanding of the intricate dynamics shaping clade diversification.
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