Abstract
AbstractPairwise ecological resemblance, which includes compositional similarity between sites (beta diversity), or associations between species (co‐occurrence), can be measured by >70 indices. Classical examples for presence–absence data are Jaccard index or C‐score. These can be expressed using contingency table matching components a, b, c, and d—the joint presences, presences at only one site/species, and joint absences. Using simulations of point patterns for two species with known magnitude of association, I demonstrate that most of the indices converge to a similar value and they describe the simulated association almost identically, as long as they are calculated as a Z‐score, that is, as deviation of the index from a null expectation. Further, I show that Z‐scores estimate resemblance on average better than raw forms of the indices, particularly in the face of confounding effects of spatial scale and conspecific aggregation. Finally, I show that any single of the matching components, when expressed as Z‐score, can be used as an index that performs as good as the classical indices; this also includes joint absences. All this simplifies selection of the right resemblance index, it underscores the advantage of expressing resemblance as deviation from a null expectation, and it revives the potential of joint absences as a meaningful ecological quantity.
Highlights
Ecological resemblance (Legendre and Legendre 2012) is a fundamental ecological quantity that encompasses both similarity of species composition between sites and co-occurrence patterns among species, which are the Q and R mode analyses respectively (Legendre and Legendre 2012, Arita 2017)
I expect the same conclusions to be obtained for beta diversity, since the mathematics of the raw beta diversity is identical to the association metrics, only the indices are applied to a transposed site-by-species matrix (Arita 2017)
None of the indices gave perfect correlation with the association represented by parameter alpha (Fig. 1), which I expected since the association was distorted by varying conspecific aggregation, numbers of individuals, varying spatial grain, and the by fact that spatially implicit method was used for spatially explicit simulation
Summary
Ecological resemblance (Legendre and Legendre 2012) is a fundamental ecological quantity that encompasses both similarity of species composition between sites (beta diversity) and co-occurrence patterns among species, which are the Q and R mode analyses respectively (Legendre and Legendre 2012, Arita 2017). Among the many measures of ecological resemblance, popular are indices of pairwise similarity or association for binary presence/absence data, with around 80 proposed, as reviewed by (Hubálek 1982, Koleff et al 2003, Rajagopalan and Robb 2005, Legendre and Legendre 2012, Ulrich and Gotelli 2013) (Appendix 1). These reviews provide guidance for the selection of appropriate indices, based on criteria such as symmetry, additivity, sensitivity to number of sites or species, or interpretability. All of the indices can be used in both Q- and R- mode, i.e. for rows or columns of a species-by-site incidence matrix
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