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.