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1 2 3 4 5 Supporting Information 6 7 8 9 Testing species assemblage predictions from stacked and 10 11 joint species distribution models 12 13 14 Damaris Zurell, Niklaus E. Zimmermann, Helge Gross, Andri Baltensweiler, Thomas Sattler, 15 16 Rafael O. Wüest 17 18 19 20 This supporting information contains the following items: 21 For Peer Review 22 • Table S1. Forest species included in analyses. 23 • Table S2. and species included in the analyses. 24 • Fig. S1. Distribution of bird and tree prevalence levels. 25 26 • Fig. S2. Spatial blocks used in 5-fold spatial block cross-validation. 27 • Fig. S3. Predictor variables for forest bird and tree species analyses. 28 • Fig. S4. Single species model performance. 29 30 • Fig. S5. Spatial autocorrelation in model residuals. 31 • Fig. S6. Prevalence of species with higher JSDM or SDM performance. 32 • Fig. S7. Assemblage sensitivity and specificity. 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Page 23 of 2260 Journal of Biogeography

1 2 3 Supplementary Tables 4 5 6 7 Table S1. Forest bird species included in the analyses. For each species, we list the predictive performance achieved in the single-species ensemble SDMs and JSDMs (cf. Fig. S3). 8 9 JSDM SDM 10 11 Latin Name English Name AUC Sens Spec TSS AUC Sens Spec TSS 12 Accipiter gentilis Northern 13 Goshawk 0.61 0.83 0.34 0.17 0.85 0.81 0.75 0.56 14 Accipiter nisus Eurasian 15 Sparrowhawk 0.56 0.79 0.32 0.10 0.85 0.85 0.75 0.59 16 Aegithalos Long-tailed 17 caudatus Bushtit 0.67 0.89 0.37 0.27 0.83 0.80 0.72 0.52 18 Anthus trivialis Tree Pipit 19 0.83 0.79 0.77 0.56 0.90 0.88 0.78 0.66 20 Asio otus Long-eared Owl 0.54 0.46 0.71 0.17 0.94 0.91 0.90 0.80 21 Bonasa bonasia Hazel GrouseFor Peer0.60 0.12Review0.95 0.07 0.94 1.00 0.79 0.79 22 Buteo buteo Common 23 Buzzard 0.85 0.77 0.77 0.54 0.90 0.78 0.84 0.62 24 25 0.83 0.89 0.67 0.56 0.89 0.94 0.70 0.64 26 Certhia Short-toed 27 brachydactyla Treecreeper 0.88 0.85 0.77 0.62 0.92 0.88 0.81 0.68 28 Certhia Eurasian 29 familiaris Treecreeper 0.74 0.61 0.73 0.34 0.83 0.74 0.75 0.48 30 Coccothraustes Hawfinch 31 coccothraustes 0.76 0.87 0.54 0.41 0.86 0.77 0.78 0.54 32 Columba oenas 33 0.75 0.93 0.53 0.46 0.88 0.93 0.71 0.64 34 Columba Common 35 palumbus Pigeon 0.89 0.83 0.80 0.63 0.92 0.87 0.81 0.68 36 Corvus corax Northern Raven 0.58 0.60 0.52 0.12 0.79 0.82 0.62 0.44 37 Corvus corone Carrion Crow 38 corone 0.82 0.68 0.83 0.51 0.89 0.79 0.86 0.65 39 Cuculus canorus 40 0.63 0.49 0.74 0.24 0.78 0.77 0.65 0.41 41 Dendrocopos Great Spotted 42 major Woodpecker 0.81 0.73 0.75 0.48 0.87 0.74 0.84 0.58 43 Dendrocopos Lesser Spotted 44 minor Woodpecker 0.83 0.85 0.64 0.49 0.90 0.95 0.71 0.67 45 Dryocopus Black 46 martius Woodpecker 0.72 0.91 0.43 0.34 0.83 0.88 0.62 0.50 47 Emberiza Yellowhammer 48 citrinella 0.82 0.75 0.75 0.50 0.89 0.85 0.76 0.61 49 Falco subbuteo Eurasian Hobby 50 0.78 0.92 0.54 0.46 0.90 0.91 0.74 0.65 51 Ficedula European Pied 52 hypoleuca Flycatcher 0.75 0.90 0.55 0.45 0.85 0.88 0.67 0.55 53 Garrulus Eurasian Jay 54 glandarius 0.81 0.80 0.67 0.48 0.90 0.76 0.85 0.60 55 Hippolais Icterine warbler 56 icterina 0.75 0.50 0.88 0.38 0.95 0.98 0.85 0.83 57 Lanius collurio Red-backed 58 Shrike 0.66 0.91 0.34 0.25 0.84 0.73 0.79 0.52 59 Loxia Red Crossbill 60 curvirostra 0.79 0.74 0.73 0.47 0.86 0.87 0.70 0.57 Journal of Biogeography Page 24 of 2260

1 2 3 Luscinia Common 4 megarhynchos Nightingale 0.91 0.78 0.85 0.63 0.95 0.98 0.83 0.82 5 Milvus migrans Black Kite 6 0.79 0.81 0.64 0.45 0.86 0.92 0.64 0.56 7 Muscicapa Spotted 8 striata Flycatcher 0.79 0.86 0.63 0.49 0.86 0.89 0.65 0.55 9 Nucifraga Spotted 10 caryocatactes Nutcracker 0.88 0.91 0.74 0.65 0.92 0.90 0.80 0.70 11 Oriolus oriolus Eurasian Golden 12 Oriole 0.90 0.88 0.79 0.67 0.93 0.97 0.79 0.76 13 Parus caeruleus Blue Tit 0.92 0.90 0.83 0.73 0.96 0.91 0.85 0.75 14 15 Parus cristatus European 16 Crested Tit 0.81 0.81 0.65 0.46 0.88 0.79 0.79 0.58 17 Parus montanus Willow Tit 0.86 0.83 0.82 0.65 0.91 0.85 0.83 0.69 18 Parus palustris Marsh Tit 0.82 0.80 0.74 0.54 0.89 0.84 0.75 0.59 19 Pernis apivorus European Honey 20 Buzzard 0.58 0.90 0.25 0.15 0.87 0.95 0.69 0.64 21 Phoenicurus CommonFor Peer Review 22 23 phoenicurus Redstart 0.61 0.77 0.43 0.20 0.81 0.76 0.72 0.49 24 Phylloscopus Western Bonellis 25 bonelli Warbler 0.68 0.55 0.75 0.30 0.86 0.85 0.70 0.55 26 Phylloscopus Wood Warbler 27 sibilatrix 0.74 0.79 0.63 0.41 0.85 0.80 0.74 0.54 28 Phylloscopus Willow Warbler 29 trochilus 0.69 0.87 0.49 0.36 0.84 0.81 0.72 0.53 30 Picus canus Grey-headed 31 Woodpecker 0.80 0.79 0.70 0.49 0.90 0.92 0.79 0.71 32 Picus viridis European Green 33 34 Woodpecker 0.67 0.71 0.54 0.26 0.81 0.72 0.74 0.46 35 Prunella Dunnock 36 modularis 0.77 0.64 0.77 0.41 0.86 0.75 0.80 0.55 37 Pyrrhula Eurasian 38 pyrrhula Bullfinch 0.79 0.74 0.69 0.43 0.87 0.72 0.83 0.55 39 Regulus Firecrest 40 ignicapillus 0.83 0.76 0.78 0.54 0.89 0.82 0.79 0.62 41 Regulus regulus Goldcrest 0.80 0.85 0.64 0.49 0.88 0.78 0.80 0.58 42 Serinus Citril 43 44 citrinella 0.88 0.90 0.80 0.70 0.92 0.99 0.73 0.73 45 Sitta europaea Eurasian 46 Nuthatch 0.84 0.77 0.78 0.55 0.90 0.80 0.81 0.61 47 Streptopelia European Turtle 48 turtur Dove 0.85 0.80 0.78 0.57 0.93 0.99 0.80 0.79 49 Strix aluco Tawny Owl 0.60 0.71 0.46 0.16 0.86 0.89 0.70 0.59 50 Sylvia borin Garden Warbler 51 0.69 0.56 0.73 0.29 0.81 0.72 0.76 0.48 52 Sylvia curruca Lesser 53 Whitethroat 0.84 0.80 0.80 0.60 0.91 0.89 0.78 0.67 54 Tetrao tetrix Black Grouse 0.94 0.97 0.80 0.78 0.96 0.96 0.88 0.83 55 Turdus pilaris Fieldfare 0.65 0.81 0.45 0.26 0.81 0.65 0.82 0.47 56 Turdus Ring Ouzel 57 torquatus 0.94 0.98 0.84 0.82 0.96 0.99 0.85 0.84 58 59 Turdus Mistle 60 viscivorus 0.79 0.77 0.70 0.47 0.87 0.79 0.77 0.56 Page 25 of 2260 Journal of Biogeography

1 2 3 4 5 Table S2. Tree and shrub species included in the analyses. For each species, we list the predictive 6 performance achieved in the single-species ensemble SDMs and JSDMs (cf. Fig. S3). 7 8 JSDM SDM 9 Latin Name English Name AUC Sens Spec TSS AUC Sens Spec TSS 10 Silver 11 0.82 0.79 0.71 0.50 0.88 0.86 0.72 0.58 12 Acer campestris Hedge Maple 0.82 0.76 0.74 0.50 0.92 0.99 0.74 0.73 13 Acer opalus Italian Maple 0.67 0.00 1.00 0.00 0.97 1.00 0.93 0.93 14 Acer platanoides Norway Maple 15 0.74 0.88 0.55 0.43 0.93 0.95 0.82 0.77 16 Acer Sycamore 17 pseudoplatanus Maple 0.75 0.80 0.60 0.39 0.85 0.72 0.79 0.51 18 Alnus glutinosa Black 0.82 0.84 0.68 0.53 0.97 1.00 0.92 0.92 19 Alnus incana European Alder 0.68 0.76 0.51 0.27 0.90 0.93 0.70 0.64 20 Alnus viridis Green Alder 21 For Peer0.90 0.80Review0.83 0.63 0.94 0.98 0.78 0.76 22 Berberis vulgaris Barberry 0.81 0.64 0.87 0.51 0.97 0.99 0.90 0.89 23 Betula pendula Weeping 0.74 0.79 0.57 0.36 0.87 0.89 0.68 0.57 24 Carpinus betulus Hornbeam 0.89 0.94 0.76 0.70 0.95 0.96 0.86 0.83 25 26 Castanea sativa Sweet Chestnut 0.89 0.71 0.92 0.63 0.99 0.99 0.94 0.93 27 Clematis vitalba Old Mans 28 Beard 0.82 0.79 0.73 0.52 0.93 0.98 0.81 0.78 29 Cornus sanguinea Red Dogwood 0.82 0.61 0.80 0.40 0.92 0.96 0.74 0.70 30 Corylus avellana Hazel 31 0.74 0.82 0.57 0.39 0.84 0.78 0.73 0.51 32 Crataegus Common 33 monogyna Hawthorn 0.76 0.75 0.66 0.41 0.92 0.90 0.79 0.68 34 Crataegus English 35 oxyacanta Hawthorn 0.81 0.85 0.65 0.50 0.94 0.98 0.77 0.75 36 Daphne Paradise 37 mezereum 0.54 0.47 0.60 0.07 0.97 0.92 0.92 0.84 38 Euonymus European 39 europaeus Spindle Tree 0.86 0.65 0.84 0.48 0.95 0.98 0.82 0.80 40 Fagus sylvatica Beech 41 0.92 0.87 0.83 0.70 0.95 0.87 0.87 0.74 42 Fraxinus excelsior Ash 0.82 0.82 0.72 0.54 0.89 0.88 0.71 0.59 43 English Ivy 0.85 0.91 0.67 0.58 0.91 0.89 0.80 0.69 44 Ilex aquifolium English Holly 0.82 0.91 0.61 0.53 0.95 0.94 0.85 0.79 45 46 Juglans regia Walnut 0.81 0.92 0.63 0.55 0.95 0.97 0.88 0.85 47 Juniperus Common 48 communis Juniper 0.82 0.68 0.76 0.44 0.95 0.96 0.86 0.82 49 Juniperus Common 50 communis ssp Juniper (Ssp 51 alpina Alpina) 0.87 0.75 0.85 0.59 0.96 0.97 0.88 0.86 52 European 53 0.79 0.67 0.78 0.45 0.88 0.77 0.81 0.58 54 55 Ligustrum vulgare Common Privet 0.82 0.37 0.88 0.25 0.92 0.96 0.76 0.72 56 Lonicera alpigena Alpine 57 Honeysuckle 0.67 0.74 0.50 0.24 0.94 0.95 0.82 0.77 58 Lonicera caerulea Blue 59 Honeysuckle 0.60 0.18 0.87 0.05 0.99 0.98 0.97 0.95 60 Lonicera nigra Black Honeysuckle 0.66 0.74 0.52 0.26 0.94 0.94 0.84 0.78 Journal of Biogeography Page 26 of 2260

1 2 3 Lonicera European Fly 4 xylosteum Honeysuckle 0.71 0.84 0.51 0.35 0.85 0.74 0.77 0.51 5 Norway 6 0.75 0.74 0.64 0.38 0.88 0.73 0.88 0.61 7 Pinus cembra Swiss Stone 8 Pine 0.95 0.89 0.90 0.79 0.98 0.99 0.91 0.90 9 Pinus mugo Mountain Pine 10 arborea (Var Arborea) 0.86 0.04 0.99 0.03 0.98 0.98 0.92 0.91 11 Pinus mugo Mountain Pine 12 prostrata (Var Prostrata) 0.91 0.68 0.89 0.57 0.98 1.00 0.94 0.94 13 Scots Pine 0.73 0.83 0.54 0.36 0.88 0.86 0.75 0.62 14 15 tremula Aspen 0.70 0.52 0.75 0.28 0.94 0.94 0.86 0.80 16 Prunus avium Sweet Cherry 0.80 0.84 0.64 0.48 0.88 0.88 0.71 0.59 17 Prunus padus European Bird 18 Cherry 0.79 0.62 0.85 0.46 0.97 0.98 0.91 0.88 19 Prunus spinosa Blackthorn 0.78 0.25 0.91 0.16 0.95 0.97 0.84 0.81 20 21 Pseudotsuga DouglasFor Fir Peer Review 22 menziesii 0.85 0.81 0.77 0.58 0.98 0.99 0.93 0.92 23 Quercus petraea Eych 0.85 0.92 0.65 0.57 0.92 0.97 0.77 0.74 24 Quercus Downy Oak 25 pubescens 0.84 0.45 0.96 0.41 0.99 1.00 0.96 0.96 26 Quercus robur Common Oak 0.88 0.88 0.74 0.62 0.93 0.97 0.75 0.72 27 28 Rhamnus frangula Alder 29 Buckthorn 0.78 0.60 0.79 0.39 0.97 1.00 0.90 0.90 30 Rhododendron Rusty Leaved 31 ferrugineum Alpenrose 0.89 0.58 0.93 0.51 0.95 0.98 0.82 0.79 32 Ribes alpinum Mountain 33 Currant 0.54 0.00 1.00 0.00 1.00 0.97 0.97 0.94 34 Robinia Black Locust 35 pseudoacacia 0.92 0.70 0.92 0.61 0.99 1.00 0.97 0.97 36 Rubus fruticosus Blackberry 37 spec 0.75 0.15 0.96 0.10 0.92 0.92 0.77 0.69 38 39 Rubus idaeus American Red 40 Raspberry 0.64 0.07 0.97 0.03 0.95 0.94 0.85 0.79 41 Salix caprea Goat Willow 0.61 0.74 0.45 0.18 0.83 0.75 0.74 0.50 42 Sambucus nigra Common Elder 0.81 0.75 0.74 0.49 0.89 0.86 0.75 0.61 43 Sambucus Red Elderberry 44 racemosa 0.61 0.71 0.46 0.17 0.91 0.90 0.78 0.68 45 Sorbus aria Whitebeam 46 0.69 0.62 0.65 0.27 0.85 0.78 0.75 0.53 47 Sorbus aucuparia Rowan 0.72 0.72 0.62 0.34 0.84 0.77 0.74 0.51 48 Taxus baccata Yew 0.67 0.00 1.00 0.00 0.99 0.98 0.97 0.95 49 Tilia cordata Small-Leaved 50 Lime 0.83 0.88 0.66 0.53 0.94 0.96 0.87 0.82 51 52 Tilia platyphyllos Large-Leaved 53 Lime 0.75 0.92 0.51 0.42 0.94 0.95 0.85 0.80 54 Ulmus glabra Scots 0.71 0.92 0.46 0.38 0.87 0.84 0.74 0.58 55 Vaccinium Black 56 myrtillus Whortleberry 0.69 0.00 1.00 0.00 0.98 0.97 0.91 0.87 57 Viburnum lantana Wayfaring- 58 Tree 0.76 0.53 0.79 0.31 0.90 0.95 0.70 0.65 59 Viburnum opulus Guelder Rose 60 0.78 0.75 0.69 0.44 0.93 0.97 0.75 0.73 Page 27 of 2260 Journal of Biogeography

1 2 3 Supplementary Figures 4 5 6 7

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17 0 0 18 0.0 0.2 0.4 0.6 0.8 0.0 0.2 0.4 0.6 0.8 19 Prevalence Prevalence 20 21 For Peer Review 22 Figure S1. Distribution of bird and tree prevalence levels. 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 Figure S2. Spatial blocks used in 5-fold spatial block cross-validation. 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Journal of Biogeography Page 28 of 2260

1 2 3 4 5 6 Aspect Aspect 7 Slope Slope TPI Topography TPI 8 TWI 8.6 cm TWI Radiation Radiation BIO-1 BIO-1 9 BIO-2 BIO-2 BIO-3 Climate BIO-3 10 BIO-4 BIO-4 BIO-5 BIO-5 11 BIO-6 BIO-6 BIO-7 BIO-7 12 BIO-8 BIO-8 BIO-9 BIO-9 13 BIO-10 BIO-10 BIO-11 BIO-11 BIO-12 BIO-12 14 BIO-13 BIO-13 BIO-14 BIO-14 15 BIO-15 BIO-15 BIO-16 BIO-16 16 BIO-17 BIO-17 BIO-18 BIO-18 17 BIO-19 BIO-19 DDEG-0 DDEG-0 18 DDEG-5 DDEG-5 Moist. balance Moist. balance Moisture index Moisture index 19 PET PET PET winter PET winter 20 PET summer PET summer PET ratio s/w PET ratio s/w 21 PREC winter For Peer ReviewPREC winter PREC summer PREC summer 22 PREC ratio s/w PREC ratio s/w Avg. height Avg. height 23 p10 height p10 height p25 height Vertical p25 height 24 p95 height p95 height SD height vegetation SD height CV height 8.6 cm CV height 25 FHD structure FHD COV COV 26 DNS DNS Ratio p25-p95 27 UHD Edge length canopy Horizontal 28 Edge length under/midstory vegetation Edge length matrix 8.6 cm 29 Total edge length Clumpy under/midstory structure 30 Clumpy canopy 31 32 0 5 10 15 0 5 10 15 20 25 30 35 33 Figure S3. Predictor variables for forest bird and tree species analyses. The barplots indicate the number of 34 times each predictor variable was selected in the individual SDMs. Red stars indicate the five globally selected 35 predictor variables that were used for the JSDMs and global SDMs. Blue circles indicate the five predictor 36 variables selected for (individual) MEMs. Please refer to main text for description of the predictor variables 37 and variable selection. 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Page 29 of 2260 Journal of Biogeography

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0 Individual Ensemble 33 . 0 34 AUC Sensitivity Specificity TSS 35 36 Figure S4. Single species performance for forest birds (top) and tree species (bottom). Global GLM and Global 37 Ensemble refer to SDMs estimated using the same globally selected predictor set as in JSDMs. Individual GLM 38 and Individual Ensemble refer to SDMs estimated using species-specific predictor sets. Outliers are not 39 shown. 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Journal of Biogeography Page 30 of 2260

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24 0 25 26 27 Figure S5. Spatial autocorrelation in single species model residuals. Presented are the distances up to which 28 spatial autocorrelation in SDM and JSDM residuals was significant. Residual autocorrelation is low in all 29 models compared to autocorrelation in raw data. 30 31 32

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49 e e r r 50 P P 2 2 . . 51 0 0 52 0 0 . . 53 0 n = 0 63 6 57 16 47 0 63 0 n = 20 43 18 45 45 18 18 45 54 AUC Sensitivity Specificity TSS AUC Sensitivity Specificity TSS 55 56 57 Figure S6. Prevalence for species with higher JSDM performance and with higher SDM performance in terms of AUC, sensitivity, specificity and TSS. Left panels show comparison of JSDMs against ensemble SDM, right 58 panels JSDMs against GLMs. Numbers below the boxplots indicate the number of species exhibiting higher 59 JSDM performance and higher SDM performance, respectively. Outliers are not shown. 60 Page 31 of 2260 Journal of Biogeography

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23 e e 24 p p S S 25 26 0 0 27 SDM JSDM bin prob prr corr SDM JSDM bin prob prr corr 28 29 Figure S7. Assemblage specificity and sensitivity. Results are separated for different underlying model types 30 (SDMs vs. JSDMs), different stacking procedures (binary vs. probabilistic), and for the application of 31 ecological assembly rules without and with bias correction of the macroecological constraints. Assemblage 32 sensitivity represents the proportion of species correctly predicted as present. Assemblage specificity 33 represents the proportion of species correctly predicted as absent. 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60