Inferences about nested subsets structure when not all species are detected

Comparisons of species composition among isolated ecological communities of different size have often provided evidence that the species in communitie s with lower species richness form nested subsets of the species in larger communities. In the vast majority of studies, the question of nested subset s has been addressed using information on presence-absence, where a "0" is interpreted as the absence of a given species from a given location. Most o f the methodological discussion in earlier studies investigating nestedness concerns the approach to generation of model-based matrices corresponding to the null hypothesis of a nonnested pattern. However, it is most likely t hat in many situations investigators cannot detect all the species present in the location sampled. The possibility that zeros: in incidence matrices reflect nondetection rather than absence of species has not been considered in studies addressing nested subsets, even though the position of zeros in these matrices forms the basis of earlier inference methods. These samplin g artifacts are likely to lead to erroneous conclusions about both variatio n over space in species richness, and the degree of similarity of the vario us locations. Here we propose an approach to investigation of nestedness, b ased on statistical inference methods explicitly incorporating species dete ction probability, that take into account the probabilistic nature of the s ampling process. We use presence-absence data collected under Pollock's rob ust capture-recapture design, and resort to an estimator of species richnes s originally developed for closed populations to assess the proportion of s pecies shared by different locations. We develop testable predictions corre sponding to the null hypothesis of a nonnested pattern, and an alternative hypothesis of perfect nestedness. We also present an index for assessing th e degree of nestedness of a system of ecological communities. We illustrate our approach using avian data from the North American Breeding Bird Survey collected in Florida Keys.