SUBJECT INDEX

Note: Page numbers followed by f and t indicate figures and tables, respectively.

AAbiotic factors

Antarctic hard bottoms, 327–328cobbles and caves, 290–292coral reefs

bleaching, 298comprehensive analysis of, 293continental shelf reefs, 295dictyoceratids, 295food for sponges, 299–303geographic edges, 298hurricanes, 297–298Mycale laxissima, 296ordination techniques, 294physiological sensitivity, 298–299role of light, 298–299subhabitats, 294temperature, 298Verongula gigantea, 296

coral reefs—cryptic spaces, 315–316intertidal shores—tropical and

temperate, 325–326mangroves, 317–322sediment-dominated habitats,

seagrass meadows, 322–324walls, plateaus, canyons, 282–284

exploration of, 283Haliclona caerulea, 283–284Jania adhaerens, 283–284sand-sized sediment, 282–283sponge diversity and biomass, 283water movement, 282

Amplified fragment lengthpolymorphisms (AFLPs), 364

Aphanocapsa feldmanni, 240–242, 241fAphrocallistidae, 35–36Aplysina red-band syndrome (ARBS),

250, 251f

Asexual propagules, 376–379external buds, 378internal gemmules, 378–379patchy distributions, 378ftypes of, 377f

Astrophorida, 28–29Axinyssa, 31

BBelize, role of sponges in

Carrie Bow Cay, 215f, 216fCCRE research areas, 215fecology

bioerosion, 255–257, 256fcommercial sponge fishery,

250–253, 251f, 253fdistribution and factor regime,

228–237, 234fimpact of sediment, 254–255, 254fspecies interactions, 237–250,

238f, 241f, 247fmethods

data gathering, 217observational and monitoring

techniques, 217scientific illustration, 218

natural products chemistry andallelopathy, 259–260

reproduction and developmentreproductive biology, 227fTEM, 226–228

silica, carbonate environment,257–259, 258f

systematicsinvasive species, 225new species and taxonomic

revisions, 218–224, 219f, 220f,221f

411

412 Subject Index

Belize, role of sponges in (cont.)

phylogeny and molecular genetics,224–225

Bioerosion, 255–257, 256f

CCalcarea, molecular phylogeny, 42,

46–47Calcaronea, 45–46Calcinea, 44–45Leucosolenida I, 46Leucosolenida II, 46ribosomal RNA-gene sequences, 44ftaxonomic overview of, 42–43

Calcispongiae, 133–139Calcinea and Calcaronea, 137Clathrina, 134t, 137–139, 138fMinchin–Bidder hypothesis, 136–137

Caribbean Coral Reef Ecosystems(CCRE), 213–214, 215f, 217,245–246, 250

Chimerism, 383Chondrosida, 24Clathrina clathrus, 18Clonality, 379–382Coral reefs

abiotic factors

bleaching, 298comprehensive analysis of, 293continental shelf reefs, 295dictyoceratids, 295food for sponges, 299–303geographic edges, 298hurricanes, 297–298Mycale laxissima, 296ordination techniques, 294physiological sensitivity, 298–299role of light, 298–299subhabitats, 294temperature, 298Verongula gigantea, 296

ecological interactionscompetition, 304f, 307–312food for sponges, 299–303macroscopic organisms, 303–307,304f

predation, 313–315

Corticium candelabrum, 15f, 39f, 54fCytochrome oxidase subunit 1 (COI),

351, 355–356, 357, 359,369–370

DDemospongiae, 144–159, 148f

“G4” clade, 25–32Haploscleromorpha, 152, 153fHeteroscleromorpha, G4, 152–159

polyphyletic orders, 155–159,157f, 158f

Spongillida, 154Tetractinellida, 155

Keratosa, 22–23, 147–149marine Haplosclerida, 25mitochondrial genomes, 17Myxospongiae, 23–25, 149–152

Chondrilla, 149–150, 151tChondrosida, 149–150Verongida, 150–152

phylogenetic relationships of, 20ftaxonomic overview of, 19–22

Dendroceratida, 22–23Dictyoceratida, 23Dissolved organic nitrogen (DIN),

242–243Dysidea etheria, 227f

EEcological interactions

Antarctic hard bottoms, 328–329coral reefs

competition, 304f, 307–312food for sponges, 299–303macroscopic organisms, 303–307,

304fpredation, 313–315

coral reefs—cryptic spaces, 316–317intertidal shores—tropical and

temperate, 326–327mangroves, 319–322sediment-dominated habitats,

seagrass meadows, 324–325walls, plateaus, canyons, 284–290,

286fAplysina aerophoba, 289–290

Subject Index 413

Caulerpa, 285cavity-dwelling sponges, 285Clathria pyramida, 288Dendrilla membranosa, 286fHalichondria panicea, 284Haplodoris nodulosa, 288microhabitat protection, 288mollusc and echinodermspongivores, 286f

Mycale acerata, 286fMycale hentscheli, 288Ophiothrix fragilis, 288–289photosynthetic symbionts,284–285, 290

spongivorous fishes, 287–288symbiotic associations, 288–289topography, 287–288

Ecology, spongesbioerosion, 255–257, 256fchimerism, 383clonality, 379–382commercial sponge fishery

ARBS, 250, 251ffine-structure examination, 250Geodia papyracea, 251fHippospongia gossypina, 252, 253f

cryptic speciation and ecologicalrepercussions, molecularmarkers, 352t

allozymes, 351AMOVA, 355–356ATP synthetase, 357–359biodiversity, 349–350Callyspongia vaginalis, 360Chondrilla nucula, 355–356Chondrosia reniformis, 357cosmopolitan sponge species, 350cytochrome oxidase subunit 1,351

genetic and cytological studies,355

ITS sequences, 351Plakina trilopha, 355Scopalina blanensis, 358fScopalina lophyropoda, 358f

distribution and factor regimeIndo-Pacific reefs, 232

Pelican Cays, 230–231physico-chemical determinants,

232–237principles of horizontal

distribution, 228–229submarine caves, 229–230

functional genesbibliometric data, 386fbiomineralization, 385–388cDNA sequence, 387implications, 391–392pollutants, stress, and gene

expression, 388–390symbioses and horizontal gene

transfer, 390–391impact of sediment, 254–255, 254finteractions. See Ecological

interactionspopulation genetics and

phylogeographyallozymes, 362–363amplified fragment length

polymorphisms, 364genetic differentiation, 365–372,

366tmicrosatellites, 364–365mitochondrial gene sequences,

363–364nuclear gene sequences, 363small-scale genetic structure,

372–373temporal genetic structure, 373–374

species interactionscompetition and predation,

237–240, 238fendobioses, 246–250, 247fepizoism, 245–246, 247fphotosynthetic organisms,

240–245, 241fsponge asexual propagules, 376–379,

377f, 378ftrends in, 392–395

Eighth Sponge World Conference ofGirona, 90–91

Epizoism, 245–246, 247fExpressed sequence tag (EST), 4, 5,

55–56

414 Subject Index

FFluorescence in situ hybridization

(FISH), 228

GGastrulation, 52–55, 54f“G4” clade, Demospongiae, 25–32

Spongillina, 27–28Tetractinellida, 28

Agelasids, 29–30Astrophorida, 28–29axinellids, 29–30Clionaidae and Spirastrellidae, 31dictyonellids, 29–30Halichondridae and Suberitidae, 31heteroxyids, 29–30Poecilosclerida sensu stricto, 32Polymastiidae, 31raspailids, 29–30Spirophorida, 29Tethyidae and hemiasterellids,31–32

HHalichondrida, 156, 157–159, 157f, 158fHalisarcida, 24Haplosclerida, 25Heteroscleromorpha, 152–159

polyphyletic orders, 155–159, 157f,158f

Spongillida, 154Tetractinellida, 155

Hexactinellidamitochondrial genomes, 17molecular and morphological data

sets, 131–133, 132f

skeleton of, 131types of spicules, 132f

molecular phylogeny, 33, 37status of, 34–36taxonomic overview of, 33–34

Hexactinosida, 34–35Homoplasy, 108–112

Astrophorida, 111Crambe crambe, 110, 111fMerlia deficiens, 110, 112fMerlia normani, 110, 112f

Homoscleromorpha, 139Levi’s classification, 140molecular phylogeny, 38–39, 41–42

Corticium, 40–41internal relationships of, 40fPlakina, 40–41Pseudocorticium, 40–41taxonomic overview of, 39–40

Oscarella, 40–41, 140–143morphological, anatomical,

cytological and ecologicalcharacters, 145t

Oscarella balibaloi, 144fOscarella lobularis, 144fOscarella tuberculata, 144fOscarella viridis, 144fvacuolar cells, 146fWorld Porifera Database, 141t

IIGP. See Intragenomic polymorphisms

(IGP)Integrative taxonomy, 101–105

data sets, 102–104, 104tintegration by congruence, 104–105integration by cumulation, 104–105Minchin–Bidder hypothesis,

136–137polymorphic morphology, 104–105taxonomic circle, 101–102, 102f, 103f

Internal transcribed spacers (ITSs),347–348, 351, 356–357

IGP, 363nuclear ribosomal, 368phylogeographic studies, 363sequences, 368–369variability of, 364–365

Intragenomic polymorphisms (IGP),347–348, 363

Ircinia, 167–168ITSs. See Internal transcribed spacers

(ITSs)

KKeratosa, 22–23, 147–149

Dendroceratida, 22–23Dictyoceratida, 23

Subject Index 415

LLyssacinosida, 34–35, 35f

MMarine Haplosclerida, 25Mesoamerican barrier-reef ecosystem,

Belize. See Belize, role ofsponges in

Metabolic fingerprinting, 128–130, 129fMitochondrial DNA (mtDNA)

genomes of sponges, 16–18phylogenetic inference, 18

MLGs. SeeMultilocus genotypes (MLGs)Molecular ecology era, sponges

biomineralization, 385–388chimerism, 383clonality in sponge populations

Casex index, 381genetic composition, 380microsatellites, 381–382MLG, 380–381molecular techniques, 382

cryptic speciation and repercussions,352t

AMOVA, 355–356ATP synthetase, 357–359Callyspongia vaginalis, 360Chondrilla nucula, 355–356Chondrosia reniformis, 357genetic and cytological studies,355

Plakina trilopha, 355role of molecular markers,349–351

Scopalina blanensis, 358fScopalina lophyropoda, 358f

ecological implications, 391–392genetic differentiation, geographical

scales, 365–372, 366tintraspecies level

allozymes, 362–363amplified fragment lengthpolymorphisms, 364

microsatellites, 364–365mitochondrial gene sequences,363–364

nuclear gene sequences, 363

pollutants, stress, and geneexpression, 388–390

small-scale genetic structure,372–373

sponge asexual propagules, 376–379external buds, 378internal gemmules, 378–379patchy distributions, 378ftypes of, 377f

symbioses and horizontal genetransfer, 390–391

temporal genetic structure, 373–374trends in, 392–395

Molecular Operational TaxonomicUnits (MOTUs), 175

Molecular phylogenyCalcarea, 42, 46–47

Calcaronea, 45–46Calcinea, 44–45Leucosolenida I, 46Leucosolenida II, 46ribosomal RNA-gene sequences,

44ftaxonomic overview of, 42–43

Demospongiae, 18–19, 32–33“G4” clade, 25–32Keratosa, 22–23marine Haplosclerida, 25Myxospongiae, 23–25phylogenetic relationships of, 20ftaxonomic overview of, 19–22

Hexactinellida, 33, 37status of, 34–36taxonomic overview of, 33–34

Homoscleromorpha, 38–39, 41–42Corticium, 40–41internal relationships of, 40fOscarella, 40–41Plakina, 40–41Pseudocorticium, 40–41taxonomic overview of, 39–40

MOTUs. See Molecular OperationalTaxonomic Units (MOTUs)

mtDNA. See Mitochondrial DNA(mtDNA)

Multilocus genotypes (MLGs),380–381

416 Subject Index

Myxospongiae, 23–25, 149–152Chondrilla, 149–150, 151tChondrosida, 24, 149–150Halisarcida, 24Verongida, 24–25, 150–152

O2-5’-Oligoadenylate synthetase (OAS),

390

PPad one homologue (POHL), 389–390Pelican Cays, 230–231Petrobiona massiliana, 45–46Phylogeography, 362–375Phylum Porifera. See SpongesPoecilosclerida sensu stricto, 32POHL. See Pad one homologue

(POHL)Polychlorinated biphenyl (PCB),

388–389Polymastia mamillaris, 167Polymastiidae, 31

RRemotely operated vehicles (ROVs),

83, 88–90, 89f

SSarostegia, 35–36SBP. See Sponge Barcoding Project

(SBP)Scanning electron microscopy (SEM)

choanocyte chambers, 119fcinctoblastula larvae, 123fcyanobacteria, 251flithistid sponge, 221fmicrostructures of microscleres, 107Scopalina ruetzleri, 227fuse of, 107

Sclerocyte (sc), 39fSEM. See Scanning electron

microscopy (SEM)Simple sequence repeats (SSRs), 348,

364–365Single nucleotide polymorphisms

(SNP), 393

Spatial genetic structure (SGS), 373Spirophorida, 29Sponge Barcoding Project (SBP), 125Sponges

abiotic factors

Antarctic hard bottoms, 327–328cobbles and caves, 290–292coral reefs, 292–315coral reefs—cryptic spaces,

315–316intertidal shores—tropical and

temperate, 325–326mangroves, 317–322sediment-dominated habitats,

seagrass meadows, 322–324walls, plateaus, canyons, 282–284

Aplysina cauliformis, 259biotic factors, 290–292Calcarea, 42, 46–47

Calcaronea, 45–46Calcinea, 44–45Leucosolenida I, 46Leucosolenida II, 46ribosomal RNA-gene sequences,

44ftaxonomic overview of, 42–43

Calcispongiae, 133–139Calcinea and Calcaronea, 137Clathrina, 134t, 137–139, 138fMinchin–Bidder hypothesis,

136–137Callyspongia vaginalis, 300chemical characters

chemotaxonomical characters,126–127

metabolic fingerprinting,128–130, 129f

Chondrosia reniformis, 116fClathrina clathrus, 115fCliona delitrix, 300–301cytology and choanosome anatomy,

113–120, 115f, 117t, 119f, 120fdata sets, 106tDemospongiae, 18–19, 32–33,

144–159, 148fcomposition of, 144–147“G4” clade, 25–32

Subject Index 417

Haploscleromorpha, 152, 153fHeteroscleromorpha, G4,152–159, 157f, 158f

Keratosa, 22–23, 147–149marine Haplosclerida, 25Myxospongiae, 23–25, 149–152,151t

phylogenetic relationships of, 20ftaxonomic overview of, 19–22

distribution and abundance, 278–280community dynamics, 279–280Great Barrier Reefs, 278sponge communities, 278Tedania ignis, 278–279trophic interactions, 280

diversity, 281DNA barcoding, 125ecological interactions

Antarctic hard bottoms, 328–329coral reefs, 299–315coral reefs—cryptic spaces, 316–317intertidal shores—tropical andtemperate, 326–327

mangroves, 319–322sediment-dominated habitats,seagrass meadows, 324–325

walls, plateaus, canyons, 284–290,286f

ecologyabiotic factors, 234fAphanocapsa feldmanni, 240–242,241f

asexual propagules, 376–379, 377f,378f

bioerosion, 255–257, 256fbiotic interactions, 239Callyspongia vaginalis, 247fCervicornia cuspidifera, 254fchimerism, 383clonality, 379–382commercial sponge fishery,250–253, 251f, 253f

competition and predation,237–240, 238f

cryptic speciation, 349–362, 352t,358f

Desmapsamma anchorata, 238f

Dictyonella funicularis, 241fDIN, 242–243endobioses, 246–250, 247fendobiotic algae and microbes, 241fepizoism, 245–246, 247ffast-growing sponges, 240functional genes, 384–392, 386fHalecium bermudense, 245–246Haliclona tubifera, 254fhorizontal distribution, 228–229impact of sediment, 254–255, 254fIndo-Pacific reefs, 232Lissodendoryx colombiensis, 238fLysmata pederseni, 247f, 248mangrove roots, 237–239Mycale laxissima, 241fOphiotrix lineata, 247fParazoanthus parasiticus, 246Pelican Cays, 230–231photosynthetic organisms,

240–245, 241fphysico-chemical determinants,

232–237, 234fPlakortis halichondrioides, 242–243population genetics and

phylogeography, 362–375, 366tseagrass meadows, 240Spheciospongia vesparium, 254fsubmarine caves, 229–230Synechococcus spongiarum, 240–242Tectitethya crypta, 254fTwin Cays, 233, 234f

Escherichia coli, 300–301evolution of sponge development,

57–58Amphimedon queenslandica, 48animal embryonic development

progresses, 48blastomere reorganization, 54fvs. eumetazoan development,

55–56gastrulation, embryogenesis,

52–55, 54fmultiplication of, 58parenchymella larva, 50–52, 50freproduction and spermatozoon

ultrastructure, 49

418 Subject Index

Sponges (cont.)external features, 112–113, 114f,

115f, 116fHemimycale columella, 114fHexactinellida, 33, 37, 131–133

skeleton of, 131status of, 34–36taxonomic overview of, 33–34types of spicules, 132f

Hexadella pruvoti, 115fHexadella racovitzai, 115fhigher-level non-bilaterian

relationshipsanalysis of 18S rDNA, 10–11Ctenophora, 5EST data, 5Metazoa, 6–7, 6fmonophyletic/paraphyletic,7–13, 8t

phylogenetic signal, 4phylogenomic analyses, 4–5status of, 13–16, 14f, 15f

Homoscleromorpha, 38–39, 41–42,139

Corticium, 40–41internal relationships of, 40fLevi’s classification, 140Oscarella, 40–41, 140–143, 141t,144f, 145t, 146f

Plakina, 40–41Pseudocorticium, 40–41taxonomic overview of, 39–40

international sponge conferences, 82fLamellodysidea chlorea, 301–302methods

data gathering, 217observational and monitoringtechniques, 217

scientific illustration, 218molecular markers

phylogeny and systematics, 124–126a-taxonomy, 124

Monachora arbuscula, 259monographs, 84fmtDNA in sponge phylogenetics

genomes of, 16–18phylogenetic inference, 18

natural products chemistry andallelopathy, 259–260

Petrosia ficiformis, 116fPhorbas fictitius, 114fpropositions for

Linnaean classification, 170–173,174t

phantom species, 175PhyloCode, 173–174, 174tSystema Porifera, 176–178

reproduction and early developmentDysidea etheria, 227fFISH, 228Scopalina ruetzleri, 227fTedania ignis, 227fTEM, 226–228

reproductive strategies, 120–124external fertilization, 123flarvae of Calcispongiae, 122fovoviviparity, 120–122, 121f

silica, carbonate environment,257–259, 258f

skeletonsdiversity of, 107, 108f, 109fhomoplasy, 108–112, 111f,

112fvirtual 3D isosurface, 109f

spherulous cells, 120fSpiculidendron corallicolum, 257–258,

258fsponge biology, 83tsponge taxonomy

errors/uncertainties, databases,161–162

geographical areas/biotopes,87–90

Indian Ocean and Mediterraneanelephant ear sponges, 169

loss of knowledge, 160–161loss of type material, 162–168,

163tMediterranean/NE Atlantic

Hymedesmia–Phorbas paupertas,169–170, 169f

molecular phylogeny, 90–91Systema Porifera, 85–87, 159–160

sunlight, 301

Subject Index 419

systematicsAgelas clathrodes, 220fChondrilla caribensis, 220fCliona caribbaea, 222–223Coelosphaera biclavata, 218, 219fGastrophanella cavernicola, 221f,223–224

Haliclona magnifica, 220finvasive species, 225Iotrochota birotulata, 223–224Lissodendoryx, 224multidisciplinary work, 222Mycale citrina, 220fphylogeny and molecular genetics,224–225

SEM micrographs, 221fSpheciospongia vesparium, 221, 254fSvenzea zeai, 220fTedania klausi, 220f, 223–224

theoretical frameworkcladistics and morphology, 91–93integrative taxonomy, 101–105,102f, 103f, 104t

Linnaean classification toPhylocode, 93–101, 95f, 97f, 99t

SSRs. See Simple sequence repeats(SSRs)

Sycon, 46

TTEM. See Transmission electron

microscopy (TEM)Transmission electron microscopy

(TEM)Acrochaetium filament, 241fcyanobacterium, 251fSvenzea, 226–228

VVerongida, 24–25

WWorld Porifera Database (WPD),

85–86, 163tChondrilla, 151tClathrina, 134tHomoscleromorpha, 141tMOTUs, 175taxonomic changes,

159–160