Beta diversity at different scales
Three distinct scales were considered in this study: large (archipelago scale), intermediate (island) and small (habitats within an island) scale. At the large scale, beta diversity was calculated among all selected islands, merging all selected cells within an island and using the island as grain size (Supplementary Material 2). In the case of the intermediate and small scales, grain size corresponded to cells of 500 x 500 m. At the intermediate scale, beta diversity was calculated within each island, among all grid cells of the three selected habitats, irrespective of each cell’s habitat type (Supplementary Material 2). At the smallest scale, beta diversity was calculated among all cells of each habitat within an island (e.g. cells covered with native forest in Terceira Island) (Supplementary Material 2). At this scale, each habitat patch was only considered in the analyses when there were more than 20 contiguous cells occupied by the same habitat at > 99% cover (see above and Supplementary Material 2). Therefore, we could only consider native forest patches from Flores and Terceira islands, naturalized vegetation patches from Pico, São Jorge and São Miguel, and seminatural pastures patches from Faial, Pico, São Jorge and São Miguel.
Turnover was estimated in each of these scales using the multiple site Simpson’s index (βSIM, Baselga et al., 2018). We used multiple site βSIM instead of average pairwise βSIM between units because we were interested in quantifying the heterogeneity in species composition among several spatial units at a given scale (e.g. islands for large scale or cells for intermediate and small scales). This way, beta diversity is interpreted as an attribute of the whole scale and not an attribute of a given pair of units. Multiple site βSIM was implemented using the beta.multi function from the R package betapart(Baselga et al., 2018). Multiple site βSIM was then computed at the archipelago scale, within islands and within habitats in islands. We complemented our analyses by calculating pairwise βSIM implemented in the beta.pair function to estimate the turnover between pairs of islands, between pairs of habitats within islands, and thus address the similarity in native plant composition between Azorean islands. Finally, to correlate climatic and geographical distance to beta diversity, we also computed pairwise β SIM between cells within islands (see below).
Because islands and habitats had a different number of cells, we re-calculated all measures of multiple βSIM by standardizing the number of cells to 20 to deal with a similar sampling effort. We then repeated this procedure 1000 times with replacement to obtain the mean and 95% confidence interval of each βSIM. The significance of the differences in the multiple site βSIM was estimated as the degree of overlap between the 95% confidence interval obtained from the bootstrapping procedure. This procedure was not implemented for multiple βSIM at the large scale (between islands) since we only considered 6 islands. All results presented correspond to the standardized values.