Ancon, RepublicofPanama Matthieu Leray Matthieu Holbrook [email protected] author,*corresponding E-mail: USA USA MA, Dietary partitioning promotesDietary partitioning th type :Article Original Article DR. MATTHIEU LERAY (Orcid ID : 0000-0002-7327-1878) This article is protected by copyright. All rights reserved. AllrightsThis articleis protectedby reserved. copyright. doi: 10.1111/mec.15090 lead ofRec thisversion between todifferences andtheVersion andproof been through typesetting, thecopyediting, pagination accepte This articlehas been 5 4 Santa Barbara, USA CA,93106, 3 Barbara,CA, 93106,USA Barbara, Santa 2 1 National MuseumofNatural History,Institution, Smithsonian W Computationaland SystemsBiology, MassachusettsInstitute of DepartmentEvolution andMarineBiology, Universit ofEcology, I Smithsonian TropicalResearch AcceptedInstitute,o University MarineCoastal Research Science Center, Article 2,3 , SchmittRussell J. 1 *, Alice L.*, Alice Alldredge d for publication and undergone fu and d forpublication 2,3 , Nancy Knowlton nstitute, SmithsonianInstituti e coexistence of planktivorousof coexistence e 2,3 ,

JoyY. Yang 5 , Andrew J. Brooks , AndrewJ. 4 , ChristopherP.Meyer ord. Please cite thisarticle as Please ord. ll peer review buthasnot review ll peer reading process, whichmay process, reading on, Panama City, Balboa, City, on, Panama f California SantaBarbara,f California ashington, DC20013, y Santa ofCalifornia species on coral reefs species coralreefs on Technology, Cambridge, Cambridge, Technology, 3

5 , Sally J. , Sally J. to whichfoodpartitioning contri Chromis This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. diet than species despitetheirseemingly differences significant prey revealed their diversezooplankton Chromis viridis intraspecific partitioni dietary ecosystems remains Here, approac a molecular we unresolved. use categorizations based uponbroad wi tohave appear numerousspecies Yet, ecological nichespace. atl partition ifthey morelikelyto co-occur that speciesare high diversificationTheories involvingto explain levels niche ABSTRACT day, explained more than 19% ofthevariationindietarycompos morethan day,explained copepod, omna rvosytogt Accepted common aspreviously thought. They resolution. nichelevelsthat oftaxonomic re alsosuggest webs intro trophic underscore theimportanceofcharacterizing reefa amongspecialization coral findings Our shifted during ofbothfishspecies. the ontogeny Finally, p suggestsfeedingbehaviour. intrinsicdifferencesin Article . Chromis Labidocera sp Dascyllus ) that commonly co-occur inbran ) thatcommonlyco-occur , whereas didnotsignificantly of shiftitsdietinthepresence ., found in low density and higher in the water column during t column water higher foundinlowdensity inthe ., and Chromis ng twospeciesofdamse between similar feeding strategies. strategies. similarfeeding butes to species coexistence i coexistence butes tospecies ssociated species have likely havelikely species ssociated of resource use or functional ofresource use tended toselect calanoid A large prey larger items. ching corals. Species-level ide Species-level corals. ching Dascyllus east one dimension of their east onedimensionoftheir rey composition significantlyrey n hyperdiverse tropical n hyperdiverse of tropical diversity propose propose diversity oftropical show that levels ofdietary show thatlevels been underestimated, andthey been underestimated, in diet composition between dietcomposition in dundancy may not be as may notbe dundancy lfish ( traits. In particular, the extent Intraits. theextent particular, pical ecosystems at higher ecosystems pical dely overlappingdely niches ition between h to investigate inter- and h toinvestigate inter- exhibited a more diverse a morediverse exhibited Dascyllus flavicaudus Dascyllus Chromis Dascyllus ntification of , which he and ,

reconstruction of food webs to sufficient taxonomic levelsreconstruction tosufficient has food webs taxonomic of andunresolved subje remains contributes tospeciescoexistence Talbot conspicuous (Collette& nocturnalacti 2001). Diurnalversus competiti and hasbeenlinkedto (Sampayo, Hoegh-Gu Franceschinis, dinoflagellate zooxanthellae: (McClanahan, & Raso,1999);Echinoidea: (Iglesias Malacostraca: Lassig,& 1980) (Robertson [Actinopterygii: frequently observed with spatialpartitioningconsistent 2015).Fine& scale Jones, ecosystem,th mostdiverse marine arguably the coral On reefs, (Bonin, ofinterspecific competition evidenceexistence for the (Kartzinel etal.,2015). c result ofoverly pairsisa broad observedmany among species Siepielski & Thisraises ofwhether McPeek, thequestion 2010). res of evidence littleornoapparent show species co-occurring foods(dietary p different niche niche partitioning)orconsume microhabitats pa (spatialniche space, onedimensionoftheirniche sufficientlyalong atleast thought is Interspecific tober competition Hutchinson, 1961). species setsofre thatusedifferent over longtimescalesthan l are asimilarrangeexploit theory, ofresources that species A functionsthey ecological asthe provide. assemblages aswell the persi and maintaining biodiversity topredicting is central This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Accepted Article Understanding themechanismsthatcontributeto maintenance rtitioning), have asynchronous a asynchronous rtitioning), have , 1972). By contrast, the extent the extent , 1972).By contrast, on forlimitedhabitat availabi vity patterns suggesting te patternssuggesting vity INTRODUCTION INTRODUCTION ess likely to be able to coexist abletocoexist tobe ess likely sources (Chesson, 2000a; (Chesson, sources stence of species-rich species-rich stence of e.g., they may occupy different e.g., theymay occupy a niche based model is model anichebased lity (Munday, Jones, & Caley, Jones, (Munday, lity mporal partitioning also are partitioningalso are mporal artitioning). However, many artitioning). Boström-Einarsson, Munday, Boström-Einarsson, educed when specieswhen differ educed ource segregation (Sale, 1978; segregation ource been challenging because of of because challenging been ctivity patterns (temporal patterns ctivity to whichfoodpartitioning ccording to classicniche to ccording haracterizations of resources ofresources haracterizations ct to debate. The ct todebate. the apparent nicheoverlap apparent the ; Gastropoda: (Kohn, 1980); ; Gastropoda: 1988); symbiotic 1988); ldberg, & Dove, 2007)] &ldberg, Dove, 2007)] ere is a wealth of is awealth ere of tropical tropical of are found in a majority of families of coral reef fishes (e.g., families reef fishes a majority ofcoral are of found in from t ingest planktonicanimals This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Acceptedand i fishes A diversearrayof and interspecific ofintra- samples, anddidnotcomparelevels preliminary2015). Despite providing insights, studiesin these bymore species consumed had been rev using sequencing invertivorous fishspecies high-throughput t among dietary comparisons Mills, &For example, Meyer, 2012). Leray,Morris, Akins,& 2013; Mills,&Meyer, Steinke, Agudelo, intofun thatgrouped fooditems instudies previously obscured ofgut identifications c DNA-based co-occur between dietary differences identified morepronounced Nugues, vanderVelde,Wartenbergh, et al.,2007;Nagelkerken, and orcombinationsofgutPratchett content Berumen, & 2008)], Article& 2015;Allgeier,Adam,Burkepile, 201 Ruttenberg,Burkepile, & for and corallivorous [i.e., observationsbehaviors offeeding Talbot, Russell,& Anderson, 1978).Studiesemploying alternati 2007;Pereira,Barros Longenecker, Hobson, 1974;K Hiatt &Harmelin-Vivien, Strasburg, 1979; 1960; & Gladfelter & Bellwood, 2003; 1986;Depczynski Bouchonnavaro, diets(An overlapping widely invertivores, had orplanktivores) associa reef concluded thatcoral foo of semi-digested studies using classification morphological &Glynn, 20 interactions (Enochs structure inwhichthese occur the high involvedintrophicinteractionsand richness species he water column afeedinghe water st as ted taxa within feeding guildswithin feeding ted taxa ontents suggested very comple suggested ontents , Zemoi, & Ferreira,Zemoi, & 2015;Ra , than one of the predator spec predator the thanone of nvertebrates associated withco nvertebrates associated Pomacentridae, Holocentridae, Holocentridae, Pomacentridae, herbivorous fish (Adam,fish Kelley, herbivorous the complex three-dimensional the complex differences in diet. indiet. differences cluded limitednumbersof (e.g., browsing herbivores, herbivores, browsing (e.g., d remains in gut contents ingutd remains contents derson et al., 1981; etderson ctional groups (Côté,Green, ctional groups rategy. Planktivorous species Planktivorous rategy. ealed that only ~20% of preyonly ~20% of that ealed 17). The vast majority of vast 17). The ve strategies suchas field ve strategies & Pratchett, 2009) have 2009) &Pratchett, stable isotope analyses (Ho (Ho analyses stableisotope ring species. More recently, More recently, ring species. ndall, 1967; Ross,1986; ndall, 1967; x feeding behaviors feeding x ies (Leray,&ies Meyer, Mills, 2013; Leray, Boehm,Leray, 2013; 7; Pratchett, 2005,2007; hree coral-dwelling coral-dwelling hree ulbicki etal.,2005; ral reefs capture and capture ral reefs Johnson, 1983; Johnson, considered to have broadly overlapping diets based ontheirhig based considered broadly tohave diets overlapping . theirdiet partition they in part,because planktonic-f two partitioning,these temporal andspatialniche InSchmitt & Brooks, thatgiv 2011). we thisstudy, hypothesize Schmitt& 2016;Holbrook,Brooks, Leichter, &(Hanson, Schnarr si feeding corals they commonlyare inbranching together found Holbrook, Schmitt,& Ladd,Bur& Brooks, 2011;Shantz, Schrack, Brooks, S (Holbrook, nutrients intheformofnitrogenous waste growthIn theypromote zooplankton. exchange, corals tocapture inthewate theyswim Schmitt & feeding, Holbrook, 1999).While branches of ( coralho their amongthebranches of co-occur resources asthey f a range of provide habitat branching Pocilloporid for corals thus p and feeding strategy some ofwhichshareaplanktivorous F Frédérich, quantified (butsee c on planktivorous organismspartitionavailablefood resources di 2016). Despitetheirabundance, foodwebs (Ha of oligotrophiccoral reef the benthiccomponents This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. li al., 2008),anditisacritical trophic mode,withupto50%oftotalfishbiomasscomprised P brittlestars,andpolychaetes. sponges, bivalves, tunicates, bythe holes andcrevices created nutrient acquisition& (Houlbrèque in heterotrophy on rely corals andBalistidae) many Apogonidae, AcceptedDascyllus flavicaudus Article Pocillopora ) and blue green damselfish ( bluegreendamselfish ) and which afford a refuge from predation (Holbrook & predation(Holbrookfrom Schmitt, 2002 a whichafford refuge nk in the transfer of organi the transferof nk in abri, Lepoint,& Par Vandewalle abri, three-dimensional structure o three-dimensional versity and functional role, and functional versity Ferrier-Pagès, 2009). Numero Ferrier-Pagès, Chromis

viridis Chromis viridis c matter from the waterfrom columnto the c matter and lanktivory can beadominant can lanktivory D. the degree to which which to the degree eeding fish are able to coexist, arefish able tocoexist, eeding f reefs also filter plankton,i.e., filter reefs alsof hly similar feeding strategies feedingstrategies similar hly oral reefs isnotwell currently oral st. The yellowtail dascyllusst. The en the lack of significant en thelack

mentier, 2009). 2009). mentier, chmitt, & Stewart, 2008; chmitt, & Stewart, otentially compete for food compete for otentially planktivores (DeMartini et (DeMartini planktivores flavicaudus multaneously during theday multaneously nson, Schnarr, & Leichter,& nson, Schnarr, additiontoautotrophyfor of their host by releasing by releasing oftheirhost us invertebrates livingin us invertebrates r column directly above the directly r column Stewart, 2008;Holbrook, kepile, 2015). Notably, Notably, kepile, 2015). ) reside among) reside the ishes and invertebrates, and ishes have been ; species are found residing in and hovering over coral colonies residingcoral species over found are inandhovering structure of species branching occupyingthe viridis Sample collection consumers. of wide range acrossa in diverse and ecosystems complex decipher to approach the potentialofmetabarcoding guts tissuetothespec fish andcoral from recovered sequences was library sequences ofreference Thiscurated (Meyer, 2017). inMoorea conducted study The was b been built COI barcodes has DNA waters. insurrounding conducted counts ofzooplankton into theirfeeding (i.e.,fe behavior insightsand gainfurther the consumer. Tocharacterize a se intothepoorlydiet of coral hoststogaininsights known We resolution. level of taxonomic specific differencesbetw dietary a high-throughput A sequencing Iallowed subunit gene ustocharacc. Oxidase Cytochrome (COI) than stronger coronoidprocess This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Accepted Article 2006). &Parmentier, Vandewalle, inthemorphology differences ofthe minor column andhaveonly suction veryon visiontodetect s and Bothand apparatus. rely (hereafter referred toas referred (hereafter In the lagoon of Moorea, French Polynesia, In ofMoorea, thelagoon pool of prey that thethreeplank poolofpreythat MATERIALS AND METHODS MATERIALS METHODS AND Dascyllus C. viridis een the two coral-dwelling fis twocoral-dwelling een the used the same sequencing appr usedthesamesequencing Dascyllus y >3,5 BIOCODE projectfor the pproach targeting hypervariathe . and , French Polynesia, where an where Polynesia, , French

Pocillopora flavicaudus Chromis Dascyllus flavicaudus ) are the two mostabundantfish ) arethe two has larger caniniform teethanda haslarger corals. Individuals corals. ofthesetwo eding selectivity), weselectivity), also eding ssile and more passive ssile andmore mall prey items inthewatermall prey items hes with an unprecedented with anunprecedented hes in large ormulti- mono- ies level. Our results highlight results Our ies level. tivorous species had access to to hadaccess tivorous species used to classify many classify used to mechanisms ofresourceuse mechanisms oach tissuesofthe onpolyp jaw (Frédérich, (Frédérich, jaw terize intra-andinter- terize 00 marine species species 00 marine ble mitochondrial ble mitochondrial extensive library of extensive and Chromis This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Dascyllus Brooks, Schmitt& 2008; Stewart, Schnarr(Hanson, theday corals during column abovetheirhost planktivores specific visual bothspeciesare aggregations, and 149.8088 eydouxi corals, hereafter small handnetsandtheanaestheticquinaldine(2-methylquinoli Pocillopora colonies that had been outplanted toasand flatintheMaharep colonies thathadbeenoutplanted and 0.4 m in height, and wereand 0.4minheight, l and appro coloniesusedinthestudy were experimental of thethree Accepted 1.4m(mean 0.04m) abovethebottom andtheotherpumpsampling to each of t adjacent King, inpairs deployed 2009).Pumpswere meters, 200 20, 2008,using planktonpumpsoutfittedwithpre-c submersible hand1530o 1400 the day during between and 0330hagain ontheboat. 7.5), DMSO,NaCl-saturated] DMSO sterile clipped off in andstored coralwere experimental immediately tothelab atthe boat -80°C uponreturn andfrozen individually1200 h.Fish und were bagged and 2008 between1130 determined by visualobservations Holbrook, 1996;Schmitt collecte were Fishes & Holbrook,1999). moving target fishfrom betwee on asandplain,whichprevented Article Zooplankton samples were collected during 60-min periodsatnig 60-min during Zooplanktoncollected sampleswere colonies found within the Maharepa lagoon onthenorthernside lagoon theMaharepa within found colonies o and W) approximately two monthspriortoinitiationofthestudy, approximately two W) colonies with one pump sampling the water column 0.3m (mean ± colonieswithonepump samplingwater column0.3m(mean the P m mesh cod ends,and2.5cminside m meshcod Chromis Pocillopora individuals) resident on three experimental individuals)resident onthreeexperimental A, B and C, were representative of naturally occurring occurring representative of A,B naturally andC,were ocated at a depth of 2m.Thec a depthof at ocated Holbrook,Schmitt& Brooks, 20 made over several days (Brook several madeover diameter intakepipeopenings that actively feed in the water feed inthewater thatactively orals were spaced 10 m apart 10mapart spaced were orals a lagoon (17.4751 a lagoon ximately 1.0 min diameterximately 1.0 oratory. Three branch tipsper Three branch oratory. ne) sulfate. Experimental Experimental ne) sulfate. he three outplanted outplanted three he buffer [0.25MEDTA(pH & Leichter,& 2016;Holbrook, alibrated, internal flow alibrated, internal n colonies (Schmitt & (Schmitt n colonies s, pers. com.) on 21August s, pers.com.) d after peak feeding as d afterpeakfeeding ver three days,August 18- ver three erwater, placed on onice erwater, 11). All fishes(including 11). All Pocillopora eydouxi Pocillopora ± SD=1.420.09m) of the island. Each theisland. of were collected usingwere collected ht between 0200h ht between SD =0.32± (Alldredge & o S, P.

intake. By contrast, the lower digestive tracts contained only digestiveintake. By thelower tractscontained contrast, copepods) (e.g., and hard-bodied eggs) (e.g., undigested soft- utilized tostandardizeutilized c raw a dissecting enumeration using f formaldehyde bufferedand returned in2% preserved tothelab & were King, 2009). (Alldredge1530 hwhen theplankton sampled whenremain stablebetween thefish noon w inMoorea abundances the stomachcontentsof This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Acceptedstored at-20 was the each fish digestivetract of entire (gwet The weight). Sample processing 2005-2016). Polynésie (Protocoled'Accueil Francaise (DTRT) the Government issuedby under permits was Researchcompleted Rech Polynesia àla (Délégation of assumptions meet to where necessary transformed the datalog significanwere for statistical tested inabundance differences ¾moonwaslocated whilea mi all bright samples were collected Article substant plankton countsindicated removed from wereThese four samples cod end. captured inthe tofive In the36samples,one 4of Dascyllus thebottomande corals above tothemaximum above thebottom.Sampling corresponded heights FishesSeptember 2008,measured were (totallength thawed on2 and ° C in numbered Eppendorf tubes containing 95% ethanol. Visual ex ethanol. Visual 95% tubescontaining C innumberedEppendorf Chromis had been observed to feed (Brooks, pers. com.). Daytime plank Daytime (Brooks, com.). pers. tofeed hadbeenobserved Dascyllus ount data to numbers observed per ount datatonumbers microscope and plankton wheel. F wheel. and plankton microscope erche) anderche) theHaut-commissariat stimated maximum distance abov distance stimated maximum (n = 34) and (n=34) ial feeding in thecodendby ial feeding Dascyllus or Chromis Chromis (n = 27) revealed a range of of a range (n=27)revealed hadenteredtheintake pipeand were ce using Student undigested hard parts,undigested most hard n removed and individuallyand n removed prey from the morning prey from the the captured fish.Nightcaptured the cubic meter of water filtered. filtered. ofwater cubic meter or sorting, identification and sorting,or normality. normality. dsky. Height andday/night the analyses because low because analyses the de la République en delaRépublique low meter datalow meter were e the bottom where e thebottom ere sampled and 1400- ere sampled Plankton samples were Planktonsampleswere height oftheoutplanted in mm)and weighed of French ’ s t-testswith amination of ’s food ton This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. from the tipwasper branch excised & Tissuekitfollowing instructions. manufacturer’s using transferredt extraction toindividual2mL DNA tubes for removed only. fromthestomach focused our we taxa, ofsoft-bodied avoid themisrepresentation ofthed asnapshot day.likely Toobtain theprevious ingested Amplification (PCR).A negative minimize potentialinhibitionclean-up during to kit(MO-BIO) P t purifiedusing DNAwassubsequently Genomic completely lysed. overnigh were withproteinaseK incubated andsamples necessary, theamountinitial volumeoflysis on was adjustedbased buffer interferewi DMSO bufferthatcould excess remove waterfree to High throughput sequencing contaminants. for potential check performed to mlCOIintF and jgHCO2198 (Geller, Meyer, Parker, & Hawk, 2013; L mlCOIintF &(Geller, 2013; Parker, Meyer, Hawk, and jgHCO2198 AcceptedI subunit c. Oxidase wi region (COI) (~313bp) oftheCytochrome al., 2013). (Leray, Haene adaptors ofindexed incorporateda ligation using incorporated during PCRamplification PCR using primers indexed (TableS1) two indices,was implemented for samplemultiplexing w istagged each sample which by approach, tagging hierarchical Article Using sterile tools, the contents of each fish stomach andcora stomach fish ofeach Using thecontents tools, sterile To reduce the per sample cost of sequencing on the Roche FLX pl Roche onthe cost ofsequencing theper sample To reduce First, cleaned DNA extracts (n = 64) were used to amplifya hyp to =64)were (n used extracts First, DNA cleaned control extraction andnegative controlextraction

Pocillopora skeleton and thoroughly rinsed withDNA- rinsed skeletonandthoroughly A small tissue subsample (1cm x 1cm) A smalltissuesubsample(1cmx iet for comparative analysis and and analysis iet forcomparative of starting material if material ofstarting he QIAGEN DNeasy Blood DNeasy he QIAGEN molecular analysis on prey molecular l, & Bourlat, 2016; Leray 2016; et Bourlat, l, & DNA purification were were purification DNA olymerase Chain Chain olymerase ith a unique combination of ith auniquecombinationof th downstream analysis. The The th downstream analysis. th versatile PCRprimers th versatile . The first index was index first . The t or untiltissueswere t . The second tag was. Thesecond he PowerClean DNA DNA he PowerClean l tissues were were l tissues eray et al.,2013) eray ervariable fragment ervariable atform, a a atform, This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. in 12 MinElutecolumn purifiedusingremoval dimers, QIAGEN ofprimer pooled, gel exc persample, wereconducted Three PCRreplicates found canbe The PCRcocktailandtouchdowntemperatureprofile r PCR ineach wereincluded S2) annealin al., 2013;Vestheim 2008),consumer-specific & Jarman, therecove DNAisknowntoprevent consumer co-amplification of Index2-mlCOIF/jgHCO-inIndex1-mlCOIF/jgHCO-index1; Sample2: 1: each in identicaland reverse for indicesprimer ontheforward &Bohmann, Gil assignment totagreads (Schnell, of jumping due 2017).To & (LerayKnowlton, detection significant biasinOTU were sequences at least3bp.Theseindex by sequence differing was included sequence & (LerayKnowlt samples for benthic asshownrecently abundance Despiteamplification somelevel bias,thisprimer of set provi invertebra ofmarine thediversity across known toperform well concentration was aft normalized concentration 1.5%agarose contaminants(nobandabsence on of confirmed the (Invitrogen, U Carlsbad,California, Accepted ligateBasel The Switzerland). FLXLibrary the S1) using TitaniumRapid Identifiers (Table MID Ipswitch,BioLabs, USA)followedby Massachusetts, the ligation perpoolfor ofPCRproduct wasused atotalof500ng Second, QuickDNASample PrepReagentSet2ch tailed usingthe NEBNext with each poolcontaining amplic Article μ l of elution buffer. A PCR reacti A PCR buffer. l ofelution at the 5’ end of each PCR primer( each PCR the5’endof at d PCR products were purified usin productswere d PCR eaction at ten times theconcent times at ten eaction er quantification using the dsD usinger quantificationthe ons generated with eachofthe generated ons SA) and equimolar amountso SA) and on performed withnegative con on performed Tables S1 and S2), with each index S1andS2),with eachindex Tables des useful estimatesofrelative des useful dividual sample (e.g., Sample (e.g., dividual sample shown toinduce no shown tes (Leray et al.,2013). tes (Leray NA Qubit Fluorometer Qubit NA ration of versatile primers. ration ofversatile eight indexed primerpairs.eight indexed g Agencourt AMPure beads gAgencourt avoid the erroneous avoid the of unique 454Multiplex 454Multiplex ofunique g blocking primers (Table g blocking primers ised toensurecomplete f each sample were pooled, weref each pooled, sample bert, 2015), we used bert, 2015), gel). PCR product gel).PCR Adaptors Kit(Roche, Adaptors ry of some prey (Leray et prey (Leray ry ofsome in Leray (2013). in et al. on, 2015). A 6bp index A6bpindex on, 2015). s andtheproducteluted emistry(New England end-repair and dA- end-repair trol extractions extractions trol dex2). Because the dex2). This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Analysis ofthe sequencedata eluted in40 (Beckman CoulterGenomics), 2012; Meyer 2017), an all-taxa biodi an all-taxa 2012; Meyer 2017), builtbyBo COI (Leray,BIOCODE barcodes database of the Moorea usedtoalign & 2011)was Delsuc, (Ranwez, un Harispe, Douzery, Following this initialquality t filtering, inQII function using thetrie dereplicated and thedatasetwas (Schlossetal.,2009),the sequences primer indices inMothur files werefastahomopolymer then regions The longer than8bp. mismatches inprimer sequences onem than indices, (2)hadmore (1) a if they didnotincludeforward thendiscarded Reads were inMothur(Sc & 2011)implemented Lanzen, Turnbaugh, Davenport, generated anddenoise from.sfffiles flow fileswere inMothur Note thatadditionalsamplesunrelated tothisstudyalso were S2.S provided inTablesS1and 454r PCR andsequencingin two Accepteddifferingby orfewe three implemented inMothur to merge reads prec an initial used we clustering, downstream and speed-upthe further reduc codons orframeshiftsforsubsequent To analysis. invertebrate s andretained only mitochondrial translationcode insertion/de ornucleotide tonucleotidesubstitution frame due detects interru and aminoacidlevel performs atthe alignments Article We used a data analysis procedure previously described in Leray in described previously procedure usedadataanalysis We amples of both species were rand amples ofbothspecieswere , (4) had any ambiguous base calls (e.g., “N”),calls (e.g., base ambiguous had any , (4) ismatch in primer index sequenc ismatch inprimerindex uns. Details of the experimental uns. Details ofthe versity theis inventory of he option “enrichAlignment” implemented inMACSE implemented he option“enrichAlignment” μ l of TE buffer, and pooled prior toemulsion and pooledprior l ofTEbuffer, ME (Caporaso etal.,2010). (Caporaso ME included in these runs. included intheseruns. letion. Weselectedthe of both 454 runs wereof both454runs pooled land ecosystem. MACSE land ecosystem. equences without any without stop equences d using Pyronoise (Quince, Pyronoise d using ptions intheopen reading nd reverse and primers nd e the variability in the dataset e thevariabilityin thedataset lustering approach approach lustering demultiplexed basedon demultiplexed r bases. This algorithm first This r bases. omly assigned to each run. each assignedomly to es, (3) hadmorethantwo (3) es, design of each run are each of design ique reads tothereferenceique ehm, Mills& Meyer, ehm, hloss etal.,2009). et al. (2013). First, etal.(2013). or (5) had any any (5) had or reference barcode between 97% and 85% were assigned tothe phyl assigned 97%and85% were reference barcode between assigned common to the lowest 9 at > multiplespecies Inan OTUmatched 2009). thecasewhere Hashig (Machida, wasatleast97% databases in oneofthethree a species-level consideredwas thatthere arefere theirlevelto ofsimilarity on based three categories settings & (Ratnasingham 20 engine[search withdefault Hebert, This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. = size word GENBANK (BLASTn: =11,eva (BLASTn: wordsize BIOCODE reference database Moorea thethre within abundant sequences then mergesand rar theirabundance of ranks inorder sequences falses of positives(splitting by providin groupingamongreflect invertebrates species marine todel shown previouslybecause itwas defined-l3and-u4 We differ similarityaccount for to and lower(-l) withinuser-defined 5%), CROPgenerates clusters on thenatural dissimilarity. distributionofsequence Rathert inputfo as an wasused filtered dataset resulting The quality that delineatesOperational Taxon Bayesianmodel Chen, 2011),a (singletons). by sequence asingle Knight, 2011) implemented inMothurbe Knight, 2011) implemented Haas (Edgar, forUCHIME using chimeras thenscreened Reads were Accepted ass taxonomic usedfor OTUwas per One representative sequence repre each of searches similarity ran We strategy. an iterative et al.,2013). Article ingle taxa) and false negatives false andingle taxa) ences in rates of sequence evol ofsequence inrates ences taxonomic rank. OTUs withaseque taxonomic rank. shold specified (Huse, Welch, shold specified 11, e value = 1e-20) and the Barco = 1e-20)andthe 11,evalue “match” when the similarity to a reference sequence sequence reference when thesimilarity toa “match” fore discarding all remai fore discarding (lumping of multiple taxa) (Leray(lumping multipletaxa) of nce: > 97%, 97-85%, < 85%. We <85%.We 97-85%, >97%, nce: han using a hard cut-off (e.g., cut-off usinga hard han ution among taxonomic groups.taxonomic among ution sentative sequence againstthe sentative sequence ineate OTUs thatcloselyineate OTUs uchi, Nishida, & Nishida, uchi, Nishida, e sequences with more more with e sequences g the lowest frequency of the lowest g upper (-u) boundlevels of (-u) upper 07)] to classify OTUs in to classify 07)] Morrison, & Sogin, Morrison, 2010). 7% similarity, itwas omic Units (OTUs) based omic Units(OTUs) ning preclusters represented represented preclusters ning um of the closestmatchas of the um r CROP (Hao, Jiang,& r nce similarity to a similarity nce , Clemente, Quince, &, Clemente,Quince, lue = 1e-20), lue de ofLife Data ignments following This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Diversity analysis analysis. referredtoa contingency sampleby A observation table (later and fishsummarizing OTU bu ofreads per gut per the number was themet of any using assigned confidently 2015).OTUs&(Leray, Mills, Meyer cutoff posterior probability taxonomic and accepted sequence) OTUrepresentative (i.e., each homologues GENBANKfrom ( retrieved SAP to build10,000 allowed unrootedphyloge Nielsen, 2008).We Statistical Assignment Package (S approac tophylaCOIa phylogenetic wereusing assigned barcode etal.( recommended Ransome by dissimilarity based on the Jaccard and the Bray Curtis metrics and theBrayCurtis dissimilarity Jaccard onthe based Accepted (259). sample containedinthedataset tothesmallest numberall sampleswas ofreads scaleddown of an alter usedtocreate subsampling was (rarefaction) procedure the positiverelationship between of andnumbe sequences number to bedetected. sampling ef thatplateausindicates2006). Acurve asufficient u ofaccumulation at increasing levels and samplesrespectively byrand computed Thecurveswererarefaction were curves built. Article To illustrate the extent of the sequencing effort, individual- individual- effort, ofthesequencing To illustrate theextent The rarefied OTU table was used to compute distance matrices of was usedtocomputedistance matrices OTU table The rarefied alpha and beta of estimates can reads affectUnequal numbersof 2017). Finally, OTUs with<85% Finally, 2017). AP) (Munch, Boomsma, HuelsenbeBoomsma, (Munch, AP) > hods above were labelled “unidentified”. were labelled hods above 70% sequence similarity) for each query sequence similarity) queryfor sequence each 70% sequence fort remain rare asonly OTUs within the R package Vegan within theRpackage native OTU table in which the the table inwhich OTUnative sing EstimateS(Colwell, number of sequences that a that sequences number of that could notbe thatcould omly resamplingomly sequences assignments atan80% h implemented inthe h implemented r of OTUs. Hence, a OTUs. r of ilt for downstream ilt fordownstream netic trees with 50 netic trees and sample-based and sample-based similarity to a reference similaritya reference to s OTU table) s OTU ck, Willerslev, & ck, Willerslev, diversity because of because of diversity community

This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. “ R Studiov.0.98.1056 programmingenvironment for thecomputati toeach fitted plot. were models with95%confidenceintervals Bray-Curtis dissimilarities i data. tothelossofsequence of ecological patterns respective 9 and12samples, of ledtotheremoval reads (which 2001). Allstatisticalanalyses w between individual (position ofgroups inmultivariate of space) samples were test plots.DifferencesMetric MultidimensionalScaling inme (NMDS) abundant OTUs. Bray-Curtis havelower will samples sothat OTUs thanJaccard, Bray-Curt incommon. OTU not haveany indicates thatsamplesdo of ofOTU identical abundance compositionexactly interms and avalueof0 samples; ofreads between inabundance differences incommon.Bray-Cunot haveanyOTU do 1 indicatesthatsamples samples value of0indicatesthat metaMDS).Jacca =(binary true,infunction Jaccard calculating toapres inputtablewas(Oksanenet converted al.,2009).The graphics. (Wickham, 2009)for AcceptedVega Article n” We further examined ontogenetic changes in fish diet bydiet infish plottin changes ontogenetic furtherWe examined in two-dimensio compositionPatterns ofspecies were visualized

package (Oksanen et al., 2009) for community analysis and analysis community etal.,2009)for (Oksanen package Dascyllus n relation to differences in size insize n relationtodifferences collected on different corals using PERMANOVA (Anderson, (Anderson, using PERMANOVA corals collectedondifferent ere repeated with OTUtables r with repeated ere have exactly the same OTUcom thesame haveexactly (total lengthLinear inmm). ed between species and species between ed ence/absence matrix priorto matrix ence/absence arefied down to900and1200 arefied down We usedthestatistical We ly) to test for therobustness ly)to testfor rd ranges from 0 to 1. A 0to1. from rangesrd indicates thatsamplesare indicates values if they share share values ifthey reads whereas a value of 1 a valueof reads whereas position whereas a value of a valueof position whereas on of all statistics, the statistics, on ofall an diet composition composition an diet is gives lessweightis torare rtis takes intoaccount the “ggplot2” package g pairwise Jaccard and Jaccard gpairwise nal space usingNon nal space 1.08). Both the mean length and weight of and weight 1.08). Both length themean mm TL ± 9)and g ±SD= from ( weight (mean 51 0.49to4.34 wet were occu and 90% 1) (Fig. damselfish of one ofthetwospecies detected 6120 potentially chimeric reads that were also removed thatwere chimeric reads detected 6120potentially they interruptionswerehad inthe open readi because discarded section Methods inthe asdescribed requirements (71%) metour Diversity andabundance ofdietary items infish stomachs analysis. were inthesequencing used from with individualsbeing(F significantly larger (mean±SD= 4.04 ±3.45). 0.10 to14.66g wet weight Dascyllus on tenrandomlychosen Surveys damselfishes of that100%ofadult lagoon Moorearevealed of This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Moorea. colonies of occurring found onnaturally Atotalof42 ofthenum characteristic are abundances coral colonies.These groups ofboths hosted large corals abundant species. Several (F correlated on either Acceptedon Article Pocillopora Pocillopora There were a total of 354,753 reads after denoising thedataset readsafter a totalof354,753 Therewere Pocillopora Dascyllus . The abundances of . Theabundances 1,8 A and significantly heavier (F Aand significantly heavier = 0.02,P Fig.= 1). 0.8915; B and 3 from B and ranged in size from 13 to 84 mm TL (mean ± SD = 50 ±16)andf from13to84mmTL ±SD= insize ranged 50 (mean Dascyllus A or C. Of these individuals, 34 or C.Oftheseindividuals, A Chromis and 32 and Pocillopora Chromis and P. eydouxi RESULTS Dascyllus Dascyllus C) and 27 C)and Dascyllus 2,39 2,39 Pocillopora eydouxi Pocillopora were collected from the three experimental experimental fromthethree werecollected = 11.33, P=0.0001)on = 8.67,P=0.0008)on (Holbrook et al., 2015) in thelagoonsin (Holbrook etal.,2015) of tended tobethemoreconsistently differed among the three coral colonies among threecoral differed the onthesetencolonieswere not Chromis Dascyllus Chromis P. eydouxi pecies (Fig. 1). 1). pecies (Fig. bers of these twospecies bers ofthese ng frame. Finally, Uchime frame. ng (all from . The final dataset contained dataset final . The pied by both pied ranged in size from31to65 size ranged in (13from . An additional 53,932reads . Anadditional were occupied by at least wereoccupied mean ± SD =2.48 ± SD mean ± corals in the Maharepa inthe corals but only 251,933 251,933 butonly Pocillopora Pocillopora Pocillopora Pocillopora Chromis B than B than C) rom rom and A,18 This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. mean±SD=8003 (Overall: 2748±690; sam per of reads (54%) with anumber 191,881 high reads quality Accepted se ofthe for 11.8%and44.9% pha larval composed ofa planktonic totaxa (29%) belonged OTUs whereas 201 planktonic lifecycle, 11.1%matchedrespectively). and (52%, 37.1%,61.3% a Mollusca Annelida, Arthropoda, InBOLDcontrast,(Fig. OT GENBANK 2B). or BIOCODE, barcodes in (87.5%)and (77.8%) Echinodermata Bryozoa to Chordata (90.4%), A ma (16%). followed byOTUs and 21%respectively) unidentified Chordata and (31 OTUs). Arthropoda (73 OTUs),ChordataAnnelida by (6 followed diverse (302OTUs), unidentified remained Fig.while 110(15.8%) 2B), taxonomic a higher assigned to Article (<97%simila 426 OTUs thatdidnotmatchany barcode reference additional OTUsmatchedbarcodes i similar 97% (> BIOCODE in sequence a reference 236 OTUsmatched OTU leavinga totalof699eukaryotic removed fromthedataset, species (i.e., contaminants (e.g., OT were seven asprokaryotes, identified reads) seven OTUs (189 mean ±SD= 1181±472; The Bayesian clustering CROPdelineated a tool totalof716OTU A total of 36 OTUs (5%) were assigned to taxonomic groupswere assigned totaxonomic known A totalof36OTUs(5%) Arthropoda which 14 animalphyla,among OTUsa totalof spanned Dascyllus flavicaudus Homo sapiens Pocillopora quences in the guts inthe of quences level (>85%similarity inGenBa ) and (14,643reads)as belonging threeOTUs tothehost nd Nemertea were lessrepresent nd Nemertea , Chromis viridis Chromis viridis se and a benthic adult phase a benthic and se n GENBANK or BOLD (> 97% simi orBOLD (>97% n GENBANK also comprised the highest n thehighest also comprised : mean±SD = 7330±660) Dascyllus (labelled “unidentified” in F (labelled “unidentified” : mean±SD= 3589±1380; and Dascyllus Pocilloporaeydouxi (mean ±SD=9 ±8.1)and (mean . Planktonic taxa accounted . Planktonictaxa s (175,914 reads). A totalof reads). (175,914 s nk or SAP assignment, see nk orSAP with a bipartite life cycle with abipartite lifecycle ple ranging 279to from ple Us (1135 reads) as reads) (1135 Us ed in barcode databases databases barcode ed in rity), 316 couldbe 316 rity), umber of sequences (45% sequences umber of 3 OTUs) and Mollusca 3 jority of OTUsjority belonging of matched representative representative matched ity) (Fig. 2A) and 37 (Fig. 2A) ity) Us inthephyla s. Among them, them, s. Among larity). Out of the larity).Out was most the to have a strictly a strictly tohave ). These were ). Thesewere ig. 2A). ig. 2A). Chromis : number of OTUs per sample ranged from 17 to 96 (Overall: mean ± 17to96(Overall: from ranged sample number ofOTUs per at thetimeofsampling 3 (Fig. characterizerequired th tobetter additional fishandcoral Thus examining thedietof analysed. toclimbwit continued OTUnumbersindividuals ofeach species, because By contrast, gut wereOTUs inany particular detected. 3 (Fig. effort for sufficient allsamplesindicating sequencing This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Chromis OTUs with at least ten sequences) (Fig. S3). (Fig. S3). OTUs withatleasttensequences) of OTUs withtw 97%similarity > reference (32.6% barcodes with Leray, themostabundantOTUswere 2015), &2015; Mills, Meyer etal. analysis (Al-Rshaidat commonly inmetabarcoding observed 92%,respectiv and (73% >10sequences with byOTUs represented an Chordata (23%proportion ofrare ofdoubletons)whereas OTUs Molluscacomp The phylum 10sequences. OTUs containedlessthan rare byIn ofOTUs(Fig.represented were S1). two total,12.7% Accepted Article sequences bya large of number Few OTUswere represented respectively). ofprotists,fungi(10%, 25%and9% under-represented largely OTUswere Non-animal 2727 sequences). multicellular algae (Phaeophycea representatives andprotists, eight (115sequences) fungi OTUs con also parasitic. Thedataset Pocillopora Individual-based cur rarefaction (mean ± SD = 41.6 ± 19.7), respectively, versus 4.1%ofthese versus respectively, ±19.7), (mean±SD=41.6 tissues(mean±SD= know OTUs 3.8±6).Five belonged totaxa tained ten OTUs (236 sequences) sequences) (236 tained tenOTUs B).Both offishconsume species e diversity of dietary items dietary e diversityof e: 5 OTUs and 30 sequences;Rho e: 5OTUsand30 and algae OTUs had>97%mat OTUs and algae ves reached a plateau between 1 between aplateau ves reached consumed on Moorea coral reefs Moorea reefs coral consumed on A). In mostofthe otherwords, A). samples would have been would samples d a very diverse diet. The diversediet. d avery of major groups of of major of differences among of differences belonging to majorgroups belonging of sequences only and 38.7% of onlyand 38.7% sequences h additional samples , 2016; Leray, 2016; Knowlton, & o sequences; 42%of o sequences; d Poriferawere mostly dophyta: 17OTUsand dophyta: more likely to match SD = 52 ±17; SD= 52 ely) S2).Asis (Fig. in barcode libraries inbarcode

ch toreference barcodes, while many OTUs were while many rised the highest rised thehighest ,000 and 2,000 reads ,000 and2,000 quences from quences n to be n Dascyllus : 0.75) orbetween richness inthedietbetween compared to and was positively correlated with the number of reads persamp reads thenumberofwith and wascorrelated positively R there was evidence for interspecific dietary partitioning.Mean thereevidence forinterspecific dietary was Patterns indietcomposition dissimilarity of = 0.003). Post hoc Tukey tests indicated a higher meantests indicated diversit ahigher = 0.003).PosthocTukey vs. This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. F (ANOVA: dataset based onboththenon-rarefied totalnumberofwas OTUs significant 0.001) (Fig. S4).Themean mean ±SD= 60±17; rarefied for to259readsaccount F 0.002; significant between all pairs of species based on Jaccard ( basedonJaccard all pairsofspecies significant between supported by PERMANOVA tests (Jaccard: F supported byPERMANOVA tests(Jaccard: mean dietc in 4A; Bray-Curtis, andthesedifferences Fig. 4B), separated on well were threespecies (Table 1).Samplesofthe theJa thanwithinspeciesforboth were species between higher F the difference in Bray-Curtis dissimilarityBray-Curtis the difference in between π π 2 1,59 2,61

Accepted =0.07, Article Pocillopora =13.7,R =8.2,R Dascyllus

Using the dataset rarefied to 259 reads to control for differen to control to259reads Using rarefied thedataset A totalof14OTUsmostly belong p <0.001; Chromis 2 =0.21, 2 : F =0.19, vs. Pocillopora Pocillopora π 1,35 Pocillopora (non-rarefied: (non-rarefied: Chromis =2.2,R Chromis p < 0.001) (Table 2). Differences in OTU composition werealso composition <0.001)(Table 2). Differences inOTU p <0.001; Pocillopora and 2 vs. =0.06, : mean±SD= 43±10; : F Chromis Pocillopora Chromis differences in sequencing sequencing in differences π 1,35 p <0.001; rarefied: <0.001;rarefied: =2.8,R p and <0.001)and Bray ing to Arthropoda and Chordata to Arthropoda ing (non-rarefied: (non-rarefied: vs. Dascyllus π : F 2,61 Pocillopora 2 = 0.07, π 1,28 =3.5,R (2,61) Chromis =2.4,R (non-rarefied: (non-rarefied: =9.5, Pocillopora p p = 0.002) but no difference inthe =0.002)butnodifference Chromis p < 0.001). <0.001). 2 =0.97;rarefied: =0.1, : F – and Curtis ( 2 depth (ANOVA: F (ANOVA: depth pairwise =0.08, p π omposition wereomposition statistically NMDS plots (Jaccard, Fig. (Jaccard, NMDS plots y ofOTUs in 1,28 ccard and Bray-Curtis indices ccard and <0.001)andthedataset le (Pearson: r=0.47, le (Pearson: Dascyllus ly different among species ly different =4.2,R vs. p : mean±SD= 41±29) <0.001;Bray ces in sequencing effort, effort, insequencing ces Chromis p Dascyllus p = 0.12; rarefied: rarefied: = 0.12; <0.001; β diversity values values diversity contributed 50% of contributed 2 (Table 3). One (Table 3).One =0.13, p Dascyllus vs. = 0.71). =0.71). : F (2,61) Dascyllus Dascyllus – π Curtis: 1,59 p =6.3, = p =4.7,

< p = : p

significantly different from from significantly different (F = 0.08, This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. 17.1%ofthe copepod alsocontributed indietarythan 19%ofthevariation composition between thetw large OTU, identifiedasavery stomachs of R where Dascyllus and 2%tothedissimilarity. and Annelida eac belongingadditional OTUsmostlyto Arthropoda (Jaccard: F (Jaccard: OTUs identifiable as calanoid andcyclopoid were copepods calanoid detec OTUs identifiableas planktonava 4) andbettercompare themto (Table three species di elucidate tofurther was assessed category a majortaxonomic food it absence) of (or presence generatin preyitems OTU ormorenumerous consumed, withlarger S3). (Table sequence data Resultsshowthatthepat 1,200reads. rarefied downto900and explained 6.2%, 6.1% and 5.6%ofthedi 6.2%,6.1%and explained Dascyllus Pocillopora 2 π

Accepted =0.08, Article 2,31 =1.2,R Chromis The dataset also revealed evide also revealed The dataset The number of reads reflects the individual size as well as the aswell as theindividualsize reflects readsThe numberof p = 0.005), whereas no significant differences wereno significantfound using differences =0.005),whereas from different and p π 1,19 . By contrast, noOTUcontributedto thediss disproportionally . Bycontrast, =0.11;Bray Dascyllus 2 Pocillopora Pocillopora =1.16,R was absent. We repeated NMDS and PERMANOVA analyses withdatas PERMANOVAanalyses and repeatedNMDS We absent. was =0.07, collected on collected p 2 = 0.14) (Table 2). Pairwise tests showed that prey composition testsshowedthatprey 2).Pairwise =0.14)(Table Pocillopora – =0.05, Curtis: F (Table 3). One unidentified OTU unidentified (Table 3). One Dascyllus planktonic copepod inthegenus planktoniccopepod ems in the gutcould becl ems that p =0.14;Bray π Pocillopora 1,14 coral hosts based on the Jaccard index (F index basedontheJaccard coralhosts collected from collectedfrom Bray-Curtis dissimilarity nce for differences in OTUcompo in fornce differences =0.92,R fferences between these betweenthese fferences C,where – 2 Curtis: F = 0.06, Pocillopora Chromis p π 1,19 = 0.58) and =0.58) , a red alga and an annelid and red, a alga early identified andassigned to identified early =0.94,R terns are robust to thelossof terns are robust fferences in dietamong the in fferences

between between ilability. Almost allof the Almost ilability. o fish species. Thesame fish species. o Labidocera A (Jaccard: F A(Jaccard: two species while>10 two species ted in the fish stomachs, fishstomachs, ted inthe also occurred, was not was alsooccurred, h contributed between 4% contributed between4% h g more reads. Thus, the reads. Thus, gmore abundance of each of abundance the Bray-Curtis index Bray-Curtis index the Pocillopora 2 = 0.05, sition between Chromis imilarity between , explained more , explained π π 2,31 1,14 p and =0.55), =1.3,R =1.17, B in ets ets 2

species ( amounts of the variance ( amounts ofthevariance absence to calculate calculate absence to lower proportion of the variance (adjusted r (adjusted lower proportion ofthe variance relationship wasalsosignificantfor (tot size and differences infish index Bray-Curtis between the of forparticularlymarked 4A and4B).The onNMDS plots(Fig. during fishontogeny based Dascyllus This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. isopods, ostracods, insto gastropods,and polychaetes tanaids, in samplesof identifia OTUs the reads of but therewerealmost twiceasmany but notfor 6A). 6A). shrimps and crabs compared to compared to shrimps andcrabs identifiedas yielded oftheOTUs morereads stomach samples and the number of OTUs in the stomach contents of of in thestomachcontents OTUs and thenumberof Ontogenetic dietaryshifts gutsabsent fromthe analysed. present in shrim and harpacticoidcopepods, than

Acceptedβ Article diversity. A simple linear model explained 37% ofthevariance 37% diversity. modelexplained Asimplelinear Chromis There was a significant linear negative relationship between negativerelationship fi There linear asignificant was Chromis had a greater diversity of fish O fish of diversity greater hada Pocillopora Dascyllus indicatingthat Dascyllus : p <0.001; β (adjusted r (adjusted diversity (Jaccard), the relationships also were significant f therelationships diversity(Jaccard), tissues. Mysids, and the cephalochordate, tissues.Mysids,cephalochordate, andthe Chromis than Chromis Dascyllus Dascyllus Chromis Dascyllus 2 when prey abundance was taken into account in calculationsin takenintoaccount was abundance whenprey =0.01, p, polychaetes, appendicularian p, polychaetes, : adjustedr Dascyllus . There were more OTUs identifiable as amphipods, moreOTUs. There identifiable were has a much broader diet than than broader diet hasamuch : p p < 0.001), but the model explained relativelylow <0.001),butthemodelexplained stomach samples.Only stomach TUs, most certainly consumed certainly TUs, most = 0.5) (Fig. 5). Prey composition appeared to shift appeared Prey =0.5)(Fig.composition 5). 2 = 0.02). When taking =0.02).When 2 =0.09; ( p < 0.001) but the model explained a much < 0.001)butthemodelexplained Chromis Dascyllus (adjusted r mach samples of mach samples al length) (Fig. 6B). The The 6B). al length) (Fig. Labidocera : adjustedr ble as harpacticoid copepods copepods ble asharpacticoid Branchiostoma sp s, and gastropods were gastropods s, and a few OTUs ofcyclopoid OTUs a few into account presence- into account gradual change in diet was was change indiet gradual in the relationship relationship the in Chromis sh size (total length) (total sh size 2 =0.39, as eggs. as sp. and larvae of andlarvae sp. 2 =0.02)(Fig. . Samplesof Dascyllus p or both Chromis <0.001) ., were

night. Eggs were about half as abundant at night as duringas atnightnight. the asabundant Eggs were abouthalf Labidocera larvae, thep crustacean larvae,other isopods, crab andshrimp Pocillopora contributed 13% at 1.4 m and6%a contributed 13%at1.4m at which contributed33% 31% at0.3mheight aboveavailable prey itemsat1.4mand the Daytime sampleswere plankton coral reefs. The lack of taxonomic resolutioninprey taxonomic lack The of coral reefs. identific potential mechanisms understanding This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. both depths(t=6.573, signi were items ofplanktonicprey the abundance anddiversity all provided importantinsightsintothefoodavailabilityfor samples.However, ambient zooplankton the precluded sequencing level thanprovidedbytaxonomic th copepods tospecies,identificat m all larvalformstospecies larvae dominated bycrustacean Diversity andabundance ofdietar Accepted 20itemsm lessthan low,averaging Daytime were abundances Zooplankton at relatively thetwo distributed was homogeneously Article Resolving andindividualspartitiontheirfood species whether Zooplankton hyperdiversethis was diversity in expected system sp. and polychaetes were rare i wererare sp.andpolychaetes does) compared to during the day when the fish and coral both both thefishandcoral during thedaywhen to does)compared p = < 0.001) when =<0.001)when 1.4mand51%at0.3gastropod orphologically difficulty and the ion of the ambient zooplankton zooplankton ambientthe ion of and copepods. Given theimpossib and copepods. dominated bysmall copepodswhich t 0.3 m (Table. 5). Large-bod 5). t 0.3m(Table. e sequencing approach. Avail approach. e sequencing y items collected byplankton ly allowing a diversecommuni lya allowing DISCUSSION Chromis n thedaytime samplesbutrelat and Dascyllus three planktivores studied.Both three planktivores of identifying most ofthe most of identifying ation, thediversity ofpotential redatory calanoid copepod redatory calanoid day (Table 5). (Table day -3 wasa generallyhigher at ficantly higher at night at at night higher ficantly bottom, followed byeggs bottom, atbothdepths (Table5). ied taxa suchasamphipods, ied taxa depths during the day. depthsduringthe day. donotfeed(butthe able monetary resources resources able monetary protoconchs which protoconchs ilityalmost ofidentifying these samples still samples these ty of species to coexist on tocoexist species ty of pumps pumps made up41%ofthe made resources key is to to be very high and to bevery ively abundant at ively feed.

This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Acceptedand 10.9timeshigher inthedietof the totalnumberofsequences int lifeOTUs cycle withastrictlynot asdiverse were planktonic ofthesequenc (29%and 35.7% ofOTUs helped ide resolution levelprey species database. Nonetheless, orlarva depths consumedaseggs tomorphologically species, b cryptic belong uncollected likely life islandofM ofthe themarine at cataloguingand barcoding effortsoftheBI reflects theextensive andprobably ecosystem belongingto 14 699OTUs with ofpreyrange foundadiverse We This isrelatively high barcode. areference 273 (39%) matched Machida,Leray,Knowlton, 2017). & Ho, databasescurated ofmet oflarge combined withthedevelopment contents) owingto methodological primerse (i.e., improvements Article mor (i.e., powerful totraditional ofdiets analyses complement Ferrie & (Leal webs todecipher food it hasseldombeenapplied mitochondrial usedextens gene. has been thisapproach Although onthemolecular Ouranalysis dietary investigationfocused of fishspecies throughputits associatedplanktivorous using high promotingin coexistenc selectivity role ofdietarysuggest the planktivor among co-occurring differences interspecific dietary In thisstudy,reefs. guilds identifyfeeding fort we oncoral althoughsmall particulateprey, planktivores thatfeedonthey Itb differences. quantify dietary confidently has and identify habit reef ofthe structuralcomplexity andthe food resources, e, or micro-zooplanktonic taxa taxa e, ormicro-zooplanktonic he dataset with an averageco withan he dataset Chromis es) consumed atthelarval consumed es) thanin Dascyllus he first time, pronounced firsttime,pronounced he een particularly challenging for particularlychallenging een at have hindered efforts to hinderedefforts at have e on coral reefs. reefs. on coral e represent one ofthedominant represent one (36), they represented 23.4% of 23.4%of represented they (36), and phological analysis of gut analysis of phological OCODE project (Meyer, 2017) OCODE project sequencing of a hypervariable of sequencing oorea. Species thatremain Species oorea. ntify 201 benthic preyntify species 201 benthic enthic taxa living at greater livinggreater at enthic taxa ntribution of holoplankton 4.6 holoplankton ntribution of ous fish species, which ous fishspecies, for a hyperdiverse tropical a hyperdiverse for r-Pagès, 2016). Itr-Pagès, a 2016). isnow ts for short amplicons) short ts for still under-represented inthe ively in microbial ecology, in microbialecology, ively azoan sequences (Ryuji J J (Ryuji azoan sequences Pocillopora or eggstages.Although or a coral host and two of of a hostandtwo coral phyla, of which of phyla, , respectively. , respectively. This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. sequence on These estimatesbased Interestingly, consistent withpredictionsofnichetheor a pattern (Table 1), levels of dissimilarityinterspecificwere dietary than higher very consumed corals branching feeding despite having similar highly that Ourreveal findings co-occur fish species that morphologies, thetwoplanktivorous Labidocera of thepr gutsbeen itemsfromthe also possiblethatsomeofther trans to the contribute equally link an essentialtrophic are theyconfirmed thatplanktivores unidentifiedin OTUspossibly remained someplanktonic because using for stable isotopes[34-55% might notstrongly for compete inthe suggests thatthetwospecieshaveintrinsicdifferences Dascyllus be driven largely by their ability to detect prey of different of ability to detect prey their by be drivenlargely evasive prey items. However, the items. evasive prey Acceptedrely dietary specializatio and the visionforfeeding, ontheir an feeding alternative substratetheyalso the as pickprey off ran observed thisbehavior, the i Although beenreported ithasnever resources. of wider array whyexplain et al.,2006),which could sucking (Frédérich prey givecoronoid processinthemandible Article are both visual particulate feeders that use suctionfeedingt both visualparticulatefeedersthatuse are , feed on other zooplankton. , feedonother Dascyllus did not significantly shift its diet in the presence of shiftitsdietinthepresenceof notsignificantly did fer of nutrients from the pelagi from nutrients fer of ge of benthic prey in stomachsge benthic o prey of arer species catalogued asprey speciescatalogued arer food (i.e., no competitive displ nocompetitive (i.e., food different portionsoftheavaila different presence of stronger caninifor ofstronger presence ey items themselves assomeo ey itemsthemselves Dascyllus data aredata slightly than lower Dascyllus in the lagoon of Moorea (Hanson 2011)] inthelagoon 2011)] Moorea(Hanson of an ability to seize prey in addition to an ability prey in toseize pigmentation, shape or behavior. orbehavior. shape pigmentation, n of n intraspecific dietary dissimilarity intraspecific dietary c to the benthic food web. It foodweb. is c tothebenthic strategy. Zooplanktivorous fish strategy. ir feeding behavior and hence, andhence, behavior ir feeding y (Chesson, 2000b). and that not all species and thatnotall for the fish may fish for have the infact acement). n the literature and we never never and we n theliterature f in close proximity in in closeproximity ble resources. Levels of resources. ble they are able to feed on a on tofeed able they are previous estimates made estimates previous m teeth and anenlarged and m teeth f thezooplankton,including Chromis Dascyllus our dataset. Nevertheless, Nevertheless, our dataset. behaviors and and behaviors o capture individual o capture Chromis and couldsuggestthat Chromis Dascyllus and . This may At favoured by This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. individual movingwith vari prey thefish also contingent prey onwhether is capture of detected afunction properties ofthephysical 1987),whichis (Lazzaro, bod able todiscriminatevarious shownto hasbeen fish thevisibilityForto a example, of prey both fishspecies(i.e., a asKing, wellasbeing 2009) (0.4-1 combined taxa othercopepods 2.5 mmlength) thanallthe fromt sp.out Labidocera singled although stillsmallerthanmos μ averaged andpolychaetes megalops, crab decapod larvae, reve Moorea contentofplanktonfrom Measurements thecarbon of by consumed primarily and polychaetes fromit. catching enable behavior thatmight t the dietary compositionbetween calanoid copepod predatory Jaffe & 2005; Brooks pers.observation). Genin, & 2 (Holbrook night Schmitt, anddonot feedduring thatperiod observations indicate that water c are abundantinthe more Acceptedg animal C Article an average of 27 of an average Prey size may also play a role in dietary separation. The The a roleindietaryPrey separation. play mayalso size -1 Dascyllus respectively, while the small copepods, crustaceans and gastro crustaceansand respectively,while thesmallcopepods, μ g C animal g C Labidocera sp. Labidocera

averaged between 2and16 between averaged Chromis Chromis Labidocera sp highly significant food item. W item. food significant highly t of the larger prey consumed by t ofthelargerprey y structures from the backgroun y fromthe structures -1 olumn at night, both night-time both olumn atnight, ous motion patterns and escape patterns and escape ous motion he other copepods taxa because taxa he othercopepods wo fish species (Table 3),has (Table wo fish species ,

and amphipods favoured by to detect it more readily, or might prevent might prevent or todetectitmorereadily, , decapod larvae, amphipods, isopods, and polychaetes) larvae,amphipods,isopods,andpolychaetes) , decapod Dascyllus Chromis ., that explained morethan19% ofthevariationin ., thatexplained are among the largest prey available. available. are prey thelargest among shelter from predators in their hostcorals shelterfrom at predatorsintheir μ g animal C 42 Dascyllus μ depend upon how well it is howwell dependupon is able to discriminate among isabletodiscriminate of the eyes. The successful The eyes. ofthe g C,18 hile prey by consumed mainly -1

a characteristic glidinga characteristic Chromis d (i.e., light contrast) (i.e., light d video recordings and diver videorecordings anddiver Labidocera 002; Yahel, Yahel,Berman, 002; Yahel, (Alldredge & 2009). King, it was so much larger (1.5- largermuch itwasso .2 mm length) (Alldredge &.2 mmlength) (Alldredge strategies. For example, the For example, strategies. aled that aled that were an exception werean exception μ g 70 C, . We deliberately. We , decapod larvae, , decapod Labidocera pod larvae pod larvae Dascyllus μ g C,and44 ,

larger individuals of both species tend to feed in theupperspecies pa tendtofeedin larger individualsofboth quantifyby offoraging patterns Chromis abundant nearer the surface during abundant nearer surface the the surface. exp wouldbe prey abundances However, &(Alldredge 2009). King, unstrati lowandrelatively was planktonabundance as expected, Duringfor nearthebot we zooplankton this study, sampled only was swimming drivenby upward p in responsetostrong predation bacupper 50cmoftheshallow copepod a King showedthat (2009) Reidenbach,& Sebens, 2010;Holzman, Monismith,Koseff, Genin, consistently a some taxa more mar reported Several studieshave groups the swim predators, Inabsence of the volumes ofwater. ofboth prey. Theschoolingbehavior th caused by also may be differences fed Dietary inourstudy. a genus sometimes seen as synonymousas a genussometimesseen withthe including copepods of on several species This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Accepted Article Moreover, caught& issimilar(AlldredgeKing, 2009). pumps tendtocollectfewer zooplanktonthandiver-towednets, underestimation prey pumps.Ho oftheavailable bythe plankton a high ofselectivitydamselfishe degree onthepartoftwo Dascyllus Alternatively, concentrations of certain prey species inthest species ofcertain prey concentrations Alternatively, may occasionally forage higher up in the water column. Althou may upinthe forage higher occasionally that exceed their measured con measured their thatexceed Labidocera in particular is highly attracted to light and tolightattracted was particularishighlymuch likely in bundant towards the surface surface the bundant towards k reef of Moorea (2.4m) during th during (2.4m) Moorea of k reef the two species of fish in the twospeciesof the ked vertical stratification of vertical stratification ked the day (Alldredge 2 & theday King, nd veliger larvae were tim larvae 3-8 nd veliger Chromis centrations inthewatercolumn centrations Corycaeus sp. Corycaeus and Farranula Dascyllus Dascyllus (Hanson, Schnarr & Leichter,& 2016) (Hanson, Schnarr (Heidelberg, O’Neil,(Heidelberg, Bythell, & sp. water column during water thisstudy, column allows exploration oflarger allowsexploration rt of the water columnrt ofthewater while zooplankton on reefs, with onreefs, zooplankton s or non-random collection or ornon-random s e uneven spatial distribution of distribution spatial e uneven

on which it also selectively on whichitalso high in the water column. inthe high fied during the day fied during theday the diversity of the organisms oftheorganisms the diversity tom and in midwater, where, midwater, where, tom andin 009) suggesting that 009) wever, while the plankton wever, while e day. This vertical zonation vertical zonation This e day. isknowntoselectivelyfeed es more abundant inthe abundant es more ressure near the sea floor. sea the near ressure omachs of 2005). Alldredge and 2005). ected to be higher nearer ected tobehigher gh we didnot gh could reflect either reflect could Chromis more more and , This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. (Brooks,closer host pe totheircoral smaller individualsfeed pull backintotheirmouthoncese stings andpullthemtowardsthe Perissinotto, &indiv First, Schleyer, 2010). immobilize polyps day duringandn zooplankton both tocapture feedingstrategies Acceptedlikely amounts ofDN make they upnegligible However, approach. detectionis unavoi ofsecondary prey dietary partitioning. The (Sh richness prey artificiallyincreasing prey ofa thus prey), se co-amplify may also 2013).Polymerase Chain Reaction Jarman, (Deagle,Th taxa of per sequences biases intherelativenumber Knowlton, 2016;Pompanonet example, primermis al.,2012).For information dietary hereused provided approach molecular The Yet, italsohasshortcoming ofresolution. level unprecedented (Leal etal.,2014). of herbivory nutrition in coral microalgae, numerous tissuealsocontained form Coral offeces. as sm eggs, present inthemucus fish, contained adiversity of revealed Our study ofpreyingested. therange likely broadens Article 2008). & 2003;Palardy,Ferrier-Pagès, Grottoli, Rodrigues, growth (Ferrier-Pagès,Witting, Tambutté,& 2003;Houlb Sebens, of forthemaintenance are essential corals,scleractinian and Asexpected, Zooplankton sou are asignificant position inthewater column. species. segregationresponsib islikely column than in thewater do tendtofeedhigher Pocillopora le for both inter- and intra-spe both inter-and le for mouth. Second, polyps extrude mouth.Second, hasavery its and, feedingits distinctdietowing mode to veral prey have been trapped. been veral have prey Dascyllus , which indicates that verticalthat , whichindicates eppard et al., 2005) and inflating andinflating et al.,2005) eppard Pocillopora cific dietary differences inboth dietary differences cific metabolic processes and skeletal andskeletal metabolic processes rs. com.). In rs. com.). addition, all larvae and possibly and all larvae in the dable with this sequencing dable withthissequencing s (Creer et al., 2016; Leray& 2016; et al., s (Creer that idual prey nematocyst using rce of nutrients for nutrients rce of omas, Shaffer, Trites, &omas, Shaffer,Trites, This passive feeding strategy strategy passivefeeding This ight (Séré, Massé, (Séré, ight confirming the importance confirmingthe importance mucus webs thattheymucus webs then rèque, Tambutté, & rèque, matches likely create create likely matches condary prey (i.e., the prey (i.e., condary Pocillopora A, are likely highly highly likely are A, with an usestwomain tissues Chromis

This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. duringt specimens and catalogued Poupin Joseph andothers Arthur Anker, thankGustavPaulay,We on coralree biodiversity of forspecialization themaintenance interactions thecomplexitytools forunderstanding trophic of rarefaction),levelrare of and OTUs) sequencing effort (i.e., thebe partitioning regardlessof sh analyses Our inthisdataset. for ofthesequences only 1.8% (e.g., protists,fungi andalgae) possiblesecondary thatare p example, OTUset al.,2005).For assig in thedataset(Sheppard digestedand toprimary therefore ac likely incomparison prey, AcceptedAUTHOR’S CONTRIBUTIONS FrancaiseRépublique enPolynésie and th Recherche) (Délégation àla Government French Polynesian completed underwas p awards).OCE 1637396andearlier Research Research Long Ecological Coral Reef Term History Moorea and the Betty theSantChairofSmithsonianNatioFoundation, Moore workwas This qualitysignificantlyimproved the ofthiswork. who providedco reviewers anonymous manuscript aswellthree Ecology subjecteditorofMolecular thankDr.PimBongaerts, We KwesMatthew supportaswell logistical and Jeffrey Huntfor Smithsonian NationalMuseum History. ofNatural Weespeciallya i conducted were data analyses Article n and with the support of the L.A ofthe n andwiththesupport ta diversity metric used (i.e. used ta diversitymetric

ACKNOWLEDGMENTS ACKNOWLEDGMENTS he Moorea BIOCODE project.BIOCODE All he Moorea (DTRT) (Protocole d'Accueil 2 (DTRT) (Protocole , equal or little weight given to orlittleweight , equal rey for the planktivores account planktivores for the rey pointing to the value ofthese value to the pointing fs. fs. and the role of dietary and therole owed clear patterns of dietary ofdietary clear patterns owed count for very few sequences few sequences count forvery supported by the Gordonand supported by ned to non-metazoan groups ned tonon-metazoan .B. facilities ofthe .B. facilities kin for informatics support. informaticssupport. kin for nal MuseumofNatural , for handling this , 005-2018). 005-2018). who collected, identified who collected, nstructive feedback that feedback nstructive e Haut-commissariat dela e Haut-commissariat cknowledge Robin Turner RobinTurner cknowledge ermits issued by the ermits issued (LTER) program (NSF (LTER) of the laboratoryand ofthe Anderson, G. R. V, Ehrlich, A.H.,E Anderson, G. R.V,Ehrlich, This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Figshare (https://doi.org/10. fromalso bedownloaded table can multiplexing strategy (https://doi.org/10.6084/m9.figshare.7550 multiplex identifier (https://doi.org/10.6084/m9.figshare.75501 thel conducted the samples.ML ALA,AJB, RJS,CPM study. andML ALA, AJB, SJH, SJ the designed Allgeier, J. E.,Adam,T.C., &Allgeier, J. B Anderson, M. J. (2001). A new method for non-parametric multiva (2001). A new methodfornon-parametric Anderson, M.J. Accepted M.(2009).Near-surface enrichment J. L.,&King, Alldredge, A. Devine, A.M Al-Rshaidat, M.D.,Snider,A.,Rosebraugh, S., Adam, T.C.,Kelley, Ruttenberg,I.,B.Burkepile, D.E. & M., REFERENCES Article SAMN10780924-SAMN10780987) accessions: https://doi.org/10.6084/m9.figshare.5808621)the NCBIand Short (https://doi.org/10.6084/m9.figshare.5808618 and are files Raw sequencedata DATA ACCESSIBILITY manuscript. to thefinalversionof discussedt manuscript withinputfromALA Allauthors and AJB. theplanktonsur CPM andNK conducted contributed reagents.ALA 117 Austral Ecology of the Royal Society B: Biological Sciencesof theRoyalSocietyB: Biological coral nichesamong herbivorous traitsspecies-level fortrophic doi:10.1007/s00338-009-0534-4 doi:10.1098/rspb.2017.0307 Talbot, F. H. (1981). The community The Talbot, F. H.(1981). shallow back reef: Implications for coral reef food webs. food Implications reef for coral shallow backreef: 724 northernR coral reefsinthe ofJordanian overlooked diversity DeepL.,Leray, COI(2016). sequencin … M. reefs. drivesfunctionalin parrot diversity along multiplenicheaxes (4), 476 – 737. doi:10.1139/gen-2015-0208 737. doi:10.1139/gen-2015-0208 Oecologia – 495. doi:10.1086/283729 495. doi:10.1086/283729 , , 26 179 (1), 32 (4), 1173 (4), available fromFigshare available – aboratory work. ML and JYY analy ML andJYY work. aboratory 46. urkepile, D. E. (2017). Theim D.E.(2017). urkepile, – hrlich, P. R., Roughgarden, hrlich, P.R., 1185. doi:10.1007/s00442-015-3406-3 1185. doi:10.1007/s00442-015-3406-3 structure of coral reef fis coral reef structureof . Sequences ofPCRprimer . Sequences , 284 g of standardized benthic samples unveils gstandardized benthicsamples of (1856), 20170307. (1856), Coral Reefs (2015). Resource partitioning(2015). Resource 83), a description of the of a description 83), portance of individual and of portance 6084/m9.figshare.7551026). 180) and the completeOTU and the 180) J. D.,Russell,B. C.,& J. of zooplankton overa ofzooplankton ., Devine, T. D.,Plaisance, T. ., Devine, Read Archive (BioSample Read he results andcontributed he results fishes on Caribbean coral coral onCaribbean fishes riate analysis of variance. riate analysis ofvariance. reef fishes. fishes. reef ed Sea. ed Sea. hes. zed the molecular data. molecular data. zed the vey. ML the vey.wrote H and RJScollected American Naturalist , s and 454 Genome 28 (4), 895 (4), Proceedings Proceedings , 59 – 908. (9),

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J.,Kuzmina,M. ., Kress,W. er space causes density- causes er space n assemblage of n assemblage pical scleractinian corals. pical scleractinian lution, feeding behaviours, behaviours, lution, feeding t of zooplankton availabilityt ofzooplankton (10), 2855 ers in marine food webs and foodwebs ers inmarine , & Genin, A.(2005).Near- , &Genin, u-Tham, G., & Wantiez, L. G., & Wantiez, u-Tham, 0). Ironing outthewrinkles 0). t greatest risk from lossof greatest riskfrom t in the scleractinian coral in thescleractinian hips with zooplankton hips withzooplankton lagoonsNew of – 530. s composition, s composition, – 2868. 2868. , , 95 65 Conus (882), 137 , (2), 539 296 , 112 (2),

(26), – , – Machida, R. J., Hashiguchi,Machida, S.(200 Y.,Nishida,M.,& R.J., Nishida, (2016).PreparationQ., &Bourlat, S.J. Leray, of M.,Haenel, Machida, R. J., Leray, N.(2017).Me & Ho, S.-L.,Machida,Knowlton, R.J., M., N. (2016).Ce Leray,&Knowlton, M., Leray,N. (2015) &Knowlton, M., C.,&Meyer, P.(2012).M T.,Mills,S. Leray,Boehm, C. J. M., This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Devil d inthedetails:high-resolution K. (2007). Longenecker, Leal, C.,Calado,R.,Thompson,M.E.,Fr M.C.,Ferrier-Pagès, Leray, M., & Knowlton, N. (2017). Random sampling causes thelo Leray,N. (2017).Randomsampling causes &Knowlton, M., Leray,Mills, S.C.,&Meyer, P.(2013).Ef N., M.,Agudelo, C. Leray, C.P.,& M.,Meyer, Mills,S.C.(2015).Metabarcoding d AcceptedLeray, Y.,Meyer, J. M.,Yang, C.P.,Mills,S.C.,V., …Machida,R. Agudelo, N.,Ranwez, Article analysis through single-gene sequencing of a community sample. community ofa sample. sequencing analysis through single-gene Inmethod. Bourlat (Ed.), S.J. Illumina marinemetabarcoding eukaryotes using MiSeq:Thead of 438. doi:438 10.1186/1471-2164-10-438 438. doi:43810.1186/1471-2164-10-438 doi:10.1073/pnas.1424997112 oftheUnitedStatesAmerica Academy ofSciences diversity. marinebenthic samples reveal patterns of 1-4939-3774-5 Methods andProtocols 8 sequence reference datasets for taxonomic assignment of environ assignment fortaxonomic datasets reference sequence fishes. reef coral common predatory interactions: predator-prey libraryas atoolforunderstanding doi:10.1016/j.margen.2016.02.003 ecology.coral their potentialusefor basic assumption of reef-fish diversitymodels. basic assumptionofreef-fish Molecular Ecology C.(2014).Coralfeeding onmicroal J. Sciences century. eukaryotic OTUs in Illumina COI metabarcoding. Illumina in COIeukaryotic OTUs metabarcoding. coralreef inthegut contents oftwo prey revealed unexpected blocking versus characterizatio restrictionenzymes primers for doi:10.7717/peerj.3006 highly partitioned, generalisthighly diet. partitioned, of theminorcontribution dwellingfish demonstrates predatory J. (2013).Anew primers versatile J. fish gut contents. region metazoan diversity: forch formetabarcoding application (4), e58076. doi:10.1371/journal.pone.0058076 (4), e58076.doi:10.1371/journal.pone.0058076 , Philosophical Transactions of the Royal Society of London. Series B,Biological oftheRoyalSocietyLondon.Series Philosophical Transactions 371 (1702), 20150331. doi:10.1098/rstb.2015.0331 (1702), 20150331. Frontiers inZoology Frontiers , 23 (15), 3870 (15), (Vol. 1452,pp.209 (Vol. . 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Zooplankton ietary analysis of coral ofcoral analysis ietary – tazoan mitochondrial gene mitochondrial tazoan – insights intothedietof 388. 388. iversity in the twenty-first thetwenty-first in iversity – t of the mitochondrial COIt ofthe 7. fish species. fish species. w reproducibility of rarew reproducibility of n of generalist diets: n ofgeneralist 555. coral mutualists totheir coral mutualists aracterizing coral reef coral reef aracterizing ng of standardized of ng ar trophic markers. ar trophic mental samples. mental samples. BMC Genomics – apter ligation apter 2081. PLoS One , 10 , , Munday, P. L., Jones, G. P., & Caley, M. J. (2001). Interspecif (2001). P., &Munday, Caley,L., G. M.J. P. Jones, P., Huelsenbeck, E.,&Munch, K.,W., Boomsma, J. Willerslev, N C FASTA data.Merritt: Project Biocode Meyer, C.(2017).Moorea guild inaseaurchin and Coexistence McClanahan, T.R.(1988). This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. (2 &Lanzen,Davenport, P.J. Turnbaugh, R.J., A., Quince, C., Pratchett,L. variat Interspecific M.S.,& M. (2008). Berumen, but Pratchett,Dietaryselection by coral-feeding M.S.(2007). L. & The Grottoli,A.G.(2008). J., Palardy, E.,Rodrigues, J. Oksanen, L.S. Nugu J., Wartenbergh, Velde,I., G., Nagelkerken, der van Pereira,Zemoi,B., B.Ferreira, P.H.C.,Barros, P.(20 R.,& Pompanon, F., O.C.,Brown, B.E.,Symondson, Deagle, W. D.S., AcceptedPratchett,Dietary M.S.(2005). Article in aguild ofcoral-dwelling fishes. Biology usingBayesian StatisticalDNA sequences assignment of phylogen 2016±05±14. Retrieved ark:/%0D13030/m5478zfg from Biocode 13030/m5478zfg.Lib Collectionark:/ CaliforniaDigital diversity and degradation. 38 9658(2001)082[2177:icacia]2.0.co;2 Scientific Data pyrosequenced amplicons. amplicons. pyrosequenced Chaetodontidae).(Teleostei: butterflyfishes coral reef Australia. Barrier Reef, on theGreat 373 Marine BiologyandEcology Journal ofExperimental and requirements bleached ofhealthythe daily carbon metabolic http://vegan.r-forge.r-project.org/ http://cran.r-project.org/, 1.1 version Rpackage community(2009). Vegan: ecology package. doi:10.1111/j.1095-8649.2009.02303.x butterflyfishes (Chaetodontidae). components (2009). Cryptic dietary 1730 doi:10.1016/j.jembe.2008.09.015 and food partitioning of and foodpartitioning of Reviews inFishBiologyandFisheries Molecular Ecology iseatingwhat:P. (2012).Who dietassessmentusing gener next (Chaetodontidae) at Lizard Island, northern Great Barrier Reef. LizardIsland, Great at (Chaetodontidae) northern – J., Kindt,R., Legendre,J., Simpson, G.L.,B., P.,O’Hara, P.,…Wagner, H. Solymos, 382. doi:10.1007/s00227-005-0084-4 – 1747. doi:10.1111/j.1095-8649.2008.02062.x , 57 (5), 750 , 4 (January), 170027. doi:10.1038/sdata.2017.27 (January), 170027.doi:10.1038/sdata.2017.27 , – 21 757. doi:10.1080/10635150802422316757. 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(2), 180 tterflyfishes tterflyfishes its applications to coral reef tocoralreef itsapplications (6), 1123 ielsen, R.(2008). ielsen, Jarman, S. N., & Taberlet, S.N.,& Taberlet, Jarman, ollection: Moorea

review of the genusdiet. ofthe review ation sequencing. Marine Biology , 171 corals at two depths. attwo corals rary Version1: sympatric sympatric – etics. etics. 5-3. Retrieved from Retrieved 5-3. 188. – 176. – 1143. 1143. Systematic Systematic , 73 , 148 (7), (2), Ross, S. T. (1986). Resource partitioning in fish assemblages - Ross, S.T.(1986).Resourcepartitioning infishassemblages Lassig,Robertson, D.R.,&(1980). Spatialdistributionpat B. TheBOLD: &Ratnasingham,Barcode P.D.N.(2007). Hebert, S., Sale, P. F. (1978). Coexistence of co of Sale, P.F.(1978).Coexistence Schloss, P.D.,Westcott, L.,S. R.,Hartm Ryabin, T.,Hall,J. L.,Dove,O., & Hoegh-Guldberg, Sampayo,Franceschinis, E.M., Ranwez, V., Harispe, S., Delsuc, F., & Douzery, E. J. P.(2011) J. Delsuc,&E. F.,Ranwez, V.,Harispe,S., Douzery, Schmitt, R. J., & Holbrook, S. J. (1996).Local-scale patterns &Schmitt, R. Holbrook,S.J. J., This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. E.(1967).Food habitsofr Randall, J. Ransome, E., Geller, J. B.,Timmers Ransome, E.,Geller,J. Schnell, I. ju Schnell, K., &Bohmann, M.T.P.(2015).Tag B., Gilbert, (1999).Mortality &Schmitt, R. Holbrook, S.J. J., of juvenile AcceptedL.Séré, Perissinotto, R.,& M.G., Massé, Schleyer, M., M.H. Article Alignment of Coding SEquences accounting for frameshifts andst for Alignment SEquencesaccounting ofCoding 6 Copeia 30 reef. Barrier from group territorial theGreat damselfishes of ode=GeneralSearch&qid=7&SID=3DOF2GlLjfAhkdiHKKi&page=1&doc=1 http://apps.webofknowledge.com.gate1.inist.fr/full_record.do?pr (www.barcodinglife.org). Applied and Environmental Microbiology Applied andEnvironmental micro comparing and forcommunity-supported describing software Biology ofFishes 3721 partitioning symbioticrelated ofclosely dinoflagellates. e0175066. doi:10.1371/journal.pone.0175066 e0175066. doi:10.1371/journal.pone.0175066 09 Introducingmo C.F.Weber, (2009). planktivorous damselfish - Do they predict recruitment? recruitment? planktivorous damselfish-Dothey predict Oceanography measure cryptic diversity on Mo’orea coral reefs, French Polynesia. reefs, coral onMo’orea measurecryptic diversity Research doi:10.1890/0012-9658(1999)080[0035:MOJDIF]2.0.CO;2 doi:10.1890/0012-9658(1999)080[0035:MOJDIF]2.0.CO;2 sequence-to-sample misidentific sequence-to-sample thatdetermineabundance. assessing processes study using autonomous reef monitoring structures (ARMS)andstudy me usingautonomous reef structures monitoring C. P.(2017).Theimportanceofs Resources Journal of Experimental Marine BiologyandEcology Journal ofExperimental heterotrophic feeding on th on heterotrophic feeding (9), e22594.doi:10.1371/journal.pone.0022594 , 187 – 3733. doi:10.1111/j.1365-294X.2007.03403.x , – 2 203. , , 352 , 47 15 (2), 449 (2), (6), 1289 (6), – , 388. 5 , 665 , 3 , 85 – 463. doi:10.1071/mf9960449 463. – – 847. 847. – 1303. doi:10.1111/1755-0998.12402 102. Molecular EcologyNotes e sexual reproduction of reproduction of e sexual , M., Leray,, M., Mahardini, M., ral reef fishes-a lottery fishes-a ral reef ations inmetabarcoding studies. eef fishes of the West I theWest fisheseef of tandardization for biodiversit for tandardization thur: open-source, platform- thur: open-source, , 75 (23), 7537 (23), Ecology , Pocillopora verrucosa 7 , (3), 355 for living space. space. for living , 395 ndies. ann, M. – 80 Molecular Ecology of larval settlement ina of settlement larval Marine andFreshwater damselfish: implications for damselfish: terns and coexistence ofaterns andcoexistence 7541. doi:10.1128/aem.01541- a review of field studies. review of a (2010). Influence of (2010). mps illuminated - reducingmps illuminated . MACSE: Multiple (1), 35 (1 A., Sembiring, A., Sembiring, Bulletin of Marine Science Bulletin ofMarine – S. (2007). Niche S. (2007). – 2), 63 Studies in Tropical of Life Data Life System of y comparisons: Acasey comparisons: 364. Retrieved from 364. Retrieved , Hollister,E.B., …

oduct=WOS&search_m independent, independent, Molecular Ecology Molecular – op codons. op codons. 50. bial communities. bial communities. tabarcoding to tabarcoding – PLoS One 71. Environmental in aquaria. in A., …Meyer, , 16 PloS One , (17), 12 (4), , , This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Ladd,& A.A., D.E.(20 Burkepile, C., Schrack,E., Shantz, M. Siepielski, A.M.,& evidencefor On McPeek, the M.A.(2010). Sunderl Sheppard, S.K.,Bell,J.,

Talbot, F. (1978).Cor C., & H.,Russell,B. G. R.V. Anderson, Yahel, R., Yahel, G., Berman, T., Jaffe, J. S.,& Genin, J. T.,Jaffe, A.(20 Yahel, G.,Berman, R.,Yahel, S. N.(2008).Blocking toenhan Vestheim, primers H.,& Jarman, Accepted Wickham, H.(2009). Article doi:10.1016/j.jembe.2010.08.014 hotspots shape coral reef benthic communities. benthic hotspots shapecoralreef 2152. doi:10.1890/14-2209.1 2152. doi:10.1890/14-2209.1 critique of the coexistence program. critique ofthecoexistence doi:10.1111/j.1365-294X.2005.02742.x generalist predators. invertebrate bypredation ofthe PCR analyses (2005). Detection ofsecondary 50 0154.1 unstable, high diversity systems. doi:10.2307/2937241 crepuscular changes of zooplankton over a coral reef. overa reef. coral ofzooplankton changes crepuscular Frontiers inZoology preyDNA inA on study samples-acase inmixed rare sequences (3), 930 – 944. doi:10.4319/lo.2005.50.3.0930 944. doi:10.4319/lo.2005.50.3.0930 ggplot2: elegantgraphicsfordataanalysis ggplot2: , 5 , 12. doi:1210.1186/1742-9994-5-12 and, K. D., Fenlon, J., Skerv J., Fenlon, and, K.D., Ecological Monographs Molecular Ecology Molecular Ecology , 91 Ecological Applications (11), 3153 (11), , 14 Limnology andOceanography (14), 4461 in, D.,& O.C. Symondson, W. 05). Diel pattern with abrupt 05). Dielpattern , al reef fish communities - communities fish al reef 48 15). Fish-derived nutrient Fish-derived 15). – species coexistence: a coexistence: species . New York: Springer. . New York:Springer. 3164. doi:10.1890/10- ce PCRamplificationce of (4), 425 gut contents of gut contents ntarctic krill stomachs. krill ntarctic – 4468. – 440. , 25 (8), 2142 – , This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Figure 1. Accepted Article corals inthelagoon ofMoorea. Co-occurrence of planktivorous damselfishes surveyed on ten surveyed onten of planktivorousdamselfishes Co-occurrence Pocillopora eydouxi Pocillopora

This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. individualfishandc presented per breakdown (B)aretaxonomic OTUand illustrated. diversity(C) ofCOI metabarcoding sequencing of Figure 2. H Bacillariophyta, Dinophyceae, The ca Hemichordata, Nemer Echinodermata, anim “Other category “unidentified”. The assigne could notbeconfidently Blasthits(if>85%similarity,and M closest see Package (SAP) implemented in approach phylogenetic Bayesian to phylaa using with<97%similarity COI OTUs reference to was than97%. higher BIOCODE GenBankBOLDif the or database, sequence intheMoorea

Accepted Article Chromis viridis tegory “Other non animals” comprises members of Phaeophyceae, Rhodophyta, Rhodophyta, ofPhaeophyceae, animals” comprisesmembers non “Other tegory Diversity of OperationalDiversity Taxonom of (n=27), Dascyllus flavicaudus d using any ofthemethodsabov d using eterokonta, Amoebozoa andFungi. Amoebozoa eterokonta, . The proportion ofOTUsidentif . Theproportion oral. An OTU was considered An OTU oral. tea, Platyhelminthes, Sipuncu als” comprises Bryozoa, Chaetognatha, Bryozoa, Chaetognatha, als” comprises ic Units (OTUs) recovered from (OTUs)recovered ic Units (n=34) and (n=34) Pocillopora eydouxi Pocillopora ethods section). OTUs that OTUs ethods section). e were labelled e were labelled to match a reference a reference to match abundance (D) are also (D)are abundance the Statistical Assignment ied (A) and their and ied (A) barcodes were assigned assigned were barcodes

la and Xenacoelomorpha. la andXenacoelomorpha. level ofsimilarity level dietary analysis analysis dietary (n=3) using (n=3)

This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. sequences resampling by randomly Figure 3. Accepted Article ofdietaryitems. thediversity characterize usedinthi depth thesequencing whether indicate accumulation, Individual Rare rarefactionand sample(B) based analyses. (A) and samples respectively at in and samplesrespectively s study sufficientto was creasing levels of creasing faction curves,built

This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Figure 4. from the rarefied OTU table (n OTUtable from therarefied credit: (fish),GustavPaulay Jeffrey(coral) Williams Accepted Article notapply does to the scalebarfor size Bray-Cur based metric(A)and scaling plots multidimensional Ordination plots

comparing the composition of prey items. Non-metric ofpreyitems. Non-metric the composition comparing =259) to control for differences for differences =259) tocontrol tis (stress = 0.22), an abundance- =0.22), an tis (stress were computed using Jaccard (str Jaccard using were computed Pocillopora samples. Beta diversity was samples.Beta calculated diversity in sequencing depth. Photos depth. in sequencing based metric (B).Notethat metric based ess = 0.22), anincidence- = 0.22), ess

Dascyllus from the rarefied dataset (n=259) to control for differences(n=259) in tocontrolfor from therarefieddataset This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Figure 5.

Accepted Article intervals. fitted with95%confidence : Y = 37.8 - 0.1*X, adjusted r : Y=37.8-0.1*X, Diversity of OTUsinrelationt Diversity of Chromis 2 =0.01, o fish size (total length inmm o fishsize(totallength : Y = 53 - 0.5*X, adjusted r = 53-0.5*X,adjusted : Y

p = 0.5. The number of OTUs was calculated wascalculated OTUs = 0.5.Thenumberof sampling effort. effort. sampling ). A linearmodelis 2 =0.39,p<0.001;

Jaccard dissimilarity 0.6 0.7 0.8 0.9 1.0 AJaccard - 0204060 Dascyllus This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Figure 6. Bray-Curtis, for differences (n=259)tocontrol OTUtable from therarefied r Jaccard, toeachplot. fitted were intervals confidence Bray-Curti based metric(A)and were inprey computedusi composition mm). Pairwisedifferences 2 =0.09,

Accepted Article : Y = 0.77 + 0.001*X, adjusted r : Y=0.77+0.001*X, p Correlation between prey composition and differences infishsi and differences composition prey Correlation between Difference in total length (mm) < 0.001; Jaccard, <0.001;Jaccard, Chromis : Y = 0.50 + 0.014*X, adjusted r : Y=0.50+0.014*X,adjusted Dascyllus s, an abundance based metric(B) based abundance s, an Chromis Dascyllus : Y = 0.88 + 0.001*X,adjusted r : Y=0.88 2 = 0.02, =0.02,

Bray-Curtis dissimilarity 0.4 0.6 0.8 1.0 p < 0.001. Beta diversity was calculated calculated was <0.001.Betadiversity B - Bray-Curtis - B Chromis 2 0204060 =0.37, : Y=0.80+0.002*X,adjusted in sequencing depth. depth. in sequencing p <0.001;Bray-Curtis, . Linear with95% models . ng Jaccard, an incidence anincidence ng Jaccard, Difference in total length (mm) 2 = 0.02, = ze (totallength in ze p =0.001;

This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. (259). ra the dataset calculated using and theBray-Curtis diagonal)metrics. Bet dissimilarity (above Table 1 Accepted Article Intraspecificmeans Pocillopora Dascyllus Chromis Species Intra- measured dietary overlap usingthe Jac andinterspecific Chromis Chromis 0.96 0.86 0.83 refied to the lowest number ofr refied tothelowest Dascyllus Dascyllus 0.89 0.92 0.88

Pocillopora eads that a sample contained eads thatasample 0.90 0.96 0.94 a diversity values were were values a diversity card (belowdiagonal) card Intra-specific Intra-specific means means 0.91 0.79 0.65

This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Table 2 differences in diet. Intra-specificwas dietpartitioning indiet. teste differences hosts(A,Bcoral andC). collected ondifferent ( Intraspecific Interspecific Accepted Article Dascyllus) Permutational multivariate analy Bray-Curtis Jaccard Bray-Curtis Jaccard Beta Species Species Residuals Species of variation Source Residuals Residuals Coral host Residuals Coral host Residuals sis (PERMANOVA) testing inter- sis (PERMANOVA)testing inter- Df 31 31 61 61 2 2 2 2 17.4 21.8 9.8 0.7 0.9 4.7 2.5 SS 11 F Model d between individual individual d between 1.2 1.3 8.2 3.5 0.93 0.07 0.92 0.08 0.79 0.21 0.9 0.1 r 2

<0.001*** <0.001*** <0.001*** <0.001*** 0.005** P-value and intra-specific and intra-specific 0.14 Dascyllus

* = This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Accepted theindicatedof ismarkedwi preypair thatconsumesmore item assignedany ofthemethodsabovewerel using Blast hits(if>85% OTUs methodsection). similarity, that see implemen approach phylogenetic <97% similaritywere COI toreference assigned tophyl barcodes higher was BOLD ifthelevel ofsimilarity or database, GenBank int sequence reference tomatcha wasconsidered OTUs). AnOTU bold(cumulate are in highlighted ofspecies each pairs between to50% OTUsthattogethercontribute diets. between differences Table 3 Article Dascyllus

Similarity Percentage Analysis (SIMPER) identifyingcontrib the Phylum Heterokonta Chordata Chordata Rhodophyta Unidentified Arthropoda Annelida Rhodophyta Annelida Rhodophyta Chordata Annelida Chordata Arthropoda Echinodermata Arthropoda Arthropoda Unidentified Chordata Arthropoda Arthropoda Chordata Unidentified Arthropoda ; x = ; x

Pocillopora Thalassoma amplycephalum (Labrid fish) Labroides dimidiatus(Labrid fish) unicornisNematonereis (Polychaete) (Polychaete) Nereididae Cirripectes quagga (Blenny) Polychaeta Pseudocheilinus hexataenia (Wrasse) (HarpacticoidScutellidium copepod) Acanthaster planci (Sea star) (Fly)Chironomidae (Pomacentrid) nigricans Stegastes Maxillopoda Farranula gibbula (Cyclopoid copepod) Scarus psittacus(Parrotfish) Labidocera (Calanoid copepod) Lowest taxon

ted intheStatistical Assignment

abelled “unidentified”. The member of each “unidentified”.The abelled #1.4 Chromis Dascyllus Contribution (%) to differences between (%) todifferencesContribution between could not be confidently could notbe #19.3 #19.3 d contribution ofranked *0.2 *0.2 #1.5 *1.6 *1.6 #1.6 *1.7 *1.7 *2.0 #2.5 *2.6 *2.9 *4.2 *5.6 *1.1 *1.1 *0.2 *0.1 0.0 0.0 0.0 0.0 0.0 0.0 th asymbol. #= of the total difference indiet difference ofthetotal than 97%. OTUs with OTUs than97%.

a using a Bayesian Bayesian a a using Package (SAP) andclosest (SAP) Package

he Moorea BIOCODE he Moorea vs. vs.

x 6.2 x 2.4 x 2.4 x 2.6 x 3.2 x 3.7 x 4.0 x 5.7 ution ofOTUs to ution Chromis Pocillopora species species #17.1 x 2.2 2.2 x # 2.0 #1.4 #1.5 #0.5 #1.0 #1.5 #0.8 #0.6 #0.3 #2.3 #0.9 #0.7 #2.4 #2.7

vs. Chromis

Dascyllus Pocillopora x6.1 x0.4 *1.1 *0.8 *0.8 *1.7 *1.5 *1.9 *0.3 *2.2 *2.8 *2.7 *6.2 *1.6 x2.2 *2.3 x2.3 x2.4 x2.5 x3.2 *3.6 *3.8 x5.6 0.0

; vs

This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. (https://doi.org/10.6084/m9.figshare.7551026) from Figshare downloaded be can complete OTUtable outfromothe sp.wassingled Labidocera consumed asfisheggs. ind identifiableare number of OTUs and thetotal each predator each taxonomic found for of reads Table 4 AcceptedFish Branchiostoma sp. Appendicularia Polycheates Gastropod (larvae) (larvae) Stomatopod Shrimp (larvae) (larvae)Crab Article Tanaids Mysids Ostracods Other Isopods Gnathid isopods Amphipods Harpacticoids Cyclopoids Other Calanoids Labidocera sp. Summary of metazoan OTUs by taxonomic group. Summary OTUs ist bytaxonomic SumofReads metazoan of 12572 24545 2192 1592 1176 1129 219 119 838 CV 16 0 0 0 0 1 6 0 6 SUM ofSUM READS 23112 6440 3307 9929 936 159 494 134 138 127 757 DC 24 75 73 0 4 0 0 group. ofidentifi Thenumber 508 807 152

33 29 P 0 0 0 0 0 0 0 0 0 0 8 7 0

CV identifiable 10 10 25 29 17 8 0 0 1 1 0 2 8 1 0 0 8 2 Number of in gutin DC 18 11 39 45 12 6 2 0 3 4 0 7 8 1 0 1 1 9

OTUs P 0 0 0 0 0 0 0 2 1 0 1 7 0 0 4 2 0 1 identifiable identifiable icated. Fish wereicated. mostly OTUs Total able OTUs consumed by consumedby able OTUs r calanoid copepods. The copepods. r calanoid 12 19 12 57 59 15 19 2 0 3 5 0 7 9 1 0 1 2

he totalnumber Crab zoea zoea Crab Tanaids Mysids Ostracods Other Isopods Gnathid isopods Amphipods Cyclopoids/Harpactioids Other Calanoids Labidocera Total Eggs Fish larvae sp. Spadella Branchiostoma Appendicularia Polycheates Gastropods Stomatopod larvae Shrimp larvae decapod Other Crab megalops sp. experimental corals. corals. experimental This article is protected by copyright. All rights reserved. AllrightsThis articleisprotectedby reserved. copyright. Table 5 Accepted sp. Article Abundance of major zooplankton taxa in thecolumn attwo water zooplanktontaxa Abundance ofmajor No. m <0.1 <0.1 16.9 10.4 23.7 83.0 2.0 0.1 0.0 0.2 3.8 7.5 0.0 0.2 0.3 0.0 0.4 0.9 0.9 0.3 5.0 8.0 2.5 ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± 1.4 m -3 37.4 0.7 0.1 0.0 0.0 0.4 2.3 6.0 0.0 0.2 10.7 0.4 7.1 0.0 0.4 1.2 0.6 0.3 3.0 2.0 12.1 2.2

NIGHT 100.0 20.4 12.5 28.6 2.4 0.1 0.0 0.0 0.3 4.6 9.0 0.0 0.2 0.4 0.0 0.5 1.1 1.1 0.3 6.0 9.7 3.0 %

No. m <0.1 <0.1 <0.1 12.5 38.8 3.8 0.0 0.0 0.1 1.1 1.4 0.0 0.4 0.5 0.1 0.2 0.1 0.2 1.4 3.4 1.4 9.1 3.0 ± ± ± ± ± ± ± ± ± ± ± 0.3 m ± ± ± ± ± ± ± ± ± ± ± 0.1 0.3 0.0 0.1 0.3 1.8 1.6 3.1 5.8 4.8 6.1 9.1 1.6 0.0 0.0 0.0 0.2 0.8 1.4 0.0 0.2 0.3 -3

100.0 23.4 32.2 0.2 0.5 0.0 0.2 0.5 3.5 8.9 3.7 7.8 9.7 0.0 0.0 0.0 0.4 2.8 3.6 0.0 1.1 1.3 %

No. m 18.3 0.1 0.5 0.0 0.0 0.4 0.1 0.0 0.3 4.5 2.7 0.1 6.1 0.0 0.0 0.0 0.0 0.2 2.4 0.0 0.0 0.7 ± ± ± ± ± ± ± ± ± ± ± 1.4 m ± ± ± ± ± ± ± ± ± ± ± 0.1 0.3 0.1 0.0 0.4 0.2 0.1 0.3 2.0 2.2 0.2 8.7 3.6 0.0 0.0 0.0 0.1 0.3 1.5 0.0 0.0 0.6 -3

DAY 100.0 24.9 14.9 33.2 13.2 heights above the above heights 0.4 2.6 0.2 0.0 2.1 0.7 0.2 1.7 0.7 0.0 0.0 0.0 0.2 1.3 0.0 0.0 3.8 %

No. m <0.1 <0.1 <0.1 <0.1 <0.1 15.5 0.1 0.1 0.0 0.4 0.3 0.6 0.3 3.7 1.1 0.1 7.8 0.0 0.0 0.0 0.1 0.9 0.0 0.0 ± ± ± ± ± ± ± ± ± ± ± 0.3 m ± ± ± ± ± ± ± ± ± ± ± -3 0.1 0.0 0.1 0.0 0.3 0.3 0.5 0.3 1.8 0.4 0.1 2.0 2.9 0.0 0.0 0.0 0.0 0.3 0.5 0.0 0.0 0.0

100.0 50.6 23.8 0.0 0.0 0.0 0.0 0.7 6.0 0.0 0.0 0.0 0.4 0.0 0.7 0.0 2.4 2.0 4.2 1.8 7.1 0.3 %