CoML Census of Coral Reef Ecosystems (CReefs)
Dr. Nancy Knowlton, PI
Department of Invertebrate Zoology
National Museum of Natural History, Smithsonian Institution
PO Box 37012, MRC-163, Washington DC 20013
Phone: 202-633-0668 (direct line) Fax: 202-357-3043 E-mail: knowlton@si.edu
Dr. Julian Caley, PI
Australian Institute of Marine Science, PMB 3
Townsville MC, Queensland 4810 Australia
Phone: +617-4753-4148 Fax: +617-4772-5852 E-mail: J.Caley@aims.gov.au
Dr. Russell E. Brainard, PI
Chief, Coral Reef Ecosystem Division, Pacific Islands Fisheries Science Center
National Oceanic and Atmospheric Administration (NOAA)
1601 Kapiolani Blvd., Suite # 1110
Honolulu, HI 96814 USA
Phone: (808) 944-2110 Fax: (808) 941-8705 E-mail: Rusty.Brainard@noaa.gov
Megan Moews, Project Manager, Education/Outreach Network Liaison
Joint Institute for Marine and Atmospheric Research, RCUH
Coral Reef Ecosystem Division, Pacific Islands Fisheries Science Center
National Oceanic and Atmospheric Administration (NOAA)
1601 Kapiolani Blvd., Suite # 1110
Honolulu, HI 96814 USA
Phone: (808) 944-2120 Fax: (808) 941-8705 E-mail: Megan.Moews@noaa.gov
Mary Wakeford/Shawn Smith - Project Manager, OBIS Liaison
Australian Institute of Marine Science, PMB 3
Townsville MC, Queensland 4810 Australia
Phone: +617-4753-4399 Fax: +617-4772-5852 E-mail:
M.Wakeford@aims.gov.au/S.Smith@aims.gov.au
Dr Laetitia Plaisance, Postdoctoral Fellow
Department of Invertebrate Zoology
National Museum of Natural History, Smithsonian Institution
PO Box 37012, MRC-163, Washington DC 20013
Phone: 202-633-0684 (direct line) Fax: 202-357-3043 E-mail: plaisancel@si.edu
http://www.coml.org/descrip/c-reefs.htm
http://www.creefs.org
1. 2008 ACCOMPLISHMENTS & SCIENTIFIC HIGHLIGHTS
Field Efforts
Hawaii
CReefs Hawaii and the National Oceanic and Atmospheric Administration (NOAA), led a multinational scientific expedition in October 2006 to improve understanding of the biological diversity of
understudied invertebrate, algal, and microbial species at French Frigate Shoals (FFS) in the largest
fully protected marine conservation area on the planet—the Papahanaumokuakea Marine National
Monument. Initial estimates predicted discoveries of over 100 new species and records, using a wide
variety of new and proven methods over a diverse range of habitats. As a follow up to this effort,
since 2007, scientists from NOAA’s Pacific Islands Fisheries Science Center, the University of
Hawaii’s Hawaii Institute of Marine Biology, Bishop Museum, Instituto de Ciencias do Mar at the
Universidade Federal do Ceara in Brazil, Woods Hole Oceanographic Institution, the Florida Museum
of Natural History, and the Natural History Museum of Los Angeles County have been sorting,
identifying, and curating the 4,150 sample lots and estimated 2,100 unique morphospecies collected
during the cruise. Over 1,2790 DNA subsamples were collected for the Barcode of Life initiative.
Complementing the data obtained from the French Frigate Shoals sampling effort and
Autonomous Reef Monitoring Structure retrieval (see ARMS discussion below), CReefs scientists are
analyzing samples of the algal and invertebrate communities living on derelict fishing gear collected
during a September/October 2007 NOAA marine debris removal expedition in the Northwestern
Hawaiian Islands. Specific goals for the survey were to bring together a skilled scientific team to
assess the diversity of species living on derelict fishing nets, document and preserve the specimens
found for analysis, and create end products that spatially depict the findings in a way that is useful to
managers and future researchers. Investigations could assist managers in finding out if the debris
serves as a possible vector for accelerating the introduction of alien species to the region. The Report
from this effort includes a database of species found living on the debris and could contribute
significantly to effective management of invasive species globally (Godwin et al, 2008).
Multi-institutional scientists analyzing samples from these efforts have recently submitted an update of
specimens currently being processed.
~1600-2150 Unique morphospecies
~1279 DNA subsamples
Most photographed alive
Algae:
366 specimens catalogued (~160 morphospecies)
179 described taxa reported previously at FFS (Vroom, 2006)
7+ genus/species records
Undergoing nuclear LSU, mitochondrial COI barcode, plastic UPA sequencing
General Invertebrates:
At least 30-50 new species and at least 100 new records for region
Probable new species among sponges, corals, anemones, flatworms, segmented worms, hermit and
other crabs, sea slugs, bivalves, gastropods, octopus, sea cucumbers, sea stars, and sea squirts
(6 octopus were collected representing 6 different species, 3 may be new)
Ascidians:
>50 species documented, new species and family records for the Northwestern Hawaiian Islands
(NWHI), new species
Only 67 species previously recorded from entire Hawaiian Archipelago
Opisthobranchs:
~500 species reported previously from HI, 140 from NWHI
62 species collected
48 likely new records for FFS
27 likely new records for NWHI
4 new records for HI
3 may be undescribed
Annelids:
~1052 individuals among 115 morphospecies in 28 families were found. (Eunicidae, Syllidae, and
Nereidae dominant)
Cryptic polychaetes and other worms underrepresented due to sampling methodology
Most specimens undergoing ID
Undescribed genus of sabellid found on Oahu practice dive
Undescribed Haplosyllis with undescribed parasite found
Potential new genus for a eunicid
Crabs & symbionts:
1 new hermit
1 new HI record hermit
likely 2 new anemones
2 new flatworms
likely new oyster
At least 7 families of decapods and ~20 genera and 33 species reported from FFS for the first time
Many HI and NWHI genus, and species records, undescribed species
According to Dr. Tito Lotufo in Brazil, many species of didemnids of the genus Leptoclinides,
have been found in the FFS samples. Lotufo informed the project that although it is a common genus
in the Pacific, it usually is not abundant or diversified, so this appears to be a peculiarity of the
ascidian fauna from that region.
Recently, in 2008, a paper was published regarding a new record for the Hawaiian
Archipelago: Godwin, L.S. and I. Baums. 2008. The hermit crab Calcinus isabellae Poupin
(Crustacea: Decapoda: Anomura: Diogenidae), a new record for the Hawaiian Archipelago, including
a review of the genus Calcinus Dana in Hawaii. Bishop Museum Occasional Papers 100: 52-54. The
following manuscript submitted to Zootaxa is pending: Martin, J.W., L.S. Godwin and R. Moffitt. 2008.
Additions to the decapod crustacean fauna of the Hawaiian Islands, I. A new species of the crab
genus Sakaila Manning and Holthuis, 1981 (Decapoda, Brachyura, Calappoidea) from French Frigate
Shoals, Northwestern Hawaiian Islands. Godwin et al. 2008 recently provided a report summarizing
invertebrate fauna found on derelict fishing gear recovered by NOAA at FFS in 2007.
Identification and analysis of these specimens can be a time consuming process, thus there
are likely to be many more discoveries as the specimens are further analyzed. Such discoveries will
be documented in multiple joint publications and the data placed in OBIS. By providing scientists and
managers with a more complete picture of what exists in coral reef ecosystems, they will be better
equipped to manage them and in particular watch for and manage changes over time. With the
integration of further investigations, there can be a greater understanding of biodiversity over
gradients of human disturbance.
CReefs and NOAA have been invited to collaborate with several institutions of the Palmyra
Atoll Research Consortium (PARC), including the California Academy of Sciences, the American
Museum of Natural History, University of Hawaii, University of California San Diego, Stanford
University, and Victoria University, to develop a funding proposal to the Gordon Moore Foundation
and a ship time request to NOAA to conduct a comprehensive CReefs biodiversity census at Palmyra
and Kingman Atolls in the central Pacific. This proposal will be submitted in November 2008 and the
proposed field surveys, if funded, would be conducted in 2010.
Autonomous Reef Monitoring Structures (ARMS)
CReefs scientists are continuing the development and testing of Autonomous Reef Monitoring
Structures (ARMS) as a systematic, consistent, and comparable method to monitor indices of cryptic
invertebrate diversity and a CoML legacy. These long-term collecting devices, designed to roughly
mimic the structural complexity of a coral reef and attract colonizing invertebrates, are being
developed and used as a standard method for taxonomic and molecular analysis to assess indices of
invertebrate biodiversity and improve the ability to measure and monitor the biodiversity of these
understudied organisms on a global scale over time. With an increasing scarcity of trained
invertebrate taxonomists, ARMS will enable researchers to obtain information utilizing molecular
techniques that would otherwise be challenging and time consuming using traditional morphological
analyses. Furthermore, while coral reefs are highly diverse ecosystems, methods to assess this
diversity can be problematic, particularly for small and cryptic organisms. Through retrospective
analysis and the development of this monitoring tool, ARMS have the potential to greatly enhance the
capacity for ecosystem-based management and increase the ability to monitor and predict ecological
impacts of global climate change, particularly ocean warming and ocean acidification.
Beginning in the Hawaiian Archipelago and expanding globally, ARMS have been deployed
throughout the Hawaiian Archipelago (Main Hawaiian Islands and the Papahanaumokuakea Marine
National Monument), Line Islands, Phoenix Islands, American Samoa, Australia, and Brazil, with
proposed deployments in Panama, Reunion (Indian Ocean), Mariana Islands, Turks and Caicos,
Cayman Islands, along with other locations that are currently being discussed. Schematics of the final
ARMS design have been created to allow future production to occur in-country utilizing standard
materials and labor. Consequently, ARMS deployed during the recent 2008 Australia field efforts
were produced by the AIMS workshop and are scheduled for re-collection during the second round of
trips in 2009.
The first set of ARMS deployed in 2006 at French Frigate Shoals, were recovered in October
2007 and initial identification of invertebrates colonizing the ARMS is currently underway, with
molecular and taxonomic analyses continuing through 2008. These ARMS were deployed at sites
selected on the basis of habitat characterization and the analyses were designed to look at both the
effectiveness of the instruments across the range of habitats and the taxa collected. ARMS were
most productive in sampling mollusks (28%), ascidians (24%), crustaceans (19%) and bryozoans
(11%) in fore reefs and lagoon patch reef habitats. These results suggest that coupling ARMS with
taxonomic and molecular analyses can be an effective method to assess and monitor understudied
coral reef invertebrate biodiversity. Interestingly, Godwin et al. 2008 found three new records of alien
species colonized on the ARMS at French Frigate Shoals, suggesting that ARMS may serve as a
useful tool to detect cryptic alien species.
In 2008, NOAA’s Pacific Reef Assessment and Monitoring Program (RAMP) deployed 81
ARMS throughout the Line and Phoenix Islands and American Samoa, 75 ARMS throughout the
Northwestern Hawaiian Islands, and 36 ARMS in the Main Hawaiian Islands. In addition, CReefs sent
9 ARMS to Brazil that were collaboratively deployed on the Abrolhos Reefs as part of the Pro-
Abrolhos Reef Project. These structures will remain in the field collecting data for approximately 1-2
years.
Additional ARMS development and testing is currently taking place off the coast of Oahu,
Hawaii, where 14 ARMS were deployed in August 2007. They will be retrieved in December 2008, as
part of a planned Workshop on ARMS Recovery, Processing, and Analyses. This workshop will bring
together leading taxonomists and molecular biologists to jointly develop and test methods for retrieval,
sorting, processing, and analyzing the samples using both molecular and taxonomic methods.
As a spinoff to the ARMS development effort, CReefs and the NOAA PIFSC Coral Reef
Ecosystem Division are exploring the development of similar systematic and comparable calcification
plates to monitor spatial and temporal patterns of calcification in response to ocean acidification. The
goal is to develop simple, inexpensive, and stable structures (with minimal footprint) that will improve
our understanding of the ecological impacts of ocean acidification.
Australia
CReefs Australia began field expeditions this year and has now completed three of nine
planned expeditions to three Australian sites. Each expedition will be 3 weeks long and involve
approximately 25 people. This field program has been generously supported by BHP Billiton, the
world’s largest resources company. This funding will continue until 2011. Milestones reached to date
include:
 A CReefs Australia Steering Committee has been established and its Terms-of-Reference
agreed between CReefs PI Julian Caley and a representative from each of five Australian
Museums (recently expanded to six), in November 2007. The Steering Committee has
communicated through a series of face-to-face meetings, conference calls and email
correspondence. A thorough examination and assessment of gaps in taxonomic knowledge
has been completed and a list of priority taxa established that will be targeted in surveys of the
three Australian field sites.
 Completion of three field expeditions – Lizard Island (Apr 08), Ningaloo Reef (June 08) and
Heron Island (Aug/Sep 08). These expeditions were very successful collecting hundreds of
new species and adding new locations for many others. These expeditions ran smoothly
without incident and received considerable media attention.
 Activities supporting these expeditions included extensive logistical planning, upgrading and
updating AIMS’ staff diving and first aid qualifications, management of OHS&E risks
encompassing the many different collaborating institutions, hazards specific to each field
location, sampling protocol revision, implementation of a collection database for linking images
and data, uploading existing taxonomic classifications and allowing automated searching, and
sample tracking. These procedures will be further developed and refined for use during
upcoming expeditions.
 In April 2008, the project was endorsed at the institutional level by the Council of Australian
Museum Directors. This endorsement allows the institutions’ contributions to be officially
acknowledged through a variety of means including use of their logos on CReefs materials
and websites. It also creates greater opportunity for these institutions to co-invest in the
project while contributing to their strategic needs.
 The Australian Biological Resources Study (ABRS), the main funding body for taxonomy and
systematics in Australia, agreed in early June 2008 to co-invest with the CReefs Australia
Project an additional $600,000 to support the taxonomic and systematic analyses of the
samples collected as part of the project. The process for allocating the CReefs funds for
taxonomy support and the additional funds from ABRS has also been agreed upon.
 The Manager of Science Communications at AIMS, Steve Clarke has been involved in
developing a communications plan for the CReefs Australian project and attended the Census
of Marine Life, All Programs Meeting in Auckland in November 2007.


A large library of high quality imagery (stills and video) documenting CReefs activities and
collection material has been established. Gary Cranitch, a Queensland Museum
Photographer, was awarded the 2008 Professional Science, Environment and Nature
Photographer of the year award by the Australian Institute of Professional Photography based
on his photography associated with CReefs expeditions.
Recruitment of a Postdoctoral Fellow to the CReefs Australia Project, Dr. Rebecca Fisher, has
been completed. She will officially begin work 17 November 2008. Her role will be to focus on
the analysis of large-scale coral-reef biodiversity patterns.
CReefs Collection Database (Long-term Legacy)
The CReefs Collection Database was used as the central data management system for all
three 2008 Australia collection trips. Gavin Ericson developed an access database based on the
format of the Excel spreadsheets used during the first CReefs cruise to French Frigate Shoals, with
the aim to create a product that was user-friendly, simplified data entry and image storage, provided
features to assist subsequent taxonomic analysis and provide much greater data security than is
possible with spreadsheets. During the Australian field expeditions, each group of researchers had a
copy of the database loaded on their computer and entered data directly into the database, rather
than into spreadsheets to be verified and uploaded at a later date. The table structure reflected the
need to have mandatory fields for referential integrity and also to match the OBIS structure.
Researches were able to upload pre-existing classifications into the database to be accessed via
drop-down lists whist entering taxonomic information. The process of matching Specimens with
photographs was greatly simplified by having a button on the form “Add Images” that allowed
researches to search for relevant folders and images on the desktop, select a number of images
which were then automatically copied, renamed, saved and linked in the database to the relevant
Specimen. Each Specimen could also have an entry in the DNA table and Lots table. To make data
entry more efficient, a Defaults section allowed researches to set default values for a range of fields,
i.e. Custodian, Habitat, Substrate, Relaxant and Fixative. The Participant table could be updated and
Collector Groups created allowing a group name to be entered rather than several entries for each
participant. Searches of the data, particularly by taxonomy, allowed images for all entries of a
particular species to be viewed and compared - which was a very useful tool for parataxonomists and
when a new morphospecies was created. Upon completion of the trip, researchers took a copy of the
database with them or exported Specimen data by selecting the fields of interest and saving as an
Excel spreadsheet. All data from the databases were appended to one location and reside at AIMS.
Future updates to taxonomy by researchers at museums around Australia will be done via 1) a web
login system and 2) a synchronized access database. These two applications are currently being
developed.
Indian Ocean and East Africa rollout
Three arenas remain promising for extending CReefs to the Indian Ocean:
 The Royal Society-Chagos Archipelago Project (Contact: Dr Alex Rogers, Zoological Society
of London). The Royal Society contacted CReefs concerning a proposal to work in the Chagos
Archipelago. The proposal is for lengthy research programmes (5 years) including expeditions
employing the methods CReefs has developed for standardized sampling. The Chagos
Archipelago is of particular interest as a CReefs field site for a number of reasons: 1) the
remoteness and hence relatively pristine nature of these reefs, 2) the general lack of
information for reefs of the Indian Ocean, and 3) the role of the Chagos as a stepping stone for
dispersal in the region. However, we have not received any word about the success of their
proposal.
 Western Indian Ocean Marine Science Association (WIOMSA) Conference. CReefs PI Dr.
Julian Caley met with interested parties at the WIOMSA Conference in Durban (Oct. 2007) to
discuss potential funding opportunities and collaboration to expand CReefs into the Indian
Ocean. Opportunities exist to develop sites for CReefs off the East African coast, the

Seychelles, and Reunion Is. ARMS deployment in this region is generating considerable
interest and is likely to be achievable before funding can be secured for full fledged sampling
expeditions.
ARMS deployments in Western Indian Ocean. CReefs PI Dr. Rusty Brainard initiated
collaborative discussions with Dr. Henrich Bruggemann at the University of Reunion and Dr.
Gustav Paulay at the University of Florida Museum of Natural History regarding deployments
of ARMS in 1) Reunion - restricted access sanctuary zones have been established on the reef
flats and outer reef slopes as part of the new MPA; 2) the uninhabited French Eparse Islands
situated along a South-North gradient in the Mozambique Channel (Europa, Juan de Nova,
Mayotte, Gloriose Islands) and Tromelin located NE of Madagascar. These islands are strict
sanctuaries with military presence; and 3) Seychelles - a BIOTAS mission.
All Taxa Biotic Survey
Knowlton has been invited by the Keck Foundation to submit a proposal for the first all taxon
biotic survey of a coral reef, now in the final stages of preparation, for ~1.3 million dollars. This project
will be in collaboration with Philippe Bouchet, Gustav Paulay, Chris Meyer, and the Marine Barcode of
Life initiative. If funded, the two-year project will begin in July 2009, and will focus initially on mass
molecular sampling of reef multicellular organisms in order to obtain an estimate of how much coral
reef biodiversity remains to be documented (narrowing the scope of the unknown) and what is being
lost associated with reef degradation.
Molecular approaches for categorizing marine biodiversity of coral reefs
A paper on the diversity of crustaceans in Moorea (French Polynesia) and in the Line Islands
has been submitted to Coral Reefs, in collaboration with Dr. Christopher Meyer, of the Smithsonian’s
National Museum of Natural History/Univ. California Moorea Biocode Project and Dr. Gustav Paulay,
of the University of Florida’s Florida Museum of Natural History. In this study, >400 individual
crustaceans were sequenced, and 135 distinct sequences detected. Although most could be
morphologically assigned to described species or species complexes, none matched at the species
level any sequence in GenBank, indicated how lacking are the genetic data for reef organisms.
Strikingly, this relatively small sample (collected from just 22 heads of dead coral) contained 65
species of brachyuran crabs, 30% of the total described for Europe and 1% of the global total. The
data from this study will be served in the Barcode of Life data system.
Quantitative sampling of reef-associated organisms has taken place in all three Australian
localities investigated in 2008 (Lizard and Heron Island and Ningaloo reef). DNA barcoding is
underway for these collections. Initial identification of invertebrates colonizing the surfaces of ARMS
retrieved from French Frigate Shoals is also underway, with molecular and taxonomic analysis
continuing through 2008. Numbers of samples are: Lizard Is, GBR: 670 (all taxa); Heron Is, GBR:
1100 (all taxa); Ningaloo, Western Australia: 600 (all taxa); ARMS (Hawaii): 800 (crustaceans only).
In addition to DNA barcoding, which is now widely used for species identification, discovery
and inventory, we are actively developing environmental sampling and high throughput sequencing
methods. These methods will allow determination of thousands of sequences from a single collection;
it is especially useful for those groups of organisms that are too small to voucher effectively and in
groups for which species richness is often overlooked. This will be the subject of a field workshop in
December 2008, using the Hawaiian ARMS to be collected at that time.
New Species Descriptions
Seven papers are published or in press with news species descriptions from the Knowlton lab
(see CoML database). These concern snapping shrimp in the genus Alpheus, the archetypal megadiverse reef group which may have over 1000 species in total. In addition to publications, species
pages are available on a Smithsonian website. Other species descriptions are underway associated
with a large number of taxonomists who participated in the Hawaiian and Australian expeditions, for
example a paper in press in Crustaceana on a new species of isopod.
2. PROJECT MANAGEMENT & INTERNAL COMMUNICATION
The project is led by the three PIs: Dr. Nancy Knowlton, Dr. Julian Caley, and Dr. Russell Brainard
and is coordinated by project managers residing at each node. Each node has different areas of
responsibility, as follows:



Smithsonian’s National Museum of Natural History/Scripps Institution of Oceanography- Nancy
Knowlton (PI), Penny Dockry- (Admin. funded by SIO), Laetitia Plaisance (postdoctoral fellow
funded by CReefs). Knowlton, with Plaisance, coordinates the development of molecular tools
and analyses and is responsible for developing a Caribbean field project. She also provides
links with efforts being undertaken by the World Bank Coral Reef Targeted Research Program,
the BioCode Project in Moorea, the Santo Project and future all taxa survey run by Philippe
Bouchet (with Plaisance), marine Bar-Coding projects, and other CReefs-associated projects
in Palmyra.
Pacific Islands Fisheries Science Center, Coral Reef Ecosystem Division (CRED), NOAARussell Brainard (PI), Megan Moews (node coordinator/outreach liaison funded by
CReefs/Sloan Foundation), Russell Moffitt (database/field specialist funded by CReefs/NOAA),
Molly Timmers (invertebrate/field specialist funded by CReefs/NOAA), Bonnie DeJoseph
(outreach/field specialist funded by CReefs/NOAA), Daniel Merritt (engineer/methods
development, funded by NOAA). Brainard, with Moews, is responsible for coordinating all
CReefs Central, Western (except Australia) and South Pacific projects, NOAA Pacific RAMP,
and education/outreach. Moffitt and Timmers assist the project ~50% of their time providing
database, methods development, and field assistance. Merritt provides engineering expertise
for ARMS and the upcoming ocean acidification measurement methods. DeJoseph assists
50% of her time with logistics and outreach/education. The project is continuously provided
support by CRED staff.
Australian Institute of Marine Science- Julian Caley (PI), Mary Wakeford (Project Manager),
Shawn Smith (CReefs Australia Field Manager), Gavin Ericson (CReefs Database
developer/administrator). Caley, with Wakeford/Smith/Ericson, is responsible for delivering
relevant coral reef records into OBIS, undertaking a series of field expeditions to 3 Australian
reef sites (see above), and development/management of the CReefs Collection Database.
The three nodes each have clearly defined milestones that are addressed at the node level.
For milestones concerning CReefs as a whole, coordination between the nodes is maintained by
email contact, conference calls and occasional face-to-face meetings. A web-based content
management system in Plone serves as the central hub for project documents, milestone progress,
meeting minutes, forums and upcoming events.
3. 2008 EDUCATION & OUTREACH EFFORTS
Websites
A partnership has been established between renowned photographer Susan Middleton,
CReefs, NOAA, the Papahanaumokuakei Marine National Monument, Scripps Institution of
Oceanography, AIMS, the Smithsonian, and the US Fish and Wildlife Service to create a web
presentation prototype from the 2006 FFS photographs and engage the general public with powerful
imagery to convey the importance of understanding marine biodiversity and the function of lesser
known organisms in coral reef ecosystems. This project was awarded funding by the 2008
International Year of the Reef Initiative (IYOR 2008) and is currently in progress. Because of the
quality of Middleton’s work as well as the success of her previous endeavors, it is anticipated that this
effort will be highly successful, reaching a wide audience of internet users.
Also in conjunction with IYOR 2008, CReefs and ad2 developed the CReefs Biodiversity
Resource Locator (CBRL) in time for the International Coral Reef Symposium in July 2008, where
CReefs held a booth (as well as presented). CBRL (http://www.creefs.org/resourcelocator.html),
housed on the CReefs website (www.creefs.org) has been designed as a searchable, web-based
database updated by its users, allowing users (individuals needing information about a given area,
species, etc associated with coral reefs) to connect with institutions, managers and scientists
associated with coral reef biodiversity around the world. The site was developed so that further
expansion can take place, allowing for additions such as literature and database search capabilities.
By adding such content, CBRL will be an invaluable tool allowing users to research multiple facets of
available material relating to coral reef biodiversity. While its initial introduction at ICRS was a
success, drawing in 82 members, CBRL (along with other CReefs efforts) was further introduced at
the Hawaii Conservation Conference as well as through business cards and brochures. A largescale, web-based announcement will take place in November 2008.
In addition to the CBRL, CReefs, partnering with AIMS and NOAA, is focusing on further web
expansion during 2008 and 2009 to transform the site into a one-stop site for coral reef biodiversity
information. CReefs is also pursuing the possibility of partnering with the Smithsonian Ocean Portal
(ocean.si.edu/oceanhall) as the Portal is developed. This website, associated with the opening of the
Smithsonian’s Sant Ocean Hall, featured several pieces on conservation related to coral reefs written
by Knowlton and her assistant Christine Hoekenga.
Australian Field Expeditions
The 2008 Australian field expeditions were launched at the Museum of Tropical Queensland
on 31 March by BHP-Billiton, the Great Barrier Reef Foundation and AIMS with many CReefs
participants and local dignitaries present. The launch received much positive press coverage and the
events of each expedition were extensively blogged on the CReefs website (www.creefs.org). The
three expeditions undertaken in 2008 were the subject of a very successful global media campaign,
developed in partnership with the Education and Outreach group of the Census of Marine Life. Media
coverage included all the major wire services, media pieces in 18 languages across 51countries (see
the summary under construction online at http://spreadsheets.google.com/ccc?key=p
Rwdzmg01IrRpiC7PrOQTXA&hl=en), and at least 55 media pieces in Australia. A large library of high
quality imagery (stills and video) has also been generated documenting CReefs activities and
collection material. Gary Cranitch, a Queensland Museum Photographer, was awarded the 2008
Professional Science, Environment and Nature Photographer of the year award by the Australian
Institute of Professional Photography. The prize-winning images were all from Gary’s participation in
the Lizard Island expedition of CReefs. Richard Morris joined the Heron Island expedition and
produced high resolution video on CReefs activities and interviews. This footage, along with stills
imagery, was put to extensive use in the recent media campaign. Discussions have also been held
between the Education and Outreach group of the Census and CReefs Australia about possible
opportunities for a television documentary on coral reefs.
As part of CReefs Education and Outreach activities, the most recent CReefs Australia
expedition was joined by a science teacher from San Diego, Zamaria Rocio who was sponsored by
the ARMADA Program. Zamaria worked primarily as an assistant to Laetitia Plaisance, who is
sampling biodiversity in dead coral heads. Zamaria reported back to her classes on her activities
directly from Heron Island and will use her experience of the expedition in curriculum development.
CReefs Australia is discussing opportunities with BHP Billiton to include an Australian science teacher
on a CReefs expedition as a prize in the BHP-Billiton Science Awards
Other Press and Public Conferences
During the AAAS meeting in Boston in February 2008, Knowlton was one of four presenters at
a press conference on the topic of climate change and acidification, and discussed these themes with
respect to coral reef biodiversity. She was also the plenary speaker for the US Coral Reef task force
and a speaker for the coral reef panel of the Congressional Hill Ocean Week, where she discussed
resilience and biodiversity. Finally, at the International Coral Reef Symposium in July 2008, she was
a participant for a press conference and a TV/web interview on coral reef biodiversity extinctions, and
participated on a panel consisting of scientists and media representatives, led by Seaweb, to help the
two groups work together more effectively.
Brainard provided an interview about coral reef biodiversity for the syndicated National
Geographic Weekend radio show hosted by Boyd Matson. He is also working closely with Greg
Marshall of National Geographic on a long-term documentary about monitoring the impacts of climate
change on coral reef biodiversity. Greg is presently (October 2008) participating on a NOAA Pacific
RAMP research cruise in the main Hawaiian Islands.
4. SOCIETAL BENEFITS, IMPACT & APPLICATIONS
Marine Policy
Press conferences described made a strong recommendation for the importance of local
protection as a builder of coral reef resilience in the face of global change. Related to this theme,
Knowlton was one of three scientists asked by the chairman of the White House Council on
Environmental Quality, James Connaughton, to brief the Council and affiliated agencies on the
importance of the central Pacific atolls with respect to evidence for the efficacy of local protection; the
presentation was so well received that the panel was asked to repeat it for representatives of
recreational fishing organizations. As part of the same effort to assess increasing protection and
conservation of the Pacific Remote Islands areas of the central Pacific, several islands in the Northern
Mariana Islands, and Rose Atoll in American Samoa, Brainard was asked to lead a series of three
scientific presentations about the coral reef ecosystems of the Pacific region to Chairman
Connaughton. Knowlton was also asked to participate in a panel on a related topic for congressional
staff on the use of the term “resilience” in coral reef management, followed by a visit to key staff
members; the term was later included in legislative language. Knowlton was one of four scientists
invited to a senate breakfast discussion of climate change organized by Senator John Kerry. Finally,
she led Senator Chris Dodd on a tour of the new Sant Ocean Hall, including a discussion of the
threats to coral reefs which are prominently displayed in the only living portion of the exhibit.
The results of the 2006 FFS CReefs/NOAA census provided managers with information cited
in the Papahanaumokuakea World Heritage Site Nomination. Furthermore, the significance of this
large scale census has led to a request by PARC that CReefs conduct a census at Palmyra and
Kingman Atolls in the Line Islands. The importance of obtaining/utilizing coral reef ecosystem
biodiversity information is further becoming a priority within NOAA as well.
As a result of the Fall 2007 investigation which examined biofouling organisms associated with
derelict fishing gear in the Pāpahanaumokuākea Marine National Monument (in conjunction with a
study conducted in 2000), the need for future debris removal efforts to note and collect rare fauna
recruiting to debris will likely be factored in to future management decisions. There were 8 new
records from 4 different phyla recorded for the NWHI during this preliminary effort. All these records
were cryptic species that are difficult to obtain, except during efforts focused on species inventory for
the purpose of assessing biodiversity (“The marine invertebrate species associated with the biofouling
of derelict fishing gear in the Pāpahanaumokuākea–Marine National Monument: A focus on marine
non-native species transport,” Preliminary Report, Godwin, et. al, 2008).
New Technologies
It is a CReefs goal that sampling methodologies and protocols developed for CReefs field
operations be adopted by researchers when assessing the status of understudied coral reef species
as well as climate change. In particular, CReefs is developing and testing Autonomous Reef
Monitoring Structures (ARMS) as a CoML legacy (see section 1). The schematics for ARMS
construction have been standardized to support efforts to measure indices of invertebrate biodiversity
on a universal level. As noted previously, in association with NOAA Pacific RAMP and CReefs
efforts, ARMS have been deployed throughout the Hawaiian Archipelago (Main Hawaiian Islands and
the Papahanaumokuakea Marine National Monument), Line Islands, Phoenix Islands, and American
Samoa. Other CReefs associated ARMS deployments are taking place in Australia and Brazil, with
proposed deployments in Panama, Reunion (IO), Mariana Islands, Turks and Caicos, and the
Cayman Islands. The interest in ARMS continues to increase globally.
The “suction sampler”, which gently suctions/filters invertebrates and sand, originally
developed by Philippe Bouchet, is also expanding its horizons from Santo Vanuatu to the Hawaiian
Archipelago; it is currently being utilized in Moorea by Gustav Paulay and team associated with the
affiliated Moorea Biocode Project. In addition, a method of standardized biodiversity sampling in
natural habitats that has been used in Hawaii, the Line Islands and Australia, consists of sampling the
biodiversity inhabiting in dead coral heads (Pocillopora).
Two papers that report scientific results related to these efforts were presented at the
International Coral Reef Symposium in Florida, July 2008, and one paper was presented at the Ocean
Sciences meeting in Florida, March 2008.
 Plaisance, L., Meyer, C. Paulay, G., Brainard, R., Hall, A., Caley, M. J., and Knowlton, N.
2008. Standardized sampling and molecular approaches for assessing marine biodiversity of
coral reefs. 11th International Coral Reef Symposium, Ft. Lauderdale, USA.

Hall, A., Brainard, R., Caley, M. J. et al. 2008. Autonomous Reef Monitoring Structures
(ARMS): a tool for monitoring indices of biodiversity. 11th International Coral Reef Symposium,
Ft. Lauderdale, USA.

Plaisance, L., Meyer, C. Paulay, G. and Knowlton, N. 2008. Molecular approaches for
categorizing marine biodiversity of coral reefs. 2008 Ocean Sciences Meeting, Orlando, USA.
CReefs and the NOAA PIFSC Coral Reef Ecosystem Division are currently exploring the
possibility of developing settlement and accretion plates. The goal during 2008-2009, is to develop
simple, inexpensive, and stable structures (with minimal footprint) that will help create a better
understanding of acidification in tropical reef areas, for use on a global scale.
In addition to the collection protocols, CReefs will encourage the use of the CReefs Collection
Database as a data repository and sample management tool for similar biodiversity studies requiring
data identification, storage, update, and tracking. Requests to use this database have been received
from other marine biodiversity survey projects. Data from this database will be served to OBIS.
CReefs collection data will provide valuable baseline information for future monitoring studies at
selected locations. CReefs outreach (see Outreach/Education section), and in particular the CReefs
website, will provide significant coral reef biodiversity information and will be linked with the CReefs
Database via the newly developed resource locator (described above). Discussions are now
underway to link the CReefs website with the Smithsonian’s Ocean Portal, which will be launched in
2009.
5. PARTNERSHIPS & COLLABORATIONS
Organization Name
Point-of-Contact (Name)
Nature of Relationship
Nancy Knowlton
CReefs Lead Principal Investigator
links with Northern Line Islands
cruises and other biodiversity
scientists
Nancy Knowlton
CReefs Lead Principal Investigator
links with other biodiversity
scientists and Sant Marine
Initiative
Nancy Knowlton/Marea Hatziolos
CReefs Lead Principal Investigator
chairs targeted coral reef research
project, whose network links 4
centers of excellence (Univ.
Queensland, Philippines, Mexico,
Zanzibar) and >50 reef scientists
worldwide
Russell Brainard, Megan Moews
CReefs Principal Investigator
(Brainard), NOAA Pacific Islands
Fisheries Science Center, Coral
Reef Ecosystem Division leads
integrated coral reef ecosystem
assessments and monitoring at 50
islands and atolls across the
Pacific as part of NOAA Pacific
Reef Assessment and Monitoring
Program.
Australian Institute of
Marine Science (AIMS)
Julian Caley, Shawn Smith, Mary
Wakeford, Gavin Ericson, Rebecca
Fisher
CReefs Principal Investigator
(Caley), links with other AIMS and
Australian reef scientists,
web/marketing consultants
photographers, videographers,
journalists
BHP-Billiton
Melinda Buckland
Scripps Institution of
Oceanography
Smithsonian’s National
Museum of Natural History
World Bank
National Oceanic and
Atmospheric Administration
(NOAA)
Group Manager Community
Programs HSEC &Sustainability
NOAA: NCCOS; Coral
Reef Conservation
Program; NWHI-MNM;
CoRiS
Mark Monaco; Andy Collins
National Centers for Coastal
Ocean Science; outreach;
outreach/NWHI-MNM co-trustee
management agency; Pacific
Region Integrated Data Enterprise
(data integration);
Florida Museum of Natural
History
Gustav Paulay, John Starmer, Sea
McKeon, Arthur Anker
Collaborative biodiversity surveys
and systematic projects
Museum national d'Histoire
naturelle
Philippe Bouchet
Collaborative Projects throughout
Pacific, including Santo Expedition
and New Caledonia
Berkeley/Smithsonian
Moorea Biocode Project
Christopher Meyer
Project Coordinator Moorea
Biocode Project
National Geographic
Society
Enric Sala
Coordination with Smithsonian in
web and other ocean efforts
Hawaii Institute of Marine
Biology
Jo-Ann Leong; Scott Godwin
Scientific Collaboration for Pacific
Islands and with ARMS
University of Hawaii
Tom Schroeder; Alison Sherwood
JIMAR resources; UH Botany
CSIRO, AIMS
Roland Pitcher, Peter Doherty
PIs for Seabed Biodiversity Project
U.S. Fish and Wildlife
Service
Don Palawski, Jim Maragos
NWHI-MNM co-trustee
management agency
NBII Pacific Basin
Information Node
Mark Fornwall, Derek Masaki
OBIS Regional Node, CReefs web
host, data management
Bishop Museum
Lu Eldredge, Richard Pyle
Advisory Committee
Natural History Museum of
Los Angeles County
Joel Martin, Leslie Harris, Gordon
Hendler
Collaborative biodiversity surveys
and systematic projects
Ocean Biogeographic
Information System
Mark Costello, Tony Rees
Collaboration, advisor
State of Hawaii
Dan Polhemus
NWHI-MNM co-trustee
management agency
University of Miami
Carla Hurt
DNA barcoding (alpheid shrimp)
Brown-Marine Biological
Laboratory/ICoMM
Mitch Sogan, Linda Amaral Zettler
Microbial consultation, ICoMM
San Diego State University
Forest Rohwer, Katie Barott
Australian Museum
Patricia Hutchings
Western Australian
Museum
Diana Jones
Scientific collaboration (molecular
analysis of environmental
samples)
CReefs Australia Steering
Committee
CReefs Australia Steering
Committee
Museum and Art Galleries
of the Northern Territory
Barry Russell
South Australian Herbarium
Andy Lowe
University of Puerto Rico,
Ernesto Weil, Emmanuel Irizarry
CReefs Australia Steering
Committee, Department of Natural
Resources Environment and the
Arts, Northern Territory
CReefs Australia Steering
Committee
Scientific Consultation
Caribbean
University of the Philippines
University of Hawaii
University of Kansas
Independent Pacific
Invertebrate Specialist
Independent Photographer
Universidad Federal do
Ceara, Brazil
National Park Service
National Park Service
Independent systematist
Soto
Ed Gomez
Cheryl Squair, Celia Smith, Les
Watling, Kris Coontz
Daphne Fautin
Corydon Pittman
Susan Middleton
Tito Lotufo
Rebecca Most
Caroline Rogers
Kevin Tilbrook
Scientific Consultation
Scientific Consultation
Scientific Consultation
Scientific Consultation
Outreach and Education
(see outreach section)
Scientific Consultation
Scientific consultation
Scientific consultation
Scientific Consultation, Bryozoan
taxonomists
Palmyra Atoll Research
Consortium (PARC-partnership of 10
institutions)
Healy Hamilton, Eleanor Sterling,
Stuart Sandin
Palmyra Atoll Research
Consortium (Calif. Acad. Of Sci,
Amer. Mus. of Nat. Hist., UCSDSIO) collaboration to conduct
CReefs biodiversity census at
Palmyra and Kingman Atolls.
University of California,
Merced/ICoMM
Monica Medina
Microbial consultation
Murdoch
Rainbo Dixon
PhD algal taxonomy
Australian Institute of
Marine Science
Dr Katharina Fabricius
Octocoral taxonomist
Queensland Museum
Dr Merrick Ekins, Dr Monika
Schlacher, Patrisha Hendricks, Dr
Niel Bruce; John Hooper, Gary
Cranitch
Octocoral/sponge/isopod
taxonomists; CReefs Australia
Steering Committee (Hooper),
photographer (Cranitch)
Museum Victoria
Dr Phil Bock, Dr Magda Blazewicz,
Tim O’Hara
Bryozoan/tanaid/echinoderm
taxonomists; CReefs Australia
Steering Committee (O’Hara)
CERF
Dr. Camille Mellin
Post doc
Museum and Art Gallery of
the Northern Territory
Dr Chris Glasby, Dr Charlotte
Watson, Gavin Dally, Steven
Gregg
Polychaete taxonomists,
taxonomic support
South Australian Herbarium
/University of Adelaide
Dr Fred Gurgel, Elizabeth Perkins,
Algal taxonomy
Western Australian
Herbarium /Murdoch
University
Dr John Huisman
Corey Bradshaw
Algal taxonomist
Museum Victoria
Ms Joanna Browne
PhD student- Gelatinous
zooplankton
National Geographic
Mr. Greg Marshall, Birgit Buhleier
Outreach and Education.
Documentation of scientific efforts
to conserve coral reef biodiversity
6. LIAISONS
CoML Group
Liaison / Primary Point of Contact
Email
Synthesis
OBIS
Mapping & Visualization
Barcoding
Education & Outreach
Nancy Knowlton
Mary Wakeford
David Crossman
Nancy Knowlton
Russell Brainard, Megan Moews
Knowlton@si.edu
m.wakeford@aims.gov.au
d.crossman@aims.gov.au
Knowlton@si.edu
Rusty.Brainard@noaa.gov,
Megan.Moews@noaa.gov
7. APPENDICES
7A. Synthesis Plans: Broad overarching synthesis themes/outcome from your project
 More precise estimation of coral reef diversity worldwide.
 Contribution to the identification of patterns of species diversity for understudied reefassociated groups.
 Estimation of biodiversity loss across gradients of human disturbance.
 Identification of prospects for maintenance of species diversity on reefs suffering from
various levels of human impacts.
 Identification of taxonomic and ecological information required to manage reefs
effectively.
 Development of effective tools to monitor and assess coral reef biodiversity (ARMS).
 Development of a resource locater as a tool for the scientific community to research coral
reef biodiversity information.
 Complete interoperability with OBIS
Synthesis management structure for your project
Title
CReefs
Synthesis
Team
Leader
Name
Nancy
Knowlton
Contact
nknowlton@ucsd.edu
CReefs
Synthesis
Writing
Team
Nancy
Knowlton,
Rusty
Brainard,
Julian
Caley
Julian
nknowlton@ucsd.edu
Rusty.Brainard@noaa
.gov
j.caley@aims.gov.au
Responsibility
To ensure the synthesis proceeds on
schedule, solicitation and coalition of the
groups opinions, communication with CoML
secretariat and to provide the lead for the
CReefs Synthesis Plan
Synthesis write-up will involve a team of
CReefs associated scientists. A committee
will further be designated for compilation of
sections and editing.
j.caley@aims.gov.au
To synthesize the major activities in the
Western
Pacific/Indi
an Ocean
region
synthesizer
Central and
Western
(nonAustralia)
Pacific
region
synthesizer
Caley
Russell
Brainard
(Megan
Moews,)
Rusty.Brainard@noaa
.gov
Same as above
Caribbean
region
synthesizer
Molecular
methods
synthesizer
Nancy
Knowlton
nknowlton@ucsd.edu
Same as above
Laetitia
Plaisance
plaisancel@si.edu
Outreach
Megan
Moews
Megan.Moews@noaa
.gov
Methods
Developme
nt
Megan
Moews,
Russell
Moffitt
Russell
Moffitt,
David
Crossman
Shawn
Smith
Megan.Moews@noaa
.gov,
Russell.Moffitt@noaa
.gov
Russell.Moffitt@noaa
.gov
To summarize the various molecular and
sampling methods developed for CReefs and
by others, and to summarize molecular
results
To develop publication plans and establish
links with related efforts and existing media;
finalize informational website
To summarize the CReefs sampling methods
(other than molecular)
Mapping &
Visualizatio
n
Database
synthesizer
region, both directly sponsored by CReefs
and in parallel with CReefs efforts. Identify
databases for incorporation.
s.smith@aims.gov.au
Hawaii Liaison for Synthesis Mapping and
visualization
To coordinate the accession of new
information for databases and the methods
needed for uploading this information now
and in the future
Outline of your chapter for Contributed Synthesis Volume
The Known (Status of discipline prior to Census)
 Basic coral reef biology (see Knowlton 2008 review in Curr. Biol.)
 Historical perspective on coral reefs studies (Knowlton chapter in Cote volume provides a
short working history to start with).
 Historical perspective on biodiversity studies (Bouchet chapter provides a good starting
summary)
 Web-based analysis of what has been published in what fields prior to start of CReefs, with
special emphasis on biodiversity
From Unknown to Known (Evolution of discipline during the Census)
 Major gaps relate to the lack of information on poorly studied organisms that make up the
bulk of the biodiversity; this is true even on well studied reefs. This is a reflection on both
the scale of the problem (upwards of 9 million species worldwide) and the lack of effort
(including the demise of taxonomy in universities)
 To close these gaps requires both new technologies and new scales of approach – business
as usual will mean that it could take centuries to describe all coral reef life. Massive



application of standardized sampling methods and molecular analyses are essential – we
will not be able to put a name on all the diversity that is detected.
Major findings include a better estimate of global reef diversity, an estimation of
biodiversity loss associated with habitat destruction, and the fact that even with preliminary
sampling, we are uncovering substantial proportions of previously recorded diversity (e.g.
brachyuran crab species on 22 dead heads of corals from a single depth on 5 central Pacific
Islands totaled 30% of all named European crab species. In addition, most coral reef
species are rare, and genetic barcodes for these species are almost entirely lacking in major
databases such as GenBank. Finally, even for well known groups such as corals, our
understanding of species relationships is very poor – our recent analysis showed that 17/18
families of scleractinian corals were not properly defined.
Primary ramification of these discoveries is that coral habitat destruction could result in
widespread extinctions, comparable in terms of percentages to past mass extinctions.
Because of the scale of the diversity and the difficulty of caring for these organisms, a
“California condor” approach to the conservation of reef biodiversity will not succeed
(although aquaria might serve as a shelter of last resort for some species). The loss of
biodiversity on this scale could have many consequences to human health (e.g. drugs from
sea such as cone shells provide) in addition to impoverishing the planet in a more general
sense.
New questions include what mechanisms underlie the staggering diversity of reefs, and the
related question, how do rare species persist?
The Currently Unknown (remaining gaps)
 By the end of the census, we will still have at best an imperfect knowledge of coral reef
biodiversity – the scale of the problem is enormous (e.g. compare the number of species
that live in the plankton with the number of species that live on coral reefs). We will have
partial censuses at a number of sites, and a complete census will have been started (in New
Caledonia) for a mega-diverse site, and we will have molecular results from ARMS from
around the Pacific. However, it will still be difficult to extrapolate to reefs around the
globe.
 We will have an inkling of the anticipated patterns of loss related to global change (e.g.
warming, ocean acidification) and local degradation (e.g. effects of overfishing and poor
water quality) from several surveys across gradients of human disturbance. However,
accurate predictions of future human actions and the details of ecosystem responses to these
actions will still be out of reach.
How Can we Move From Unknowable to Knowable (novel approaches)
 We need to scale up efforts from partial censuses (e.g. limited number of taxonomic
groups) to all taxa inventories, and we need to scale up the number of sites for which large
or all taxa inventories are attempted.
 We need to push the limits because we have so much to learn about the staggering amount
of diversity on reefs, and we are in clear danger of losing it (e.g. 80% loss of Caribbean
coral cover in three decades). Conservation priorities cannot be established without having
a better idea of what is at stake and where.
 Our primary dream to “move the goalposts” involves real time sequencing at centers of reef
biodiversity, which is planned for the first time in New Caledonia in 2009 and 2010. We
would also like to make a global effort at reef environmental sampling and barcoding, by
using these methods at key sites in the Atlantic, Pacific and Indian Oceans. The key
obstacle is money (e.g. a 454 sequencing effort for a single environmental sample costs $510,000).
Conclusions (major findings and major gaps, how to move forward)
 The major conclusion is that reef diversity still verges on the unmeasurable, that we may be
on the verge of massive reef extinctions, and that we are still struggling with the methods to
characterize reef diversity and its loss.
 We need to expand the number of reefs that are well sampled from a handful to at least
twenty.
 We need to use quantitative sampling to estimate how diversity compares across nested
geographic scales at all twenty sites.
 We need to improve methods of molecular analysis and apply them globally. Of particular
importance is to develop reliable methods of sampling the small organisms that are larger
than bacteria but too small to easily barcode in a time efficient fashion. CReefs will have
made important progress in this regard, but there will be more work to do because of the
variation in individual biomass, abundance, and ease of amplification that makes this a
much harder task than it is with microbes.
Within-project synthesis plans
For science audiences:
 Book on coral reefs (Knowlton, probably Island Press). This book will be about 200 pages
and cover coral reefs present, past and future. It has already been outlined and some
chapters written.
 CReefs website – Resource Locater
 Input of reef biodiversity data collected by others into databases (OBIS, Genbank), OBIS
interoperability
 Overall analysis of molecular data generated by quantitative reef surveys (initial results
from New Caledonia would be submitted to Science or Nature)
 Coordination with bar-coding efforts (via Smithsonian)
 Synthesis of methods for assessing biodiversity sampling (Marine Biology?)
 Other scientific papers, and perhaps a special issue journal (Coral Reefs?)
For public audience:
 General CReefs website and Smithsonian Ocean Portal coral reef entries
 CReefs photos taken during the French Frigate Shoals expedition and Australian
expeditions
 Popular articles on expeditions
 Documentary production
For marine stakeholder audience:
 Synthesis of quantitative methods for assessing biodiversity sampling
 Collection and data management protocols of use to state and federal monitoring efforts
(e.g. NOAA, GBRMPA)
For policy audience:


CReefs and Smithsonian web portals articles on coral reef conservation, and coordination
with National Geographic ocean web initiative
Presentations as requested for state and national governments (e.g. see above for activities
of Knowlton and Brainard during past year)
Cross-project synthesis plans (what product and who?)
 “Role of the Rare”: Knowlton and Caley are participants and will be attending organizing
meetings in 2009. Our quantitative surveys clearly indicate that ~half of all coral reef
organisms are singletons in collections, so that reefs are highly relevant to this discussion.
 Barcoding: Knowlton (with L. Plaisance) will continue to contribute to this initiative – it is
a core component of CReefs.
 “How many species live in the oceans”: Caley is a participant.
 “New Biogeographies”: Caley is a participant.
 A-Z book for the public on marine biodiversity (Knowlton, being coordinated by CoML
with National Geographic Society if possible)
Visualization outputs for your project
 Coral Reef book (some maps)
 Images from expeditions (e.g. pictures of singletons to illustrate beauty of the rare)
 Graphs of potential numbers of new species to be detected based on knowledge at hand
 GIS biodiversity animation
Timelines/milestones for your deliverables
 July 2008 – International Coral Reef Symposium (accomplished)-PIs met in person
 July 2008 – Outline of plans for Knowlton/Bouchet Philippine Initiative (accomplished)
 Fall 2008 –Annual Report submitted (accomplished)
 Oct 23-25 – Russell Moffitt (NOAA) and David Crossman (AIMS) representing CReefs at
Mapping and Visualization Workshop (Durham, NC USA)
 Nov 2008 –planning session with Moffitt and Crossman post-M&V workshop
 Nov 2008 – Proposal to Keck Foundation to fund all taxa survey project in New Caledonia
(accomplished)
 Nov 2008 – Proposal to Moore Foundation to conduct CReefs biodiversity census at
Palmyra and Kingman Atolls
 Dec 2008 – Summary of Hawaii census results
 Dec 2008 – Launch of newly populated CReefs website and photos from the CReefs
expedition to French Frigate Shoals
 Dec 2008 – Detailed outline of Coral Reef book developed
 Dec 2008 – Field workshop on ARMS retrieval, processing, and analyses
 Jan 2009 – Submission of NSF grant to fund systematics of snapping shrimp (Knowlton)
 Jan 2009 – Submission of Synthesis proposal for 2010
 Feb 1-5, 2009 – Synthesis workshop aboard the Queen Mary (Long Beach, CA)
 Feb 2009 – AAAS symposium on ocean conservation success stories (incl. coral reefs) Mar 2009 – Pacific Science InterCongress, Biodiveristy Session, Tahiti
 May 2009 – Public symposium at Smithsonian associated with International Marine
Conservation Congress on ocean conservation success stories (incl. coral reefs)
 July 2009 – Beginning of New Caledonia survey project (pending funding)











Aug 1, 2009 – Draft Cross-Project synthesis outputs due for review by Synthesis Group
Aug 1,2009 – Draft within-project synthesis (Macintyre chapter) due
Fall 2009 – Summary of first Australia census
Dec 1, 2009 – Final Cross-Project synthesis outputs due (incl. chapter, A-Z book)
Dec 1, 2009 – Final Individual Project chapters due to Synthesis Group
July 2010 – Completion of coral reef book
Jan 2010 – Summarize results of 2nd and 3rd Australia censuses
August 2010—all remaining processed CReefs data entered into OBIS
Summer 2010 – Final version of website launch
Summer 2010 – First molecular counts of New Caledonia reef diversity announced if
project is funded – major finding to be used at Grand Finale. Note that although this survey
will continue beyond the Census, important molecular analyses will be completed by the
time of the time of the grand finale. In the event that Keck funding is not received, we will
use molecular data from other sites that have already been censused. Regardless of the
source, this will be a major finding as it will be the first such attempt that includes the small
in usually unstudied mega-diversity of reefs.
Oct 4-7, 2010 – Census “Grand Finale”
7B. Milestones
7C. OBIS Report
Provided by: Mary Wakeford
Project Manager, OBIS Liaison
Australian Institute of Marine Science, PMB 3
Townsville MC, Queensland 4810 Australia
Phone: +617-4753-4399 Fax: +617-4772-5852
E-mail: M.Wakeford@aims.gov.au
1. Has the person responsible for liaison with OBIS from your project been in communication with
OBIS?
The CReefs project has not served additional records to OBIS since the last reporting period, as the focus in
2008 centered on completing 3 field expeditions - the data from which will be served to OBIS once taxonomic
identifications have been verified by Australian Museums (2009). In preparing for the Australian Collection
trips considerable effort was directed toward developing the CReefs Collection Database to facilitate data entry,
imagery attachment and taxonomic classification/updates. Consequently communication with OBIS has been
minimal for 2008. A number of datasets from various Australian Museums have been identified for delivery to
OBIS in 2009.
2. Has dialogue begun with OBIS on how the OBIS portal may benefit your project (e.g. through
personal communication to the OBIS Chair or by answering questionnaires)?
J. Caley attended the OBIS Biogeography Meeting at the All Programs meeting in Auckland, New Zealand in
November 2007 and discussed opportunities and developments regarding the OBIS portal.
3. Please provide numbers on the following as published through OBIS at this time:
Name
AIMS - GBR Nearshore Coral
Date
Served
16-Jun-06
Records
16,489
Species
285
Genera
69
Locations
176
Diversity
AIMS - Bioresources Library
16-Jun-06
1,093
580
340
462
AIMS - Baited Remote Underwater
Video Stations (BRUVS)
18-Aug-06
18,541
638
233
610
AIMS - LTM Nearshore Corals
18-Aug-06
8,906
310
97
75
AIMS - LTM Fish
16-May-07
41,695
236
52
267
Northern Barrier Marine Life
(Aquarium Fish Trade)
28-Jun-07
869
216
100
6
AGRRA - Benthic (Scleractinia)
28-Jun-07
66,248
26
60
731
AGRRA – Fish
28-Jun-07
50,088
26
69
675
203,929
2,317
1,020
3,002
4. Please provide numbers on following as projected to be published through OBIS and indicate, to the
best of your knowledge, when these will published (Month and Year):
To be published in OBIS
Datasets
Number
Anticipated date (month, year)
1) NOAA CRED
345 datasets
2,500spec w/ location
345 unique locations
25,000 total by location
25,000 more
Dec 2008
Dec 2008
Dec 2008
Dec 2008
Dec 2010
2) NOAA NCCOS
10,000
Dec 2009
3) Australian Museums
– serve taxonomic information from
various Australian Museums as
available (many of the datasets may be
served to OBIS through OZCAM)
TBA
Nov 2008 – Dec 2009
4) CReefs Australia Collection Trips
2008
TBA
Dec 2009
5) All remaining processed CReefs
data
TBA
August 2010
5. How many species do you expect your project to observe and/or collect as part of CoML-related
efforts through 2010? Ultimately, how many new species would you estimate may be described as a
result of CoML activities, even if this work continues beyond 2010?
The first CReefs collection trip took place in Oct 2006 to French Frigate Shoals in the Northwestern Hawaiian
Islands. Preliminary analysis indicate that ~1611-2151 unique morphospecies were documented, with >100 new
species/new records. There have been delays in serving this data in 2008, and the revised date is 2009. Three
Australian Collection sites (Lizard Island, Heron Island and Ningaloo Reef) are to be sampled 3 times over the
next 4 years. The first round of trips was completed in September 2008 using similar sampling protocols/effort
to those employed during the French Frigate Shoals trip. Successive collections at each of the sites are likely to
result in reduced collection numbers. The target for serving the 2008 Australian collection data to OBIS is Dec
2009. The following summarizes findings so far:
Ningaloo Reef
950 sample lots were given field identification – of which some will be split into separate species and others
grouped at a later date. 305 unique species were identified in the field.
Lizard Island
1781 sample lots were given field identification. 150 distinct species.
Heron Island
Field trip completed September 2008, data not yet summarized.
6. Has discovery metadata been provided directly to OBIS for each dataset published?
Yes, discovery metadata was provided for each dataset published and has been updated or added to as requested
by OBIS. Metadata has been provided to OBIS through Phoebe Zhang (Institute of Marine and Coastal
Sciences Rutgers) and Melanie Meaux (for NASA’s Global Change Master Directory data).
7. Are there any particular difficulties in publishing data through OBIS?
AIMS has served data to OBIS since 2006 and the process has developed to reflect the changes occurring at
OBIS for this process. An online document builder is now used to create metadata records.
8. Are you using any controlled vocabularies in your data management (e.g., taxonomic reference lists,
gazetteer/locality names standard list, habitat types, biological sampling protocol, physical
oceanography parameters, etc.)? If so, please list these below and indicate how/where they originated
(e.g., in-house or via another source – list source). This information is essential for data integration.
The taxonomic reference, Catalogue of Life, was used for all data sets submitted to date. During the 2008
CReefs Australia collection trips, taxonomists from Australian Museums used their own preferred classifications
– however it is proposed that the Catalogue of Life classification will be followed when these records are served
to OBIS. The CReefs Collection Database also has drop-down lists for habitat and substrate selection (created
in-house)
9. What ecological information are you recording in your data management system (e.g., habitat type,
temperature, salinity, pH, nutrients, etc.)? And would you be willing to share this with OBIS? This
information will help OBIS design an interface to help link species to habitats and ecosystems.
Various types of ecological information are associated with each of the datasets - general habitat descriptions,
i.e. depths, fore-reef, back reef, lagoon, seabed. There is also abundance information. In many cases
researchers are less willing to make this type of data available (especially species abundance) although this
would be negotiable through direct contact with the data custodian.
10. Have you used data in OBIS (other than those provided by your project) for research or analyses? If
so, please provide brief description of study and, if applicable, citation for publication.
Not to date.
7D. Current Funding Report
Provided as a separate appendix
7E. Future Funding Needs Report
Provided as a separate appendix
7F. Shiptime Report
Provided as a separate appendix
7G. Images
Numerous images from the Australian expeditions have already been provided, from which you are
free to choose.