The fellow developed a new birth-death model of diversification in which speciation and extinction rates evolve instantaneously according to a Geometric Brownian Motion (GBM) on reconstructed phylogenetic trees including neontological and paleontological information. Rates of speciation and extinction that can vary at any time for any lineage is theoretically expected from the interplay of intrinsic (e.g. species traits such as body size) and extrinsic factors (e.g. environment such as ambient temperature) acting at a given time on species, and opens new modeling and computational possibilities in the study of macroevolutionary dynamics. Before, no mathematical expression nor computational algorithm existed to apply this model. The fellow was able to overcome these obstacles and developed the necessary mathematical and computational tools, provided in an efficient open-source software package, to enable inference of this model using empirical data (Fig 1). The fellow implemented the model in Julia, with a suite of new functions to manipulate, plot and input/output phylogenetic trees, using Data Augmentation within MCMC, achieving high performance. The new model development uncovered a clear signal of an early-rise of modern mammals, suggesting that the angiosperm radiation opened substantial ecological opportunities for these lineages to diversify in the Late Cretaceous and up to the present (Fig 2). Furthermore, the fellow achieved integrating fossil information, allowing for different fossil recovery rates across time, validated the model, and is currently being applied across clades of plants and animals (Fig 3).
Finally, the fellow developed the math and code to jointly infer rates of diversification with trait evolution following a relaxed Brownian motion (biotic variable) and with a fixed dependent function (abiotic variable). This model however, is currently being validated to then perform inference on empirical phylogenetic trees.
Dissemination and engagement: While the COVID pandemic hampered many venues for dissemination and public engagement, the fellow presented the work at conferences and external laboratories, taught three workshops on Julia and flexible diversification methods, mentored two master students, and disseminated current achievements in social media, will continue to do so.
