Supplementary Material

Supplementary Table 1: Complete list of bird species and their synanthropy, functional group and special species status.

Species / Abbreviation / Synanthropy / Functional Group / Special or indicator species
Acorn Woodpecker / ACWO / non-synanthropic / own group / yes
American Crow / AMCR / synanthropic / corvidae omnivores / no
American Goldfinch / AMGO / synanthropic / own group / no
American Robin / AMRO / non-synanthropic / seed eaters, frugivores and ground foragers / no
Anna’s Hummingbird / ANHU / synanthropic / hummingbirds / yes
Ash-throated Flycatcher / ATFL / non-synanthropic / vireos, sparrows, warblers / no
Barn Swallow / BASW / synanthropic / swallows / no
Black-capped Chickadee / BCCH / synanthropic / bark foragers / no
Bewick’s Wren / BEWR / synanthropic / seed eaters, frugivores and ground foragers / no
Brown-headed Cowbird / BHCO / synanthropic / seed eaters, frugivores and ground foragers / no
Black-headed Grosbeak / BHGR / synanthropic / seed eaters, frugivores and ground foragers / no
Black Phoebe / BLPH / synanthropic / flycatchers / no
Brown Creeper / BRCR / non-synanthropic / own group / no
Black-throated Grey Warbler / BTGW / non-synanthropic / foliage gleaners / no
Ban-tailed Pigeon / BTPI / synanthropic / own group / no
Bullock’s Oriole / BUOR / synanthropic / own group / no
Bushtit / BUSH / synanthropic / bark foragers / no
California Quail / CAQU / synanthropic / own group / no
Cassin’s Vireo / CAVI / synanthropic / seed eaters, frugivores and ground foragers / no
Chestnut-backed Chickadee / CBCH / non-synanthropic / bark foragers / no
Cedar Waxwing / CEWA / synanthropic / foliage gleaners / no
Chipping Sparrow / CHSP / synanthropic / seed eaters, frugivores and ground foragers / yes
Common Raven / CORA / synanthropic / corvidae omnivores / no
Common Yellowthroat / COYE / synanthropic / foliage gleaners / no
Dark-eyed Junco / DEJU / non-synanthropic / seed eaters, frugivores and ground foragers / no
Downy Woodpecker / DOWO / non-synanthropic / bark foragers / no
European Starling / EUST / synanthropic / seed eaters, frugivores and ground foragers / no
Evening Grosbeak / EVGR / synanthropic / seed eaters, frugivores and ground foragers / no
Grey Jay / GRJA / synanthropic / corvidae omnivores / no
Hairy Woodpecker / HAWO / non-synanthropic / bark foragers / no
Hermit Warbler / HEWA / non-synanthropic / foliage gleaners / no
House Finch / HOFI / synanthropic / own group / no
House Wren / HOWR / synanthropic / seed eaters, frugivores and ground foragers / no
Hutton’s Vireo / HUVI / non-synanthropic / vireos, sparrows, warblers / no
Lazuli Bunting / LABU / synanthropic / seed eaters, frugivores and ground foragers / no
Lesser Goldfinch / LEGO / synanthropic / seed eaters, frugivores and ground foragers / no
McGillivray’s Warbler / MGWA / synanthropic / bark foragers / no
Mourning Dove / MODO / synanthropic / own group / no
Nashville Warbler / NAWA / non-synanthropic / foliage gleaners / no
Northern Flicker / NOFL / synanthropic / bark foragers / no
Orange-crowned Warbler / OCWA / synanthropic / own group / no
Olive-Sided Flycatcher / OSFL / synanthropic / flycatchers / no
Pine Grosbeak / PIGR / synanthropic / own group / no
Pileated Woodpecker / PIWO / non-synanthropic / bark foragers / no
Pacific-slope Flycatcher / PSFL / non-synanthropic / flycatchers / no
Purple Finch / PUFI / synanthropic / seed eaters, frugivores and ground foragers / no
Red-breasted Nuthatch / RBNU / non-synanthropic / bark foragers / no
Red-breasted Sapsucker / RBSA / non-synanthropic / own group / no
Rufous Hummingbird / RUHU / synanthropic / hummingbirds / no
Red-winged Blackbird / RWBL / synanthropic / seed eaters, frugivores and ground foragers / no
Western Scrub Jay / SCJA / synanthropic / corvidae omnivores / yes
Sooty Grouse / SOGR / non-synanthropic / own group / no
Song Sparrow / SOSP / synanthropic / seed eaters, frugivores and ground foragers / no
Spotted Towhee / SPTO / non-synanthropic / seed eaters, frugivores and ground foragers / no
Steller’s Jay / STJA / non-synanthropic / corvidae omnivores / no
Swainson’s Thrush / SWTH / non-synanthropic / foliage gleaners / no
Townsend’s Warbler / TOWA / non-synanthropic / foliage gleaners / no
Violet-green Swallow / VGSW / synanthropic / swallows / no
Warbling Vireo / WAVI / synanthropic / vireos, sparrows, warblers / no
White-breasted Nuthatch / WBNU / synanthropic / bark foragers / yes
White-crowned Sparrow / WCSP / synanthropic / vireos, sparrows, warblers / no
Western Bluebird / WEBL / non-synanthropic / foliage gleaners / yes
Western Tanager / WETA / non-synanthropic / foliage gleaners / no
Wild Turkey / WITU / non-synanthropic / corvidae omnivores / no
Wilson’s Warbler / WIWA / non-synanthropic / foliage gleaners / no
Winter Wren (now Pacific Wren) / WIWR / non-synanthropic / seed eaters, frugivores and ground foragers / no
Western Meadowlark / WMLA / non-synanthropic / seed eaters, frugivores and ground foragers / yes
Western Wood Peewee / WWPE / synanthropic / flycatchers / no
Yellow-breasted Chat / YBCH / non-synanthropic / vireos, sparrows, warblers / no
Yellow Warbler / YEWA / synanthropic / foliage gleaners / no
Yellow-rumped Warbler / YRWA / synanthropic / vireos, sparrows, warblers / no

Supplementary Table 2. Sampling intensity of individual bird species.

Species Code / Sampling Intensity / Species Code / Sampling Intensity / Species Code / Sampling Intensity / Species Code / Sampling Intensity
ACWO / 72% / CAVI / 79% / MGWA / 44% / SPTO / 68%
AMCR / 58% / CEWA / 62% / MODO / 44% / STJA / 81%
AMGO / 72% / CHSP / 76% / NOFL / 64% / TOWA / 44%
AMRO / 74% / COYE / 89% / OCWA / 56% / VGSW / 71%
ANHU / 62% / DEJU / 82% / PIGR / 44% / WBNU / 70%
BASW / 44% / DOWO / 47% / PIWO / 44% / WCSP / 73%
BCCH / 68% / EUST / 68% / PSFL / 65% / WEBL / 79%
BEWR / 74% / HEWA / 44% / PUFI / 62% / WETA / 78%
BHCO / 71% / HOFI / 69% / RBSA / 50% / WIWR / 44%
BHGR / 74% / HOWR / 74% / RUHU / 58% / WMLA / 44%
BRCR / 78% / HUVI / 68% / RWBL / 48% / WWPE / 69%
BUOR / 74% / LABU / 66% / SCJA / 54% / YBCH / 72%
BUSH / 44% / LEGO / 62% / SOSP / 64% / YEWA / 58%

Supplementary Table 3. List of functional groups resulting from Cluster Analysis (see text for description of analysis). Species codes given in Table 5.

Group / Species Included / Group / Species Included
1 Acorn Woodpeckers / ACWO / 11 Brown Creepers / BRCR
2 Corvidae omnivores / AMCR, CORA, SCJA, WITU, GRJA, STJA / 12 Orange-crowned Warblers / OCWA
3 Seed eaters, frugivores, ground foragers / AMRO, BHGR, EUST, EVGR, PUFI, SPTO, BEWR, HOWR, WIWR, WREN, CAVI, BHCO, WMLA, LABU, SOSP, LEGO, CHSP, RWBL, DEJU / 13 Red-breasted Sapsuckers / RBSA
4 Bark foragers / BCCH, BUSH, CBCH, DOWO, HAWO, PIWO, WBNU, MGWA, NOFL, RBNU / 14 Swallows / BASW VGSW
5 Flycatchers / BLPH, WWPE, PSFL, OSFL / 15 House Finches / HOFI
6 Foliage gleaners / BTGW, HEWA, SWTH, NAWA, COYE, WIWA, YEWA, CEWA, WEBL, WETA, TOWA / 16 Pine Grosbeaks / PIGR
7 Vireos, Sparrows, Warblers / ATFL, WAVI, YRWA, HUVI, YBCH, WCSP / 17 California Quails / CAQU
8 American Goldfinches / AMGO / 18 Sooty Grouses / SOGR
9 Bullock’s Oriole / BUOR / 19 Band-tailed Pigeons / BTPI
10 Hummingbirds / ANHU, RUHU / 20 Mourning Doves / MODO

Supplementary Table 4: Candidate explanatory variables for canonical correspondence analysis (CCA) and generalized linear models (GLM). See text for additional information on how each variable was measured and/or calculated.

Abbreviation used, if any / Unit / How variable was measured / Included in CCA / Included in GLM
Local (site) scale variables
Average canopy height / CanopyHeight / m / Field estimates using laser rangefinder / yes / yes
Average canopy cover / CanopyCover / % / Field measurements using densitometer at 0, 90, 180 and 270º, one meter from estimated centermost tree / yes / yes
Height diversity / HD / # / Field measurements using ruler and a laser rangefinder and calculated using methods discussed in Moss (1978) / yes / yes
Number of snags and logs / SnagsAndLogs / # / Field counts within 0.04 ha of center of site / yes / no*
Number of tree stems (total) / TotalStems / # / Field counts within 0.04 ha of center of site / yes / yes
Number of large tree stems (total) / Total Large Stems / # / Field counts of trees >8 cm within 0.04 ha of center of site / yes / yes
Number of seedling tree stems / # / Field counts of trees <2.5 cm within 0.04 ha of center of site / no† / no†
Number of sapling tree stems / # / Field counts of trees 2.5-8 cm within 0.04 ha of center of site / no† / no†
Basal area / # / Calculated based on number of each size of tree measured / no† / no†
Tree species diversity / # / Counted number of trees in each of eight families (including one unidentified) within 0.04 ha of center of site / no† / no†
Presence of cuts / y/n / Field observations within 50 m of center of site / no‡ / no‡
Presence of grazing / y/n / Field observations within 50 m of center of site / no‡ / no‡
Understory vegetation (Rhus diversilobs, Rubus discolor, tree saplings, other) / % / Field estimates within 0.01-ha of center of site / no† / no†
Ground cover (grasses/forbes, bare ground, impervious surface, water) / % / Field estimates within 0.01-ha of center of site / no† / no†
Number of next boxes / # / Field counts within 50 m of center of site / no‡ / no‡
Impervious area / % / Field estimates within 50 of center of site / no† / no†
Water / % / Field estimates within 50 m of center of site / no† / no†
Patch scale variables
Area** / Area / m2 / Calculated using Hawth Tools and landcover data in ArcGIS / yes / yes
Core area (amount of area 50 m from any edge) ** / m2 / Calculated using Hawth Tools and landcover data in ArcGIS / no† / no†
Perimeter** / Perim / M / Calculated using Hawth Tools and landcover data in ArcGIS / yes / yes*
Area:perimeter** / M / Calculated using Hawth Tools and landcover data in ArcGIS / no† / no†
Landscape scale variables
Amount of surrounding oak forests** / Oak / % / Calculated using Hawth Tools and landcover data in ArcGIS / yes / yes
Amount of surrounding other forests** / Forest / % / Calculated using Hawth Tools and landcover data in ArcGIS / yes / yes
Amount of surrounding development** / Develop / % / Calculated using Hawth Tools and landcover data in ArcGIS / yes / yes
Amount of surrounding agriculture** / Ag / % / Calculated using Hawth Tools and landcover data in ArcGIS / yes / yes
Amount of surrounding “other” (everything not included in other four matrix variables)** / % / Calculated using Hawth Tools and landcover data in ArcGIS / no† / no†
Distance to nearest oak** / m / Calculated using Hawth Tools and landcover data in ArcGIS / no† / no†

*removed based on multicollinearity

†removed based on inclusion in other variables

‡ removed based on distribution and simple regressions

**Used Trimble Juno and a TruPulse 360B Rangefinder in the field to map patch perimeters. ArcGIS was then used to calculate this variable.

Supplementary Table 5: Generalized linear model results for diversity of all identified species (richness, abundance), for synanthropic species (richness, abundance), for non-synanthropic species (richness, abundance), for functional groups (richness, evenness and abundance) and for individual species (abundance). Functional group abundances are listed by the description of the functional group and are given only for groups with more than one species. A more detailed account every species in each functional group is listed in Supplementary Table 3. When the null model is one of the viable models (AICc=AICcmin±2), only the null is reported. All AIC values, ΔAIC, and weights (Wi) are listed for each model run up to AICcmin±2 in Supplementary Table 6. R2 was calculated as 1-(residual deviance/null deviance). Codes: HD=height diversity; Develop, Ag, Oak, Forest = % of development, agriculture, oak or other forest in the surrounding matrix, respectively.

Scope / Diversity Indicator / Model Predictors (∆AICc ± 2) / Best Model / R2
Overall / Richness / HD (+) Total Stems (-) Canopy Cover (+) Canopy Height (+) Develop (-) Total Large Stems (+) / HD(+) / 0.100
Abundance / Ag (+) Canopy Height (+) Total Large Stems (+) Oak (-) Canopy Cover (+) / Ag (+) CanopyHeight (+) Total Large Stems (+) / 0.262
Non-synanthropic / Richness / Null / HD (+) / 0.0635
Abundance / Null / Null / -
Synanthropic / Richness / Null / Canopy Height (+) / 0.0709
Abundance / Oak (-) Canopy Height (+) Area (+) Ag (+) / Oak (-) / 0.114
Functional Diversity
(where only functional group is listed, the abundance of that group was evaluated) / Richness / Null / Null / -
Corvidae omnivores / Oak (-) Forest (-) Develop (-) Ag (-) HD (+) Total Stems (-) Canopy Height (-) Total Large Stems (+) Canopy Cover (+) / Oak (-) Forest (-) Develop (-) Ag (-) HD (+) Total Stems (-) / 0.474
Seed eaters, frugivores, ground foragers / Canopy Height (+) Total Large Stems (+) Total Stems (+) Area (+) Ag (+) / Canopy Height (+) Total Large Stems (+) / 0.146
Bark foragers / Canopy Cover (+) Area (-) Oak (-) / Canopy Cover (+) / 0.109
Flycatchers / Ag (+) Develop (-) CanopyHeight (+) Forest (+) / Ag (+) / 0.109
Foliage gleaners / Area (+) Forest (+) Develop (-) Total Large Stems (-) Total Stems (+) Canopy Cover (+) HD (-) Ag (+) / Area (+) Forest (-) Develop (-) Total Large Stems (-) / 0.0382
Vireos, Sparrows, Warblers / Null / HD (+) Total Stems (-) / 0.108
Hummingbirds / Null / Develop (+) / 0.124
Swallows / Null / HD (-) / 0.144
Evenness / Ag (-) Total Large Stems (-) Area (+) Total Stems (-) Forest (-) Develop (-) Oak (-) / Ag (+) Total Large Stems (-) / 0.193
Acorn Woodpecker / Abundance / Canopy Height (+) HD (-) Total Large Stems (+) Canopy Cover (+) Oak (-) / Canopy Height (+) HD (-) / 0.196
Chipping Sparrow / Abundance / Develop (-) Total Stems (-) Area (+) Canopy Height (+) / Develop (-) / 0.113
Western Scrub Jay / Abundance / Develop (+) Forest (-) Canopy Height (-) / Develop (+) / 0.129
White-breasted Nuthatch / Abundance / Ag (+) HD (+) Total Stems (-) Total Large Stems (-) Forest (+) / Ag (+) HD (+) Total Stems (-) / 0.274

Supplementary Table 6: Results from all Generalized Linear Models for all viable models (AIC=AICmin+2)