Supplementary Material:
Partitioning the multi-scale effects of human activity on the occurrence of riparian forest birds
Robert J. Fletcher, Jr. and Richard L. Hutto
Appendix Model selection strategies for developing parsimonious models at each spatial scale to further use in variation partitioning analyses aimed at estimating effects of scale and human disturbance on bird distributions.
To develop models used for variation partitioning, we first compared a series of candidate models at each scale and selected the most parsimonious model using Akaike’s Information Criterion, adjusted for sample size (AICc). At the local scale, candidate model sets were developed by first classifying each species into coarse categories based on nest location (ground, shrub, tree, cavity), nest height (<2.5m, <5m, >5m, >10m), and foraging tactic. Information on these characteristics was taken from the literature (Ehrlich et al. 1988; Tewksbury et al. 2002; Poole 2005; Table A1). We then used the following decision rules based on these characteristics to identify a candidate set of models for comparison within each species (Table A2). For each species, we only considered local variables relevant to known nest sites. For example, for species that nest in cavities, we considered models that included the number of snags. For cavity nesters we also included tree density b/c often portions of trees are dead or dying and used by cavity nesters. From nest height information, we included ground and shrub measures for species known to nest near the ground (<2.5 m). For foraging tactics, we considered the following decision rules for model comparisons. For bark foragers and ground foragers, we included tree density measures and ground measures, respectively. For foliage foragers (gleaners), we included shrub and tree density measures that may reflect indirectly the total amount of foliage available in an area. Finally, for all species we considered measures of canopy height and cover, under the assumption that these factors could influence both nesting and foraging for all species (see Table A3 for results of these model comparisons). At the local level, we also separately developed models to explain the effects of exotics by comparing three models: one that included total exotic cover, one that included exotic diversity, and one that included both measures (Table A4).
At the patch scale, we compared three candidate models: one that included patch width only, one that included patch shape only, and one that included both measures (Table A4). At the landscape scale, we compared candidate models that included forest area (as a measure of potenital habitat loss), patch density (as a measure of configuration and potential fragmentation), and the distance and area of the nearest patch (as a measure of connectivity). We compared all combinations (Table A4), under the assumption that each factor—loss, fragmentation, and connectivity—could influence each species.
References
Ehrlich PR, Dobkin DS, Wheye E (1988) The birder’s handbook: a field guide to the natural history of North American birds. Simon and Schuster, Inc., New York
Poole A (ed) (2005) The Birds of North American Online: http://bna.birds.cornell.edu/BNA/. Cornell Laboratory of Ornithology, Ithaca, New York
Tewksbury JJ, Black AE, Nur N, Saab VA, Logan BD, Dobkin DS (2002) Effects of anthropogenic fragmentation and livestock grazing on western riparian bird communities. Studies in Avian Biology 25:158-202
Table A1. Life history/natural history characteristics of species and the inclusion of different types of local vegetation variables in the development of bird distribution models.
Characteristic / Considered in candidate local habitat models?Species* / Species code / Nest
location / Nest height / Forage tactic / Ground cover / Shrubs / Trees / Canopy / Snags
American Goldfinch / AMGO / ground/shrub / >5m / foliage / Y / Y / Y
American Robin / AMRO / tree/shrub / <5m / ground / Y / Y / Y / Y
Black-billed Magpie / BBMA / shrub / >2.5m / ground / Y / Y / Y
Black-capped Chickadee / BCCH / cavity / >2.5m / bark / Y / Y / Y
Brown-headed Cowbird / BHCO / parasite / ground / Y / Y / Y / Y
Black-headed Grosbeak / BHGR / shrub / <5m / foliage / Y / Y / Y
Bullock’s Oriole / BUOR / tree / >5m / foliage / Y / Y / Y
Cedar Waxwing / CEDW / tree/shrub / >5m / foliage / Y / Y / Y
Common Yellowthroat / COYE / ground/shrub / <2.5m / foliage / Y / Y / Y / Y
Downy Woodpecker / DOWO / cavity / >5m / bark / Y / Y / Y
Eastern Kingbird / EAKI / tree/shrub / >5m / aerial / Y / Y / Y
European Starling / EUST / cavity / >5m / ground / Y / Y / Y / Y
Gray Catbird / GRCA / shrub / <2.5m / ground / Y / Y / Y
House Finch / HOFI / tree / >5m / ground / Y / Y / Y
House Wren / HOWR / cavity / <5m / ground / Y / Y / Y / Y
Least Flycatcher / LEFL / tree/shrub / <10m / aerial / Y / Y / Y
Mourning Dove / MODO / tree/shrub/ground / <10m / ground / Y / Y / Y / Y
Northern Flicker / NOFL / cavity / >5m / ground / Y / Y / Y / Y
Red-naped Sapsucker / RNSA / cavity / >5m / bark / Y / Y / Y
Red-winged Blackbird / RWBL / ground/reeds / <2.5m / ground / Y / Y / Y
Song Sparrow / SOSP / ground / <2.5m / ground / Y / Y / Y
Spotted Towhee / SPTO / ground / <2.5m / ground / Y / Y / Y
Tree Swallow / TRES / cavity / >5m / aerial / Y / Y / Y
Warbling Vireo / WAVI / tree/shrub / >5m / foliage / Y / Y / Y
Western Kingbird / WEKI / tree / >5m / aerial / Y / Y
Western Wood-pewee / WEWP / tree / >5m / aerial / Y / Y
Willow Flycatcher / WIFL / shrub / <2.5m / aerial / Y / Y / Y
Yellow-breasted Chat / YBCH / shrub / <2.5m / foliage / Y / Y / Y / Y
*Scientific names listed in Table 2 of the main text.
Table A2. Different models types considered (n = 22) for developing a parsimonious local model for describing bird occurrence. Note that for each species, not all models were considered (see Table A3 for summary of model comparison for each species).
Ground cover / Shrub cover / Tree density/structure / CanopyModel description
(abbreviation) / Ka / Grasses / Forbs / Litter / Total shrubsb / Shrub diversityc / # of deciduous treesb / #of conifer trees / Tree diversityc / Canopy heightb / Canopy coverb / # of snagsb
Ground cover (g) / 5 / X / X / X
Shrub cover (sh) / 3 / X
Shrub diversity (shd) / 3 / X
Tree density (t) / 4 / X / X
Conifer density (co) / 3 / X
Tree diversity (td) / 3 / X
Canopy cover (c) / 3 / X
Canopy height (ch) / 3 / X
Snag density (sn) / 3 / X
Ground + shrubs (g+sh) / 7 / X / X / X / X / X
Ground + canopy (g+c) / 7 / X / X / X / X / X
Shrub cover + diversity (sh+sd) / 4 / X / X
Canopy cover + height (c+ch) / 4 / X / X
Shrubs + canopy (sh+c) / 6 / X / X / X / X
Canopy + tree density (c+t) / 6 / X / X / X / X
Canopy + snag (c+sn) / 5 / X / X / X
Conifer +snag (co+sn) / 4 / X / X
Shrub + tree density (sh+t) / 5 / X / X / X
Shrub + tree diversity (sd+td) / 4 / X / X
Ground + shrub + canopy (g+sh+c) / 9 / X / X / X / X / X / X / X
Ground + snag + canopy (g+sn+c) / 8 / X / X / X / X / X / X
Ground + tree density + snag (g+t+sn) / 8 / X / X / X / X / X / X
aK = minimum number of parameters (fixed effects shown, plus intercept and random site effect). For species showing non-linear correlations with habitat, additional quadratic terms were included.
bNonlinear effects considered by comparing a univariate marginal model to one that included a quadratic term. If the quadratic term lowered the AICc, nonlinear effects were included in all subsequent models.
cSimpson’s index of diversity.
Table A3. Comparison of candidate local models, based on ∆AICc, for 28 species using riparian habitat, 2004-2005. Model with the most support (∆AICc = 0) is indicated by bold type and was used for subsequent analyses.
Species code** / g / sh / shd / t / co / td / c / ch / sn / g
+sh / g
+c / sh
+sd / c
+ch / sh
+c / c
+t / c
+sn / co
+sn / sh
+t / sd
+td / g+sh
+c / g+sn
+c / g+t
+sn
AMGO / 3.6 / 3.5 / 0 / 3.2 / 1.7 / 1.9 / 3.2 / 5.5 / 3.9 / 8.1 / 6.0 / 1.6 / 3.8
AMRO / 9.7 / 5.4 / 6.2 / 1.6 / 0.7 / 3.6 / 4.5 / 0 / 12.4 / 7.9 / 7.4 / 2.0 / 6.1 / 1.3 / 2.5 / 5.6 / 12.1
BBMA / 4.0 / 1.5 / 0.9 / 4.0 / 0 / 3.7 / 1.1 / 3.0 / 0.7 / 3.1 / 4.2
BCCH / 0 / 0.1 / 3.5 / 2.4 / 3.3 / 2.3 / 3.4 / 3.7 / 4.6 / 1.1
BHCO / 28.3 / 30.1 / 28.9 / 27.8 / 31.2 / 30.5 / 27.2 / 0 / 24.6 / 6.2 / 30.6 / 1.9 / 4.4 / 5.1 / 29.5 / 30.6 / 7.8
BHGR / 5.6 / 4.1 / 5.4 / 5.4 / 5.5 / 3.2 / 0 / 6.1 / 1.8 / 4.2 / 5.4 / 7.5 / 6.2
BUOR / 23.5 / 29.0 / 32.3 / 30.3 / 27.0 / 31.0 / 6.9 / 25.2 / 0 / 2.4 / 3.0 / 27.4 / 26.1
CEDW / 7.4 / 8.4 / 10.9 / 10.3 / 10.8 / 7.2 / 0 / 8.1 / 1.6 / 1.9 / 4.9 / 8.6 / 10.2
COYE / 11.4 / 5.9 / 10.6 / 1.5 / 4.2 / 9.6 / 8.4 / 10.9 / 12.7 / 13.7 / 8.0 / 10.4 / 8.9 / 5.2 / 0 / 10.9 / 11.6
DOWO / 12.8 / 13.3 / 15.2 / 5.5 / 0.4 / 14.2 / 0 / 2.0 / 3.1 / 15.0
EAKI / 2.6 / 10.8 / 9.2 / 9.2 / 10.5 / 8.3 / 8.5 / 4.3 / 9.4 / 2.4 / 12.1 / 0 / 12.4
EUST / 51.5 / 41.5 / 49.6 / 41.3 / 47.7 / 6.2 / 34.3 / 2.7 / 5.4 / 4.3 / 1.4 / 36.3 / 0 / 36.9
GRCA / 29.8 / 22.9 / 31.9 / 39.4 / 17.0 / 23.7 / 0 / 21.2 / 17.7 / 5.8 / 0.9
HOFI / 8.9 / 3.7 / 5.5 / 5.8 / 4.1 / 0 / 4.7 / 1.9 / 4.6
HOWR / 18.5 / 19.2 / 15.7 / 9.2 / 17.6 / 13.7 / 15.6 / 20.2 / 3.5 / 0
LEFL / 15.4 / 18.9 / 1.5 / 20.2 / 13.1 / 11.0 / 4.3 / 12.6 / 3.3 / 0 / 1.2 / 2.3 / 14.7
MODO / 8.1 / 14.7 / 10.7 / 3.6 / 4.4 / 12.1 / 12.8 / 4.2 / 8.7 / 0.5 / 12.8 / 6.2 / 4.4 / 0 / 5.5 / 10.7 / 0.9
NOFL / 20.9 / 21.3 / 22.3 / 18.2 / 22.8 / 2.8 / 16.6 / 0 / 0.3 / 0.4 / 0.3 / 16.1 / 0.4 / 15.4
RNSA / 6.4 / 16.5 / 3.2 / 14.7 / 0 / 11.4 / 1.4 / 1.7 / 0.9 / 13.4
RWBL / 9.4 / 9.3 / 11.8 / 13.5 / 9.9 / 0 / 5.5 / 9.6 / 10.2 / 11.0 / 6.8
SOSP / 68.9 / 59.8 / 49.2 / 68.2 / 32.1 / 43.1 / 26.4 / 44.3 / 28.0 / 0
SPTO / 0 / 0.6 / 1.0 / 0.8 / 0.2 / 3.8 / 4.2 / 2.5 / 2.5 / 5.9 / 8.0
TRES / 1.1 / 1.0 / 7.2 / 11.3 / 5.8 / 6.3 / 6.1 / 1.3 / 4.1 / 0
WAVI / 0.1 / 9.5 / 14.7 / 13.4 / 14.2 / 14.5 / 14.1 / 0 / 16.1 / 3.0 / 18.9 / 1.7 / 11.4
WEKI / 0 / 8.7 / 9.1 / 4.4 / 5.8 / 5.8 / 5.0
WEWP / 19.4 / 28.5 / 24.9 / 28.1 / 0 / 1.1 / 1.0
WIFL / 18.4 / 16.9 / 16.8 / 17.0 / 5.3 / 21.8 / 0 / 18.9 / 4.9 / 9.0 / 2.4
YBCH / 14.5 / 11.6 / 11.4 / 2.6 / 2.5 / 11.6 / 11.2 / 7.7 / 18.2 / 15.7 / 13.5 / 9.7 / 13.8 / 0 / 4.2 / 13.5 / 20.1
*Candidate model names taken from abbreviations listed in Table A2
**See Table A1 for Full species names
Table A4. Comparisons of candidate models for invasives, patch, and surrounding landscape predictors, based on ∆AICc, for 28 species using riparian habitat, 2004-2005. Models with the most support (∆AICc = 0) are indicated by bold type. Note that each species has 3 best supported models that are used for further analyses, one for invasives, one for patch predictors, and one for landscape predictors.
Species code / Div / Abun / Div + Abun / Wid / Shp / Wid + Shp / Loss / Frag / Con / Loss + frag / Loss + con / Frag + Con / Loss + Frag + Con
AMGO / 0 / 0.3 / 0.2 / 0 / 1.9 / 1.9 / 0 / 0.1 / 1.7 / 1.8 / 3.6 / 3.0 / 4.7
AMRO / 0 / 0.7 / 2.0 / 0 / 3.4 / 1.6 / 0 / 0.1 / 2.3 / 1.9 / 4.0 / 4.2 / 6.0
BBMA / 0 / 3.5 / 1.7 / 0 / 2.3 / 0.7 / 0 / 1.2 / 2.7 / 2.6 / 3.1 / 4.2 / 4.1
BCCH / 0.3 / 0 / 2.1 / 0 / 8.4 / 2.1 / 0.5 / 6.0 / 3.1 / 2.5 / 0 / 5.1 / 1.3
BHCO / 0 / 1.7 / 1.5 / 4.6 / 7.6 / 0 / 13.9 / 14.3 / 1.9 / 15.9 / 3.8 / 0 / 1.2
BHGR / 0.9 / 0 / 2.0 / 0 / 1.3 / 1.8 / 8.2 / 0.6 / 8.5 / 0 / 10.6 / 1.7 / 2.2
BUOR / 0.5 / 0 / 2.0 / 0.9 / 0 / 0.5 / 0 / 9.3 / 7.9 / 0.7 / 2.1 / 8.1 / 3.8
CEDW / 0 / 0.3 / 2.0 / 1.2 / 0 / 2.0 / 0.2 / 0 / 0.4 / 1.8 / 2.3 / 2.4 / 4.4
COYE / 0.3 / 0 / 2.0 / 0 / 1.1 / 2.1 / 0 / 0.9 / 2.6 / 1.7 / 4.1 / 4.4 / 5.7
DOWO / 1.2 / 0 / 1.9 / 0 / 8.5 / 2.1 / 5.8 / 0 / 6.5 / 1.3 / 8.5 / 4.1 / 5.3
EAKI / 8.3 / 0 / 0.9 / 0 / 7.3 / 2.0 / 4.8 / 5.9 / 2.1 / 5.6 / 3.2 / 0 / 1.7
EUST / 0 / 1.5 / 0.7 / 9.6 / 0 / 2.0 / 1.6 / 5.2 / 0 / 3.4 / 1.2 / 2.0 / 3.1
GRCA / 0 / 6.9 / 0.7 / 4.6 / 0 / 1.7 / 3.4 / 6.1 / 0 / 5.3 / 0.2 / 1.8 / 1.3
HOFI / 0 / 0.3 / 2.1 / 0 / 6.0 / 2.0 / 1.3 / 0 / 1.9 / 2.0 / 3.9 / 3.0 / 5.0
HOWR / 0.3 / 0 / 1.9 / 0.1 / 0 / 1.2 / 0 / 0.1 / 1.8 / 2.0 / 3.8 / 3.3 / 5.3
LEFL / 1.3 / 0 / 2.0 / 0 / 13.6 / 1.4 / 6.7 / 0 / 2.6 / 1.9 / 4.0 / 0.9 / 1.5
MODO / 2.6 / 0 / 2.1 / 4.2 / 1.7 / 0 / 3.6 / 5.7 / 5.4 / 3.7 / 0.3 / 6.8 / 0
NOFL / 0 / 0.1 / 1.9 / 0 / 0.7 / 0.1 / 0 / 0.1 / 1.7 / 2.0 / 3.8 / 3.8 / 5.8
RNSA / 0 / 0.3 / 1.5 / 2.9 / 0 / 3.9 / 0 / 1.1 / 1.0 / 2.0 / 1.8 / 3.1 / 3.7
RWBL / 0.5 / 0 / 1.0 / 1.7 / 9.8 / 0 / 14.4 / 12.8 / 9.8 / 14.8 / 10.8 / 0 / 2.0
SOSP / 3.3 / 0 / 2.0 / 25.6 / 0 / 0.6 / 13.7 / 22.6 / 8.9 / 13.8 / 7.3 / 6.0 / 0
SPTO / 1.3 / 0 / 1.4 / 0.9 / 0 / 3.0 / 0.1 / 0 / 1.7 / 2.0 / 3.8 / 3.8 / 5.9
TRES / 3.6 / 6.5 / 0 / 2.3 / 0 / 2.0 / 0 / 3.4 / 1.8 / 1.2 / 0.8 / 3.7 / 0.7
WAVI / 7.7 / 0.7 / 0 / 5.5 / 0.1 / 0 / 2.3 / 6.0 / 0.1 / 3.6 / 1.5 / 1.2 / 0
WEKI / 0.5 / 0 / 1.2 / 1.9 / 0 / 3.5 / 0 / 0.8 / 2.2 / 2.0 / 3.8 / 4.2 / 5.9
WEWP / 0 / 0.1 / 2.0 / 0.9 / 0 / 1.7 / 0 / 0.1 / 1.8 / 2.1 / 3.6 / 3.9 / 5.7
WIFL / 0 / 0.1 / 1.6 / 0.2 / 0 / 0.1 / 0.4 / 0 / 2.1 / 2.1 / 4.1 / 1.7 / 3.8
YBCH / 4.7 / 0 / 2.0 / 1.4 / 0 / 3.2 / 0 / 2.0 / 3.3 / 1.3 / 3.9 / 4.7 / 3.6
Div = diversity, Abun = abundance, Wid = patch width, Shp = patch shape, Loss = amount of forest cover, Frag = patch density (# patches/amount of forest cover), Con = distance to nearest patch + area of that patch.