This is a repository copy of The Effects of Restoring Logged Tropical Forests on Avian Phylogenetic and Functional Diversity..

White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/117037/

Version: Accepted Version

Article: Cosset, C.C.P. and Edwards, D.P. (2017) The Effects of Restoring Logged Tropical Forests on Avian Phylogenetic and Functional Diversity. Ecological Applications. ISSN 1051-0761 https://doi.org/10.1002/eap.1578

Copyright by the Ecological Society of America, Cosset, C. C.P. and Edwards, D. P., The Effects of Restoring Logged Tropical Forests on Avian Phylogenetic and Functional Diversity. Ecol Appl., doi:10.1002/eap.1578.

Reuse Unless indicated otherwise, fulltext items are protected by copyright with all rights reserved. The copyright exception in section 29 of the Copyright, Designs and Patents Act 1988 allows the making of a single copy solely for the purpose of non-commercial research or private study within the limits of fair dealing. The publisher or other rights-holder may allow further reproduction and re-use of this version - refer to the White Rose Research Online record for this item. Where records identify the publisher as the copyright holder, users can verify any specific terms of use on the publisher’s website.

Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request.

[email protected] https://eprints.whiterose.ac.uk/ Accepted Article This by is protectedarticle reserved. Allrights copyright. doi: 10.1002/eap.1578 lead to differences between this version and the throughbeen the copyediting, pagination typesetting, which process, may and proofreading hasThis article been accepted publicationfor andundergone peerfull but review not has Articles : type Article community—and on functional diversity, with important implications implications for protectionof with important diversity, the community—and onfunctional diversity—the all totalevolutionaryphylogenetic within historyacross a shared species avian inforests restoringBorneo on This studyinvestigatesof vines. impactslogged the of cutting and liberation planting enrichment via logged forests, to protect obtaining funding Deforestation ForestDegradati and from conserving old-growth forests. Re primary, to thenext best alternative protection is that their suggestionsbiodiversity to leading o substantial amount a harbour still ofstructure, selectively logged forests degradation forest Selective logging the is most prevalent land-use inchange the tropics. Despite theresulting Abstract Email address: *Corresponding author. 1 Cindy C.P. CindyCosset C.P. Department ofAnimal andPlant Sciences,University ofSheffield,S10 2TN, UK The Effects of Restoring Logged Tropical Forests on Running head: diversityBird in restored logged forest

Avian Phylogenetic and Functional Diversity Diversity Functional and Phylogenetic Avian [email protected] 1* , David P. Edwards P. , David

on (REDD+) schemes is a potential method formethod potential (REDD+) isa schemes on storing carbon stocks under Reducing Emissions 1

Version of Record. Please Version as this cite ofRecord. article f Accepted Article

This by is protectedarticle reserved. Allrights copyright. Restoration, Selective logging, Silviculture, Keywords: where breaks betweenregimes are incorporated. restoration onlyon the mo tofocus is important To future perverse it REDD+ agreements. questionable biodiversity outcomes, under reduce the biodiversit levels, making unlogged forest weighedmust be against loss the of phylogenetic apparent diversityfunctional and from potential and timberharvests, future sequestration, Whilethere forests. are additional benefits to unlogged niches compared intherichness understorey birdcommunity and thus occupied in functional Restoration toareduction led the community. also in functional clustering specialized traits inrestored forests compared morewith species strategies and of functional loss a significant community experienced found ina primary indicating forest, more clos MNTDtaxon thatcommunity had (mean nearest distance) returnedlevels towards lower the speciesmore closely to related compared pairwise distance) leaving bird overall communityan less total of evolutionary and history (mean MPD diversity and lossin phylogenetic significant causeda Restoration respectively. studiedcommunitiesunderstorey were avifaunal speciesevolutionarily provision the unique manyservices. of and ecosystem Overall and Biodiversity, Birds, Liana cutting, Payments for Ecosystem Services, REDD+, Services, Ecosystem Liana for Payments cutting, Birds, Biodiversity, Southeast Asia, Sustainable forestmanagement unlogged the bird understorey while forests, y-friendliness of sequestration carbon schemes of restoration forregeneration, forest carbon to of unlogged to led which that forests, ely species related pairs. Theoverall bird using point count and mist-netting surveys, surveys, mist-netting and using pointcount ly reduced threat of forest conversion, this conversion, forest threatof ly reduced st degraded areas or at reduced intensity degradedorst areas atreduced

Accepted Article 2012, Edwards 2012, disturbance sensitive-specieshumid that dark,(Baraloto understorey require conditions timber estates and are expected to remain under forest cover (Asner coverunder to expected are and remain estates timber forest permanent in are tropics in the forests hectares of 400million more than presently, 2005 and, for biodiversity conservation (Meijaard and Sheil 2007, Chazdon andSheil 2007, (Meijaard biodiversity conservation for selective logging next asthe has beenproposed Meijaard (Sheil and Peres concessions 2005, agriculture by threatened are to conversion permanent of outside fall those that species and andfires, by invasion alien hunting, moreprone todegraded are have logging byselective been Foreststhat 2011). activities (Edwards regenerate (Putz (Putz regenerate to trees ability of the impedes forest following which bamboos often overthe logging, run 400% more likely than primary forests in the Amazon (Asner Brazilian than primarylikely forests 400% more Padmanaba2006, andSheil 2014, Abood instead ofprimary old-growth forest todominate selectively the expansion forest globally, cover of biodiversity logged forest in climatic conditions (Holdsworth and Uhl 1997, Laporte (Holdsworthin climatic andUhl1997, conditions This by is protectedarticle reserved. Allrights copyright. (Barlow are that valuable functionally to species detrimental and deforestation particularly from with2013), losses to degradation in the Brazilian Amazon largeas as conservation losses combination, degradationhabitat biodiversity causes decline (Wilcoveto drastically INTRODUCTION Selective loggingSelective degraded activities 20% of tropical worldwide 2000–forests from Protecting logged forests from risks other associatedagriculture to loggedconversion from and forests with Protecting loggingSelective most is the land-useextensive change in tropical ecosystems et al et al . 2016). . 2014b, Asner 2014b, . et al et al . 2014b). Because tropical forests forests Because tropical 2014b). . . 2008, Osazuwa-Peters 2008, . et al . 2009), causing structural damage and short-term changes changes damage short-term causing and 2009), structural . is amajor conservation concern. et al . . 2015) –withagricultural up conversion to best protecting to forests alternative primary et al et . 2015) and reduces the survival of of survival the reduces 2015) and . harbour thehighest of amounts et al et . 2007). 2007). . Climbing vines and et al et et al . 2009, Edwards 2009, . . 2009, Blaser et al et . 2006). In 2006). . et al et et al et al et et alet et al . . . . . Accepted Article community composition tree of (Wheeler Wheeler better carbon sinks and encourage more ra more encourage sinksand better carbon Kobayashi Previous have 2007). studies shown competing vines, bamboos, herbaceous plants,or early successional trees (Putz planting enrichment (1) together: individually or which twokeytypes canbe methods, restoration of applied There are and Putz 2009). bi erode will destructive that carbon-farming there danger is a that these techniques cause further damage to logged-over forests, and are and Wintle 2008,and Wintle Edwards loss, accelerate imp forest regeneration, and This by is protectedarticle reserved. Allrights copyright. the logging used (Edwards regime with biodiversityhigh levels, retain can forests forest, the selectively alteredconditions in logged the (1) despite because: is This 2011). to the reduced opportunity revenues (Fisher to thereduced foregone timber costsof al payments (Edwards activities would enhance the background rate of sequestrationcarbon toyield carbon mechanism to acquire such funding (Chazdon In 2008). the context oflogging, restoration Emissions Deforestationfrom andForest De degraded forests under payment ecosystem for service schemes such astheReducing critical a thus is agriculture conversion to al or (Edwards to areas currentused protected theseenlarge connect logged be could forests . 2015); (2) it can be more cost-effective to protect due to logged (2)it can bemorecost-effective than 2015); forests primary forests . . 2014b). Obtaining funding and political will to protect these Obtaining2014b).political protectthese logged from and to . forests fundingwill Some suggestSome restoringthat logged forests et al. 2016). 2016). suggestsResearch positive also some onthe diversity effects and et al . 2010).. et al . 2010, Gourlet-Fleury. 2010, et al . 2011, Putz 2011, . pid forest regeneration (Gourlet-Fleury (Gourlet-Fleury pid forest regeneration et al. rove timber harvests (Kobayashi harvests rove Bekessy 2007, timber ological value (Putz and Redford 2009, ological value Sasaki (Putz andRedford 2009, issue. Enhancing carbon stocks stocks Enhancingvia restoring issue. carbon the degree of retention in part dependent upon dependent part in of retention degree the gradation is apotential (REDD+) program that thesethat two methods make logged forests has potential benefits to reversebenefits has to potential biodiversity 2016), understorey avian (Edwards understorey avian 2016), of native trees, and (2) liberation cutting of of cutting (2) liberation and trees, native of et al et et al . 2012, Bicknell 2012, . . 2013). However, 2013). suggest others . et al et et al et . 2011b); and(3) 2011b); . . 2014, Martin 2014, Martin . et al et al et . 2001a, . . 2013, . et al et et et . Accepted Article traits and resulting ecosystem functions (Redding and Mooers 2006, Jetz Jetz Mooers 2006, (Reddingand functions ecosystem resulting and traits biodiversity into beincluded – can represents Evolutionary distinctiveness evolutionary amount – the metrics unique of aspecies history are also important for conservation planning(Cadotte are also conservation important for uniquenesscommunity functionalof andpatterns relationships in (measures functionala community) ofspecies diversity orand metrics Phylogenetic (measures diversity of evolutionarymetrics history and of evolutionary patterns traifunctions asthey unique possess which arevital for ecosystem processes. itsthat areevolutionaspeciesunderstand impacts on toconservationan accepted asrestoration strategy, weneed before effective be can (Pavoine and Bonsall 2011), ecosystem(Pavoine 2011), and Bonsall functioning (Petchey Gossner This by is protectedarticle reserved. Allrights copyright. Ansell2009, 2011, Bässler Bässler 2011, a community’s functioning than does speciesri a community’s functioningthan and Macediversity Functional 2009). assessmentscanbetter the reveal state andof resilience and (Díaz resilience community species to an ecological compared tocommunity species richness (Isaac revisionsare less andmoresensitive affected by non-native inclusions taxonomic of to insights into responsescommunity to environm al . 2004, Cadotte Species that are locally evolutionarily distinct are important for local ecosystemlocal for important are distinct locallythat are evolutionarily Species Incorporating phylogenetic and functional di andfunctional phylogenetic Incorporating et al et al et et al et . 2013). These metrics can inform us on community assembly processes assemblyus oncommunity informcan metrics These 2013). . et al . 2014), intrinsic conservation value (Mace (Mace conservation value intrinsic 2014), . . . 2011) (Edwards andinvertebrate . 2009, Mouillot. et al . 2007, Cadotte et al ts and occupy uniqueniches (Jetz . 2013). . conservationpreserve strategies to unique these chness or community composition (Petchey composition or community chness ental ental change. diversity Phylogenetic metrics functional trait distribution incommunities) distribution trait functional versity metrics provides us with important important with provides us metrics versity rily distinct or functionally important and orfunctionally important distinct rily et al et al . 2012).. et al et . 2012) communities. However, 2012)communities. . et al et al et . 2011, Rolland Rolland 2011, . . 2004,. Cadotte, . 2003, Winter 2003, . et al et et alet . 2004,. Meiri et al et al et al et alet . 2014). 2014). . . 2014). . . 2012,. . 2013) . . 2009, . et Accepted Article logged restored previously forests that were and forests loggedthe same at time as sampled (Myers STUDY SITE STUDY SITE AND METHODS MATERIALS responses to loggingresponses to in forests. forests. selectively logged to protect enhancement fundingusing supportfor carbon lend further would so, if if and, biodiversity restorationcan to determine conservation aid results will help emerging agendaGiven restoration forest the diversity communities. avian functional of affects the restoration how loggeddetermine forest (2) and communities; avian phylogenetic diversity of the affects restoration forest logged how thusto: were aims (1) determine The controls. as logged forests regenerating naturally and unloggedcompared forests were then to primary logged of forests restoring The impacts bamboos.climbing on vines and species cutting wasperformed liberation tree and with native Restorecosystem2006). functioning (Sekercioglu well-known taxonomically, have aglobal taxonomically,phylogeny well-known (Jetz and communities. Birdsare avian both understorey entire(overall) for the diversity impacts This levels. forest primary towards biodiversity selectively can thatareunhuntedand recovery forests also logged unburned the aid of examine whether restoration management toimprove stocks structure forest and incarbon manylogging for hasbeenresponsible (Wilcove species extinctions local This by is protectedarticle reserved. Allrights copyright. hotspot of Borneo hotspot ofBorneo (Myers The study was conducted in the global biodiversity hotspot of the islandthe of the studywas biodiversityglobal of Borneo The conducted in hotspot This study investigates the effects of restor of effects the study investigates This et al . 2000). Three habitat 2000). naturally. types (unlogged regenerating primary forests, other taxa (Edwards othertaxa et al . 2000), where 2000), extensive. habitat selectivedegradation from globally (Pistorius and Freiberg 2014), the 2014), andFreiberg (Pistorius globally onstudy phylogenetic and focuses functional et al et ing logged forests in the global biodiversity inthe ing forests logged ed logged forests were enrichment planted were forests enrichment ed logged . 2014a) and play important roles for roles 2014a) andplay . important et al . 2012), are 2012),. good of indicators et al . 2013). We 2013). . Accepted Article This by is protectedarticle reserved. Allrights copyright. (Fisher timber for valuable (Dipterocarpaceae) trees dipterocarp large Conservation Area and adjacent Palum Tambun reserves,Watershed which aredominated by Within YSthe concession is45,200 haof unlogged in primary forests the Danum Valley onehectarethe Yayasan Sabahmillion (YS)logging in Sabah, Borneo. concession Malaysian of forests dry dipterocarp lowland the in surveyed were forests) logged regenerating naturally of timber removed per per of timber (Fisher hectare removed (DBH) were harvested using high lead cable ex cable using lead harvested (DBH) high were system in which all commerciallyvaluable trees (US-MFR). Forest Reserve Ulu Segama-Malua adjacent in the forest logged represented our unlogged and primary forests, planting lines immediately before and 3 months after and3months plantingplanting lines enrichment immediatelyafter (seeAnsell before enrichment planting. Non-commercial understorey plantswere also along removed the afteryears and 3 before 6months and vines, bamboos climbing all cutting and liberation of along line species planting (5%) and wildfruit Restoration involved2011). planting a enrichment native variety (95%) with of dipterocarp were re-logged between 2001 and 2007 (Edwards 2007(Edwards re-logged 2001and between were as roads, logging dumps and skid trails that landscape skidtrailsthe fragment (Pinardroads, loggingand forest as dumps understorey and vegetation cl of unlogged logged Forinstance, forests. forest stru the logging, selective of result As a forests. (INFAPRO), with another 14,000 hectares designated for future restoration (Ansell (Ansell hectares restoration for 14,000 designated future with another (INFAPRO), Rehabilitation Project Rainforest Foundation 1993 and2011bytheInnoprise-FACE Laporte The US-MFR was selectivelywas19761991 US-MFR betweenThe and usinga modified logged uniform About 11,000 hectares of About 11,000 once-logged in US-MFR forests the betweenrestored were et al . 2007). imbing (Berry bamboos et al . 2011b). Although some oftheareas US-MFR 238,000 ha naturally regenerating and restored restored and regenerating naturally ha 238,000 s at densities of 200 seedlings per ha or lower of 200seedlings haor s at densities per cture of logged forests is very different to that to verylogged is forests different of cture traction and tractor techniques, with ~113 m ~113 with techniques, traction andtractor canopies have more gaps, a higher density of higher density of gaps, a more havecanopies of more than 60 cm diameter at breast heightbreast 60 diameter at thancm more of et al et et al . 2011), we focus ononce-logged the wefocus 2011), . . 2008,. Ansell et al et et al . 2011), as well. . 2011a)and. et al et . 2000, . et alet et al 3 . .

Accepted Article This by is protectedarticle reserved. Allrights copyright. restored between 2002 and (SBE; 2003inthe Sabah Biodiversity Hector Experiment Additionally, 500 2011 details). further ha offor once-logged inthe forest US-MFR were both communities were extracted from Ansell Ansell from were extracted both communities Data for community. understorey bird the and community whole) bird (i.e. overall the 1999): AVIFAUNAL SAMPLING AVIFAUNAL ha. withliberationcuttingplanting2011), andenrichment densities of at about 60seedlingsper species’unknown. trueabundance, is which All on any was takenas days of three the our estimate of maximum abundance butnot the highest habitat different Thenumber oftypes. speciesindividual recordedfor birds a certain (within or be temporal effects andany year, was onlysampled in one site Each 1000 h. daysconsecutive 0545– from independent (Hill 2004). and Point-coun Hamer that bird points or transectscensus by separated mist-net than 200 more m arestatistically shown forestshavein tropical Studies forests)S1a). 12 SBE) inrestored (AppendixS1:Fig count stations in unlogged 24 forests, in natura sampled 12we stations point-count persite with each station separated by250 m(48point- sites MaySeptember At 2008and Maytype,from habitat –June2009. created within – each treatment. restored with sampled 14-16yearslogging, (5-6years SBE) forests post in restoration postyears sampled 16-22 andthus in SBE), 1993and(2002 and2003 planted between 1995 previously betweenharvested were 1987 logged) l regenerating (naturally loggedSampled forests Two avian communities were sampled communities duringTwo avian thedrierseasons (Walsh were and Newberry Overall bird community: Point count surveys with unlimited-radius were Point conducted bird Overall unlimited-radius surveyscount community: with tween years) were minimized by rotating sampling betweenthe byrotatingyears) sampling tweenminimized were

et alet lly regenerating forests, and 36 (24 INFAPRO; (24 36 and forests, lly regenerating ogged forests and restored forests that were andrestoredforests forests ogged t surveys 15 for onthreeoccurred minutes and 1991, with restoredand enrichment forests . (2011) and Edwards and Edwards (2011) . point were point counts byconducted asingle et al et . (2013, 2014a). (2013, . et al . Accepted Article This by is protectedarticle reserved. Allrights copyright. MEASURES & DISTINCTIVENESS DIVERSITY PHYLOGENETIC EVOLUTIONARY specieswere recorded in themist netsurveys across all habitattypes. 100 of isunknown. which abundance, Atotal true species’ maximum abundance, butnot a unique individuals of each species across the samplingthree gave days of anestimate only each bird with auniquelywas marked once, the Totalling leg metal ring. numbered thedifferentsampling habitat between To types. orbetween year, within years)and by wereminimized (i.e., any rotating effects temporal was three days site–consecutive occurred for from oneEach only 1200h. 0600 in sampled 2.7transect nets m;mesh 15mist sizecontained (12x 25mm)placed end end. Sampling to placed at least 500m to ensure apart statistical independence (Appendix EachS1b). S1: Fig and 18(16 SBE) INFAPRO; forests) logged withtransects 2 inrestored eachhabitat within forests transects regenerating naturally (18 logged created 18 in in unloggedforests, primary be undersampled using point counts (Blake and Loiselle 2001). Fifty-four transects were can that lower-storey birds cryptic the survey and2009 to – July May 2008 May –September count surveys resulted in 167 species across all habitat types. minimi Edwards)to P. observer (D. experienced 250 trees on the Ericsonthe on 250 trees hypothesis species of different is Sixthe other. fromevolutionary relationships that (Jetz (Jetz from http://birdtree.org/ trees downloaded were hundredphylogenetic five dataset, For each et al The following methods were conducted th were for following methods The – October Mistnetting wasconducted birdcommunity: JuneUnderstorey 2007, from . 2012)of which 250trees. were based ontheHackett et al . (2006) backbone. Each phylogenetic. treerepresents a se the potential for observer bias. The point The bias. observer potential for se the ensure that individual birds were sampled sampled were birds individual that ensure e andunderstorey overall e bird datasets. et al et . (2008) backbone (2008)backbone . and Accepted Article 7. 6. 5. 4. 3. This by is protectedarticle reserved. Allrights copyright. 2. 1. were for calculated ofdistinctiveness eachphylogenetic 500 Thesewere: the trees. of local evolutionary onemetric and diversity metrics abundance-weighted phylogenetic

Evolutionary Distinctiveness (ED)Evolutionary species given that richness andfor opposite isthe sesMNTD negative valuetrue for have thanexpected higher MNTD sesMNTD values communities of imply that Positive (sesMNTD) ofMNTD size effect Standard (MNTD)Taxon Distance Nearest Mean giventhat species richness andthe oppositetrue is for sesMPD negativevalues; for expected higher have than MPD that communities sesMPD imply values of Positive effectStandard size of MPD (sesMPD) across clades,while low MPD values indicate community.Highvalues a MPD of individuals Distance (MPD) Pairwise Mean that it has no extant close relatives and vice versa. versa. vice and relatives close no has extant it that byrepresented aspecies aphylogeneticwithin ahighvalue tree. Aspecies indicates ED MNTD values suggest that they occur in the community; low while the community, in co-occur do not closely related areindividuals that that suggestvalues non-conspecific High closest MNTD relative. their individuals and between expectedthan for thatgiven species richness andthe oppositetrue isfor negative values; species pool. Positive values sesPDof sugges species richness, which are created by drawing species random at from the regional of PD community ofnull thePDofobserved equalcommunities the with comparing Standard effectStandard size of PD (sesPD) DiversityPhylogenetic (PD) correlated with with speciescorrelated richness (SwensonLi 2014, – the total ofamount evolutionary in history community; a – the average distance on a phylogenetic tree between phylogeneticaverage tree all the ona distance – –PD taking into account species richness, as PD is – the amount of unique evolutionary history unique evolutionaryhistory of amount – the – the average distance on a phylogenetic tree a phylogenetic on distance average – the – MPD taking into into –MPDtaking account species richness. – MNTD taking into account species account richness. into taking –MNTD that species are phylogeneticallythatspecies are clustered; t that higher have t that communities values PD indicate indicate that species are widely distributed et al . 2015). SesPD 2015). . is bycalculated s; Accepted Article countsample and each mist-net transect. EDthe value werediversity and calculated 500trees metrics eachpoint median all from for account for phylogenetic uncertainty, meanthe values of each ofthe sixphylogenetic calculated using the fair proportions method (Isaac fair proportionsmethod calculated usingthe FUNCTIONAL DIVERSITYFUNCTIONAL MEASURES This by is protectedarticle reserved. Allrights copyright. using the S1:Sec Supplementary Appendix Materials (see maintaining local ecosystem function (Crozier 1997, Hidasi-Neto 1997, (Crozier function ecosystem local maintaining of global EDbecause species that locall are species poolwhilst maintaining species richness Local 2000). (Gotelli ED wasused instead with anindependent swap whichdraws algorithm random species theregionalat from generated models usingwere null These nullcommunities communities. 999 null against standard effect size (ses) for PD, MPD MNTD, the and observed communitycompared was functionally important (Flynn functionally important usingresource evaluated diversityFunctional was (http://www.hbw.com/), following Edwards following (http://www.hbw.com/), extracted Smythies from (1960) and Handbook ofthe Birds of the World Alive was matrix on the used). more information Data for trait traits S1:S2 for Appendix Table physical ofcategory the speciesdetermined the (seemorphological attributes bodysize) (e.g. the wassallying);(e.g. obtained howthe foodstrategy item and ground); determined foraging types food eaten of (e.g. foragingfruit); where foragingsubstrate determined (e.g. place takes we Morphological) strategy, Foraging substrate,

The following methods were conducted th were for following methods The A full description and equations of the phylogenetic phylogenetic the metrics description equationsof and are inthe given A full picante package (Kembel et al et alet . 2009). Traits from four categories (Diet, Foraging Foraging categories(Diet, four from Traits 2009). . . 2010) in R (R Core Team 2016). the Tocalculate R(RCoreTeam 2010)in . et al.

y evolutionarily distinct are for y important distinct are evolutionarily (2013). (2013). re used – the diet category the used –thediet re determined tion S1). All seven metrics Allseven were tion S1). calculated -use traits, which studies have shown to be studies have which shownto traits, -use et al e andunderstorey overall e bird datasets. . 2007) (Appendix S1: Table S3). To S3). Table (Appendix S1: 2007) . et al . 2015).. ED was Accepted Article arithmetic average (UPGMA) (Blackburn clustering categorical, continuous and multi-choice nominal variables (Podani and Schmera 2006). The 2006). andSchmera nominal (Podani categorical, variables continuous and multi-choice co measuring fora suitable measuredistance is al was createdusingthe functional dendrogram The dendrogram. a into and functional intoa distance then matrix converted matrix trait Supplementary Materials (seeAppendix S1:Section FD S1). was calculated starting with a 5. 4. This by is protectedarticle reserved. Allrights copyright. 3. 2. 1. measured:

. 2009) using the 2009) using the . more specialized,more while communitieswith low FSpe values are less specialized. communityis that a indicate High values regional FSpe speciespool. the to compared SpecializationFunctional (FSpe) lowcommunity; FDiv that there is low niche differentiation; thatHigh community. FDivthere implies is differentiation within high a niche DivergenceFunctional (FDiv) and under-utilised; under-utilised; and and utilised, while occupied indicate values low thatniches FEve maybe under-occupied acrossfunctionalcommunity space.indicate that niches Highvalues are evenly FEve Functional Evenness Functional (FEve) while thecommunity opposite is true for values;low niches lots by are inthe occupied of High suggest that values FRic species community. Richness (FRic)Functional (Petchey andGaston 2002); Diversity (FD)Functional A full description and description of equations the A full are functional metrics given in the Using the trait data, five complementary measures of functional diversity were data, of diversitywere measures functional complementary five trait Using the vegan package (Oksanen – the total length of branches on a dendrogram functional ona length branches of total –the – of the amount functional space occupied by species in a – describes the distribution species thedistribution of abundances – a describes in – describes patterns of nichein a differentiation patternsof – describes –measures the uniquenessfunctional of community a extended Gower distance measure (Pavoine extended Gowerdistance measure mbination of variable of variable mbination types binary, including et al . 2016) and an unweighted pair-group 2016) andan . et al . 2005). The 2005). extended. Gower et Accepted Article This by is protectedarticle reserved. Allrights copyright. Thefunctionalwas dendrogram2006). thenused tocalculate FD using the accurately preserves the pairwise distances of the original datapoints (Petchey and Gaston community: 0.77; understorey birdcommunity: 0.81), which suggests that the dendrogram UPGMA highest producedthe method clustering cophenetic coefficient bird (overall in R (Kembel in R from the the from weresampled included LMMsas random effects.estimated were using maximum likelihood typeHabitat was included inthe as model a fixed while effect, sampling andtheyear site level, is which unaffected by theimbalanced total number ofpointcounts between habitats. we community, used linear mixed-effects models (LMMs). Analysis point atthe is count overallbird the diversity metrics for functional phylogenetic and on forests) restored logged communities. Tostudy the ofhabitat typeeffects (unlogged, naturally regenerating logged, homoscedasticity and normality. homoscedasticity andnormality. formulae and convex hull methodology ( hullmethodology andconvex formulae STATISTICAL ANALYSES matrix usingthe extendedmatrix measure Gowerdistance (Pavoine Thetr whenaccount calculating metrics. these species’ functional niche. Traits were weight aremethod, traits coordinates in multidimensionalspace functional niche whichdetermines a (Villéger (Villéger coordinate analysis outto (PCoA) wascarried sample and transect. sample mist-net each point n=8) werethen usedeach for to community: the calculate count metrics functional FRic, FEve, FDiv and FSpe were calculated using Villéger All All analyses were conducted separately for the overall birdandunderstorey bird et al lme4 et al . 2008). The PCoA axes (overall bird (overall ThePCoA 2008). . axes packageR (Bates in . 2010). for each point countsample and each mist-net transect.

FRic was the only metric that was log-transformed. Model log-transformed. was that only the was metric FRic et al FD package in R: Laliberté R: Laliberté in package ed equally and species abundance was takenwas into abundance species equally and ed . 2015).. Model residuals checkedwere for produce a matrix of of transformed coordinates amatrix produce ait matrixwas first converted to adistance community: n=6; understorey bird understorey n=6; community: et al . 2009) and then a principaland. then a 2009) et al et al . 2014). Using this Using this . 2014). .’s (2008, 2010) (2008, .’s picante package Accepted Article Schielzeth 2013) from the Schielzeth 2013)from This by is protectedarticle reserved. Allrights copyright. and random was calculatedeffects us fixed byeach model’s explained variation of amount The AICvalues. lowest the models had using was fit AkaikeInformation compared fit was tested using the using tested the was fit homoscedasticity andnormality. built using the aggregated no randomeffects intosites, nested were ANOVA The included. were models not were transects mist-net since were used; ANOVAmodels understorey community, the of dataInclusionSBEnot did from soaffect we and ourresults, present only the full analysis. conducted using Tukey posthoc tests inthe Pairwise thenconduct comparisons were selected based on their AIC values of which th 1000 repetitions.All were analyses done onRStudio(R Core Team2016). was used from the was the usedfrom autocorrelation influenced at results any thepoint (Appendix S1:the Supplementary spatial Tocheck whether S2). FigMaterials understorey overall bird both in community for areincluded and the functional metrics bird presentwe onlythe full analysis.

package (Hothorn To study the effects of habitat type on phylogenetic and functional diversity metrics for diversity metrics andfunctional phylogenetic type on habitat of study effects To the Correlation plots between the different phylogenetic between metricsdifferent between plots thedifferent the and Correlation lm function inR (R Core Team Model2016). residuals were checked for et al et spdep . 2008). Inclusion of data from SBE of datafrom Inclusion 2008). . AICcmodavg package in R (Bivand and Piras 2015) using model residuals with model and R(Bivand Piras2015)using in package MuMIn FRic was the only metric that was log-transformed. Model log-transformed. was that only the was metric FRic package R (Barton2016).in Pairwise comparisons were package in R (Mazerolle 2016). The best models were The models in 2016). best package R(Mazerolle ing Nagakawa and Schielzeth’s R Schielzeth’s and Nagakawa ing ed using Tukey post hoc tests in the testsed using in posthoc Tukey Criterion (AIC) (Anderson 2008) where theCriterion (AIC)(Anderson2008)wherebest multcomp e lowest values indicated thebest models. or transect levels, the Moran’s I statistic package inR(Hothorn did not affect our results, andsoour results, not affect did 2 (Nakagawa and et al et multcomp . 2008)..

Accepted Article sesMNTD (p>0.054,S3b) S1: Fig AppendixAppendixand Fig ED(p>0.1, S4a). S1: S1: Appendix S3a), Fig (p>0.3, pairs for habitat between MNTD difference significant Fig which did not differ1d), significantly (MPD:p=0.178; sesMPD: Therewas p=0.111). no sesMPD: Fig 1c; (MPD: sesMPD: (MPD:p<0.001; p<0.001) andunlogged forests p=0.012) sesMPD: naturallywasp=0.003; significantlycompared to regenerating (MPD: lower forests restored orunlogged (p=0.394) fo with differ forests naturally did significantly not while regenerating Fig 1b), (p=0.014, unlogged forests sesPD than Restoredsignificantly significantly Fig1a). forestshad lower (p=0.989, differ naturally not did which forests regenerating unloggedand PD (p=0.020), (p=0.003) than showed comparisons Pairwise that restored1). forestslower hadsignificantly MNTD (Table species; nets =mist S1:species) 13(Appendix TableS1). both datasetssampling components unique ofthe avian (pointcommunity counts =80 Overall Bird Community I(Moran’s models test: p>0.4). all detected anyfor ofthe residuals phylogenefor tended to be significantly (Appendixcorrelated This by is protectedarticle reserved. Allrights copyright. & DISTINCTIVENESS DIVERSITY PHYLOGENETIC EVOLUTIONARY RESULTS except allmetrics for fit improved model effect as afixed type habitat Including A total of87 species were shared betweenpoint the count mist netand datasets, with The phylogenetic metricsofThe both the bird overall theand understorey bird community rests (p=0.518). MPD andsesMPDrests (p=0.518). inrestored tic diversity and evolutionary distinctiveness S1: Fig S2). Spatial autocorrelation was not was FigS1: Spatial autocorrelation S2).

Accepted Article 2b) and 2b) FigFEve (p=0.043, unloggedand 2c)than Fig significantly Restored(p=0.880; significantly 2a). Fig lower forests had FRic (p<0.001, differ did not which forests, (p<0.001) unlogged and (p=0.023) regenerating in naturally than forests lowerinrestored FD significantly that comparisons reveal was Pairwise 1). (Table S1: Fig S4b). FigS1: S4b). Appendix Appendix S1: S1:Fig Fig S3f)Appendix sesMPD (p>0.1, andED (p>0.8, S3e), MPD S1: Fig (p>0.08, S3d), Appendix S1:(p>0.4, sesPD Fig S3c), Appendix (p>0.08, for PD notsignificantly different pairs were allhabitat that revealed comparisons Pairwise sesMNTD:not p=0.841. significantlyp=0.844; (MNTD:sesMNTD: whichdid differ 1f), Fig andunloggedp=0.008) forestssesMNTD: (MNTD: p=0.011; p=0.036) (MNTD:Fig 1e; significantly higher MNTDandsesMNTD sesMNTD,not but sesPD, sesMPDfor and ED (TableNaturally 2). regenerating forests had p>0.09). p>0.09). notwas detected for anythe residualsIof (Moran’s functionaldiversity models test:for all Sp FDiv. and FEve versus FRic and FD between correlations weak only were less strongly correlated than the phylogene This by is protectedarticle reserved. Allrights copyright. DIVERSITYFUNCTIONAL Understorey BirdCommunity Overall Bird Community MPD, PD, type MNTDand for effectas improved fit afixed model habitat Including The functional metrics of both the overall bird and the understorey bird community Models with habitat type included as a habitat fixe with a Models typeas included

than restored (MNTD:p=0.0436; sesMNTD: tic metrics (Appendix S1: Fig S2), with no or forests, while naturally while regeneratingforests, forests d effect improved model fit for all metrics allmetrics model fit for improved d effect atial autocorrelation autocorrelation atial Accepted Article strategies with morespecialized strategies species and that restorationcaused We structures. a found habitat with different livingin ecosystems detectto communities we did not or that thus against caution extrapolating theseinferences areas occurring to species our sample in onlyburned. of these The interpretation metrics oursampled we applies to communities and been not have that selectivelyapplied to loggedforests management technique a is restoration where diversity birds functional of and phylogenetic on the restoration forest impacts of economic value of these degraded (Edwardsforests lands. enhanc via Fundingagricultural carbon selectively valuesthese conversion within and toprotect forests tologged forests, from DISCUSSION S1: (AppendixS5c-f). Fig (p>0.1)(p>0.9) and FSpe FDiv FEve(p>0.4), FD (p>0.07), comparisons Fig showednosignificant Pairwise differencessignificantly for 2d). (p=0.975, not differ did which 2d), (Fig unlogged (p=0.018) forests and (p=0.031) regenerating fo inrestored FRic 2). (Table FEve andFDiv This by is protectedarticle reserved. Allrights copyright. Understorey BirdCommunity restoration (FDiv: p=0.964; FSpe: p=0.432). unaffected by were Appendix which S1: (p<0.001; S5b), FSpe Fig S1: S5a) Fig and FEve:(FRic: Logging p=0.441; p=0.369). AppendixsignificantlyFDiv reduced (p=0.039; restoredsignificantly(F with did not differ It It has become tofind of ensuringincreasinglywaysconservation urgent of theretention Including habitat type habitat Including as imprfixed a effect

Ric: p=0.147; FEve: p=0.743) or unlogged forests orunlogged p=0.743) FEve: p=0.147; Ric: traits in our sampled overall bird community community overall bird sampled our traits in rests innaturally significantly lowerthan was rests ements underements REDD+ couldincrease the oved model fit for FD and FRic, but not for for not but and FRic, FD for fit model oved loss in evolutionary history, functional et al . 2010). Here we. investigated the Accepted Article the forest understorey, with a more open underst more open understorey, a the forest with and refuge for many birdspecies (Putz many and refuge for site nesting important an also are vines The aforaging substrate. with provide them to litter andvines these shrubs understorey insectiv while al. forest conversion to agriculture (Frishkoff (Frishkoff forest toconversion agriculture such as change habitat drastic involve more that those especially change, land-use MPD with environmental filtering) (Webb filtering) environmental of different thelikeliness conditions would alter survive clades to inthatenvironment (i.e. leaves behind a community with more closely speciesrelated as different environmental naturally These reductions regenerating forest. to differ not whichdid forest, tounlogged sesPDcompared in lower resulted restoration and forests, naturally regenerating and of to unloggedcommunity compared that forests This by is protectedarticle reserved. Allrights copyright. DIVERSITY PHYLOGENETIC schemes under future REDD+ agreements is questionable. strategies Onbalance, (FRic). therefore, th perhaps indicating specialist thereturnof forest species, but with reduced functional towards distance) nearesttaxon forest levels levels, returning unlogged MNTD(mean understoreybird community sampled our metrics, community withmore species closely related Formost functional and more clustering. a forests,regenerating leaving behind andnaturally ofunlogged compared tothose 2011). Many generalists andunderstorey frugivores on the depend producedbyfruits The loss of phylogenetic diversity could result from restoration altering the structure of structure the altering restoration from phylogenetic result diversity could of loss The Restoration significantly the andsesMPD bird MPD Restoration of overall PD, decreased

et al et . 2002). Other studies have shown have studies Other decreases 2002). inPDand . et al et al et e biodiversity-friendliness of carbone biodiversity-friendliness sequestration . 2014, Prescott . 2001a). Furthermore, birds by that forage Furthermore, 2001a). . suggest of evolutionary aloss which history orey with fewer shrubs and lianas (Ansell shrubsandlianas oreyfewer with was robust to restoration, with restoration restoration with torestoration, robust was ores rely on vine tangles which trap leaf- whichtrap vine tangles ores relyon et al . 2016).. et Accepted Article effects from FD restoration,decline in a with FUNCTIONAL DIVERSITYFUNCTIONAL of restoration. species,evolutionary results these positives distinct representat nonegativeleast or impacts species to laadapted thathavebeenforested habitat types. is This not surprising considerin theacross and traits genes unique of amount similar indicating a between habitats differ overall the both of ED forests. regenerating 2011, Prescott Prescott 2011, specialists (Ansell forest likelyreturning most species, related closely of coexistence naturally tothose in regenerating forest found returned MNTD sesMNTDand theunderstoreyof from birdcommunity elevated levels in community was largely byunaffected andsubsequent logging Restoration restoration. closely related tothosethat were lost. suggestsrestoration thatspecies thatreplaced MPD decreaseAand themaintenance in of inthe overallbird community after MNTD This by is protectedarticle reserved. Allrights copyright. undisturbedsallying prefer with forests strategies (Duffy 2002, (Duffy strategies Laliberté 2002, These forest. suggestregenerating species naturallya lossof to andfunctional did notdiffer un to compared FEve and FRic lower in resulted restoration and forest, filtering effects. Changes in the resources, resources, Changes inthe filtering effects. The functional diversity of the overall bird community some overall experienced negative the diversity functional of The

The The diversityphylogenetic sesPD, MPD, sesMPD) (PD, of the understorey bird et al et . 2016), in restored andunlogged inrestored compared 2016), naturally forests . to that of et al et . 2010), which could be could which 2010), attributable to . environmentalbe clear understorey (Thiollay 1992, Ansell nds. In the context of understorey birdsandall of nds. Inthecontext relative to unlogged and naturally regenerating regenerating naturally tounlogged and relative structure and microclimate g that these habitat types would tend to harbour types wouldtend habitat these gthat bird and understorey bird community did not birdcommunity understorey bird and unlogged forest. This implies that there is there that implies This a unlogged forest. those lost after restoration were similarly were restoration those lost after logged forest, which which forest, logged of restored forests forests restored of et al . 2011). 2011). . et al . Accepted Article activities (Edwardsactivities occupying thevacant niches to androbust utilisation logging that resource is restoration and traits functional withsimilar by species offset FD is logging of from that any loss implies habitatsFEve, of FDivThe maintenance theunderstoreybird community across andFSpein tend to be affected most of removal vines by the and understorey shrubs(Putz This by is protectedarticle reserved. Allrights copyright. (Ansell resource-use niches (Edwards same traits the occupy similar with several species where clustering, functional indicates This unoccupied (Mason levels.resource-use Thisindicates lower efficiency some community, niches as remain the in community, although FRic declined below both 2012). different species and differentin speciesaretheir and functional spaceless distances regular (Villéger species disturbances niches, robusttofuture (Schleuning makingthecommunity more 2009, Cadotte these forests (Belmaker invasion resistance and ultimately ecosystem functioning (Mason stability, web implications onfood have to potential the negative hasgroups ecosystems from mammals (Flynnmammals also occurs in anurans (Ernst (Ernst anurans in occurs also

Restoration had Restoration very on impacts few the functional diversity of the understorey bird Lower FEve implies that there is a less even distribution of abundance of functionally of functionally abundance isaless evendistributionthat of there FEve implies Lower et al et . 2011, Berry 2011, . et al. et et al et 2011),somewith available inthe resources habitat likely unused. et al et et alet . 2009), and dungbeetles (Edwards and 2009), . . 2013, 2014c). 2013, . et al et . 2005). This is This 2005). tobe expected . densevegetationsince species would et al et . 2012, Edwards 2012, . et al et al . 2008) could reduce the ability sensitiveinhabit the of speciesto reduce 2008)could . . 2006), birds 2006), . (Devictor . 2013), which could increase the functional redundancy of redundancy the functional increase 2013), could which . et al et unlogged and naturally regenerating forest naturally regenerating unlogged and . 2014b). Loss. FD of habitat change after et al et al . 2014c). The loss ofloss functional 2014c). The . . 2008, Edwards . et al . 2005, Flynn 2005, . et al et al et et al . 2001a).. . 2013),. . 2008). . et al et al . . Accepted Article analyses might therefore bebiased relative other to habitats see (but Banks-Leite our in forest apparent diversity inone species type, todetect some are metrics easier fact in been shown to be a goodto bebeen shown indicatorgroup a for Leite Leite to account and failurethese fordetection biases (Banks- conclusions in leadto can erroneous habitats,species, densitiesvegetation between variationdetect observer’s in and to the ability This by is protectedarticle reserved. Allrights copyright. SAMPLING LIMITATIONS provide strongprovide(Barlow support for the ofour validity conclusions very using results different two broadly similar and between years and by sampled year including the randomterminour analyses.as Our a within types habitat amongst by sampling rotating variation in detection potential temporal with simila forest indense habitat types were changeBrazilian todet inthe Atlantic Forest land-use impacts of tropical on the results gavesimilar data using unadjusted who that show intensities areintensities frequently lower(Putz is to a need assess there region restoration where regions impacts inother logging and planting—is an important research direction. studyingthat on plants—sometrees and directly impacts of which subjectedare or to cutting al and detection probabilities in an occupancy(Welsh an framework in probabilities modelling and detection habitat-specific occupancy transectpartition statisticallyor mist-net to count each point at (Edwards . 2014a, . Barlow et al Our study only observed the impacts of restoration on one taxa; however, taxa; have on birds of restoration one Our study onlyimpacts observed the Detection biases can result from numerous sources such as the cryptic nature of species, nature of the cryptic as sourcessuch numerous from biases canresult Detection . 2014). Because we focused on spatial replication, we did not have did not enoughrepeats we onspatial Because wefocused replication, 2014). . et al . 2009,Ansell . et al . 2007). Previous . have studies used2007). birdsimpacts on restoration also et al . 2011) and (Edwards invertebrates 2011) . et al . 2001b). biodiversity responses as a whole (Edwards a biodiversity as responses ection adjusted data). However, all surveyed ection data). adjusted sample methods (point counts and mist-nets) counts sample methods(point and r vegetativeand for structure, wecontrolled This studyonly was one also in conducted et al et al et . 2007). . . 2012), suggesting 2012), . et al . 2013). If 2013). . et al . 2014 . et Accepted Article obtained from closed population obtained from population closed capture-mark-recapture models (Otis be can biases detection for accounted have that abundance of estimates data, sampled net depending composition andsize onindividual groups change a fission-fusion upofindividual is that grouping, made whereapopulation and Arnason or 1996) Design Robust (Pollock methods1982). Schwarz1965,acrossSeber estimates studies using for (Jolly 1965, years Jolly-Seber models that enough recaptures are acquired within years. 2004). Another method by Clement by Clement method Another 2004). This by is protectedarticle reserved. Allrights copyright. al account detectionfor in probability point count data include distance sampling (Buckland measures diveand phylogenetic of functional species that whenderiving which abundance important is account probability, detection for ecosystem functions within the understorey. Onecosystemthe understorey.negativeside, however, within and functions the phylogenetic species, evolutionary and evolutionarily distinct forests retains evidently history, important restorat Thus, restoration. after levels pre-logging to returned understorey birdcommunity werenot adversel positivebenefit). Onthe phylogenetic side, the andfunctional of diversitymetrics most potentially reduced of threat to (whichconversion forest agriculture if true is enormousan and improved sequestration, carbon regeneration, of considered ofloggedover within context restoration the forests forest offering CONSERVATION AND MANAGEMENT IMPLICATIONS IMPLICATIONS MANAGEMENT AND CONSERVATION . 2001), multiple observer methods (Nichols (Nichols observermultiple methods 2001), . Nevertheless, we recommend that future studies use more robust methods of estimating of methods robust more use studies future that recommend we Nevertheless, There areboth positivesnegatives mustbe these conservation, There and of which results for et al . (2015) utilises the assumption that populations have thatpopulations the assumption (2015) utilises . movements around groups. Finally, Finally, groups. mist- for around movements rsity (Jarzyna and Jetz 2016). Methods Methods to Jetz 2016). rsity (Jarzyna and It alsopossible is to obtain theseabundance et al et y affected by restoration, whileMNTD byrestoration, y affected . 2000) and N-mixture models (Royle models N-mixture and 2000) . future timber benefits, harvests plus future ion management of logged logged of management ion et al et . 1978),. provided et Accepted Article This by is protectedarticle reserved. Allrights copyright. inforest This trade-off used. is cutting regime liberation- intensive less if a especially may outweighrestoration well costs, anybiodiversity eco added the areas, degraded heavily in side, flip the On diversity. suggestand ourresults negative onphylogenetic suffer and wouldlikely impacts functional in terms sequestration degraded carbon forests would much of not benefit (Kobayashi 2007) restoring on state degraded forestsFurthermore, should the the depend of since lessforest sequestration potential. carbon and biodiversity long-term detrimental to be instead future timber yields is unlikely toprovide logging activities. Restoring forests logged under REDD+ when core a is to aim increase to future subjected will notbe that forests onlogged-over conducted be REDD+ shouldonly cultivate. most viableeconomically tool for forest restoration, given seedlings that are expensive to restoration. Research is urgentlyinto needed thus carbon sequestration, which could reduce Carson However, in a breaks 2001). these decline therate cause could of tree recovery and (Ansell forests unlogged of tothose similar microhabitats tangle dense critical toretain as so cutting regime liberation intoincorporated the be breaks that proposed been vegetation, it has on dense determine whether otherrespond taxa in a same waytotheavian communities. ecosystdistinct species, and evolutionarily above likely understorey These level. reductions living species those are change of maindrivers the that probably indicating unloggedforests, functional diversity of the overall bird community was lower in restored thanforests in The useThe ofrestoration obtainingas enhancementa tool for carbon funding under liberation cutting inSince reduces logged forests abundance species the of dependent et al . 2011), . which couldbenefit biodiversity (Levey Schnitzer and 1988, long-term benefits for carbon stocking, and may and stocking, benefits for carbon long-term the precise impacts of liberation cutting the as management strategy has been demonstrated in demonstrated strategy management has been em functions. Future research should research should emalso Future functions. the overall ecosystem theoverall benefits service of underscore losses ofevolutionary history, system service benefits of of benefits service system Accepted Article This by is protectedarticle reserved. Allrights copyright. Anderson, D. R. 2008. Model based inference in H.Abood, S.A., S. J. Burivalova,P. Lee,Garcia-Ulloa, Z. J. L. Koh.2015. and Relative CITED LITERATURE DepartmentMinister’s for permission to researchconduct Sabah. in SabahCentre, Chief Minister’s Department Economicand Planning thePrime the Unit of Biodiversity Sabah Secretary, the the FACE foundation, Committee, State Management site for access andlogistical support. Yayasan We Sabah,Valley Danum thank also Reynolds Royal andthe Society’s Southeast Glen Lodge, Rainforest andBorneo support; collaborative Suzansupport; for Benedick We thank James Graham RebeccaPrescott Gilroy, Lim, Senior Felix and for analytical ACKNOWLEDGEMENTS careensure tothat these schemes. biodiversity-friendly are representsin the REDD+an important aspectappliedfuture with this be but must agreement, this paradox 2016). (Thom and EnhancingSeidl ca reconcile whichecosystems, temperate procedures to the need new highlights and boreal for Ansell, F. A., D. P. Edwards, and K. C. Hamer. 2011. Rehabilitation of logged K. andD. rain 2011. Edwards, Rehabilitation forests: C.Hamer. F. A., P. Ansell, Springer, New York,NewUSA. York, Indonesia. Conservation Letters 8:58–67. ofthecontributions logging, oilpalm, fiber, and industries mining forest to loss in REDD+.43:504–511. Biotropica avifaunal habitat composition, structure,

Asian Rainforest Research (SEARRP) Program Asian Rainforest and implications for biodiversity-friendlyand implications for thelife sciences: primer on a evidence. rbon via restoring degraded forests still Accepted Article Barton, K.2016.MuMIn: Multi-model inference. Rpackage 1.15.6. version https://CRAN.R- Barlow, J., G. D. Lennox, J. Ferreira, E. G. Lennox, C. Berenguer,Barlow, D. Lees, A. R. J., J. Ferreira, Mac Nally, J. R. Barlow, J., Baraloto,C., B. Hérault, C. E.T. Paine,H. Massot, L. Blanc, D. Bonal, Banks-Leite, C., R. Pardini, D. Boscolo, C. R. Cassano, T. Puettker, C. S. Barros, S. C. Puettker, T. Cassano, R. C. Boscolo, D. Pardini, R. C., Banks-Leite, K. G.P., T.Asner, Rudel, T. Aide,R. M. Defries, 2009.R.Emerson. and A contemporary This by is protectedarticle reserved. Allrights copyright. J and Knapp, E. D. Keller, M. Oliveira, J.C. P. N. Broadbent, E. G.P., Asner, project.org/package=MuMIn. tropicaltree community toselective logging. Journal ofAppliedEcology 49:861–870. Nicolini, andD. 2012. Sabatier.Contrasting taxonomic functionaland responsesof a Statesof America 104:18555-18560. plantation forests. Proceedings of the National Academy of Sciences of the United tropical conservation science. Journal Of Applied Ecology 51:849-859 et al Nationalof Academy Sciences103:12947–12950. 2006. Condition and fate of logged forests in the Brazilian Amazon. Proceedings of the assessment ofchange in humid tropical forests. Conservation Biology 23:1386–1395. 535 biodiversitytropical forests Nature deforestation. double disturbance in can from loss Vaz-de-Mello, R. C. S. A. Venturieri,Veiga, and A. T. Gardner. 2016. Anthropogenic Z. F. M. Silveira, J. R. Pardini, V. G. Siqueira, Souza, Moura, N. Nunes, J. M. S. S. Oli de C. R. Cardoso, M. T. Braga, F. R. Begotti, A. R. Aragao, L. Vieira, G. Thomson,S. F.Ferraz, D. J.Louzada, V.H. F. Oliveira,Parr L. . 2014.. Assessingutility theof statistical imperfectadjustments forin detection :144-159. et al . 2007. Quantifying thebiodiversity of value tropical primary, secondary, and y,R. R.D. Solar, I. C. J. F. Molino, E.A. . N. M. Silva. Silva. M. N. . J. Barlow, Barlow, J. veira, C. C. veira, Accepted Article This by is protectedarticle reserved. Allrights copyright. Bicknell,E., J.M. Struebig, J. D. Edwards, P. and G. Z. Davies. 2014. Improved timber N.Berry,O. J.,Phillips, L. R. C. Ong, andK. C. Hamer. 2008.of Impacts selectivelogging Belmaker, J., Sekercioglu,C. H. W.and Jetz. 2012. Globalof patterns specializationand Bekessy, A., S. and B. A. Wintle. 2008. Using carboninvestment togrow the biodiversity Bates, D., M. Mächler, B. Bolker,and S. Walker.Fitting 2015. linear mixed-effects models Bässler,C.,M. R. Ernst, C.Heibl,Cadotte, J.and Müller. 2014.logging Near-to-nature Blackburn, T. M., O. L. Petchey, P. Cassey, and K. J. Gaston. 2005. Functional diversity Bivand, R., and G. Piras. ofimplementations Comparingestimation 2015. spatial methods for Blaser, J., Sarre, D. A. Poore, andS. Johnson. 2011.ofStatus tropical forest management. Blake, J. G., B. and A.Loiselle. 2001. Bird assemblagesinsecond-growthand old-growth Applied Ecology 51:939-948. influences fungalcommunity assembly processesin a temperate Journalforest. of harvest techniques maintain biodiversity in tropical forests. Current Biology 24: Landscape Ecology 23:915–929. landscape: a of theon tree diversity across spatialrainforest scale. importance coexistence in bird assemblages. Journal of Biogeography 39:193–203. bank. Conservation Biology 22:510–513. using Journal lme4. of Software. 67:1–48. Statistical econometrics. Journalof StatisticalSoftware63:1–36. R1120. mammalian predatorsmammalianand inisland extinction birds. Ecology 86:2916–2923. ITTO Technical Series 38. International Tropical Timber Organization, Yokohama, SeriesOrganization,Yokohama, ITTO Technical Tropical 38.Timber International costaforests, rica: perspectives from netsmist point and 118:304–326. Aukcounts.

R1119- of Accepted Article Devictor,R. V.,Julliard, and Jiguet. F. 2008.Distribution specialist of and species generalist This by is protectedarticle reserved. Allrights copyright. Clement, M.J., J. M. O’Keefe, and B. Walters.2015.A method for estimating abundance of L., Chazdon, R. Chazdon, R. L. 2008. Beyondrestoring deforestation: and forests ecosystemservices on M.Cadotte, W., R. Dinnage, D.and 2012. Tilman. promotes Phylogenetic diversity Cadotte,M. W., J. D. Cavender-Bares, Tilman, andH. T. Oakley. 2009. Using phylogenetic, Cadotte, M. W., K. Carscadden, and N. Mirotchnick. 2011. Beyond species: functional Buckland, T., D.R. S. Anderson, K. P.Burnham, L.J. Laake,D. L. Borchers, andL. Díaz, S., Lavorel, de S. F. F.Bello, Quétier, K. Grigulis,M. T. and Robson. 2007. and Systematics 28:243–268. Japan. diversity, phylogeny, and worth.conservation 6:184.Crozier, 1997.R. H. Preservinginformationthe content of species: genetic mobile populationsusing telemetry and ofcounts unmarked animals. Ecosphere in human-modifiedtropical landscapes. 41:142–153.Biotropica degraded Science lands. 320:1458–1460. ecosystem stability.Ecology 93:S223–S233. 4:e5695.PLoSOne functional and trait diversity to understand Ecology 48:1079–1087. diversity and the maintenance of ecological processes and services. Journal of Applied distance toThomas. 2001. Introduction Universitysampling. Oxford Press, UK. Oxford, along spatial gradients of habitat disturbance and Oikosfragmentation. 117:507–514. et al et . 2009. Beyond reserves: a researchagenda conservingfor biodiversity patterns ofplant productivity. community

Annual Review of Ecology, Evolution,

Accepted Article Edwards, A., F. Edwards, D. P.K.C. Hamer, and G. Davies.R. 2013. Impactsof logging Edwards, D. P., J. A.Tobias,E. D. Sheil, Meijaard, W.and F. Laurance.2014b.Maintaining Edwards, D. P., Edwards, D. P., T. H. Larsen, T. D. S. Docherty, F. A. Ansell, W. W. Hsu, M. A.M. Hsu, W. W. Ansell, A. F. Docherty, S. D. T. H. Larsen, T. P., D. Edwards, Edwards, D. P., B. Fisher, E.and Boyd. 2010. Protecting degradedrainforests: enhancement Edwards, D. P., A. R. Backhouse, C.Wheeler, C. Khen,V. andK.C. 2012. Hamer. Impacts This by is protectedarticle reserved. Allrights copyright. Edwards, D. P., F.Ansell, A. A.H. Ahmad, R.Nilus, and K. C. Hamer.2009. J.Duffy, E. 2002. Biodiversity and ecosystem the function: connection.consumer Oikos Ibis 155:313–326. ofconversion to rainforestpalm on oil theof functional diversityin birds Sundaland. Society B:Biological Sciences278:82–90. importance of Southeastrepeatedly Asia’s logged forests. Proceedingsof the Royal C. Hamer, and D.S. 2011.Wilcove. Degraded worthlands protecting: thebiological Evolution 29:511–520. Tr forests. tropical logged in services and function ecosystem Applications 24:2029-2049. and trade-offs forbiodiversity indicators, conservation planning. Ecological rehabilitating logged rainforest for birds. Conservation Biology 23:1628–1633. of forest carbonstocks under ConservationREDD+. Letters3:313–316. Borneo.northern Journalof Insect Conservation. 16:591–599. of rainforests communities tropical oninvertebrate in of logging andrehabilitation Incorporating plant diversityfunctional e 99:201–219. ofProceedings the National104:20684–20689. Academyof Sciences et al . 2014a. Selective-logging. oilpalm: impacts, and multi-taxon ffects in ecosystem service assessments. ends in Ecology and and Ecology in ends The valueof Derhe, K. K. Derhe, and Accepted Article This by is protectedarticle reserved. Allrights copyright. Johansson, S. U. Elzanowski, A. Britton, T. Anderson, L. C. G., P. Ericson, Edwards, A., F. D.Edwards, P.T. H.Larsen, W. W. Hsu, S. Benedick, A. Chung, C. Vun Fisher, B., D.P. Edwards, T.H. Larsen, F.A. Ansell, W. W. Hsu,C. Fisher, B., D.P. Edwards, X. Giam,and D. S. Wilcove. 2011a.highThe costs of conserving R.,Ernst, K. E. Linsenmair, andM. O. Rödel.2006.Diversity erosionbeyond the species Flynn, F.Nogeire, D. B., T. N. Molinari, M.Gogol-Prokurat, B. T. Richers, B. B.N Lin, Gossner,M. T. M., Lachat,J. Brunet,Isacsson, G. C. H.Bouget, Brustel, R. Brandl, W. D.Frishkoff, L. O., S.L. Karp, K. M’Gonigle, C. Mendenhall,D. J. Zook, Kremen,C. E. A. Conservation 17:163–173. palm oil alter Animalagriculture hotspot? diversity ina functional biodiversity Khen, D. S.Wilcove, K. and C.Hamer.2014c. Does logging forest and conversion to integration of molecular sequence data and fossils. Biology Letters 2:543–547. Ohlson, T. J. Parsons, D. Zuccon, G.and Mayr.2006.Diversification ofNeoaves: 334. Southeast Asia’s lowland rainforests. Frontiers in Ecology and the Environment 9:329– amphibiancommunities. Biological Conservation 133:143–155. Dramaticlevel:loss of functionaldiversity after selective loggingtropical two in offs inoffs Asia. Southeast Letters Conservation 4:443–450. Wilcove. 2011b. Cost-effective conservation: ca Weisser, J.Müller. 2013.and near-to-nature Current managementforesteffects on agricultural systems.agricultural Science 345:1343–1346. Hadly,andG. C. Daily. Loss2014. ofaviandiversity phylogenetic inneotropical landuse intensification across multiple taxa.12:22–33. EcologyLetters Simpson, M. M.Mayfield, andF. DeClerck. 2009. Loss offunctional diversityunder lculating biodiversity and logging trade- S. Roberts,and D. S. M. Kallersjo, J. I. I. J. Kallersjo, M.

W. . . Accepted Article Hill, J.K.,Hill, K.andC. Hamer. Determinin 2004. Hidasi-Neto, J., R. Loyola, M.V. and Cianciaruso. 2015.Global and local evolutionaryand Hector, A., C. Philipson, Saner, P. J. Chamagne,D. M. Dzulkifli,J.Snaddon, O’Brien, P L. Hothorn, Bretz, T., F. P.and Westfall. 2008. inference Simultaneous ingeneralparametric Holdsworth, A.R., and C. Uhl. 1997. Firein amazonian selectively loggedforest and rain the Hackett, S. J., This by is protectedarticle reserved. Allrights copyright. Gourlet-Fleury, S.,F. Mortier,A. Fayolle, F. Baya,Ouedra D. N. 2000. J. Gotelli, Null Ecology analysisofmodel patterns. species 81:2606– co-occurence tropicalforest structure andTrans.R.Soc. Phil. functioning. B 366:3303–3315. test Biodiversity Experiment: of a long-term role theof diversity restoring in tree Ulok, M. Weilenmann, G. Reynolds, and H. C. J.2011.SabahThe Godfray. Diversity and Distributions 21:548–559. ecologicalmamm distinctiveness ofterrestrial Science 320:1763–1768. models. Biometrical Journal 50:346–363. potential for fire reduction. Ecological Applications 7:713–725. 41:744–754. of tropical fauna:theforest importance of 368:20120302. Central Philosophical Africa. Transactionsof the SocietyB:Royal Biological Sciences 2013. Tropical forestrecoverylogging: from a24year silvicultural experiment from 27:605-614. functionaltrait composition ofsaproxylic beetles in beech forests.Conservation Biology 2621. et al . 2008. A. studybirds phylogenomic reveals their of history. evolutionary g impacts of habitat modification on diversity spatial scale.Applied Journal Ecology of als: identifyingpriorities acrossscales. ogo, F. Benedet, andN. Picard. . . Accepted Article Jetz, W., G.H. Thomas, B.Joy,J. D. W. Redding, K.Hartmann,and A. O.M Jetz, W., G.H. Thomas, B.Joy,J. K. Hartmann, A.andO. Mooers.2012. Theglobal Jarzyna, M.A. and W. Jetz.2016.Detecting the of facets multiple Trendsbiodiversity. in Isaac, N. J. N.Isaac, T. B., S.B.Collen, Turvey, and C.Waterman, E. J. M. Baillie. 2007. This by is protectedarticle reserved. Allrights copyright. Isaac,J. N. B., J.Mallet, andG. M. Mace.2004.Taxonomic inflation: its in Laliberté, E., Laliberté, E.,P.Laliberté, Legendre,and B. Shipley. 2014. diversityfunctional fromFD: measuring S. Kobayashi, of 2007.Anoverview techniquesthe rehabilitation offor degraded tropical Kembel, S. W., P.D. Cowan, M. R. Helmus, W. K. Cornwell,Morlon, H. D. D. Ackerly G.Jolly, M. 1965. Explicitestimatescapture-recapture from bothwith data death and Laporte, N. T.,J.A. Stabach, R. Grosch,T.Lin, S. and J.Goetz. S. 2007. Expansion of multiple traits,multiple other and fortools functional ecology.R package 1.0-12. version 93:1596–1603. Science Current conservation. biodiversity and forests on the basedpriorities EDGE: conservation onthreat andphylogeny.One PLoS 2:e296. diversityspace in ofbirds time. and Nature 491:444–448. Ecology and Evolution 31:527-538. macroecology andconservation. Trends inEcology 19:464–469. Evolution and ecology. Bioinformatics 26:1463–1464. 26:1463–1464. Bioinformatics ecology. P. Blomberg, and C.O. Webb. 2010. Picante: R tools for integratingphylogenies and response diversity in plant comm Biology 24:919–930. Globaldistribution of and conservation evolutionary in Current birds. distinctness immigration-stochastic model. Biometrika 52:225-247. model. immigration-stochastic etal . 2010.. Land-use intensification re unities.Ecology Letters13:76–86. duces functional redundancy and fluenceon ooers. 2014. Mammals , S. , Accepted Article Martin, P. A., A. C. Newton, M. Pfeifer, M. Khoo, and J. M. Bullock. 2015. Impacts M. Bullock. 2015. J. Khoo, and M. Pfeifer, M. Newton, A. C. A., P. Martin, Mace, G.M., J.L. Gittleman, andA. Purvis. 2003. Preservingof thetree life. Science Li,N. R., J. B. Kraft, H. andYu, 2015. H. Li.Seed plant phylogeneticdiversity This by is protectedarticle reserved. Allrights copyright. Levey, D. J.1988.Tropical wet forest treefall Laurance, W. F. 2007. Forest destruction in tropical Asia. Current Science 93:1544–1550. Meijaard, E. and D. Sheil. 2007. A logged forest in Borneo is better than none at all. N Mazerolle, M. J. 2016. AICcmodavg: model selection and multimodel inference based on Mason, N.W. H., D. Mouillot, W. G. Lee, J. B. Wilson, Setälä. H.and 2005. Functional Mouillot, D., N.Graham, A. J. D., S. Mouillot, N. Villéger, D.W. and Mason, H. 2013. Bellwood. R. Meiri, S., G.and M. Mace. 2007. New taxonomyoriginspecies.the and of PLoS Biology (Q)AIC(c). R package version 2.0-4. http version package R (Q)AIC(c). Conservation Biology 29:1552–1562. Asia. ineasternglobalhotspot within biodiversitya conservationrichness in planning 300:1707–1709. plants. Ecology 69:1076–1089. industrial loggingin central Science africa.316:1451. functional diversity. Oikos 111:112–118. richness, functional evennessand functionaldivergence: the primary components of functionalapproach reveals respons community 5:e194. 446:974–974. analysis. Forest Ecology and Management Management and Ecology Forest analysis. tropical selective logging oncarbonstorag ://CRAN.R-project.org/ gapsunderstorydistributions and of and birds 356 es to disturbances. Trends in Ecology e and tree species richness: Ameta- :224-233. package=AICcmodavg. andspecies ature ature A of Accepted Article Osazuwa-Peters, O. L., C. A. Chapman, and A. E. Zanne. 2015. Selective logging: does Pavoine, S., J. Vallet, A. S. Dufour,B. Gachet, H. and Daniel.2009. On the challengeof Pavoine, S., M.B.Bonsall.and 2011. Measuring toexplainbiodiversity community Otis, D. L., K.P. Burnham, G. C. White, D.and R.Anderson. 1978. Statistical inference Padmanaba, M., and D. Sheil. 2014. Spread of the invasive alien species via Piper the invasive aduncum Spreadof alien 2014. D. Sheil. Padmanaba, and M., Oksanen, J. F., G. Blanchet,R.Kindt, P. Legendre,R. Minchin, P. R. B. O'Hara, G. Nichols,J. J. D.,Hines, J. E. R. Sauer,F. Fallon,W. J.E. Fallon, andP. Nakagawa, S., 2013. H.ASchielzeth.and general simple and method obtaining from R2 for This by is protectedarticle reserved. Allrights copyright. N.,Myers, Mittermeier,R. A. C. G. Mittermeier, A.Fonseca,B.daG. J.and2000 Kent. ecology package.R package version2.3-5. P.Simpson, Solymos, M. H.H. Stevens, andH. Wagner. 2016. Vegan: community counts. Auk 117:393–408. detectiondouble-observer andapproach probability for estimating abundance point from functional diversity. Oikos 118:391–402. varioustreating types of variables: improvingapplicationthe measurement for of unifiedassembly:86:792–812.Reviews approach. a Biological Physiology 3:cov012. tree onimprint structure remain composition and 45 Conservationafter years? from capture dataon closed animal Biodiversity hotspots for conservation priorities. Nature 403:853–858. Nature priorities. Biodiversity hotspots for conservation generalizedmodels. linear mixed-effects Methods Ecology4:133–142. in Evolution and and 28:167–177. Evolution logging roadslogging inBorneo. ConservationTropical Science populations. Wildlife Monographs 62:1-135. https://CRAN.R-project.org/package=vegan. 7 :35-44. J. Heglund. 2000. A L. the . Accepted Article Pistorius, T., and H.Freiberg. 2014. and FromTarg Pistorius, T., This by is protectedarticle reserved. Allrights copyright. J.Peres, Barlow, Laurance. F. C. 2006. A., and W. Detecting disturbance anthropogenic in Putz, F. E., and K. H. Redford. 2009. Dangers of carbon-based conservation. Glob Pinard, M.,Pinard, M.Barker, and J.Tay.2000. Soil disturbance post-logging and reco forest Prescott, G. W., J. J. Gilroy, T. Haugaasen, C. A. Medina Uribe, W. A. Foster W. Uribe, Medina A. C. Haugaasen, T. Gilroy, J. J. W., G. Prescott, K.Pollock, H. 1982. designcapture-recapture A robustto unequal probability ofcapture. Podani, J., and D. Schmera. 2006. On dendrogram-based measures of functional diversity. Petchey, O. A. L., Hector, J. K. Gaston.and 2004.measures Howof different do functiona Petchey, O. L., andK. J. Gaston. 2002.(FD), Functional diversityspecies richness and Petchey, O. L., andK. J. Gaston. 2006. Functionalback diversity: tobasics andlooking Putz,F. E., L.K. silvicultural effectssilvicultural onforest structure,production, fruit and of locomotion arboreal International Governance of Forest Landscape Restoration. Landscape of Forest Governance International bulldozer paths inSabah, Malaysia. ForestEcology Management and 130:213–225. diversity. JournalApplied Ecology of 53:150–158. Edwards. 2016. Managingoil palmNeotropical expansion toretain phylogenetic diversity perform? Ecologydiversity 85:847–857. perform? Journal ofWildlife Management 46:757-760. Oikos 115:179–185. community composition. EcologyLetters 5:402–411. Ecologyforward. 9:741–758. Letters Environmental Change 19:400–401. tropical forests. Trends in Ecology &Evolution

Sirot, and M. andSirot, A. Pinard.management forest 2001a. wildlife: Tropical and etImplementation: to Perspectives thefor 21 :227-229. :227-229.

Forests 5:482-497. , and D. P. P. D. and , al veryon l Accepted Article Schnitzer, S.Schnitzer, and A., W. Carson. P. 2001. Treefall gapsandmaintenance the of species Schleuning, M., Sasaki, N.,F. andSasaki, Putz. 2009. Criticalneed E. Royle, J.A. 2004.N-mixture modelssize for estimatingspatially from population replicated This by is protectedarticle reserved. Allrights copyright. Rolland, J., Redding, D.W., and A. Mooers.measures 2006.Ø. into Incorporating evolutionary R Team.Core 2016. R: A language andstatistical environment for computing. R Foundation Putz, F. E., F.Putz, P. E., Sist, T. Fredericksen, D. and Dykstra. 2008.Reduced-impact logging: F.Putz, G. M. E., Blate, H.K. R.Fimbel, Redford, andJ. Robinson. 2001b. Forest Tropical wildlife inwildlife logged tropical forests. Columbia University Press, New York, pp. 11–34. animals. in:Fimbel, Grajal, R.A., A., Robinson, G., The (Eds), cutting conserving edge: for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. Austria. URL Computing,https://www.R-project.org/. Vienna, Statistical for diversitytropical ina forest. Ecology 82:913–919. toward latitudes. tropical Biology22:1925–1931.Current degradation” inglobal climate change agreements. Conservation2:226–232.Letters 8:692–694. counts. Biometrics 60:108–115. conservation prioritization. ConservationBiology conservation prioritization. 20:1670–1678. attainedthe theand attainable. Conservation Letters5:296–303. challenges and opportunities. Forest Ecology and Management 256:1427–1433. 15:7-20. Management and Conservation of Biodiversity: An Overview. Conservation Biology et al et al etal . 2012. Sustaining conservation values in selectively logged tropical forests: . 2012.. inUsing phylogenies conservation: new perspectives. BiologyLetters . 2012.of. Specialization mutualistic interactionnetworks decreases for definitionsnew of “forest” and “forest Accepted Article Walsh,D., R. P. andD. M. Newbery. 1999. The of Danum,Sabah,ecoclimatology inthe S.,Villéger, J.R.Miranda, F. D. Hernández,and D. Mouillot. 2010. Contrasting changesin S., N.W. H.Villéger, NewMason,2008. multidimensional functional D.Mouillot. and This by is protectedarticle reserved. Allrights copyright. D., E.Sheil, 2005. Meijaard. and Life after logging: wildlife Howtoreconcile conservation Sekercioglu, C.H. 2006. Increasing awarenessof Trends ecologicalfunction. in avian G.Seber,1965. A.A F. thenote on Biometrikamultiple-recapture census. 52:249-259. Schwarz, C. J., and A. N. Arnason. 1996. A general methodology for the analysis of capture- Thom, D.,Thom, and R.Natural Seidl. 2016. disturbance impactsecosystem on services and J.M.Thiollay, 1992. Influence ofselective loggingon birdspecies diversityin a Guianan Swenson,N. 2014. G. Functional andphylogenetic ecologyin R,SpringerScience & Smythies, B. E. 1960. Thebirds ofBorneo. & Oliver UK. Boyd, Business Media, New York, New York, USA. USA. York, New York, New Media, Business context ofthe world’sregions, rainforest w Ecological Applications 20:1512–1522. vs.taxonomic diversity fish oftropical habitat after communities functional degradation. 2301. diversity indices for multifaceteda ecology. in framework functional Ecology 89:2290– Ecology and Evolution 21:464–471. inrecapture experiments open populations.52:860-873. Biometrics biodiversity in biodiversity in temperate borealand Biological forests. Reviews91: rainforest. Conservation Biology 6:47–63. and production forestry in Indonesian Borneo. ITTO Tropical Forest ITTOTropical Borneo. Indonesian forestry in and production Update 15. ith particularith reference to periods dry and

760–781. 15 :12- Accepted Article Data available from Figshare: http://dx.doi.org/10.15131/shef.data.5017328 supportingAdditional mayinformation be inthefoundonline ofthis version at article M., V.Winter,Devictor, O. and Schweiger.2013. diversity nature Phylogenetic and Wilcove, D.S., X.Giam, Edwards, D. P. B.Fisher, andP. Koh. L. 2013. nightmare Navjot’s Wheeler, C. E., P.A. Omeja, C. A. Chapman, M. Gilpin, C. Tumwesigye, a Welsh, A. H., D. B. Lindenmayer, and C. F. Donnelly. 2013. Fitting and interpreting This by is protectedarticle reserved. Allrights copyright. Webb, O.,C. D. D.Ackerly, M. A.McPeek, andJ. M. Donoghue. Phylogenies 2002. and restoration. Forest Ecology and Management 373:44-55. 2016. Carbon sequestration biodiveristyand following 18years ofactive tropical forest http://onlinelibrary.wiley.com/doi/10.1002/eap.xxxx/suppinfo http://onlinelibrary.wiley.com/doi/10.1002/eap.xxxx/suppinfo whereconservation: Trends are Ecology we? Evolutionandin 28:199–204. and 28:531–540. Evolution logging,revisited: biodiversity and inagriculture, in SoutheastAsia.Ecology Trends 505. community ecology. Annual Review of Ecology, Evolution, and Systematics 33:475– occupancy models. PLOSOne 8:e52015. 354:1869–1883. their impact.Philosophical Transactions ofthe Royal SocietyB: Biological Sciences Supporting Information Information Supporting Data AvailabilityData nd S.L. Lewis.

Accepted Article Null Null -399.93 0.02 4.46 0.00 FSpe This by is protectedarticle reserved. Allrights copyright. Null 25.27 0.36 8.55 0.00 FRic FD variable Response Null 1459.30 0.32 5.70 0.00 sesPD PD variable Response Criterion; =AIC Information Akaike inbold. are highlighted Best models effects. random asnested site models AIC type habitat their to null metricsincl based values. relation in on The diversity and functional distinctiveness evolutionary phylogenetic all diversity, werefor selected TABLE 1. Model selection linear of mixed-effects fortheoverall models community. bird Models Null Null -295.47 0.03 1.75 0.00 FDiv Null Null FEve FEve Null Null 244.83 0.06 2.93 0.00 MPD Habitat Habitat 761.94 0.03 1.11 0.03 sesMNTD

sesMPD sesMPD Null variation explained by fixed effects (Habitat); Conditional R Conditional (Habitat); effects fixed byexplained variation Null Null 257.88 0.02 1.44 0.00 ED Null Null 262.32 0.24 9.57 0.00 MNTD Null Null AIC = the AIC difference between the best model and the stated model; Marginal Marginal R statedmodel; and the model thebest between AICdifference the AIC = Phylogenetic DiversityPhylogenetic Evolutionary Distinctiveness & Habitat Habitat Habitat Habitat Habitat Habitat Habitat Habitat Habitat Habitat Habitat Model AIC Model AIC Null 1453.60 1453.60 0.25 0.00 0.16 -404.39 -404.39 0.07 0.00 0.07 -297.22 -297.22 0.05 0.00 0.05 226.30 6.46 0.00 0.42 0.42 0.00 6.46 226.30 126.18 126.18 855.88 14.25 0.00 0.24 0.24 0.00 14.25 855.88 460.24 460.24 114.79 114.79 0.27 0.00 0.22 219.84 219.84 0.33 0.00 0.15 0.07 0.07 0.00 241.90 841.63 841.63 0.25 0.00 0.25 760.83 0.00 0.00 0.00 2.59e 0.00 760.83 256.44 256.44 0.05 0.00 0.05 252.75 252.75 0.33 0.00 0.25 459.49 459.49 0.04 0.00 0.04 67 .001 0.27 0.14 0.00 16.72 Functional Diversity ∆ ∆ 11.39 11.39 0.75 AIC AIC AIC AIC 2 = variation explained by the model. model. the by explained variation =

Marginal R Marginal R 0.00 0.00 0.00 0.00 ude only point and point ude only

2 2

Conditional Conditional Conditional Conditional 2.75e 0.30 0.30 R R 2 2 -20 -15 2 =

Accepted Article Null 2 374.38 6.02 0.05 1.00 -185.19 -185.19 Habita 1.00 0.05 6.02 374.38 2 Null sesMNTD Habitat 4 -181.82 3.82 0.13 1.00 94.91 94.91 1.00 0.13 3.82 -181.82 4 Habitat FSpe -61.03 1.00 0.45 0.43 130.07 4 Habitat MNTD ED Habitat 4 -150.25 2.61 0.21 1.00 79.12 79.12 1.00 0.21 2.61 -150.25 4 Habitat -197.46 FDiv 1.00 0.39 0.86 398.91 2 Null sesMPD Null 2 249.73 5.64 0.06 1.00 -122.87 -122.87 1.00 0.06 5.64 249.73 2 Null FEve -72.87 1.00 0.24 2.34 153.73 4 Habitat MPD This by is protectedarticle reserved. Allrights copyright. 12.83 1.0 0.3 1.72 -21.66 2 Null FRic FD variable Response Null 2 703.90 1.47 0.32 1.00 sesPD -349.95 PD variable Response parameters; AIC = AkaikeInformation Criterion; relation to habitat type based on their AIC values. Best models are in metrics diversity distinctiveness and functional phylogenetic all evolutionary selected for diversity, were Models community. bird understorey the ANOVA models for of selection TABLE 2.Model likelihood. Cu weights; AIC = AICWt model; stated the and Null 2 133.95 6.55 0.04 1.00 -64.98 -64.98 1.00 0.04 6.55 133.95 2 Null Habitat 4 268.60 3.69 0.14 1.00 -130.30 -130.30 1.00 0.14 3.69 268.60 4 Habitat Habitat Habitat Habitat Habitat Habitat Habitat oe AIC Model K AICModel K Null Null Null Null Null Null Null Null Null Null Phylogenetic Diversity & Evolutionary Distinctiveness t 4 127.40 0.00 0.96 0.96 -59.70 -59.70 0.96 0.96 0.00 127.40 4 4 33.23 0.00 0.56 0.56 -12.62 -12.62 0.56 0.56 0.00 33.23 4 -180.18 0.95 0.95 0.00 368.37 4 2 264.92 0.00 0.86 0.86 -130.46 -130.46 0.86 0.86 0.00 264.92 2 2 -185.65 0.00 0.87 0.87 94.82 94.82 0.87 0.87 0.00 -185.65 2 -62.82 0.55 0.55 0.00 129.64 2 2 -152.86 0.00 0.79 0.79 78.43 78.43 0.79 0.79 0.00 -152.86 2 -195.03 0.61 0.61 0.00 398.06 4 4 244.10 0.00 0.94 0.94 -118.05 -118.05 15.69 0.94 0.7 0.94 0.7 0.00 244.10 0.00 4 -23.38 4 -73.70 0.76 0.76 0.00 151.39 2 4 702.43 0.00 0.68 0.68 -347.22 2 33.67 0.44 0.44 1.00 -14.84 -14.84 1.00 0.44 0.44 33.67 2 Functional Diversity Functional Diversity m.Wt = Cumulative Akaike weights; LL maximum Cumulative= = Akaikeweights; m.Wt ∆ ∆ AIC = the AIC difference between the best model best model the between the difference AIC = AIC AIC AIC AIC AICWt Cum.WtAICWt AICWt Cum.Wt AICWt highlighted in bold. K = number of

LL LL

Accepted Article similar similar symbols indicate no significant difference. symbols indicate that there issignificant a difference betweenthehabitat types(p<0.05); the median bold represents the line respectively, visual for Theclarity. bottom and of top therepresentboxplots the andthird quartiles, first Functional Functional evenness ( (FEve); bird ( FIG Habitat 2. oneffects diversitythe overall ofthefunctional bird ( indicate symbolssignificant difference. similar no symbols indicate that there issignificant a difference betweenthehabitat types(p<0.05); the median bold represents the line respectively, (sesMNTD). The bottom and top of the boxplots represent the first and third quartiles, This by is protectedarticle reserved. Allrights copyright. FIG Habitat 1. oneffects diversity phylogeneticthe the ( bird overall of of ( PD (sesPD); (sesMPD); ( (sesMPD); understorey bird (

d ) communities. ( ) communities. e )Meannearest taxon distance (MNTD); ( c ) Mean pairwise distance (MPD); ( e , f ) communities. ( ) communities. a ) Functional diversity (FD); ( d ) Functional richness, understorey richness,) Functional (FRic). FRic is logarithmic a ) Phylogenetic diversity (PD); ( (PD); diversity Phylogenetic ) , and the points represent outliers. Different , and the points represent outliers. Different d b ) Standard effect size ofMPD size effect ) Standard f ) Functional richness (FRic); ( (FRic); Functional richness ) ) Standard effect size of MNTD a – b a – d ) Standard effect size size ) Standard effect c ) and understorey understorey ) and ) and ) and c ) Accepted Article This by is protectedarticle reserved. Allrights copyright.

Accepted Article This by is protectedarticle reserved. Allrights copyright.