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Moorea BIOCODE barcode library as a tool for understanding predator-prey interactions: Insights into the diet of common predatory coral reef fishes



Identifying species involved in consumer–resource interactions is one of the main limitations in the construction of food webs. DNA barcoding of prey items in predator guts provides a valuable tool for characterizing trophic interactions, but the method relies on the availability of reference sequences to which prey sequences can be matched. In this study, we demonstrate that the COI sequence library of the Moorea BIOCODE project, an ecosystem-level barcode initiative, enables the identification of a large proportion of semi-digested fish, crustacean and mollusks found in the guts of three Hawkfish and two Squirrelfish species. While most prey remains lacked diagnostic morphological characters, 94% of the prey found in 67 fishes had >98% sequence similarity with BIOCODE reference sequences. Using this species-level prey identification, we demonstrate how DNA barcoding can provide insights into resource partitioning, predator feeding behaviors and the consequences of predation on ecosystem function.
1 23
Coral Reefs
Journal of the International Society for
Reef Studies
ISSN 0722-4028
Coral Reefs
DOI 10.1007/s00338-011-0845-0
Moorea BIOCODE barcode library as
a tool for understanding predator–prey
interactions: insights into the diet of
common predatory coral reef fishes
M.Leray, J.T.Boehm, S.C.Mills &
1 23
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Moorea BIOCODE barcode library as a tool for understanding
predator–prey interactions: insights into the diet of common
predatory coral reef fishes
M. Leray J. T. Boehm S. C. Mills
C. P. Meyer
Received: 15 August 2011 / Accepted: 7 November 2011
ÓSpringer-Verlag 2011
Abstract Identifying species involved in consumer–
resource interactions is one of the main limitations in the
construction of food webs. DNA barcoding of prey items in
predator guts provides a valuable tool for characterizing
trophic interactions, but the method relies on the avail-
ability of reference sequences to which prey sequences
can be matched. In this study, we demonstrate that the
COI sequence library of the Moorea BIOCODE project,
an ecosystem-level barcode initiative, enables the identifi-
cation of a large proportion of semi-digested fish, crusta-
cean and mollusks found in the guts of three Hawkfish and
two Squirrelfish species. While most prey remains lacked
diagnostic morphological characters, 94% of the prey
found in 67 fishes had [98% sequence similarity with
BIOCODE reference sequences. Using this species-level
prey identification, we demonstrate how DNA barcoding
can provide insights into resource partitioning, predator
feeding behaviors and the consequences of predation on
ecosystem function.
Keywords Trophic interactions Diet analysis
Food web DNA identification Hawkfish Squirrelfish
The high biodiversity of coral reefs means that ecologists
are confronted with a complex task of species identification
in their quest for understanding community-level processes
and interactions. Subtle differences in diagnostic pheno-
typic characters, presence of morphologically cryptic and
undescribed species, and lack of identification guides for
early life stages hinder reliable species-level identification
in routine ecological studies (Hebert et al. 2003). Fortu-
nately, DNA barcoding can be used to supplement tradi-
tional taxonomy when their DNA matches species-specific
sequences available in barcode reference libraries.
Witnessing direct predator–prey interactions in the field
is challenging (Merfield et al. 2004); therefore, DNA-based
techniques are increasingly used for characterizing
predator diet from feces/gut content (King et al. 2008).
Prey-specific DNA fragments can be amplified from semi-
digested prey (Zaidi et al. 1999; Dunn et al. 2010), and
prey sequences can be identified if reference barcode dat-
abases contain a comprehensive list of species consumed.
Despite the growing availability of reference databases,
large proportions remain unidentified particularly from
generalist diets (Blankenship and Yayanos 2005; Dunn
et al. 2010).
Among various ongoing barcoding initiatives, the
Moorea BIOCODE project (
is an ‘‘All Taxa Biotic Inventory’’ whose goal is to provide
Communicated by Biology Editor Dr. Hugh Sweatman
M. Leray (&)S. C. Mills
Laboratoire d’Excellence ‘‘Corail’’ USR 3278 CNRS EPHE,
CRIOBE-CBETM, Universite
´de Perpignan,
56 Avenue Paul Alduy, 66860 Perpignan Cedex, France
M. Leray C. P. Meyer
Department of Invertebrate Zoology, National Museum
of Natural History, Smithsonian Institution, P.O. Box 37012,
MRC-163, Washington, DC 20013, USA
J. T. Boehm
Biology Department, Queens College,
City University of New York, Flushing, NY 11367, USA
J. T. Boehm
The Graduate Center, City University of New York,
New York, NY 10016, USA
Coral Reefs
DOI 10.1007/s00338-011-0845-0
Author's personal copy
a library of genetic markers for all non-microbial species of
the French Polynesian tropical ecosystem. From 2006 to
2010, teams of researchers have worked to sample mac-
robiotic species ([5,670 species C2 mm) of which 3,877
(68%) are coral reef species. All specimens were identified
morphologically to lowest taxon level, photographed and
their tissue sampled for DNA barcoding. A library of
species-specific DNA signatures amplified from a single
homologous region, the cytochrome coxidase subunit I,
was constructed for most animals. Reference specimens
were sent to museum collections. All information, from the
collection of specimens to their sequencing, was central-
ized in BIOCODE’s field and laboratory information
management systems. As of April 2011, reference data
exist for 28 marine phyla, with an emphasis on arthropods,
chordates and mollusks ( The
barcode inventory of this model ecosystem will allow
researchers to overcome many limitations inherent in
morphology-based identification when species-level infor-
mation is required, for example to understand predator
feeding ecology and food web dynamics.
Here, we used direct sequencing to identify prey
remains in the stomachs of five common predator fish on
Moorean reefs with contrasting feeding regimes: three
hawkfish, Paracirrhites arcatus,P.forsteri and P.hemis-
tictus (Order: Perciformes; Family: Cirrhitidae), and two
squirrelfish, Sargocentron microstoma and S.tiere (Order:
Beryciformes; Family: Holocentridae). The three hawkfish
species commonly occupy coral colonies of the genus
Pocillopora where they sit and wait for prey during the day
(Kane et al. 2009). In contrast, the two squirrelfish species
actively look for benthic prey at night (Arias-Gonzalez
et al. 1998; Randall 2005). We aimed to: (1) assess the
proportion of prey that matched BIOCODE reference
sequences in order to evaluate the efficacy of BIOCODE’s
efforts to inventory macro-invertebrates and fishes and
(2) investigate how species-level prey identification could
provide insights into resource partitioning and feeding
behaviors in relation to the life history traits of predators as
well as into the consequences of predation on ecosystem
function. As this is the first attempt to characterize the diet
of coral reef-associated predators using DNA-based tech-
niques, this approach provides great promise for under-
standing complex trophic interactions.
Materials and methods
Fish collection and gut content dissection
A total of 67 adult carnivorous fish (33 P.arcatus,11
P.forsteri,7P.hemistictus,8S.microstoma and 8 S.tiere)
were speared on the north shore forereef of Moorea, French
Polynesia (17°300S, 149°500W), during the Austral Winters
of 2009 and 2010. The diurnal species (Paracirrrhites spp.)
were sampled at dusk, while the nocturnal predators
(Sargocentron spp.) were collected both at dawn and 2 hrs
after dusk. We did not observe prey regurgitation while
capturing predators. Fishes were preserved in cold 50%
ethanol in situ. In the laboratory, stomach contents were
dissected, and all visually distinguishable prey items
identified to the lowest taxon possible based on morphol-
ogy. Tissue samples were then taken from these prey
remains, rinsed with distilled water, counted and placed in
individual tubes for extraction and barcoding. Remaining
stomach contents were discarded, which is likely to have
biased our results toward larger and hard prey items that
better resist digestion.
DNA analysis and sequence identification
Total genomic DNA was extracted using automated
phenol–chloroform extraction with the Autogenprep 965
(Autogen, MA) with a final elution volume of 100 ll. COI
fragments were PCRed as 20-ll reactions with 0.6 llof
10 lM of each universal forward and reverse primers
(Folmer et al. 1994), 0.2 ll of Biolase taq polymerase
(Bioline) 5 U ll
, 0.8 llof50mMMg
dNTP and 1 ll of genomic DNA. PCR conditions were as
follows: 5 min at 95°C; 35 cycles of 30 s at 95°C; 30 s at
48°C; 45 s at 72°C; and a final 5 min at 72°C. Sequences
were identified based on similarity to the BIOCODE
sequence library using BLAST (Altschul et al. 1997)
searches performed in Geneious Pro 5.0.3 (Biomatters).
COI sequences were then assigned to taxonomic groups
according to criteria defined by Machida et al. (2009) and
Plaisance et al. (2009). Sequences were considered to
match reference specimens when sequence similarity was
[98%. In order to test whether our sampling effort was
sufficient, expected species accumulation curves with
95% confidence intervals were computed using EstimateS
(Colwell et al. 2004).
Results and discussion
Of the 67 fish speared, 52 had visually distinguishable prey
remains in their stomach encompassing 102 total individual
prey items. The majority of fish had only one visually
distinguishable prey item, but number of prey items ranged
from 0 to 7 (Fig. 1). Based on the size of observed hard
parts, all crustacean and mollusks were consumed as adults
while fish had been preyed upon as juveniles. Morpho-
logical identification of crustacean appendages (62 items)
and fish fins (23 items) rarely provided identifications
lower than the family level. Only two crustacean prey
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items from two P.arcatus were identified to the species
level (Menaethius monoceros). Morphological identifica-
tion therefore achieved less than 2% success at species
level, later verified by DNA.
On the other hand, COI sequences obtained from 96
(of 102) prey items showed higher than 98% levels of
sequence similarity with BIOCODE reference sequences
(Table 1). In comparison, only 16 prey items (8 species)
had less than 98% similarity with sequences in GenBank
(excluding BIOCODE-generated sequences—Table 1).
Of the four remaining crustacean sequences without [98%
matches, one was identified to the family Parthenopidae
(85% similarity), while three remaining crustaceans could
not be confidently assigned to any taxonomic group (\80%
similarity). Two sequences matching bacterial DNA frag-
ments were discarded. Overall, 94% of the sequences were
identified to species level using COI sequences, demon-
strating the efficiency with which BIOCODE has sampled
fish, macro-crustaceans and macro-mollusks from the
Moorea reef community (GenBank accession numbers
Despite the high level ([98%) of sequence similarity,
BIOCODE reference specimens could not provide species
names to 13 prey items: 1 fish, 10 crustacean and 2 mollusks.
These vouchered specimens either are undescribed species
(e.g., Galatheidae) or require further taxonomic work for
correct identification. Two prey items matched specimens
with identical names (Chlorodiella laevissima) but are
genetically distinct (K2P dist. ±SE =0.103 ±0.014),
suggesting the presence of cryptic lineages. Taxonomic
refinement and new species descriptions are ongoing as part
of the BIOCODE project. A large proportion of the crusta-
cean database is publically available on BOLD (Project
MBMIA), and fishes will be released upon final acceptance
of a manuscript under revision. All comparative data will be
made public by July 2012 according to funding obligations.
The rarefaction curve indicates that additional fish col-
lections would be required to better characterize the diet of
these predatory species (Fig. 2). Additionally, despite these
five species being known to consume mostly other fish,
crustacean and mollusks, our dietary analysis likely missed
soft-bodied prey species that can be detected using PCR
amplification and sequencing from the whole-gut content
tissue homogenate (Jarman et al. 2004; Deagle et al. 2009).
Despite the need for additional sampling of predator diet,
we discuss how prey identification to the species level
using barcoding can provide novel insights into resource
partitioning, predator feeding behaviors and the potential
consequences of predation on ecosystem function.
Firstly, the degree to which specialization on food
resources enables species coexistence and shapes commu-
nity structure has long been debated (Jones 1991). This
debate has been limited as estimates of the degree of diet
overlap between predator species greatly depends on
taxonomic resolution achieved in dietary studies (Longe-
necker 2007). Paracirrhites forsteri and P.hemistictus,
both large diurnal ambush piscivorous species commonly
found among the branches of large pocilloporid corals
(Kane et al. 2009), had narrow and largely overlapping
diets with a majority of Chromis vanderbilti (80 and 67%
of prey items, respectively) in their guts (Table 1; Fig. 3).
Alternatively, S.microstoma and S. tiere, both mobile
active nocturnal feeders (Arias-Gonzalez et al. 2004),
have broad diets and did not have a single prey species in
common (Fig. 3). Their different diets reinforce the value
of species-level prey identifications, as familial level would
have failed to elucidate the true trophic structure of these
sister species. Paracirrhites arcatus only shared one single
prey species with its congenerics, whereas eight prey spe-
cies were shared with predators that differ in microhabitat
use and time of feeding activity (Fig. 3). These results,
which must be treated with caution due to the limited
number of samples and potentially different digestion rates,
suggest that timing of activity, habitat partitioning and
hunting mode may not accurately predict resource parti-
tioning among reef fish species. The barcode inventory of
the Moorea ecosystem provides an ideal testing ground for
further exploration of the role that resource specialization
plays in shaping patterns of biodiversity.
Secondly, our findings indicate that a few prey species
may provide a considerable source of energy to predators
in the Moorea food web. For instance, C.vanderbilti was
commonly consumed by P. forsteri and P. hemistictus and
Liocarpilodes integerrimus by P. arcatus and S. micros-
toma (Table 1), suggesting that they may be preferential
targets or highly abundant on Moorean reefs.Empirical
evidence suggests that generalist piscivorous predators
forage non-selectively and consume prey in proportion to
their abundance (Heinlein et al. 2010—study in Moorea).
Fig. 1 Number of prey items from the guts of 67 fishes belonging to
five predator species. TL total length
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Table 1 Summary of prey items successfully identified from the stomach contents of fish using COI amplification and BLAST searches in the
BIOCODE barcode library
Subphylum/class Prey ID % identity BIOCODE nBIOCODE specimen Predator ID
Actinopterygii Chromis acares 99 1 MParis0005 ST
Chromis iomelas 99.8 2 MParis0055 PH
Chromis vanderbilti 99–99.5 12 MParis0195 PA, PF, PH
Cirripectes variolosus 100 1 MParis0213 PA
Eviota disrupta 99.7 1 MParis0174 PA
Eviota sp. 99.4 1 XMOO-0047 PA
Neocirrhites armatus
99.2 2 MParis0007 PF, PH
Pseudogramma polyacanthum 99.5 1 MParis0012 ST
Synodus binotatus
98.8 1 MParis586 SM
Valenciennea strigata
100 1 MParis0906 SM
Crustacea Acanthanas pusillus 99.1 1 BMOO-02811 ST
Alpheus dolerus 99.7–100 2 BMOO-00430 PA
Aniculus retipes
100 1 BMOO-01743 ST
Axiidae 98.2 1 BMOO-01079 PA
Brachycarpus biunguiculatus 98 1 BMOO-05348 PA
Calappa gallus 100 1 BMOO-02116 PA
Chlorodiella barbata 100 2 BMOO-00324 PA, SM
Chlorodiella crispipleopa 99.5–99.7 3 BMOO-00726 PA
Chlorodiella laevissima 98.4 1 BMOO-01191 SM
Chlorodiella laevissima 99.8 3 BMOO-02899 ST
Cyclodius ungulatus 98–99.8 2 BMOO-01049 PA, SM
Daldorfia sp. 99.2 1 BMOO-05257 PA
Epialtidae 99.2 1 BMOO-03230 PA
Etisus frontalis 99.7 1 BMOO-00194 PA
Galathea mauritiana
99.5–99.8 2 XMOO-0011 PA, SM
Galathea sp.
99.5–99.8 4 BMOO-02353 PA, ST
Gnathiidae 98.5 1 No voucher PA
Gonodactylus affinis 99.4 1 jg8 PA
Huenia sp. 99.2 1 BMOO-03531 PA
Liocarpilodes integerrimus 98.8–99.8 7 BMOO-01576 PA, SM
Medaeus elegans 99.4 1 BMOO-04008 PA
Menaethius monoceros 98.5–99.5 2 BMOO-03072 PA
Menaethius orientalis 99 1 BMOO-01847 ST
Metalpheus nanus 99.7 1 BMOO-02919 PA
Palaemonella rotumana 100 1 BMOO-02250 PA
Palmyria palmyrensis 100 1 BMOO-01358 PA
Parthenopidae 85 1 No match ST
Perinia tumida 98.5 1 XMOO-0383 PA
Petrolisthes sp. 98.7% 1 BMOO-02308 PA
Phylladiorhynchus sp. 99.6 1 BMOO-03262 PA
Phylladiorhynchus integrirostris 99.2–99.7 4 BMOO-01856 PA
Pilodius flavus 99.5–100 4 BMOO-02998 PA, ST
Pilodius pugil 100 2 BMOO-01102 SM
Saron marmoratus 99 1 BMOO-02912 ST
Saron sp. 98.3 1 No voucher PA
Thalamita sp. 98 2 BMOO-05357 PA, SM
Trapezia flavopunctata 99.7 1 BMOO-02830 ST
Trapezia tigrina 100 2 XMOO-0202 PA
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Conversely, Longenecker (2007) observed a different pat-
tern for predators; despite large ephemeral increases in the
abundance of certain invertebrate prey species, they were
not increasingly consumed by predators. Invertebrate
population sizes, as well as temporal and spatial patterns
of variation in abundance, remain unknown in Moorea.
Therefore, further studies should be conducted to evaluate
diet selection and the role keystone prey species (Power
et al. 1996) play in the persistence of coral reef predators.
Finally, DNA barcoding revealed that the fish predators
feed on prey which themselves are important for habitat
maintenance and ecosystem functioning. Paracirrhites
forsteri and P.hemistictus consumed Neocirrhites armatus,
and P.arcatus had fed upon Trapezia flavopunctata and
T.tigrina, which are all known to benefit Pocilloporids.
Resident fish such as N.armatus provide nutrients to host
polyps (Holbrook et al. 2008), while Trapezia species
increase the survival and growth of their host by removing
sediment from coral tissue (Stewart et al. 2006), defending
against corallivorous seastars (Glynn 1983) and removing
parasitic vermetid gastropod nets (Stier et al. 2010).
Further investigation should determine the functional
consequences resulting from the predation pressure high-
lighted in this study.
Overall, we show that the quality of the barcode refer-
ence database in Moorea will enable researchers to uncover
the complexity and spatial–temporal dynamics of food
webs not just in French Polynesia but also throughout the
Western Pacific where taxon ranges likely extend. DNA
barcoding removes subjectivity biasing prey identification
compared to visual identification and is particularly valu-
able for reef fish prey identification given the high eco-
system biodiversity. Such promises for understanding the
functioning of natural systems should encourage further
ecosystem-based barcoding initiatives worldwide.
Fig. 2 Rarefaction curve for number of prey species as a function of
fish collected with prey in their stomach (N=52). Dashed lines
represent 95% CI
Fig. 3 Venn diagram illustrating the overlap of prey species
consumed by predator fish species. Circle sizes are proportional to
total number of prey species consumed by each predator (parenthe-
ses), and overlap area between circles is proportional to number of
shared prey species. Photographs were provided by Jeffrey Williams
Table 1 continued
Subphylum/class Prey ID % identity BIOCODE nBIOCODE specimen Predator ID
Xanthias latifrons 99.5 1 BMOO-04066 ST
Mollusk Deniatys dentifer
98 3 BMOO-02659 SM
Erato sp.
99.2 2 BMOO-02545 ST
Julia zebra 98.1 1 BMOO-03193 PA
Stomatella rosaceus 99.4 1 BMOO-01483 ST
Stomatolina sp. 99.5 1 BMOO-06132 ST
The BIOCODE reference specimen ID is reported for each prey so that photographs and additional information can be obtained at
n=number of prey. PA: Paracirrhites arcatus; PF: Paracirrhites forsteri; PH: Paracirrhites hemisticus; ST: Sargocentron tiere; SM:
Sargocentron microstoma
Indicates prey COI sequences that also had [98% similarity with sequences in GenBank
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Acknowledgments We thank the BIOCODE teams who collected
marine invertebrates and fish specimen in 2006, the ‘‘Centre de
Recherche Insulaire et Observatoire de l’Environnement (CRIOBE)
de Moorea’’, the Richard B. Gump field station in Moorea for
logistical support and three anonymous reviewers for helpful com-
ments on the manuscript. We also greatly acknowledge the Gordon
and Betty Moore Foundation, Smithsonian Institution Fellowship
Program and France American Cultural Exchange program (FACE—
Partner University Fund) for financial support.
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... Larger taxa may prefer to inhabit rubble via the passive benthic pathway as they have limited mobility (i.e., nonswimming) and/or exhibit high degrees of predator avoidance behavior (Takada et al., 2016). Decapods and cryptobenthic fishes are indeed fundamental prey of coral reef fishes (Brandl et al., 2018(Brandl et al., , 2019Glynn & Enochs, 2011;Kramer et al., 2015;Leray et al., 2012) and must remain cryptic among the reef and rubble infrastructure to avoid mortality. It seems of interest to test how rubble piece size and morphology, patch depth, and consequently, varying degrees of interstitial space, influence emigration patterns and size structuring of the cryptofauna in rubble biomes, and how they may determine the transfer of energy to higher-order taxa in a current and future ocean. ...
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Abstract Patterns of movement of marine species can reflect strategies of reproduction and dispersal, species' interactions, trophodynamics, and susceptibility to change, and thus critically inform how we manage populations and ecosystems. On coral reefs, the density and diversity of metazoan taxa are greatest in dead coral and rubble, which are suggested to fuel food webs from the bottom up. Yet, biomass and secondary productivity in rubble is predominantly available in some of the smallest individuals, limiting how accessible this energy is to higher trophic levels. We address the bioavailability of motile coral reef cryptofauna based on small‐scale patterns of emigration in rubble. We deployed modified RUbble Biodiversity Samplers (RUBS) and emergence traps in a shallow rubble patch at Heron Island, Great Barrier Reef, to detect community‐level differences in the directional influx of motile cryptofauna under five habitat accessibility regimes. The mean density (0.13–4.5 ind cm−3) and biomass (0.14–5.2 mg cm−3) of cryptofauna were high and varied depending on microhabitat accessibility. Emergent zooplankton represented a distinct community (dominated by the Appendicularia and Calanoida) with the lowest density and biomass, indicating constraints on nocturnal resource availability. Mean cryptofauna density and biomass were greatest when interstitial access within rubble was blocked, driven by the rapid proliferation of small harpacticoid copepods from the rubble surface, leading to trophic simplification. Individuals with high biomass (e.g., decapods, gobies, and echinoderms) were greatest when interstitial access within rubble was unrestricted. Treatments with a closed rubble surface did not differ from those completely open, suggesting that top‐down predation does not diminish rubble‐derived resources. Our results show that conspecific cues and species' interactions (e.g., competition and predation) within rubble are most critical in shaping ecological outcomes within the cryptobiome. These findings have implications for prey accessibility through trophic and community size structuring in rubble, which may become increasingly relevant as benthic reef complexity shifts in the Anthropocene.
... Here we investigate whether genetic divergence (a proxy for time) and genitalic divergence are correlated with the emergence of sympatric distributions among related lineages in the IWP crab subfamily Chlorodiellinae. Chlorodielline crabs are some of the most abundant crustaceans inhabiting coral reef environments in the IWP (Peyrot-Clausade 1977, Plaisance et al. 2011, Leray et al. 2012, Lasley et al. 2013, Lasley et al. 2015. Despite their ubiquity, a thorough taxonomic revision of the group is still needed. ...
Molecular studies have revealed that many species once thought to be wide-ranging in the Indo-West Pacific contain allopatric mosaics of endemic lineages. These lineages provide compelling evidence that substantial time is needed to evolve isolating mechanisms sufficient to permit successful secondary sympatry, and that divergence is initiated in allopatry. In this context, questions arise regarding the nature, timing, and origin of isolating mechanisms that permit secondary sympatry. We present a phylogeny of the crab subfamily Chlorodiellinae which displays allopatric mosaics within species. These allopatric lineages typically do not have divergent male genitalia, while older sympatric lineages do. We tested the relationship between genetic distance (proxy for time), sympatry, and the divergence of male genitalic morphology. Our results suggest that male genitalic divergence is not involved in the initiation of speciation in chlorodielline crabs, having likely occurred only after isolation began in allopatry. However, morphological evolution of genitalia seemingly does play an important role in completing the process of speciation in these crabs.
... national DNA reference database for Danish species, DNAmark; Margaryan et al. 2021). Although such initiatives are less common in coral reef ecosystems, one of the most comprehensive COI barcode databases in the world originated on the tropical island of Moorea in French Polynesia (Moorea Biocode Project; Leray et al. 2012) and has subsequently been used for marine metabarcoding primer design (Leray et al. 2013) and to assist with a taxonomic assignment (Casey et al. 2019;Nichols et al. 2022;Timmers et al. 2021Timmers et al. , 2022. That said, it is becoming more common that reference DNA sequences are generated within individual studies to close gaps in existing reference data (Shinzato et al. 2018), in most cases increasing the efficiency of taxonomic assignment (Dugal et al. 2022b; Figure 13.7). ...
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Coral reefs are globally significant repositories of marine biodiversity. Over 25% of all marine life depends on coral reefs at some point in their life cycle. Among the nine million species that live on the world’s coral reefs, many are undescribed. Climate change has emerged as an immediate threat to the survival of both described and undescribed species, disrupting the ecological integrity of coral reefs and jeopardising the livelihoods of millions of people who depend on them. The risk of biodiversity silently slipping away on coral reefs increases simultaneously with the scale and frequency of climate and anthropogenic threats. More targeted research is needed to understand the form and function of biodiversity and the extent and pace at which resident flora and fauna disappear. The development of environmental DNA (eDNA) approaches, i.e. the recovery of genetic information from environmental samples, provides exciting opportunities to revolutionise coral reef biodiversity monitoring and our ability to document the extent and rate of change in complex ecosystems. This chapter provides an overview of the field of eDNA and its strengths and challenges, focusing on metabarcoding and its relevance to biodiversity monitoring in coral reef ecosystems with a glimpse into future uses of novel eDNA technologies.KeywordsBiodiversityConservationCoral reefDetectionEcosystem monitoringEnvironmental DNAeRNAMetabarcodingWeb of life
... However, most survey studies have typically focused on conspicuous reef taxa (e.g., corals, fish and macroalgae; Huang et al., 2009;Leray et al., 2012;Wells et al., 2019), with more attention paid to microbes only in recent years (Afiq-Rosli et al., 2021;Oh et al., 2021;Pearman et al., 2019;Wainwright, Bauman et al., 2019). The paucity of empirical data on drivers of reef cryptobiome diversitycomprising organisms colonizing hidden areas within the reef structural complex-is evident . ...
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Coral reefs are among the richest marine ecosystems on Earth, but there remains much diversity hidden within cavities of complex reef structures awaiting discovery. While the abundance of corals and other macroinvertebrates are known to influence the diversity of other reef‐associated organisms, much remains unknown on the drivers of cryptobenthic diversity. A combination of standardised sampling with 12 units of Autonomous Reef Monitoring Structures (ARMS) and high‐throughput sequencing was utilised to uncover reef cryptobiome diversity across the equatorial reefs in Singapore. DNA barcoding and metabarcoding of mitochondrial cytochrome c oxidase subunit I, nuclear 18S and bacterial 16S rRNA genes revealed the taxonomic composition of the reef cryptobiome, comprising 15,356 microbial ASVs from over 50 bacterial phyla, and 971 MOTUs across 15 metazoan and 19 non‐metazoan eukaryote phyla. Environmental factors across different sites were tested for relationships with ARMS diversity. Differences among reefs in diversity patterns of metazoans and other eukaryotes, but not microbial communities, were associated with biotic (coral cover) and abiotic (distance, temperature and sediment) environmental variables. In particular, ARMS deployed at reefs with higher coral cover had greater metazoan diversity and encrusting plate cover, with larger‐sized non‐coral invertebrates influencing spatial patterns among sites. Our study shows that DNA barcoding and metabarcoding of ARMS constitute a valuable tool for quantifying cryptobenthic diversity patterns and can provide critical information for the effective management of coral reef ecosystems.
... et al., 2018) and have already proved useful in elucidating complex species and trophic interactions(García-Robledo et al., 2013). For instance, DNA metabarcoding analysis from gut content or bulk samples has illuminated different nodes across various food webs and reconstructed the trophic links in terrestrial(Gogarten et al., 2020;Wirta et al., 2014Wirta et al., , 2016Wirta, Vesterinen, et al., 2015;, aquatic(Leray et al., 2012;Leray et al., 2015), and often inaccessible environments, such as deep-sea beds, hydrothermal vents, and coldseeps(Olsen et al., 2014). Several reviews to date have summarized the history, achievements, and current applications of studying species interaction using DNA metabarcode methods across multiple fields(Clare, 2014;Evans et al., 2016;Kress et al., 2015;Pompanon et al., 2012;Symondson, 2002;Valentini et al., 2009). ...
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Plant–animal interactions (PAI) represent major channels of energy transfer through ecosystems, where both positive and antagonistic interactions simultaneously contribute to ecosystem functioning. Monitoring PAI therefore increases the understanding of environmental health, integrity, and functioning, and studying complex interactions through accurate, cost‐effective sampling can aid in the management of detrimental anthropogenic impacts. Environmental DNA (eDNA)‐based monitoring represents an increasingly common, nondestructive approach for biodiversity monitoring, which could help to elucidate PAI. Here, we aim to provide an overall discussion on the potential of using eDNA to study PAI. We assessed the existing literature on this subject from 2009 to 2021 using a freely accessible web search tool. The search was conducted by using keywords involving eDNA and PAI, including both species‐specific and metabarcoding approaches, recovering 43 studies. We summarized the advantages and current limitations of such approaches, and we outline research priorities to improve future eDNA‐based methods for PAI analysis. Among the 43 studies identified using eDNA to measure PAI such as pollination, herbivory, mutualistic, and parasitic relationships, they have often identified higher taxonomic diversity in several direct comparisons with DNA‐based gut/bulk sampling and conventional survey methods. Research needs include the following: better understanding of the influencing factors of eDNA detection involved in PAI (e.g., eDNA degradation, origin, and types), methodological standardization (sampling methods and primer development), and more inclusive sequence reference databases. If these research priorities are addressed, it will have a significant impact to enable PAI biodiversity monitoring with eDNA. In the future, the implementation of eDNA methods to study PAI can particularly benefit the scalability of environmental biomonitoring surveys that are imperative for ecosystem health assessments. Environmental DNA (eDNA)‐based monitoring represents an increasingly common, non‐destructive approach for biomonitoring, which could help to elucidate plant‐animal interaction (PAI). Here, we aim to provide an overall discussion on the potential of eDNA in studying PAI. We summarise advantages and current limitations of such approaches, and we offer research priorities that will potentially improve future eDNA‐based methods for PAI analysis. Our review has demonstrated that eDNA analysis is effective to identify PAI such as pollination, herbivory, mutualistic, parasitic relationships, they have often identified higher taxonomic diversity in several direct comparisons to DNA‐based gut/bulk sampling and conventional survey methods.
... A, Chlorodiella crispipleopa Dai, Yang, Song & Chen, 1986 (RUMF-ZC-6761, male, 5.8 × 9.1 mm); B, Chlorodiella cytherea (Dana, 1852) (RUMF-ZC-5597, male, 7.2 × 11.2 mm). Mendoza et al. (2014: 277) Dai et al. 1986;Titgen 1987;加藤 ・ 奥野 2001;Leray et al. 2012;Lasley et al. 2013;Mendoza et al. 2014 Dai, Yang, Song & Chen, 1986]. Not nigra (Forskål, 1775)]. ...
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Seven species of the xanthid genus Chlorodiella Rathbun, 1897 [C. barbata (Borradaile, 1900); C. corallicola Miyake & Takeda, 1968; C. crispipleopa Dai, Yang, Song & Chen, 1986; C. cytherea (Dana, 1852); C. xishaensis Chen & Lan, 1978; C. laevissima (Dana, 1852) and C. nigra (Forskål, 1775)], are reported based on specimens collected from the Ryukyu Islands, southern Japan. The present study represents the first record of C. corallicola from Japanese waters. It is also found that C. crispipleopa and C. xishaensis had already been recorded from several Japanese studies as C. cytherea. The specimens, tentatively identified as C. cytherea in the present study, are distinguished from C. crispipleopa by several features, although the identity of C. cytherea s.s. described by Dana (1852) is uncertain. Most of the specimens tentatively identified as C. laevissima in the present study agree with “C. laevissima form robusta” in Serène (1984), but the name “robusta” is an unavaibale name. Furthermore, this study pointed out that it is necessary to compare Serène’s (1984) two forms with Menippe martensii Krauss, 1843, which is regarded as a junior synonym of C. laevissima. The specimens identified as C. nigra in the present study included two morphological variations. For better taxonomy of C. nigra, it is necessary to determine whether these variations are intraspecific or interspecific differences and to match these specimens with nominal species currently synonimised under C. nigra.
... More direct DNA-based methods (e.g., metabarcoding of gut contents, or bulk samples -contain several organisms from different taxonomic group together, e.g, Kick-Net sampling or insect trap, that amalgamate entire organisms into a single sample, Taberlet et al., 2018) have already proved useful in elucidating complex species and trophic interactions (Garcia-Robledo et al., 2013). For instance, direct DNA analysis from gut content or bulk samples have illuminated different nodes across various food webs, and reconstructed the trophic links in terrestrial (Wirta et al. 2014(Wirta et al. , 2015a(Wirta et al. , 2015b(Wirta et al. , 2016Gogarten et al., 2020), aquatic (Leray et al., 2012;Leray et al., 2015) and often inaccessible environments, such as deep-sea beds, hydrothermal vents, and cold-seeps (Olsen et al., 2014). Several reviews to date have summarized the history, achievements, and current applications of studying species interaction using direct DNA-based methods across multiple fields (Symondson, 2002;Valentini et al., 2009;Pompanon et al., 2012;Clare, 2014;Kress et al., 2015;Evans et al., 2016). ...
... A, Chlorodiella crispipleopa Dai, Yang, Song & Chen, 1986 (RUMF-ZC-6761, male, 5.8 × 9.1 mm); B, Chlorodiella cytherea (Dana, 1852) (RUMF-ZC-5597, male, 7.2 × 11.2 mm). Mendoza et al. (2014: 277) Dai et al. 1986;Titgen 1987;加藤 ・ 奥野 2001;Leray et al. 2012;Lasley et al. 2013;Mendoza et al. 2014 Dai, Yang, Song & Chen, 1986]. Not nigra (Forskål, 1775)]. ...
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Six euxanthine crabs, Euxanthus exsculptus (Herbst, 1790), E. herdmani Laurie, 1906, Hepatoporus guinotae (Zarenkov, 1971), Hypocolpus haanii Rathbun, 1909, Hy. kurodai Takeda, 1980 and Psaumis cavipes (Dana, 1852) are reported based on specimens collected from the Ryukyu Islands, southern Japan. Euxanthus herdmani and He. guinotae are recorded for the first time from Japan and the Ryukyu Islands, respectively.
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Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well designed and validated eDNA metabarcoding approaches are ideally suited for biomonitoring applications that rely on the detection of species, including mapping invasive species fronts and endangered species habitats as well as tracking range shifts in response to climate change. Incorporating these considerations will enhance the utility and efficacy of eDNA metabarcoding for routine biomonitoring applications.
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Structural complexity provided by the living coral reef framework is the basis of the rich and dynamic biodiversity in coral reefs. In many cases today, the reduction in habitat complexity, from live coral to dead coral and rubble, has altered the abundance and diversity of many reef species with impacts on community structure, food webs and ecosystem functioning. Yet, the complex microhabitat provided by rubble can too support a great density and diversity of reef organisms, often with explicit roles in ecosystem functioning. This literature review synthesises available knowledge on the biology and ecology of coral rubble. We highlight key methodologies used to sample rubble communities, and the biological and ecological consequences of ongoing habitat degradation from coral to rubble reefs under future scenarios. We conclude with a number of key research themes that may enhance our capacity to understand the current contribution of rubble communities to reef functioning and predict their ability to modulate future impacts as net framework erosion amplifies.
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Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
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Reef-fish diversity models, unlike general diversity-gradient hypotheses, assume food specialization by reef fishes is too low to influence community structure. This assumption may be an artifact of low taxonomic resolution in studies of fish diets. I performed detailed dietary analyses on adults of eight small, cryptic, diurnal fish species from the spur-and-groove habitat outside Kaneohe Bay, Oahu, Hawaii to test whether dietary specialization may facilitate high species richness in reef fish communities. Mean dietary overlap (0.179) among these fishes is similar to overlap in communities thought to be structured by fine-scale food specialization. Dietary studies with high taxonomic resolution indicate a significant decrease in food overlap among fishes as latitude decreases. These results, along with the generally recognized increase in prey diversity toward the tropics, are consistent with diversity-gradient hypotheses and suggest that food specialization allows the local coexistence of many fish species on coral reefs. Local relative abundances of reef fishes may be influenced by prey availability. The densities of five of six fish species were related to densities of important prey. Food choice and availability may influence richness and relative abundances, respectively, in reef fishes, and reef-fish communities may be structured in the same manner as other tropical communities.
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Stony corals provide important structural habitat for microbes, invertebrates, and fishes, which in some cases has led to the evolution of beneficial interactions that may protect corals from environmental factors such as thermal stress, nutrient limitation, competitors, or predators. For example, guard crabs (Trapezia spp.) protect corals (Pocillopora sp.) from attacks by crown-of-thorn seastar and sedimentation. Here, a field experiment demonstrates that guard crabs (Trapezia serenei) also ameliorate the strong negative effects of the giant vermetid (Dendropoma maximum) on growth of Pocillopora. This experiment highlights the importance of this crab-coral mutualism: guard crabs facilitate the growth of corals in stressful environments (e.g., where vermetids are abundant), thereby preserving the ecological goods and services (e.g., food and shelter) that these corals may provide to other reef-associated species. Keywords Dendropoma maximum - Pocillopora -Symbiosis- Trapezia
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The cryptofauna associated with coral reefs accounts for a major part of the biodiversity in these ecosystems but has been largely overlooked in biodiversity estimates because the organisms are hard to collect and identify. We combine a semi-quantitative sampling design and a DNA barcoding approach to provide metrics for the diversity of reef-associated crustacean. Twenty-two similar-sized dead heads of Pocillopora were sampled at 10m depth from five central Pacific Ocean localities (four atolls in the Northern Line Islands and in Moorea, French Polynesia). All crustaceans were removed, and partial cytochrome oxidase subunit I was sequenced from 403 individuals, yielding 135 distinct taxa using a species-level criterion of 5% similarity. Most crustacean species were rare; 44% of the OTUs were represented by a single individual, and an additional 33% were represented by several specimens found only in one of the five localities. The Northern Line Islands and Moorea shared only 11 OTUs. Total numbers estimated by species richness statistics (Chao1 and ACE) suggest at least 90 species of crustaceans in Moorea and 150 in the Northern Line Islands for this habitat type. However, rarefaction curves for each region failed to approach an asymptote, and Chao1 and ACE estimators did not stabilize after sampling eight heads in Moorea, so even these diversity figures are underestimates. Nevertheless, even this modest sampling effort from a very limited habitat resulted in surprisingly high species numbers.
Pocilloporid corals in possession of obligate crustacean symbionts (xanthid crabs and alpheid shrimp) demonstrated a higher rate of survival than corals divested of their crustacean symbionts. The course of coral death in colonies without crustaceans involved polyp restriction, formation of a septic diaphanous film over the affected branches, disintegration of the polypal layer and massive tissue exfoliation within 4 days. Crude mucus production by corals was significantly greater (19%) in colonies with crustaceans than without. Coral skeletal growth (branch elongation) was also greater (21%) in colonies with crustaceans than without, but at a marginally insignificant level. The sheltering and feeding activities of crustacean symbionts produced local damage to host corals (destruction of polyps and coenosarc, and skeletal abrasion), but these sites were usually repaired and caused no apparent lasting effects. Crustacean symbionts apparently increase coral vitality by assisting their host in shedding contaminants, microorganisms, larval stages and other setting organisms. -Author
A general binomial mixture model is proposed for the species accumulation function based on presence-absence (incidence) of species in a sample of quadrats or other sampling units. The model covers interpolation between zero and the observed number of samples, as well as extrapolation beyond the observed sample set. For interpolation (sample-based rarefaction), easily calculated, closed-form expressions for both expected richness and its confidence limits are developed (using the method of moments) that completely eliminate the need for resampling methods and permit direct statistical comparison of richness between sample sets. An incidence-based form of the Coleman (random-placement) model is developed and compared with the moment-based interpolation method. For extrapolation beyond the empirical sample set (and simultaneously, as an alternative method of interpolation), a likelihood-based estimator with a bootstrap confidence interval is described that relies on a sequential, AIC-guided algorithm to fit the mixture model parameters. Both the moment-based and likelihood-based estimators are illustrated with data sets for temperate birds and tropical seeds, ants, and trees. The moment-based estimator is confidently recommended for interpolation (sample-based rarefaction). For extrapolation, the likelihood-based estimator performs well for doubling or tripling the number of empirical samples, but it is not reliable for estimating the richness asymptote. The sensitivity of individual-based and sample-based rarefaction to spatial (or temporal) patchiness is discussed.
Molecular analysis of predation, through polymerase chain reaction amplification of prey remains within the faeces or digestive systems of predators, is a rapidly growing field, impeded by a lack of readily accessible advice on best practice. Here, we review the techniques used to date and provide guidelines accessible to those new to this field or from a different molecular biology background. Optimization begins with field collection, sample preservation, predator dissection and DNA extraction techniques, all designed to ensure good quality, uncontaminated DNA from semidigested samples. The advantages of nuclear vs. mitochondrial DNA as primer targets are reviewed, along with choice of genes and advice on primer design to maximize specificity and detection periods following ingestion of the prey by the predators. Primer and assay optimization are discussed, including cross-amplification tests and calibratory feeding experiments. Once primers have been made, the screening of field samples must guard against (through appropriate controls) cross contamination. Multiplex polymerase chain reactions provide a means of screening for many different species simultaneously. We discuss visualization of amplicons on gels, with and without incorporation of fluorescent primers. In more specialized areas, we examine the utility of temperature and denaturing gradient gel electrophoresis to examine responses of predators to prey diversity, and review the potential of quantitative polymerase chain reaction systems to quantify predation. Alternative routes by which prey DNA might get into the guts of a predator (scavenging, secondary predation) are highlighted. We look ahead to new technologies, including microarrays and pyrosequencing, which might one day be applied to this field.