ece3976-sup-0006-TableS1-S2_FigS1-S5
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1 Supplement Table 1. Individual observed species and their group classifications (PR: H- Habitat, M – Microhabitat, D – Diet; HRV: 2 Nest location – N, Habitat – H, D – Diet, see Table 1) for both the Puerto Rico and Hudson River Valley data sets. Species ADWA AFCD AMKE ANEU ANMA BANA BFGR BWVI BRMA CAEL CAEG CASW COGD GRSP GRAK GREG GAGR HOSP INSI KWQD LAPE LOKI MACU Common Name Adelaide's Warbler African Collared Dove American Kestrel Antillean Euphonia Antillean Mango Bananaquit Black Faced Grassquit Black-Whiskered Vireo Bronze Mannikin Caribbean Elaenia Cattle Egret Cave Swallow Common Ground Dove Grasshopper Sparrow Gray Kingbird Great Egret Greater Antillean Grackle House Sparrow Indian Silverbill Key West Quail-Dove Lesser Antillean Peewee Loggerhead Kingbird Mangrove Cuckoo Puerto Rico Data Set Scientific Name Habitat Dendroica adelaidae Coastal Forest Streptopelia roseogrisea Coastal Forest Falco sparverius Coastal Forest Euphonia musica Wet, Upper Forests Anthracothorax dominicus Wet, Upper Forests Coereba flaveola Wet, Upper Forests Tiaris bicolor Open/Anthropogenic Vireo altiloquus Wet, Upper Forests Lonchura cucullata Open/Anthropogenic Elaenia martinica Coastal Forest Bulbulcus ibis Open/Anthropogenic Petrochelidon fulva Coastal Forest Columbina passerina Coastal Forest Ammodramus savannarum Open/Anthropogenic Tyrannus dominicensis Coastal Forest Ardea alba Open/Anthropogenic Quiscalus niger Open/Anthropogenic Passer domesticus Open/Anthropogenic Euodice malabarica Open/Anthropogenic Geotrygon chrysia Coastal Forest Contopus latirostris Coastal Forest Tyrannus caudifasciatus Wet, Upper Forests Coccyzus minor Coastal Forest Microhabitat Interspersed Forest Open Open Dense Forest Dense Forest Open Grassland Interspersed Forest Grassland Interspersed Forest Grassland Open Grassland Grassland Open Grassland Open Open Grassland Dense Forest Interspersed Forest Dense Forest Interspersed Forest Diet Insectivore Granivore Carnivore Frugivore Nectarivore Nectarivore Granivore Insectivore Granivore Insectivore Insectivore Insectivore Granivore Omnivore Insectivore Omnivore Omnivore Granivore Granivore Granivore Insectivore Insectivore Omnivore MODO NOMO NUMA ORBI ORAW PETH PTWH PUEB PREM PRFL PRLC PROR PRSP PRTO PRVI PRWO RLTH RTHA ROPI RUQD SNPI SHCO SBAN TROU WWDO YFGR ZEND 1 Mourning Dove Northern Mockingbird Nutmeg Mannikin Orange Bishop Orange Cheeked Waxbill Pearly-Eyed Thrasher Pin-Tailed Whydah Puerto Rican Bullfinch Puerto Rican Emerald Puerto Rican Flycatcher Puerto Rican Lizard Cuckoo Puerto Rican Oriole Puerto Rican Spindalis Puerto Rican Tody Puerto Rican Vireo Puerto Rican Woodpecker Red-Legged Thrush Red-Tailed Hawk Rock Pigeon Ruddy Quail-Dove Scaly-Naped Pigeon Shiny Cowbird Smooth-Billed Ani Troupial White-Winged Dove Yellow-Faced Grassquit Zenaida Dove Zenaida macrocura Mimus polyglottos Lonchura punctulata Euplectes franciscanus Estrilda melpoda Margarops fuscatus Vidua macrocura Loxigilla portoricensis Chlorostilbon maugaeus Myiarchus antillarum Coccyzus vieilloti Icterus dominicensis Spindalis portoricensis Todus mexicanus Vireo latimeri Melanerpes portoricensis Turdus plumbeus Buteo jamaicensis Columba livia Geotrygon montana Patagioenas squamosa Molothrus bonariensis Crotophaga ani Icterus icterus Zenaida asiatica Tiaris olivaceus Zenaida aurita Coastal Forest Coastal Forest Open/Anthropogenic Open/Anthropogenic Open/Anthropogenic Coastal Forest Open/Anthropogenic Wet, Upper Forests Wet, Upper Forests Coastal Forest Coastal Forest Wet, Upper Forests Wet, Upper Forests Coastal Forest Wet, Upper Forests Wet, Upper Forests Wet, Upper Forests Wet, Upper Forests Wet, Upper Forests Coastal Forest Wet, Upper Forests Open/Anthropogenic Coastal Forest Coastal Forest Coastal Forest Open/Anthropogenic Coastal Forest Open Open Grassland Grassland Grassland Open Grassland Interspersed Forest Dense Forest Open Dense Forest Dense Forest Interspersed Forest Dense Forest Dense Forest Interspersed Forest Dense Forest Open Open Open Dense Forest Open Open Open Open Grassland Open Insectivore Omnivore Granivore Granivore Granivore Omnivore Granivore Frugivore Nectarivore Insectivore Carnivore Insectivore Frugivore Insectivore Insectivore Insectivore Frugivore Carnivore Omnivore Granivore Frugivore Omnivore Omnivore Omnivore Granivore Granivore Granivore Species ACFL AMCR AMGO AMRE AMRO BAOR BASW BBWA BAWW BBCU BCCH BPWA BTBW BTNW BLJA BGGN BHVI BWWA BRCR BRTH BHCO CAWA CAWR CEDW CERW CSWA CHIP Hudson River Valley Data Set Common Name Scientific Name Acadian Flycatcher Empidonax virescens American Crow Corvus brachyrhynchos American Goldfinch Carduelis tristis American Redstart Setophaga ruticilla American Robin Turdus migratorius Baltimore Oriole Icterus galbula Barn Swallow Hirundo rustica Bay-breasted Warbler Dendroica castanea Black-and-White Warbler Mniotilta varia Black-billed Cuckoo Coccyzus erythropthalmus Black-capped Chickadee Poecile atricapillus Blackpoll Warbler Setophaga striata Black-throated Blue Warbler Dendroica caerulescens Black-throated Green Warbler Setophaga virens Blue Jay Cyanocitta cristata Blue-gray Gnatcatcher Polioptila caerulea Blue-headed Vireo Vireo solitarius Blue-winged Warbler Vermivora pinus Brown Creeper Certhia americana Brown Thrasher Toxostoma rufum Brown-headed Cowbird Molothrus ater Canada Warbler Wilsonia canadensis Carolina Wren Thryothorus ludovicianus Cedar Waxwing Bombycilla cedrorum Cerulean Warbler Dendroica cerulea Chestnut-sided Warbler Dendroica pensylvanica Chipping Sparrow Spizella passerina Nest Tree Tree Tree Tree Bush Tree Ledge Tree Ground Bush Cavity Tree Bush Tree Tree Tree Bush Ground Cavity Bush Bush Ground Cavity Tree Tree Bush Bush Habitat Arboreal Terrestrial Bush Arboreal Terrestrial Tall vegetation Open Air Arboreal Tree trunk Arboreal Arboreal Arboreal Arboreal Arboreal Arboreal Arboreal Arboreal Bush Tree trunk Ground/shrub Terrestrial Bush Ground/shrub Tall vegetation Arboreal Bush Terrestrial Diet Insectivore Omnivore Granivore Insectivore Frugivore Frugivore Insectivore Insectivore Insectivore Insectivore Insectivore Insectivore Insectivore Insectivore Omnivore Insectivore Insectivore Insectivore Insectivore Omnivore Omnivore Insectivore Insectivore Frugivore Insectivore Insectivore Granivore COGR CORA COYE DOWO EABL EAKI EAPH EATO EWPE EUST FICR GRCA GCFL HAWO HETH HOWA HOWR LEFL LOWA MAWA MODO NAWA NOCA NOFL NOMO NOPA NOWA OVEN PIWO Common Grackle Common Raven Common Yellowthroat Downy Woodpecker Eastern Bluebird Eastern Kingbird Eastern Phoebe Eastern Towhee Eastern Wood-pewee European Starling Fish Crow Gray Catbird Great Crested Flycatcher Hairy Woodpecker Hermit Thrush Hooded Warbler House Wren Least Flycatcher Louisiana Waterthrush Magnolia Warbler Mourning Dove Nashville Warbler Northern Cardinal Northern Flicker Northern Mockingbird Northern Parula Northern Waterthrush Ovenbird Pileated Woodpecker Quiscalus quiscula Corvus corax Geothlypis trichas Picoides pubescens Sialia sialis Tyrannus tyrannus Sayornis phoebe Pipilo erythrophthalmus Contopus virens Sturnus vulgaris Corvus ossifragus Dumetella carolinensis Myiarchus crinitus Picoides villosus Catharus guttatus Wilsonia citrina Troglodytes aedon Empidonax minimus Seiurus motacilla Dendroica magnolia Zenaida macroura Vermivora ruficapilla Cardinalis cardinalis Colaptes auratus Mimus polyglottos Parula americana Seiurus noveboracensis Seiurus aurocapilla Dryocopus pileatus Bush Ledge Ground Cavity Cavity Tree Ledge Bush Tree Cavity Tree Bush Cavity Cavity Ground Bush Cavity Tree Ground Bush Bush Ground Bush Cavity Bush Tree Ground Ground Cavity Terrestrial Terrestrial Bush Tree trunk Terrestrial Open Air Open Air Terrestrial Arboreal Terrestrial Terrestrial Bush Arboreal Tree trunk Terrestrial Tall vegetation Bush Arboreal Terrestrial Tall vegetation Terrestrial Bush Ground/shrub Tree trunk Ground/shrub Arboreal Terrestrial Terrestrial Tree trunk Granivore Omnivore Insectivore Insectivore Insectivore Insectivore Insectivore Omnivore Insectivore Omnivore Omnivore Insectivore Insectivore Insectivore Insectivore Insectivore Insectivore Insectivore Insectivore Insectivore Granivore Insectivore Omnivore Insectivore Omnivore Insectivore Insectivore Insectivore Insectivore PISI PIWA RBWO RBNU REVI RWBL RBGR SCTA SOSP TRSW TUTI VEER VESP WBNU WIWR WOTH WEWA YEWA YBSA YBCU YRWA YTVI 1 Pine Siskin Pine Warbler Red-bellied Woodpecker Red-breasted Nuthatch Red-eyed Vireo Red-winged Blackbird Rose-breasted Grosbeak Scarlet Tanager Song Sparrow Tree Swallow Tufted Titmouse Veery Vesper Sparrow White-breasted Nuthatch Winter Wren Wood Thrush Worm-eating Warbler Yellow Warbler Yellow-bellied Sapsucker Yellow-billed Cuckoo Yellow-rumped Warbler Yellow-throated Vireo Carduelis pinus Dendroica pinus Melanerpes carolinus Sitta canadensis Vireo olivaceus Agelaius phoeniceus Pheucticus ludovicianus Piranga olivacea Melospiza melodia Tachycineta bicolor Baeolophus bicolor Catharus fuscescens Pooecetes gramineus Sitta carolinensis Troglodytes troglodytes Hylocichla mustelina Helmitheros vermivorum Setophaga petechia Sphyrapicus varius Coccyzus americanus Dendroica coronata Vireo flavifrons Tree Tree Cavity Cavity Tree Bush Bush Tree Ground Cavity Cavity Ground Ground Cavity Ground Bush Ground Bush Cavity Tree Tree Tree Arboreal Arboreal Tree trunk Tree trunk Arboreal Bush Arboreal Arboreal Terrestrial Open Air Arboreal Terrestrial Terrestrial Tree trunk Terrestrial Terrestrial Ground/shrub Bush Tree trunk Arboreal Tall vegetation Arboreal Granivore Insectivore Insectivore Insectivore Insectivore Omnivore Omnivore Insectivore Granivore Insectivore Omnivore Insectivore Granivore Insectivore Insectivore Insectivore Insectivore Insectivore Omnivore Insectivore Insectivore Insectivore 1 Supplement Table 2. Model performance for each group classification approach (italics and 2 bold; PR: H- Habitat, M – Microhabitat, D – Diet; HRV: Nest location – N, Habitat – H, D – 3 Diet, see Table 1) and subgroup within each group classification approach calculated by 4 computing the area under the curve of the receiver operating characteristic (AUC) for both the 5 Puerto Rico and Hudson River Valley data sets. HRV All species Nest Location Bush-nest Cavity Ground-nest Ledge Tree-nest Habitat Arboreal Bush Ground/shrub Open Air Terrestrial Tree trunk Vegetation Diet Frugivore Granivore Insectivore Omnivore PR All species Habitat Wet, Upper Forests Open/Anthropogenic Coastal Forest Microhabitat Dense Forest Grassland Interspersed Forest Mean 2.50% 97.50% 0.84 0.75 0.83 0.68 0.77 0.67 0.77 0.77 0.78 0.73 0.76 0.77 0.84 0.68 0.82 0.79 0.74 0.77 0.85 0.77 0.77 0.52 0.71 0.50 0.64 0.39 0.65 0.54 0.65 0.57 0.53 0.51 0.71 0.48 0.59 0.57 0.47 0.55 0.77 0.61 0.90 0.91 0.94 0.84 0.88 0.89 0.88 0.96 0.90 0.87 0.94 0.98 0.95 0.91 0.98 0.93 0.93 0.97 0.91 0.91 Mean 2.50% 97.50% 0.80 0.75 0.75 0.76 0.75 0.74 0.73 0.74 0.73 0.76 0.68 0.68 0.68 0.68 0.65 0.66 0.65 0.63 0.85 0.82 0.81 0.84 0.81 0.82 0.80 0.83 0.81 Open Diet Carnivores Frugivores Granivores Insectivores Nectarivores Omnivores 0.76 0.71 0.63 0.72 0.76 0.75 0.67 0.74 0.70 0.54 0.47 0.64 0.67 0.67 0.53 0.64 0.83 0.82 0.78 0.80 0.83 0.82 0.79 0.83 1 2 3 4 5 1 Supplement Figure 1. Total number of detections by species for the Puerto Rico and Hudson 2 River Valley data sets. 3 4 1 2 3 1 Supplement figure 2. Posterior mean estimates of species richness with 95% posterior credible 2 intervals for the full community model and each of the three different classification approaches 3 for the Puerto Rico (top) and Hudson River Valley (bottom) data sets at each site. Black circles 4 represent observed number of species at each site and black squares represent using all of the 5 species together in the full model. Red circles represent Habitat (Puerto Rico data set) and Nest 6 location (Hudson River Valley data set), respectively; blue triangles represent Microhabitat 7 (Puerto Rico data set) and Habitat (Hudson River Valley data set), and purple lines represent 8 Diet for both data sets. 9 10 11 12 13 14 15 16 17 18 19 1 2 1 Supplement figure 3. Individual species occurrence probabilities (posterior means with 95% 2 credible intervals) in the four different habitat types (Agriculture, Forest, Urban, and Edge) of 3 the study area in southwestern Puerto Rico for four important species (ANMA: Antillean mango, 4 Anthracothorax dominicus; PRVI: Puerto Rican vireo, Vireo latimeri; PRSP: Puerto Rican 5 spindalis, Spindalis portoricensis; and PUEB: Puerto Rican bullfinch, Loxigilla portoricensis). 6 We used three different classification schemes to group species: Habitat – red, Microhabitat – 7 blue, and Diet – purple, along with using all of the species – black. 8 9 10 11 12 13 14 15 16 17 18 19 1 2 3 4 5 6 1 Supplement figure 4. Mean marginal occurrence probabilities for four priority conservation 2 species (VESP: Vesper sparrow, Pooecetes gramineus; CERW: Cerulean warbler, Setophaga 3 cerulean; BTBW: Black-throated blue warbler, Setophaga caerulescens; and SCTA: Scarlet 4 tanager, Piranga olivacea) in relation to forest fragment area in the Hudson River Valley. We 5 explored three different classification schemes for grouping species: Nest location – red lines, 6 Habitat – blue lines, and Diet – purple lines; black lines represent using all of the species. 7 Covariates have been standardized to have a mean of zero and variance of one. Although 8 uncertainty was high for all models, using all species had the lowest uncertainty (narrowest 9 credible intervals) followed by nest location, habitat, and diet models. 10 11 12 13 14 15 16 17 18 19 1 2 3 4 5 1 Supplement figure 5. Posterior mean occurrence probabilities for four priority conservation 2 species (Vesper sparrow, VESP: 2 detections at 2 sites; Cerulean warbler, CERW: 7 detections at 3 6 sites; Black-throated blue warbler, BTBW: 20 detections at 9 sites; and Scarlet tanager, SCTA: 4 141 detections at 56 sites) at individual sites in the Hudson River Valley study area. We used 5 three different classification schemes for grouping species: Nest location – red large diamonds, 6 Habitat – blue triangles, and Diet – purple small diamonds; black squares represent using all of 7 the species. 8 9
