An integrated model of population genetics and community ecology

• Published in: Journal of biogeography Vol. 46; no. 4; pp. 816 - 829
• Main Authors: Overcast, Isaac, Emerson, Brent C., Hickerson, Michael J.
• Format: Journal Article
• Language: English
• Published: Oxford Wiley Subscription Services, Inc 01-04-2019
• Subjects: Abundance; Assembly; Bayesian analysis; Biodiversity; Communities; Community ecology; community genetic diversity; Community structure; comparative phylogeography; Computer simulation; Demographics; ecological neutral theory; Entropy (Information theory); Equilibrium; Estimation; Fieldwork; Genetic diversity; Genetics; island biogeography; Mathematical models; Mitochondrial DNA; Model accuracy; non‐equilibrium dynamics; Parameter estimation; Phylogeography; Population genetics; species abundance distributions
• ISSN: 0305-0270; 1365-2699
• DOI: 10.1111/jbi.13541

Aim
Quantifying abundance distributions is critical for understanding both how communities assemble, and how community structure varies through time and space, yet estimating abundances requires considerable investment in fieldwork. Community‐level population genetic data potentially offer a powerful way to indirectly infer richness, abundance and the history of accumulation of biodiversity within a community. Here we introduce a joint model linking neutral community assembly and comparative phylogeography to generate both community‐level richness, abundance and genetic variation under a neutral model, capturing both equilibrium and non‐equilibrium dynamics.
Location
Global.
Methods
Our model combines a forward‐time individual‐based community assembly process with a rescaled backward‐time neutral coalescent model of multi‐taxa population genetics. We explore general dynamics of genetic and abundance‐based summary statistics and use approximate Bayesian computation (ABC) to estimate parameters underlying the model of island community assembly. Finally, we demonstrate two applications of the model using community‐scale mtDNA sequence data and densely sampled abundances of an arachnid community on La Réunion. First, we use genetic data alone to estimate a summary of the abundance distribution, ground‐truthing this against the observed abundances. Then, we jointly use the observed genetic data and abundances to estimate the proximity of the community to equilibrium.
Results
Simulation experiments of our ABC procedure demonstrate that coupling abundance with genetic data leads to improved accuracy and precision of model parameter estimates compared with using abundance‐only data. We further demonstrate reasonable precision and accuracy in estimating a metric underlying the shape of the abundance distribution, temporal progress towards local equilibrium and several key parameters of the community assembly process. For the insular arachnid assemblage, we find the joint distribution of genetic diversity and abundance approaches equilibrium expectations, and that the Shannon entropy of the observed abundances can be estimated using genetic data alone.
Main conclusions
The framework that we present unifies neutral community assembly and comparative phylogeography to characterize the community‐level distribution of both abundance and genetic variation through time, providing a resource that should greatly enhance understanding of both the processes structuring ecological communities and the associated aggregate demographic histories.