SiBioDy: a fast, realistic, and modular spatiotemporal ecoevolutionary simulator to understand the dynamics of biodiversity
Date:
Link to the meeting: click here
Understanding how biodiversity appears, spreads, evolves, and disappears across deep time is a major challenge of ecology and evolution. Recent global-scale simulations of eco-evolutionary processes on realistic changing landscapes have helped addressing broad questions on biodiversity dynamics, such as why some regions accumulate more species than others, how environmental change shapes the history of life, and which combinations of initial conditions, dispersal, adaptation, competition, and speciation can reproduce the large-scale patterns seen in nature. However, currently available simulators have three main drawbacks: (1) a high computational cost, limiting both the number of scenarios we can consider and the possibility to develop statistical machineries to adjust the simulator to empirical data, (2) a lack of genetic layer, limiting our understanding of how microevolutionary processes scale up to large scale biodiversity patterns, and (3) a fixed and inflexible implementation, preventing the modeling of multiple macroecological and macroevolutionary processes and scenarios.
Here, we model the dynamics of biodiversity on Earth by coupling local dispersal and population dynamics with the diffusion approximation of population genetics on paleolandscapes. New species naturally emerge as clusters of individuals become genetically isolated from others. The result, SiBioDy, is a modular simulator that can be configured through shared parameter files, inspected interactively in a web interface, and exported through command-line analysis scripts. It can produce realistic simulations at the global scale across the Phanerozoic in few minutes on a regular laptop, with high spatial and temporal resolutions (e.g., 1° and 1 Ma). We use SiBioDy to analyze the emergence of major biodiversity patterns, including the latitudinal diversity gradient, the correlation between community-scale genetic diversity and species richness, species abundance distributions, and the species-area relationship.