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S1 Detailed technical information: calculation of the TPI

The Topographic Position Index (TPI, Weiss 2001), a measure of local topographic variation, was calculated as the difference between the elevation of the focal pixel and the average elevation of all surrounding pixels within a pre-determined radius (here: 25 m). Pixels with large absolute TPI values (larger than the SD value of the TPI layer, following Weiss 2001) were categorized as being positioned in a depression (negative values) or on a ridge (positive values) while pixels with small absolute TPI values were categorized as belonging to slopes. We used slope values to distinguish between pixels located on a steep slope when their slope angle exceeded 34 degrees, as this corresponds to the maximum inclination where agriculture is practiced within the TNP (sanabria siles et al. 2012) or on a gentle slope if otherwise. The proportion of pixels in a patch belonging to each of these four categories (i.e., depression, ridge, steep slope, gentle slope) was used as indicator for local topographic variation.

Fig. S1 – Observed (Sobs), Chao2 and Incidence-based Coverage Estimator (ICE) species richness estimates per watershed plotted against the log(area) of each watershed.

Fig. S2 – Observed (Sobs), Chao2 and Incidence-based Coverage Estimator (ICE) species richness estimates per Poylepis patch plotted against the log(area) of each patch.

Fig. S3 – Species accumulation curves in the watersheds included in the analyses. One sample corresponds to one 10-species list.

Fig. S4 – Species accumulation curves in the patches included in the analyses. One sample corresponds to one 10-species list.

Variable AICw Coefficient SE

Akaike’s Information Criterion weights (AICW), values of the coefficient and standard errors (SE) of the variables included in the Generalized Linear Mixed Models analysis with Chao2 and ICE total species richness estimates at watershed and patch levels. Variables with AICW > 0.50 are shown in bold.

* indicates variables which have a coefficient value being larger than their standard errors.

TABLE S2 (continued on next five pages). Bird species with their code names observed in Polylepis fragments of the Tunari National Park with their IUCN conservation status (LC = Least Concern, NT = Near-Threatened; EN = Endangered) and the Important and/or Endemic Bird Area (IBA/EBA) to which they belong. Scientific nameCodeEnglish nameIUCNFamilyEndemism, IBA Nothoprocta ornatanotsp.Ornate tinamouLCTinamidae Nothoprocta pentlandiinotsp.Andean tinamouLCTinamidae Nothura darwiniinotDarDarwin’s nothuraLCTinamidae Patagioenas maculosapatmaCSpot-winged pigeonLCColumbidae Patagioenas fasciatapatFasNorthern band-tailed pigeonLCColumbidae Leptotila verreauxilepverWhite-tipped doveLCColumbidae Zenaida auriculatazenaurEared doveLCColumbidae Metriopelia ceciliaemetCeCBare-faced ground-doveLCColumbidaeIBA BO023 Metriopelia melanopterametmelBlack-winged ground-doveLCColumbidae Colibri thalassinusColthaGreen violet-earLCTrochilidae Colibri coruscansColCorSparkling violet-earLCTrochilidae Heliangelus amethysticollishelameAmethyst-throated sunangelLCTrochilidae Sappho sparganurussapspaRed-tailed cometLCTrochilidae Oreotrochilus estellaoreestAndean hillstarLCTrochilidae Oreotrochilus adelaoreaDeWedge-tailed hillstarNTTrochilidaeIBA BO023; EBA 056 Metallura tyrianthinamettyrTyrian metaltailLCTrochilidae Aglaeactis pamelaaglpamBlack-hooded sunbeamLCTrochilidaeCountry Coeligena violiferCoevioBolivian starfrontletLCTrochilidaeCountry Ensifera ensiferaensensSword-billed hummingbirdLCTrochilidae Pterophanes cyanopteruspteCyaGreat sapphirewingLCTrochilidae Patagona gigaspatgigGiant hummingbirdLCTrochilidae Chlorostilbon lucidusChlluCGlittering-bellied emeraldLCTrochilidae

Scientific nameCodeEnglish nameIUCNFamilyEndemism, IBA Amazilia chionogasteramaChiWhite-bellied humminbirdLCTrochilidae Aulacorhynchus coeruleicinctisaulCoeBlue-banded toucanetLCRamphastidae Andigena cucullataanDCuCHooded mountain-toucanLCRamphastidae Colaptes melanochlorosColmelGreen-barred woodpeckerLCPicidae Colaptes rivoliiColrivCrimson-mantled woodpeckerLCPicidae Colaptes rupicolaColrupSouthern Andean flickerLCPicidaeIBA BO023 Veniliornis lignariusvenligStriped woodpeckerLCPicidae Veniliornis nigricepsvennigBar-bellied woodpeckerLCPicidae Psilopsiagon aymarapsiaymGrey-hooded parakeetLCPsittacidae Psilopsiagon aurifronspsiorbMountain parakeetLCPsittacidae Bolborhynchus orbygnesiusbolorbAndean parakeetLCPsittacidae Brotogeris chiriribroChiYellow-chevroned parakeetLCPsittacidae Psittacara acuticaudatuspsiaCuBlue-crowned parakeetLCPsittacidae Psittacara mitratuspsimitMitred parakeetLCPsittacidae Melanopareia maximilianimelmaxOlive-crowned crescentchestLCRhinocryptidae Grallaria rufulagraruFRufous antpittaLCFormicariidae Grallaria erythrotisgraeryRufous-faced antpittaLCFormicariidaeCountry Scytalopus parvirostrissCyparTrilling tapaculoLCRhinocryptidae Scytalopus simonsisCysimPuna tapaculoLCRhinocryptidae Geositta tenuirostrisgeotenSlender-billed minerLCFurnariidae Xiphocolaptes promeropirhynchusxipproStrong-billed woodcreeperLCDendrocolaptidae Lepidocolaptes lacrymigerleplaCMontane woodcreeperLCDendrocolaptidae Ochetorhynchus andaecolaoChanDRock earthcreeperLCFurnariidaeIBA BO023 Pseudocolaptes boissonneautiipseboiStreaked tuftedcheekLCFurnariidae

TABLE S2 (continued).

Scientific nameCodeEnglish nameIUCNFamilyEndemism, IBA Furnarius rufusFurruFRufous horneroLCFurnariidae Upucerthia jelskiiupuJelPlain-breasted earthcreeperLCFurnariidae Cinclodes fuscusCinFusBuff-winged cinclodesLCFurnariidae Cinclodes atacamensisCinataWhite-winged cinclodesLCFurnariidae Syndactyla rufosuperciliatasynruFBuff-browed foliage-gleanerLCFurnariidae Margarornis squamigermarsQuPearled treerunnerLCFurnariidae Sylviorthorhynchus yanacensissylyanTawny tit-spinetailNTFurnariidaeIBA BO023 Lepthastenura fuliginicepslepFulBrown-capped tit-spinetailLCFurnariidae Phacellodomus striaticepsphastrStreak-fronted thornbirdLCFurnariidaeIBA BO023 Asthenes dorbignyiastDorCreamy-breasted canasteroLCFurnariidae Asthenes hartertiastharBlack-throated thistletailLCFurnariidaeCountry Asthenes heteruraasthetMaquis canasteroNTFurnariidaeIBA BO023; EBA 056 Cranioleuca albicepsCraalbLight-crowned spinetailLCFurnariidae Cranioleuca pyrrhophiaCrapyrStripe-crowned spinetailLCFurnariidae Synallaxis azaraesynazaAzara’s spinetailLCFurnariidae PhytotomarutilaphyrutWhite-tipped plantcutterLCCotingidae Ampelion rubrocristatusamprubRed-crested cotingaLCCotingidae Camptostoma obsoletumCamobsSouthern beardless tyrannuletLCTyrannidae Elaenia albicepselaalbWhite-crested elaeniaLCTyrannidae Suiriri suiririsuisuiSuiriri flycatcherLCTyrannidae Mecocerculus leucophrysmeCleuWhite-throated tyrannuletLCTyrannidae Anairetes flavirostrisanaFlaYellow-billed tit-tyrantLCTyrannidae Anairetes parulusanaparTufted tit-tyrantLCTyrannidae Serpophaga mundasermonWhite-bellied tyrannuletLCTyrannidae Pitangus sulfuratuspitsulGreat kiskadeeLCTyrannidae

TABLE S2 (continued).

Scientific nameCodeEnglish nameIUCNFamilyEndemism, IBA Casiornis rufusCasruFRufous casiornisLCTyrannidae Myiarchus tuberculifermyitubDusky-capped flycatcherLCTyrannidae Ochthoeca rufipectoralisoChruFRufous-breasted chat-tyrantLCTyrannidae Ochthoeca fumicoloroChFumBrown-backed chat-tyrantLCTyrannidae Ochthoeca oenanthoidesoChoenD’Orbigny’s chat-tyrantLCTyrannidaeIBA BO023 Ochthoeca leucophrysoChleuWhite-browed chat-tyrantLCTyrannidae Sublegatus modestussubmoDSouthern scrub-flycatcherLCTyrannidae Knipolegus aterrimusKniateWhite-winged black-tyrantLCTyrannidae Polioxolmis rufipennispolruFRufous-webbed bush-tyrantLCTyrannidaeIBA BO023 Agriornis montanusagrmonBlack-billed shrike-tyrantLCTyrannidae Myiotheretes striaticollismyistrStreak-throated bush-tyrantLCTyrannidae Myiotheretes fuscorufusmyiFusRufous-bellied bush-tyrantLCTyrannidae Cyclarhis gujanensisCyCguJRufous-browed peppershrikeLCVireonidae Vireo olivaceusviroliRed-eyed vireoLCVireonidae Cyanolyca viridicyanusCyavirWhite-collared jayNTCorvidae Orochelidon murinaoromurBrown-bellied swallowLCHirundinidae Troglodytes aedontroaeDHouse wrenLCTroglodytidae Mimus dorsalismimDorBrown-backed mockingbirdLCMimidae Catharus ustulatusCatustSwainson’s thrushLCTurdidae Turdus fuscatertursp.Great thrushLCTurdidae Turdus chiguancotursp.Chiguanco thrushLCTurdidae Turdus serranusturserGlossy black thrushLCTuridae Turdus amaurochalinusturamaCreamy-bellied thrushLCTurdidae Spinus crassirostrisspiCraThick-billed siskinLCFringillidae Spinus magellanicusspimagHooded siskinLCFringillidae

TABLE S2 (continued).

Scientific nameCodeEnglish nameIUCNFamilyEndemism, IBA Spinus atratusspiatrBack siskinLCFringillidae Chlorospingus flavopectusChlFlaCommon bush-tanagerLCThraupidae Atlapetes rufinuchaatlruFBolivian brush-finchLCEmberizidae Atlapetes fulvicepsatlFulFulvous-headed brush-finchLCEmberizidaeIBA BO023 Zonotrichia capensiszonCapRufous-collared sparrowLCEmberizidae Psarocolius atrovirenspsaatrDusky-green oropendolaLCIcteridae Cacicus chrysonotusCaCChrMountain caciqueLCIcteridae Molothrus bonariensismolbonShiny cowbirdLCIcteridae Agelaioides badiusagebaDGreyish cowingLCIcteridae Oreopsar bolivianusorebolBolivian blackbirdLCIcteridae Myioborus brunnicepsmyibruBrown-capped redstartLCParulidae Myioborus melanocephalusmyimelSpectacled redstartLCParulidae Pheucticus aureoventrispheaurBlack-backed grosbeakLCCardinalidae Saltator aurantiirostrissalaurGolden-billed saltatorLCCardinalidae Sporophila castaneiventrisspoCasChestnut-bellied seedeaterLCEmberizidae Poospiza bolivianapoobolBolivian warbling-finchLCEmberizidae Compsospiza garleppiComgarCochabamba mountain-finchENThraupidaeCountry Thlypopsis ruficepsthyruFRust-and-yellow tanagerLCThraupidae Poospizopsis hypocondriapoohypRufous-sided warbling-finchLCEmberizidae Microspingus erythrophrysmiCeryRusty-browed warbling-finchLCEmberizidaeIBA BO023 Miscrospingus torquatusmiCtorRinged warbling-finchLCEmberizidae Microspingus trifasciatusmiCtriThree-striped hemispingusLCEmberizidae Conirostrum binghamiConbinGiant conebillNTThraupidaeIBA BO023 Conirostrum ferrugineiventreConFerWhite-browed conebillLCThraupidae Conirostrum cinereumConCinCinereous conebillLCThraupidae

TABLE S2 (continued).

TABLE S2 (continued). Scientific nameCodeEnglish nameIUCNFamilyEndemism, IBA Sicalis flaveolasiCFlaSaffron finchLCEmberizidae Sicalis luteocephalasiClutoCitron-headed yellow-finchLCEmberizidaeEBA 056 Sicalis olivascenssiColiGreenish yellow-finchLCEmberizidae Sicalis luteasiClutGrassland yellow-finchLCEmberizidaeIBA BO023 Phrygilus atricepsphratrBlack-hooded sierra-finchLCEmberizidae Geospizopsis plebejusgeopleAsh-breasted sierra-finchLCEmberizidae Idiopsar brachyurusiDibraShort-tailed finchLCEmberizidaeEBA 056 Chionodacryon speculiferumChispeWhite-winged diuca-finchLCEmberizidaeIBA BO023 Catamenia analisCatanaBand-tailed seedeaterLCEmberizidae Catamenia inornataCatinoPlain-colored seedeaterLCEmberizidae Diglossa cyaneaDigCyaMasked flowerpiercerLCThraupidae Diglossa sittoidesDigsitRusty flowerpiercerLCThraupidae Diglossa mystacalisDigmysMoustached flowerpiercerLCThraupidae Diglossa carbonariaDigCarGrey-bellied flowerpiercerLCThraupidaeIBA BO023; EBA 056 Pipraeidea melanonotapipmelFawn-breasted tanagerLCThraupidae Pipraeidea bonariensispipbonBlue-and-yellow tanagerLCThraupidae Pseudosaltator rufiventrispseruFRufous-bellied mountain-tanagerNTCardinalidaeIBA BO023 and EBA 056 Dubusia castaneoventrisDubCasChestnut-bellied mountain-tanagerLCThraupidae Buthraupis montanabutmonHooded mountain-tanagerLCThraupidae Sporathraupis cyanocephalaspoCyaBlue-capped tanagerLCThraupidae Anisognathus somptuosusanisomBlue-winged mountain-tanagerLCThraupidae Anisognathus igniventrisaniignScarlet-bellied mountain-tanagerLCThraupidae Lophospingus griseocristatuslopgriGrey-crested finchLCEmberizidae Tangara sayacatansaySayaca tanagerLCThraupidae

TABLE S3 (continued on five next pages). Bird species observed in the Tunari National Park, reported per watershed (in bold) and Polylepis patch ID (second row), when applicable. Complete bird names and codes are reported in Table S2.2, above. Locations: CAN = Candelaria; CHA = ChaquiPotrero; CHO = Chorojo; ESP = Espital; ICA = Icari; LAP = Laphia; LIR = Liriuni; MOR = Morochata; PAJ = Pajcha; PAL = Palcapamapa; PINT = PintuMayu; SAM = SanMiguel; TAQ = Taquiña; THO = TholaPujru. Data from LIR, ESP and ICA were provided by J. Balderrama. SpeciesCanChaChoEspICaLapLIrMorpajpaLpIntsaMtaqtho 1212312123 NOTSP.xxxxxxxxxxx NOTDARxx PATMACx PATFASxxxxxx LEPVERxx ZENAURxx METCECxxxxx METMELxxxxxx COLTHAx COLCORxxxxxxx HELAMEx SAPSPAxxxxxxxxxxxxxxxxxx OREESTxxx OREADExx METTYRxx AGLPAMxxxx COEVIOxxx ENSENSx PTECYAxxx PATGIGxxxxxxxxxxxxxxxxxx CHLLUCxx

SpeciesCanChaChoEspICaLapLIrMorpajpaLpIntsaMtaqtho 1212312123 AMACHIxxx AULCOEx ANDCUCx COLMELxxxxxxxxx COLRIVx COLRUPxxxxxxx VENLIGxxx VENNIGx PSIAYMxxxxxxxxxxxxxxxxx PSIAURxxxx BOLORBx BROCHIx PSIACUx PSIMITxx MELMAXxxxxxxxxxxxxxx GRARUFx GRAERYx SCYPARx SCYSIMxxxxxxxxxxxxxxxxxxx GEOTENx XIPPROx LEPLACx OCHANDxxxxxxxxx PSEBOIxx FURRUFxxx

TABLE S3 (continued).

SpeciesCanChaChoEspICaLapLIrMorpajpaLpIntsaMtaqtho 1212312123 UPUJELx CINFUSxxxxxxxxx CINATAxxxxxxxxxxxxx SYNRUFx MARSQUx SYLYANxxxxxxxxxxxxxx LEPFULxxxxxxxxxxxxxxxxx PHASTRxxxxxxxxxxxxxxx ASTDORxxxxxxxxxxxxxxxxxx ASTHARxxx ASTHETxxxxxxxx CRAALBx CRAPYRx SYNAZAx PHYRUTxxx AMPRUBxxxxxxxxx CAMOBSx ELAALBxxxx SUISUIxxxx MECLEUxxxxxxxxxx ANAFLAxxxxx ANAPARxxxxxxxxxxxxxxxxx SERMUNxx PITSULx CASRUFx

TABLE S3 (continued).

TABLE S3 (continued). SpeciesCanChaChoEspICaLapLIrMorpajpaLpIntsaMtaqtho 1212312123 MYITUBxxxxx OCHRUFxx OCHFUMxxxxxx OCHOENxxxxxxxxx OCHLEUxxxxxxxxxxxxxxxxxxx SUBMODx KNIATExxxxxxx POLRUFxxxx AGRMONx MYISTRxx MYIFUSx CYCGUJxxxx VIROLIx CYAVIRx TROAEDxxxxxxxxxx MIMDORx CATUSTx TURSP.xxxxxxxxxxxxxxxxxxxx TURSERx TURAMAxx SPICRAxxxxxxxx SPIMAGxxxxxxxx SPIATRxxxx CHLFLAxxxx ATLRUFxx

SpeciesCanChaChoEspICaLapLIrMorpajpaLpIntsaMtaqtho 1212312123 ATLFULxxxxxx ZONCAPxxxxxxxxxxxxxxxxxxxx PSAATRx CACCHRx MOLBONx AGEBADxxxxxxxxxxx OREBOLxxxxxxxx MYIBRUxxxxxxxxxxxxx MYIMELx PHEAURxx SALAURxxxxxxxxxxxxxxxxxxx SPOCASx POOBOLx COMGARxxxxxxxx THLRUFx POOHYPxxxxxxxxxxx MICERYx MICTORx MICTRIx CONBINxxxxxxxxx CONFERxxx CONCINxxxxxxx SICFLAx SICLUTOxx SICOLIxxxxxxxxxxx

TABLE S3 (continued).

TABLE S3 (continued). SpeciesCanChaChoEspICaLapLIrMorpajpaLpIntsaMtaqtho 1212312123 SICLUTxx PHRATRxxxxxxxxxxxxxxx GEOPLExxxxxxxxx IDIBRAxxx CHISPEx CATANAxxxx CATINOxxxxxxxxxxxxxxx DIGCYAx DIGSITxx DIGMYSx DIGCARxxxxxxxxxxxxxxxxxxx PIPMELx PIPBONxxxxx PSERUFxxxxxxxxxxxxxxxxx DUBCASx BUTMONx SPOCYAx ANISOMx ANIIGNx LOPGRIx TANSAYxx

TABLE S4

Results from the NMDS analysis – significant species for each axis at the watershed level with the direction on first axis (Dim1) and on the second axis (Dim2) with the associated p values (pvals1 and pvals2). Bold p-values are significant (< 0.05).

Species Dim1 pvals1 Dim2 pvals2

NOTSPP -1 0.61 -1 0.01

NOTDAR 1 0.83 -1 0.012

ZENAUR 1 0.83 -1 0.012

COLCOR -1 0.279 -1 0.004

SAPSPA 1 0.013 -1 0.314

METTYR -1 0.013 1 0.314

AGLPAM -1 0.002 1 0.753

COEVIO -1 0.004 1 0.442

PTECYA -1 0.01 -1 0.486

PATGIG 1 0.013 -1 0.314

AMACHI 1 0.572 -1 0.012

PSIAYM 1 0.014 -1 0.984

MELMAX 1 0.019 1 0.003

PSEBOI -1 0.013 1 0.314

FURRUF 1 0.462 -1 0.035

CINFUS -1 0.412 -1 0.036

SYLYAN 1 0.017 1 0.212

LEPFUL 1 0.036 1 0.031

ASTDOR 1 0.029 1 0.661

PHASTR 1 0.08 1 0.031

ASTHAR -1 0.004 1 0.442

PHYRUT 1 0.447 -1 0.049

ANAPAR 1 0.036 1 0.031

TURAMA 1 0.547 -1 0.024

SPIMAG 1 0.85 -1 0.04

ATLRUF -1 0.013 1 0.314

CONFER -1 0.004 1 0.442

SICOLI 1 0.009 -1 0.377

PHRATR 1 0.022 1 0.285

GEOPLE -1 0.032 1 0.223

DIGSIT -1 0.08 -1 0.031

PSERUF 1 0.022 1 0.285

TABLE S5

Results from the NMDS analysis – significant species for each axis at the patch level with the direction on the first axis (Dim1) and on the second axis (Dim2) with the associated p values (pvals1 and pvals2).

Bold p-values are significant (< 0.05).

Species Dim1 pvals1 Dim2 pvals2

NOTSPP -1 0.007 1 0.553

PATFAS -1 0.028 -1 0.354

CHLLUC 1 0.951 -1 0.041

COLMEL -1 0.001 -1 0.765

MELMAX -1 0.029 1 0.071

SYLYAN 1 0.007 1 0.485

AMPRUB 1 0.041 -1 0.126

SUISUI -1 0.005 -1 0.111

MYITUB 1 0.131 -1 0.006

OCHFUM 1 0.22 -1 0.032

TROAED -1 0.052 -1 0.025

SPIMAG -1 0.127 1 0.026

CHLFLA -1 0.027 -1 0.351

POLRUF -1 0.928 1 0.011

ATLFUL -1 0.004 -1 0.111

AGEBAD -1 0.005 1 0.106

MYIBRU -1 0.504 -1 0.001

COMGAR -1 0.448 -1 0.008

POOHYP -1 0.001 1 0.526

CONBIN 1 0.045 1 0.249

PHRATR -1 0.951 1 0.041

GEOPLE 1 0.441 1 0.001

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