TY - JOUR T1 - Estimating species interactions from observational data with Markov networks JF - bioRxiv DO - 10.1101/018861 SP - 018861 AU - David J. Harris Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/08/05/018861.abstract N2 - Estimating species interactions from observational data is one of the most controversial tasks in community ecology. One difficulty is that a single pairwise interaction can ripple through an ecological network and produce surprising indirect consequences. For example, the negative correlation between two competing species can be reversed in the presence of a third species that is capable of outcompeting both of them. Here, I apply models from statistical physics, called Markov networks or Markov random fields, that can predict the direct and indirect consequences of any possible species interaction matrix. Interactions in these models can be estimated from observational data via maximum likelihood. Using simulated landscapes with known pairwise interaction strengths, I evaluated Markov networks and six existing approaches. The Markov networks consistently outperformed other methods, correctly isolating direct interactions between species pairs even when indirect interactions largely overpowered them. Two computationally efficient approximations, based on linear and generalized linear models, also performed well. Indirect effects reliably caused a common null modeling approach to produce incorrect inferences, however. ER -