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Supporting Information
Appendix S1. Species distribution modelling details
Table S1. Background on derivation of environmental variables for each grid cell used in the modelling
process.
Variable
roads
towns
Perth
intensive land use
habitat diversity
protected areas
coast
creeks
distance water
distance coast
remnant veg
water
forestry
visitor centres
DEC web
DEC named
Derivation
Total length of all sealed and unsealed roads (not including unmapped tracks) in each
grid cell (km)
Averaged for each grid cell from a 100m raster of Euclidean distance from the
nearest town with a population over 10,000 (km)
Averaged for each grid cell from a 100m raster of Euclidean distance from the capital
city Perth, where 75% of the population of the area live (km)
Total area of intensive land use, including residential, industrial, commercial,
recreational, intensive animal production and horticulture, calculated per grid cell
(Department of Agriculture and Food 2006)*. Converted into presence/absence to
deal with skewed distribution (0=absent,1=present)
Pre-European extent from the best large-scale vegetation map of 376 plant
associations in Western Australia (Beard 1980a; Beard 1980b)**, overlaid with a
current remnant vegetation layer. Number of different habitat types currently present
within each grid cell calculated.
Number of protected areas in each grid cell calculated from a map of all protected
areas (including IUCN levels 1-6, unallocated Crown Land and Freehold, and State
Forest/Timber Reserve) managed for conservation (by WA Department of
Environment and Conservation)
Coastline present in any part of the grid cell. Converted into presence/absence to deal
with skewed distribution (0=absent,1=present)
Total length of all permanent and semi-permanent watercourses in each grid cell
(km)
Averaged for each grid cell from a 100m raster of Euclidean distance from the
nearest saltwater or freshwater body (creek, river, ocean, lake, pool, estuary) (km)
Averaged for each grid cell from a 100m raster of Euclidean distance from the
coastline (km)
Total summed area of vegetation per grid cell calculated from the current remnant
vegetation layer (km2)
Permanent water land use present in any part of the grid cell (reservoir/dam, lake,
estuary, or creek/river), calculated by merging the data for ‘creeks’ and ‘water’, then
converting into presence/absence to deal with over-dispersion (0=absent,1=present)
Total area of forestry land use, including plantation or production, calculated per grid
cell (Department of Agriculture and Food 2006)*. Converted into presence/absence
to deal with skewed distribution (0=absent,1=present)
Averaged for each grid cell from a 100m raster of Euclidean distance from the
nearest tourist visitor centre (km)
At least one protected area in the grid cell advertised on the internet:
http://www.dec.wa.gov.au (WA Department of Environment and Conservation)
(0=absent,1=present)
At least one named (gazetted or State approved) protected area (WA Department of
Environment and Conservation), where un-named areas are largely unofficial or
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newly acquired lands (0=absent,1=present)
DEC trails
At least one marked trail (not a sealed or unsealed road) in a protected area (WA
Department of Environment and Conservation), calculated from a review of
information available for all protected areas and supplemented by overlaying a map
of tracks over the existing layer of DEC protected areas (0=absent,1=present)
urban
Point layer data of all WA towns and cities buffered by 100m and merged with urban
land use (residential) layer (Department of Agriculture and Food 2006)*. Total area
calculated per grid cell and converted into presence/absence to deal with skewed
distribution (0=absent,1=present)
recreation
Recreational land use present (e.g. local parks, gardens, cultural services)
(Department of Agriculture and Food 2006)*. Converted into presence/absence to
deal with skewed distribution (0=absent,1=present)
agriculture
Total area of dryland agricultural land use (grazing modified pastures, cropping,
seasonal horticulture), calculated per grid cell (Department of Agriculture and Food
2006)*
threatened sp
Grid overlaid on partitioned atlas survey records from between 1998 and 2002 of
only threatened species (Wildlife Conservation Act 1950 in WA) to calculate number
of threatened species detected in this time for each grid cell. Converted into
presence/absence to deal with skewed distribution (0=absent,1=present)
*Land use mapped 1: 25 000 in urban areas, 1:100 000 in agricultural areas and 1:250 000 in pastoral zones
** Remnant habitat type mapped at 1:250,000, describing pre-cleared Western Australian vegetation types
(Beard 1980a; Beard 1980b)
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Table S2. GLM of the importance of prior knowledge for predicting future surveys (response variable:
number of surveys per grid cell 2003–2007)
Covariates
Intercept
Number of surveys per grid cell 1998 to 2002
(standardised)
Null deviance
Residual deviance
Explained deviance
Estimate Std. Error z value
0.31
0.01
35.04
0.80
0.02
1773.5
1155.5
0.35
45.46
Pr(>|z|)
<0.001
<0.001
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Table S3. Model parameters for the three accessibility models.
Model
Covariates
Estimate
tourism roads
Intercept
water
DEC trails
roads
visitor centres
-1.43
0.61
0.72
1.79
-0.11
Std.
Error
0.05
0.21
0.13
0.13
0.10
access roads
Intercept
roads
intensive land use
-1.40
1.80
0.60
roads
Intercept
roads
-1.37
2.07
z value
Pr(>|z|)
-30.61
2.97
5.67
13.69
-1.13
<0.001
0.003
<0.001
<0.001
0.257
0.05
0.13
0.13
-30.65
13.95
4.73
<0.001
<0.001
<0.001
0.05
0.12
-29.91
17.11
<0.001
<0.001
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Figure S1. Distribution of model parameters showing (a) Probability of survey using logistic regression
and a threatened species and protected areas hypothesis (‘conservation concern’), with important
explanatory variables of (b) frequency of protected areas per grid cell, (c) number of different habitats per
grid cell, (d) detection of a threatened species during the main atlas period in 1998–2002, and (e) road
density, a single variable that explained a high level of deviance.
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(a)
(b) 0.8
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Predicted probability of survey
Density. Bandwidth= 0.05478
0.7
4
3
2
1
0.6
0.5
0.4
0.3
0.2
0.1
0
0.0
0.4
0.8
absence presence
predicted value
actual cell value 2003-2007
AUC= 0.829
(c)
1.0
True positive rate
0.8
0.6
0.4
0.2
0.0
0.0
0.2
0.4
0.6
0.8
1.0
False postive rate
Figure S2. Discrimination capacity of the optimal distribution model developed for surveys between 2003
and 2007 in the south-west biodiversity hotspot, showing (a) distribution of predicted probability values
associated with either surveyed (solid line) or unsurveyed (dotted line) cells, (b) a boxplot of absence vs.
presence values for 2003–2007 relative to their predicted probability of being surveyed, and (c) the ROC
curve (AUC = 0.829).
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(a)
(b)
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Predicted probability of survey
Density. Bandwidth= 0.0531
0.8
3
2
1
0.6
0.4
0.2
0
0.0
0.4
0.8
absence presence
predicted value
actual cell value 2008-2011
AUC= 0.729
(c)
1.0
True positive rate
0.8
0.6
0.4
0.2
0.0
0.0
0.2
0.4
0.6
0.8
1.0
False postive rate
Figure S3. Discrimination capacity of the optimal distribution model (‘conservation concern’), tested with
surveys between 2008 and 2011 in the south-west biodiversity hotspot, showing (a) distribution of
predicted probability values associated with either surveyed (solid line) or unsurveyed (dotted line) cells,
(b) a boxplot of absence vs. presence values for 2008–2011 relative to their predicted probability of being
surveyed, and (c) the ROC curve (AUC = 0.729).