Table S1. Principal component (gradient) scores for 56 caves on Bohol Island, the Philippines included in this study.
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1 Table S1. Principal component (gradient) scores for 56 caves on Bohol Island, the Philippines included in this study. Code on Fig. 1 PC 1: Landscape disturbance PC 2: Cave complexity PC 3: Mining PC 4: Cave development PC 5: Resource extraction PC 6: Bat hunting Agaw-gaw Cave Bakongkong Cave Batongay Cave Bayang Cave Benito Cave Bogtong Park Cave Burial Cave Calompanan Cave Cang Ihong Cave Canlusong Cave Cantijong Cave Cantumocad Cave Casampong Cave Catalina Cave Claise Cave Dagohoy Cave Dakong-Buho Cave Duguilan Cave Guimba Cave Hinagdanan Cave
2 Inorok Cave Ka Dodong Cave Ka Goryo Cave Ka Iska Cave Kabera Cave Kabjawan Cave Kabyawan Cave Kalanguban Cave Kamagahi Cave Kamira Cave Kang Mana Cave Kasabas Cave Kokok Cave Lagbas Cave Lahos-Lahos Cave Lahug Cave Langgam Cave Loboc Tourist Cave Logarita Cave Lujang Cave Lungon Cave Manlawe Cave Mesias Cave Mohon Cave
3 Nangka Cave Odiong Cave Pig-ot Cave Polito Cave Popog Cave Pou Cave Seminary Cave Tagjaw Cave Tambo 1 Cave Tambo 2 Cave Tangob Cave Tinugdan Cave
4 Table S2. Scientific names and ecological and morphological traits of 19 cave-roosting bat species captured on Bohol Island, Philippines. Scientific name Pteropodidae Code for Fig. 3 Endemic Dietary niche Foraging space Roost dependence Colony size Aspect ratio Wing loading (N m -2 ) Peak frequency (khz) Eonycteris spelaea EOSP No Phytophagous Semi-clutter Obligate Large N/A 62.1 Ptenochirus jagori PTJA Yes Phytophagous Semi-clutter Facultative Small N/A 74.2 Rousettus amplexicaudatus ROAM No Phytophagous Semi-clutter Obligate Large N/A 83.7 Emballonuridae Emballonura alecto EMAL No Insectivorous Open Facultative Small Taphozous melanopogon TAME No Insectivorous Open Facultative Medium Hipposideridae Hipposideros ater HIAT No Insectivorous Clutter Facultative Small Hipposideros diadema HIDI No Insectivorous Clutter Facultative Medium Hipposideros obscurus HIOB Yes Insectivorous Clutter Obligate Small Hipposideros pygmaeus HIPY Yes Insectivorous Clutter Obligate Small Megadermatidae Megaderma spasma MESP No Insectivorous Clutter Facultative Small N/A 22.9 Miniopteridae Miniopterus australis MIAU No Insectivorous Open Obligate Medium Miniopterus schreibersii MISC No Insectivorous Open Obligate Medium Miniopterus tristis MITR No Insectivorous Open Obligate Medium Body mass (g)
5 Scientific name Vespertilionidae Code for Fig. 3 Endemic Dietary niche Foraging space Roost dependence Colony size Aspect ratio Wing loading (N m -2 ) Peak frequency (khz) Myotis horsfieldii MYHO No Insectivorous Clutter Facultative Small Myotis macrotarsus MYMA No Insectivorous Clutter Obligate Small N/A 12.8 Rhinolophidae Rhinolophus arcuatus RHAR No Insectivorous Clutter Obligate Small Rhinolophus macrotis RHMA No Insectivorous Clutter Obligate Small Rhinolophus philippinensis RHPH No Insectivorous Clutter Obligate Small Rhinolophus rufus RHRU Yes Insectivorous Clutter Obligate Small See methods section for details regarding the selected ecological and morphological traits. Body mass (g)
6 Table S3. Species-specific threshold responses to multiple gradients on Bohol Island, Philippines. Gradient: Landscape disturbance Change-point analysis Indicator species analysis Species +/- z Obs. 5% 95% IndVal p-value Purity Reliability Emballonura alecto Hipposideros pygmaeus Taphozous melanopogon Rhinolophus arcuatus Miniopterus australis Hipposideros ater Rhinolophus rufus Miniopterus tristis Myotis horsfieldii Myotis macrotarsus Rousettus amplexicaudatus Rhinolophus philippinensis Ptenochirus jagori Miniopterus schreibersii Rhinolophus macrotis Megaderma spasma Hipposideros diadema Hipposideros obscurus Eonycteris spelaea
7 Gradient: Cave complexity Change-point analysis Indicator species analysis Species +/- z Obs. 5% 95% IndVal p-value Purity Reliability Hipposideros obscurus Taphozous melanopogon Ptenochirus jagori Megaderma spasma Myotis horsfieldii Rhinolophus arcuatus Rhinolophus philippinensis Rousettus amplexicaudatus Rhinolophus rufus Miniopterus tristis Eonycteris spelaea Rhinolophus macrotis Hipposideros diadema Miniopterus australis Myotis macrotarsus Miniopterus schreibersii Hipposideros ater Hipposideros pygmaeus Emballonura alecto
8 Gradient: Mining Change-point analysis Indicator species analysis Species +/- z Obs. 5% 95% IndVal p-value Purity Reliability Hipposideros ater Hipposideros obscurus Miniopterus australis Rhinolophus arcuatus Miniopterus schreibersii Hipposideros pygmaeus Hipposideros diadema Emballonura alecto Eonycteris spelaea Rhinolophus philippinensis Megaderma spasma Ptenochirus jagori Taphozous melanopogon Miniopterus tristis Myotis macrotarsus Rhinolophus macrotis Rousettus amplexicaudatus Rhinolophus rufus Myotis horsfieldii
9 Change-point analysis Gradient: Cave development Indicator species analysis Species +/- z Obs. 5% 95% IndVal p-value Purity Reliability Hipposideros diadema Hipposideros ater Myotis horsfieldii Rousettus amplexicaudatus Rhinolophus philippinensis Emballonura alecto Hipposideros pygmaeus Rhinolophus macrotis Miniopterus tristis Taphozous melanopogon Eonycteris spelaea Megaderma spasma Miniopterus schreibersii Rhinolophus arcuatus Myotis macrotarsus Miniopterus australis Rhinolophus rufus Hipposideros obscurus Ptenochirus jagori
10 Gradient: Resource extraction Change-point analysis Indicator species analysis Species +/- z Obs. 5% 95% IndVal p-value Purity Reliability Miniopterus schreibersii Eonycteris spelaea Miniopterus australis Rhinolophus arcuatus Myotis macrotarsus Hipposideros diadema Rousettus amplexicaudatus Taphozous melanopogon Rhinolophus philippinensis Emballonura alecto Miniopterus tristis Hipposideros obscurus Ptenochirus jagori Megaderma spasma Hipposideros pygmaeus Hipposideros ater Myotis horsfieldii Rhinolophus macrotis Rhinolophus rufus
11 Gradient: Bat hunting Change-point analysis Indicator species analysis Species +/- z Obs. 5% 95% IndVal p-value Purity Reliability Miniopterus australis Rhinolophus arcuatus Rhinolophus macrotis Ptenochirus jagori Myotis horsfieldii Rhinolophus rufus Rhinolophus philippinensis Emballonura alecto Hipposideros pygmaeus Miniopterus tristis Hipposideros ater Megaderma spasma Miniopterus schreibersii Taphozous melanopogon Myotis macrotarsus Eonycteris spelaea Rousettus amplexicaudatus Hipposideros diadema Hipposideros obscurus Change-point analysis: +/- indicates the direction of each species response (positive/negative) to a gradient, standardized z-scores, observed change points (Obs.) with bootstrap confidence intervals (5 and 95%) based on 500 bootstrap replicates. Indicator species analysis: indicator value scores (IndVal) with corresponding p-values and estimates of purity (i.e., mean proportion of correct response
12 direction (z- or z+) assignments) and reliability (i.e., mean proportion of p 0.05) based on 500 replicates. Species in bold are credible indicator species with purity > 0.90 and reliability > 0.75 for the respective gradient.
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