SUPPORTING INFORMATION APPENDIX 2: ADDITIONAL DETAILS OF
METHODS USED TO CALCULATE DIVERSITY METRICS
Site Selection
In order to control for landscape effects, we ensured that our focal sites were
embedded in a matrix of similar habitats. A large proportion of this region is
intensively managed for agriculture, and it contains a growing number of rural
lifestyle properties with large gardens. Properties conducting commercial operations
(such as cropping, dairy or orchards) were large in area (i.e. > 100 ha) and
predominately managed by a single landholder. The remaining land uses sampled
comprised rural “lifestyle” properties with large gardens. These properties were
smaller in area than those used for commercial operations (range: 2–50 ha) and
hence numerous landholders owned the properties within a 500 m radius of the focal
study sites. Nonetheless, these properties tended to be clustered within particular
regions, often dominating the land use composition within a 500 m radius. The range
in landscape composition was thus approximately between 15–50% within a 1km
radius. The remaining land uses (other than the landscapes being sampled) were
dominated by managed grasslands used as grass fodder for beef cattle or sheep
farming.
In this study, we could not provide quantitative estimates of remnant vegetation as
little to no New Zealand native remnant vegetation exists in the Canterbury
agricultural region of the South Island. Remnant vegetation maps are of little use in
the landscapes surrounding our study sites. While exotic vegetation dominates the
hedgerows and shade trees in this region, this data are not currently
comprehensively mapped hence we cannot calculate cover or composition
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quantitatively. Therefore, site selection was based upon data gathered from a range
of sources, resulting in land cover data categorized into different classes which are
quite general (e.g. arable, grazing, urban etc.). Site inspections were conducted to
verify the exact land use at the time of the study, and to result in an approximate
percentage area of land use within a 500m radius. We believe these data are as
accurate as possible for this time, as it was beyond the scope of the study to
generate new aerial photographs. We thus use a conservative definition of
qualitative land-use type, rather than quantifying landscape variables.
Functional diversity
Functional diversity indices (functional richness and functional dispersion) were
calculated using the “FD” package (Laliberté & Legendre, 2010). A correction was
first applied on the species by species functional distance matrix to ensure it was
Euclidean (Cailliez, 1983). Functional richness (Cornwell et al., 2006; Villéger et al.,
2008) is a measure used to describe the volume of the minimum convex hull (in
multidimensional trait space) that includes all species. In other words, it measures
the full spread of species in trait space, and is the multivariate analogue of the range.
Consequently, it is sensitive to species with extreme trait values. Communities
exhibiting high functional richness would have a greater range of trait values than
communities with low functional richness. Functional dispersion (Laliberté &
Legendre, 2010) is computed as the mean distance of the traits of individual species
to the trait centroid of all species (weighted by species abundances). It is the
multivariate analogue of a weighted mean absolute deviation and therefore provides
an abundance-weighted measure of functional trait diversity that is unaffected by
species richness and is less sensitive to species with extreme trait values. Note that
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Fdis and RaoQ are related (Laliberté & Legendre, 2010), hence we use only Fdis to
consistently use a trait space approach for all presented indexes. We also calculated
a dendogram-based functional richness (Petchey & Gaston, 2002). Both indices
where highly correlated in our data set (Pearson's product-moment correlation =
0.89; p < 0.001) and produced qualitatively similar results. Hence, we present the
results only for the functional diversity indices (functional richness and functional
dispersion). The quality of the functional richness reduced-space representation
based on a corrected distance matrix was good = 0.71.
Cailliez, F. (1983) The analytical solution of the additive constant problem. Psychometrika, 48, 305308.
Cornwell, W.K., Schwilk, D.W. & Ackerly, D.D. (2006) A trait-based test for habitat filtering: convex
hull volume. Ecology, 87, 1465-1471.
Laliberté, E. & Legendre, P. (2010) A distance-based framework for measuring functional diversity
from multiple traits. Ecology, 91, 299-305.
Petchey, O.L. & Gaston, K.J. (2002) Functional diversity (FD), species richness and community
composition. Ecology Letters, 5, 402-411.
Villéger, S., Mason, N.W.H. & Mouillot, D. (2008) New multidimensional functional diversity indices
for a multifaceted framework in functional ecology. Ecology, 89, 2290-2301.
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