gen3sis: a general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity
Abstract
Understanding the origins of biodiversity has been an aspiration since the days of early naturalists. The immense complexity of ecological, evolutionary, and spatial processes, however, has made this goal elusive to this day. Computer models serve progress in many scientific fields, but in the fields of macroecology and macroevolution, eco-evolutionary models are comparatively less developed. We present a general, spatially explicit, eco-evolutionary engine with a modular implementation that enables the modeling of multiple macroecological and macroevolutionary processes and feedbacks across representative spatiotemporally dynamic landscapes. Modeled processes can include species’ abiotic tolerances, biotic interactions, dispersal, speciation, and evolution of ecological traits; commonly observed biodiversity patterns, such as alpha, beta, and gamma diversity, species ranges, ecological traits, and phylogenies, emerge as simulations proceed. As an illustration, we examine alternative hypotheses expected to have shaped the latitudinal diversity gradient (LDG) during the Earth’s Cenozoic era. Our exploratory simulations simultaneously produce multiple realistic biodiversity patterns, such as the LDG, current species richness, and range size frequencies, as well as phylogenetic metrics. The model engine is open source and available as an R package, enabling future exploration of various landscapes and biological processes, representing a key step toward a numeric, interdisciplinary, and mechanistic understanding of the physical and biological processes that shape Earth’s biodiversity.
What the paper shows and why it matters (AI-generated)
Building custom eco-evolutionary simulations to test hypotheses about the deep-time origins of biodiversity patterns has traditionally meant either adapting someone else's bespoke model or building one from scratch. gen3sis is a general-purpose, open-source engine meant to remove that barrier, and its demonstration case — competing explanations for the latitudinal diversity gradient — reproduces several real biodiversity patterns simultaneously from a single simulation. Over 100 papers have built on it since, from Phanerozoic marine extinction risk to island frog diversity to the group's own recent uncertainty-analysis review, making it one of the more broadly adopted tools in macroecological simulation.