10.5061/DRYAD.D0R79
Leray, Matthieu
Smithsonian Institution
Knowlton, Nancy
Smithsonian Institution
Data from: DNA barcoding and metabarcoding of standardized samples reveal
patterns of marine benthic diversity
Dryad
dataset
2016
Tardigrada
Capitellidae
Laminariales
Caprella scaura
Halichondriidae
Enteropneusta
Bathycoccus prasinos
Leptothecata
Loxosomatidae
Electridae
Cephalothrix
Torpediniformes
Papyridea semisulcata
Corallimorpharia
Scyphozoa
Nassariidae
Champia parvula
Neogonodactylus bredini
Mesogastropoda
Coscinodiscophyceae
Imbricatea
Cirratulidae
Tricladida
Tortanus discaudatus
Teredinidae
Myliobatiformes
Ostracoda
Ampithoidae
Loxosomella aloxiata
Amphibalanus improvisus
Ceramium
Eustigmatophyceae
Bangiales
Chondrosida
Styelidae
Tanaidacea
Marphysa sanguinea
Bugula stolonifera
Enoplida
Operational Taxonomic Units
Gymnodiniales
Facelinidae
Ascidia virginea
Thecosomata
Palaeonemertea
Panopeidae
Centropagidae
Philinopsis pusa
Loxocorone allax
Tubificidae
Loxomitra mizugamaensis
Tubificoides brownae
Cardiidae
Dictyochophyceae
Petrolisthes armatus
Anthomedusae
Leptocheliidae
Dendroceratida
Hargeria rapax
Alcyonidium verrilli
Didemnum psammatode
Majidae
Veneridae
Amoebozoa
Balanidae
Echinodermata
Gobiosoma robustum
Ostrea equestris
Clymenella torquata
Chaetonotida
Caprellidae
Myzozoa
Watersipora subovoidea
Sipuncula
Aphelenchida
Ctenophora
Isopoda
Neogastropoda
Ceramiales
Cliona celata
Chelonibia testudinaria
Ensis directus
Opsanus tau
Ctenogobius stigmaticus
Coryphopterus glaucofraenum
Ostreoida
Bacillariophyceae
Rhodophyta
Acartia tonsa
Tortanidae
Dyspanopeus sayi
Sphacelariales
Thalassionematales
Cystocloniaceae
Seriata
Pseudoscourfieldiales
Clavelinidae
Entomobryomorpha
Gonodactylidae
Gobiosoma ginsburgi
Hippolytidae
Chlorellales
Homosclerophorida
Pycnococcaceae
Monocorophium insidiosum
Aphragmophora
Scleractinia
Leitoscoloplos robustus
Amphibalanus eburneus
Branchiopoda
Diadumenidae
Polynoidae
Sthenelais boa
Cilicaea
Griffithsia globulifera
Chironephthya
Tergipedidae
Schizoporella errata
Leitoscoloplos fragilis
Gracilariaceae
Nidaliidae
Lutjanidae
Plocamiales
Nudibranchia
Temora longicornis
Watersiporidae
Prasinococcaceae
Darwinella
Coullana
Anthozoa
Melosirales
Scrupocellaria
Amphinomida
Panopeus occidentalis
Bigyra
Bugulidae
Mithraculus forceps
Striatellales
Bivalvia
Cephalothricidae
Pleopis polyphemoides
Stolidobranchia
Stomatopoda
Biflustra arborescens
Polychaeta
Plakobranchidae
Polyplacophora
Agardhiella subulata
Placida dendritica
Maxillopoda
Erichsonella attenuata
Phascolion cryptum
Cephalaspidea
Hesionidae
Onslowiales
Dictyotaceae
Batrachoididae
Raja eglanteria
Jassa marmorata
Obelia bidentata
Sabellidae
Gymnodinium
Chelonaplysilla erecta
Terebellida
Enoplea
Fucales
Gigartinales
Polysiphonia
Monogononta
Prasinophyceae
Chaetognatha
Lumbrineridae
Octopoda
Evadne spinifera
Mysidae
Mytilus
Haplosclerida
Ischyroceridae
Valenciniidae
Chalinidae
Ercolania fuscata
Calyptraeidae
Urosalpinx cinerea
Onygenales
Hermaeidae
Pedinophyceae
Chordata
Dactylopodida
Proceraea fasciata
Mamiellaceae
Caprella penantis
Podarke obscura
Neosiphonia
Ophiuroidea
Hippolyte zostericola
Stephanopyxidaceae
Amphipoda
Wrangeliaceae
Actinaria
Ophiactidae
Solitaria
Calanoida
Didemnidae
Perciformes
Dendrochirotida
Triceratiales
Acoela
Plagiorchiida
Platyhelminthes
Podocopida
Hermaea cruciata
Pharidae
Centroceras hyalacanthum
Eunicidae
Surirellales
Acantholobulus bermudensis
Mamiellales
Bacillariales
Monostilifera
Nuculida
Capitellida
Crassostrea virginica
Mactridae
Orbiniidae
Rajidae
Sabellida
Polydora cornuta
Nemertea
Pleosporales
Haplotaxida
Baseodiscus cf. delineatus
Tubificoides wasselli
Platysiphonia
Ostreidae
Sarcomeniaceae
Halichondrida
Clavelina oblonga
Anopla
Aplousobranchia
Diadumene leucolena
Ilyanassa
Agaricomycetes
Eucratopsis crassimanus
Chimaeriformes
Florideophyceae
Maldanidae
Myoida
Trachymedusae
Myrianida pachycera
Sporidiales
Lumbrineris cf. perkinsi
Echiurida
Temoridae
Florenciellales
Turbellaria
Thalassiosirales
Cyclopoida
Gammaridae
Baseodiscus delineatus
Cucumariidae
Coelosphaeridae
Cassiopeidae
Vaucheria litorea
Canistrocarpus cervicornis
Placida kingstoni
Mytiloida
Lepidonotus humilis
Echiniscoididae
Phascoliidae
Chthamalus proteus
Gastrotricha
Poecilosclerida
Ctenostomatida
Palmariales
Meioceras nitidum
rotifera
Phyllodocida
Scionides reticulata
Bowerbankia maxima
Paracaprella tenuis
Ceramiaceae
Phlebobranchia
Hemichordata
Echiura
Xanthophyceae
Harrimaniidae
Membraniporidae
Oxynoidae
Semaeostomeae
Arachnida
Desmodorida
Prasinococcales
Gobiidae
Charophyta
Dasyatidae
Haminoea antillarum
Agaricales
Ascidiidae
Bryozoa
Eurotiales
Eurotiomycetes
Polyandrocarpa zorritensis
Aciculata
Poecilostomatoida
Balanoidea
Alcyonidiidae
Anthoathecata
Demospongiae
Ectocarpus siliculosus
Golfingiida
Clionaidae
Xenacoelomorpha
Gymnolaemata
Polysiphonia sertularioides
Spionida
Nuculidae
Cassiopea
Polycirrus
Elysia subornata
Bangiophyceae
Hypnea
Chthamalidae
Bittiolum varium
Nucula proxima
Arcellinida
Eurotatoria
Porifera
Centropomidae
Cerithiidae
Canuellidae
Mamiellophyceae
Clitellata
Chelonibiidae
Zygonemertes virescens
Monocorophium acherusicum
Dictyotales
Gastropoda
Symplegma rubra
Vaucheriales
Capitella
Basidiomycota
Labyrinthulea
Alpheidae
Synalpheus hemphilli
Pantopoda
Tubificoides diazi
Echiuroinea
Rhodomelaceae
Sigalionidae
Sipunculidea
Porcellanidae
Gobiesox
Siphonostomatoida
Campanulariidae
Sepiolida
Branchiomma cf. bairdi
Urediniomycetes
Amphipholis cf. squamata
Rhizosoleniales
Oomycota
Rhodymeniales
Dothideomycetes
Chlorophyta
Hadromerida
Rhizostomae
Mastigias
Discosea
Lissoclinum fragile
Glyceridae
Rajiformes
Ectocarpaceae
Mytilus edulis
Centropomus undecimalis
Poduromorpha
Hymeniacidon
meiofauna
Aspidochirotida
Dinophyceae
Podon intermedius
Veneroida
Sargassaceae
Canalipalpata
Tergipes tergipes
Decapoda
Mastigiidae
Chordariales
Crepidula convexa
Podonidae
Prasinoderma coloniale
Gracilaria vermiculophylla
Ophiothrix
Heteromysis formosa
Sagittoidea
Paguridae
Penilia avirostris
Thyonella gemmata
Squamamoeba japonica
Ampithoe valida
Leptochelia foresti
Entoprocta
Neochildia fusca
Schizoporellidae
Anguinella palmata
Tubulinea
Bhawania heteroseta
Saccoglossus kowalevskii
Eunicida
Gobiesociformes
Idoteidae
Ochrophyta
Chondrichthyes
Monhysterida
Heteronemertea
Anaperidae
Rhabditida
Ophiactis savignyi
Bankia carinata
Prionospio steenstrupi
Petaloconchus keenae
Zoobotryon verticillatum
Trematoda
Chrysopetalidae
Hypocreales
Muricidae
Champiaceae
Bowerbankia tertia
Polycladida
Dondice occidentalis
Phaeophyceae
Himatismenida
Aglajidae
Diplostraca
Gymnodiniaceae
Oxynoe antillarum
Timarete ceciliae sp. nov.
Cephalopoda
Caecidae
Batrachoidiformes
Enterogona
Terebellidae
Oscarellidae
Nemaliales
Stephanopyxis turris
Gobiesocidae
Trypanosyllis zebra
Chromadorea
Coloniales
Alderia modesta
Cercozoa
Tubulanus pellucidus
Haliclona
Syllidae
Blenniidae
Tylenchida
Darwinellidae
Peronosporales
Ceramium virgatum
Echiniscoides
Halisarca dujardini
Cnidaria
Sessilia
Mysida
Enopla
Autonomous Reef Monitoring Structures
Ascomycota
Mesostigmatophyceae
Thraustochytriida
Echiniscoidea
Ammotheidae
Gracilariales
Amphiporidae
Halisarcidae
Glycera dibranchiata
Holothuroidea
Amphibalanus amphitrite
Proceraea rubroproventriculata
Tanystylum orbiculare
Corophiidae
Crepidula plana
Eunice gagzoi
Melita nitida
Harpacticoida
Tubificoides parapectinatus
Haminoeidae
Golfingiiformes
Melitidae
Syndiniales
Bostrycapulus aculeatus
Cymatosirales
Ectocarpales
Styela plicata
Ophiurida
Botrylloides nigrum
Lutjanus griseus
Vermetidae
Candidae
Spionidae
Syndiniophyceae
Hypsoblennius hentz
Monogenea
Ploima
Ophiotrichidae
Sididae
Conopeum tenuissimum
Dasyatis americana
Narcomedusae
Perophora viridis
Lissodendoryx isodictyalis
Membranipora tenuis
Saprolegniales
Streblospio benedicti
Leotiomycetes
Sphaeromatidae
Mermithida
Trebouxiophyceae
Hydrozoa
Vesiculariidae
Acoelomorpha
Nereididae
Centropages hamatus
Acartiidae
Cheilostomatida
Siphonophora
Alcyonacea
Sargassum
Amphiuridae
Chromadorida
Lissomyema mellita
Limapontiidae
Sordariomycetes
Pagurus longicarpus
Echiuridae
Ilyanassa obsoleta
Nolellidae
Littorinimorpha
Solieriaceae
Sedentaria
Perophoridae
Oscarella
Vaucheriaceae
Caenogastropoda
Eubranchidae
Monopisthocotylea
Eubranchus exiguus
Chione cancellata
Mytilidae
Annelida
Bugula neritina
Gammarus mucronatus
Heterotardigrada
Fragilariales
Pycnogonida
Demonax
Euheterodonta
Balanus
Mulinia lateralis
Tubulanidae
oyster reefs
Chaetosphaeridiales
Malacostraca
2016-01-20T00:00:00Z
2016-01-20T00:00:00Z
en
https://doi.org/10.1073/pnas.1424997112
1686849817 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Documenting the diversity of marine life is challenging because many
species are cryptic, small, and rare, and belong to poorly known groups.
New sequencing technologies, especially when combined with standardized
sampling, promise to make comprehensive biodiversity assessments and
monitoring feasible on a large scale. We used this approach to
characterize patterns of diversity on oyster reefs across a range of
geographic scales comprising a temperate location [Virginia (VA)] and a
subtropical location [Florida (FL)]. Eukaryotic organisms that colonized
multilayered settlement surfaces (autonomous reef monitoring structures)
over a 6-mo period were identified by cytochrome c oxidase subunit I
barcoding (>2-mm mobile organisms) and metabarcoding (sessile and
smaller mobile organisms). In a total area of ∼15.64 m2 and volume of
∼0.09 m3, 2,179 operational taxonomic units (OTUs) were recorded from
983,056 sequences. However, only 10.9% could be matched to reference
barcodes in public databases, with only 8.2% matching barcodes with both
genus and species names. Taxonomic coverage was broad, particularly for
animals (22 phyla recorded), but 35.6% of OTUs detected via metabarcoding
could not be confidently assigned to a taxonomic group. The smallest size
fraction (500 to 106 μm) was the most diverse (more than two-thirds of
OTUs). There was little taxonomic overlap between VA and FL, and samples
separated by ∼2 m were significantly more similar than samples separated
by ∼100 m. Ground-truthing with independent assessments of taxonomic
composition indicated that both presence–absence information and relative
abundance information are captured by metabarcoding data, suggesting
considerable potential for ecological studies and environmental
monitoring.
PGM_RAWDATA_file1This file contains raw PGM (Ion Torrent, Life technology)
data for adaptors 7, 8, 10 and 11. See file "PGM_SequencingRun"
for corresponding samples.PGM_RAWDATA_file2This file contains raw PGM (Ion
Torrent, Life technology) data for adaptors 12, 13, 14 and 15. See file
"PGM_SequencingRun" for corresponding
samples.Metabarcode_OTU_tableThe column "source ID" presents how
each OTU was identified. SAP: Statistical assignment Package; NCBI/BOLD:
>97% match to a reference barcode in NCBI and/or BOLD barcode
databases; 2mm: match an OTU identified via DNA barcoding in the
>2mm fraction; 500μm: match an OTU identified via DNA barcoding in
the 2mm-500μm fraction The second sheet lists all OTUs that were discarded
because they matched bacterial or non-COI sequences in
NCBI.PGM_SequencingRunThe table presents the strategy used for
multiplexing samples. Full primer sequences are provided in Table
S4Metabarcode_OTUrepresentativesThe file contains one representative
sequence per OTUMetabarcode_discardedOTUrepresentativesThe file contains
one representative sequence per discarded OTU
USA
Eastern Shore
Florida
Virginia
Indian River Lagoon