The pairwise approach to analysing species co-occurrence

The analysis of species co-occurrence patterns continues to be a main pursuit of ecologists, primarily because the coexistence of species is fundamentally important in evaluating various theories, principles and concepts. Examples include community assembly, equilibrium versus non-equilibrium organization of communities, resource partitioning and ecological character displacement, the local-regional species diversity relationship, and the metacommunity concept. Traditionally, co-occurrence has been measured and tested at the level of an entire species presence-absence matrix wherein various algorithms are used to randomize matrices and produce statistical null distributions of metrics that quantify structure in the matrix. This approach implicitly recognizes a presence-absence matrix as having some real ecological identity (e.g. a set of species exhibiting nestedness among a set of islands) in addition to being a unit of statistical analysis. An emerging alternative is to test for non-random co-occurrence between paired species. The pairwise approach does not analyse matrix-level structure and thus views a species pair as the fundamental unit of co-occurrence. Inferring process from pattern is very difficult in analyses of co-occurrence; however, the pairwise approach may make this task easier by simplifying the analysis and resulting inferences to associations between paired species.