While ecology addresses the coexistence and dynamics of species depending on their adaptations to their environment at present, evolution addresses the appearance-disappearance of species and the changes in their characters over a longer term and a large spatial scale. A major challenge is to bridge the gap between ecological and evolutionary models, in order to address eco-evolutionary dynamics. Specifically, past environmental changes have determined changing regimes of population and migration dynamics, yet existing approaches do not allow investigating the long-term influence of such historical changes on extant biodiversity patterns.
We introduce a new modelling approach (and associated Python package): ecophylo, dedicated to coalescent-based simulation of neutral eco-evolutionary dynamics. The model rests on coalescent theory to simulate a shared ancestry of co-occurring individuals, under the influence of past demographic fluctuations due to, for example, habitat fluctuations, fragmentation and/or migration events among separate areas. Mutations occur over time in the genealogy, and divergent genotypes represent distinct extant species.
Results/Conclusions
The package includes tools to simulate large numbers of datasets and associated summary statistics, diverse patterns of taxonomic and phylogenetic compositions can be generated, and thus can be used either to conduct virtual experiments examining how different eco-evolutionary scenarios have shaped patterns of diversity or infer its of parameter values from real data.
As an example, we show how this model can be used to explore the remnant influence of past habitat reduction and subsequent expansion using an in silico experiment. We characterized the past restriction in refugia in terms of two parameters representing the ending time of past refugia, and the extent of habitat restriction in the refugia which we related to extant patterns of taxonomic, functional and phylogenetic diversity. We found that extant relative abundances reflect the lasting influence of more recent refugia on demographic dynamics, while phylogenetic composition reflects the influence of more ancient habitat change.
