gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity

Oskar Hagen, Benjamin Flück, Fabian Fopp, Juliano S. Cabral, Florian Hartig, Mikael Pontarp, Thiago F. Rangel & Loïc Pellissier

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 α, β, and γ 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, while outputs can be linked with a variety of empirical biodiversity patterns. This work represents a key 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)

Species numbers differ between continents and regions and change with latitude, with elevation or between islands. Such patterns arise from many processes acting together on changing landscapes: species spread, adapt, interact, split and go extinct. Most hypotheses about how they produce the observed patterns are verbal, so they are hard to test against each other. Simulation models could make them precise, as Gotelli et al. (2009) argued in calling for a general simulation model for macroecology. But the models built since were mostly made for specific questions, each with a fixed set of mechanisms. The problem the paper takes on is thus the lack of a common platform in which competing explanations can be formulated and tested.

gen3sis is a simulation engine in which the processes that shape biodiversity can be combined freely and run over landscapes that change through time. Mechanisms and landscapes are exchangeable building blocks: a user specifies how species disperse, which conditions they tolerate, how they compete and evolve, and when isolated populations become new species. From these, species richness, ranges, traits and phylogenies emerge together, so that different hypotheses can be written in one framework and each checked against several observed patterns at once. As an example, the paper implements several hypotheses for the latitudinal diversity gradient, from a null model without ecological interactions to limits on how many individuals a site can support, set by its temperature and aridity, and runs them over the Cenozoic. All of them can produce a decline in species richness towards the poles; only the model with these environment-dependent limits also matches the other patterns – the shape of that decline, local richness, range sizes and the shape of phylogenies – although only in a small fraction of its simulation runs.

**Figure 2.** Schematic example of the gen3sis engine simulation cycle of one species’ populations over a landscape evolution example containing highlands (yellow), lowlands (green), and a river acting as a barrier (blue). From Hagen et al. (2021), *PLOS Biology*, licensed under CC BY 4.0. Click the image to enlarge.

The case study does not settle what causes the latitudinal gradient; the paper notes that it covered only a few of the candidate processes. What it shows is why explanations should be judged against many patterns at once: reproducing the gradient alone is a weak test, since quite different mechanisms pass it. The contribution is the tool: mechanisms that had been described only in words become explicit, reproducible models, in an open R package. gen3sis has since been used for very different systems, among them the uneven diversity of tropical moist forests (Hagen et al. 2021, PNAS), the exchange of land vertebrates across Wallace’s Line (Skeels et al. 2023) and the freshwater fishes of the western Amazon (Boschman et al. 2023).

References

Gotelli et al. (2009). Patterns and causes of species richness: a general simulation model for macroecology. Ecology Letters 12, 873–886. doi:10.1111/j.1461-0248.2009.01353.x
Hagen et al. (2021). Earth history events shaped the evolution of uneven biodiversity across tropical moist forests. Proceedings of the National Academy of Sciences 118, e2026347118. doi:10.1073/pnas.2026347118
Skeels et al. (2023). Paleoenvironments shaped the exchange of terrestrial vertebrates across Wallace’s Line. Science 381, 86–92. doi:10.1126/science.adf7122
Boschman et al. (2023). Freshwater fish diversity in the western Amazon basin shaped by Andean uplift since the Late Cretaceous. Nature Ecology & Evolution 7, 2037–2044. doi:10.1038/s41559-023-02220-8