Transcript Macroalgal Project Overview Poster from NEAS 2014

Accessing 150 Years of Specimen Data to Understand Changes in the Marine/Aquatic Environment
Christopher Neefus and Hannah Traggis, University of New Hampshire, Department of Biological Sciences, Durham NH USA
Introduction
Macroalgal Herbarium Consortium
Workflow cont.
Fig. 4
Biological Collections
Biological collections have catalogued worldwide organismal diversity for 400 years
providing a priceless record of species distribution and ecology for local and visiting
scientists. Coupled with detailed field notes, environment and habitat information,
these collections represent invaluable tools by which biodiversity can be documented
over space and time, even allowing reconstruction of climate history (Oxford
University Herbaria, 2014).
Herein, macroalgae hold particular importance. Macroalgae are a diverse group of
aquatic photosynthetic organisms from four divisions spanning two kingdoms. They
serve as foundation species defining nearly every benthic habitat (marine, estuarine
and freshwater) providing food, shelter and substrata for other organisms. Globally,
they are important primary producers and essential participants in ecosystem nutrient
cycling. They are an important food source for humans and extractable colloids are
used in pharmaceuticals and cosmetics. Local populations of algae adapt to their
environment over time and are generally resilient. It has been suggested though that
perhaps due to local adaptation, they and the habitats they define, may be especially
sensitive to climate change.
The Macroalgal
Herbarium
Consortium
Digitization of Biological Collections and the NSF ADBC Program
Biological collections held by the U.S. are estimated to contain over one billion
specimens, yet barely 10% of these collections are accessible outside of the institution
where they are held (Plimpton, 2013). Foreign collections face the same level of
inaccessibility essentially barring this critical information to all but a few scientists
that are able to physically visit the collection. It has been recognized that there is a
“digitization bottleneck.” Recently, there has been an enormous collective effort to
digitize herbarium and museum collections worldwide making the information therein
available online, open-access to scientists and citizens.
The U.S. NSF Advancing Digitization of Biological Collections Program (ADBC) was
formed to fund activities that address this bottleneck and digitize all U.S. held
biological collections. Activities funded include: the development and advancement of
digitization technologies; development and adherence to particular standard
vocabularies, i.e. Darwin Core as set forth by the Biodiversity Information Standards
(TDWG 2014). This insures data can be universally shared. Also funded are activities
that expand georeferencing techniques and software used to locate individual vouchers
on a world map. Finally the creation and implementation of substantial digitization
infrastructure with which future collections can immediately be digitized without risk
of falling into obscurity.
The ADBC has three levels of organization. The first is a “central coordinating
organization” or hub. Integrated Digitized Biocollections (iDigBio) was created in 2011
as a national resource to serve this purpose and ingest digitized specimen data
providing a central platform on which this data is easily searchable and widely
available. Similar to the Global Biodiversity Information Facility (GBIF), iDigBio serves
as a single portal through which multiple institution collections can be accessed online.
The next level is the Thematic Collections Network (TCN) that brings together multiple
institutions’ collections under a common research theme surrounding one or more
“grand challenges” to biodiversity studies or other critically important research goal.
The third level within the ADBC Program is comprised of the collections themselves.
Collective digitized data from a TCN is gathered into one portal and then ingested for
centralized distribution with other TCNs by iDigBio.
Fig. 5a
Fig. 6
Fig. 5b
In 2013, the Macroalgal Herbarium Consortium (MHC), a Thematic
Collection Network (TCN) led by the University of New Hampshire,
received $3.3 million from the NSF ADBC Program to digitize (image,
database and georeference) all of its macroalgal herbarium specimens.
Encompassing 49 institutions including universities, museums, botanical
gardens and research field stations, the MHC represents algal collections
held in 26 states and U.S. possessions. Included are more than 1.1
million specimens collected worldwide over the past 150 years with
roughly 60% of specimens over 50 years old and 10% over 100 years
old. The major research theme for this network is the utilization of
vouchered algal specimens to determine how macroalgal biodiversity
has changed both spatially and temporally and how that relates to
changes in aquatic ecosystems. In concert with this overarching
research theme, the primary goal of the MHC is to digitize the entire
consortium holdings to facilitate biodiversity research in ecological
changes of aquatic ecosystems and also to engage the public promoting a
greater appreciation for macroalgae and natural history collections in
general. Changes in macroalgal community structure and aquatic
ecosystems can be studied in response to bioinvasions (Nettleton et al.,
2013), increased human activity and of course climate change
(Jueterbock et al., 2013). Results garnered from these collections can
also be used to advise conservation policy, track global species
distribution and increase our understanding of systematics and
phylogenetics.
To accomplish its goal, the consortium is organized into regional Primary
Digitization Centers (PDCs), Digitizing Institutions (DIs) capable of
digitizing their own collection and Contributing Institutions (CIs) that
are sending their collection to one of the PDCs for digitization.
Additional specimen collections that wish to join a MHC TCN should
work with that TCN and iDigBio to submit a Partners to Existing
Networks (PENs) grant proposal to the NSF ADBC Program.
Workflow
Predigitization
curation
(Fig. 1)
Fig. 1
Voucher
barcoding
(Fig. 2)
• Skeletal data
capture as .csv
file
High
resolution
image capture
(Fig. 3)
Image upload
to MHC Portal
(Fig. 4)
• Primary key:
barcode = NHA
catalogue #
• Additional data
Georeference
specimens
(Fig. 5a-b)
Information Usage
Bio Invasions: Increased biomass production of Gracilaria sp. in the Gulf of
Maine is attributed to a previously unidentified invasive species Gracilaria
vermiculophylla.
Nettleton JC, AC Mathieson, C Thornber, CD Neefus and C Yarish. 2013. Introduction of Gracilaria vermiculophylla
(Rhodophyta, Gracilariales) to New England, USA: estimated arrival times and current distribution. Rhodora. 115:
28–41.
Climate Change: Predicted shifts of intertidal foundation fucoid species due
to increasing ocean temperatures. Occurrence records for this study were, in
part, accessed through GBIF.
Data ingestion
by iDigBio
(Fig. 6)
Jueterbock, A., Tyberghein, L., Verbruggen, H. Coyer, J.A., Olsen, J. L., Hoarau, G. Climate change impact on seaweed meadow
distribution in the North Atlantic rocky intertidal. Ecology and Evolution. 3(5): 1356-1373, 12 APR 2013 DOI:
10.1002/ece3.541
http://onlinelibrary.wiley.com/doi/10.1002/ece3.541/full#ece3541-fig-0002
Fig. 2 1
Fig. 3
Acknowledgements
This project greatly appreciates funding from the NSF ADBC program and the intellectual and
technological support of the team at iDigBio!
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References
Biodiversity Information Standards (TDWG). 2014. Darwin Core. Retrieved April 22, 2014 from http://rs.tdwg.org/dwc/
Global Biodiversity Information Facility (GBIF). 2014. Using Data. Retrieved April 20, 2014 from http:..www.gbif.org/usingdata/sciencerelevance
iDigBio. 2014. iDigBio ADBC Overview; Citizen Outreach; Digitization Resources and Mobilizing Small Herbaria Workshop. Retrieved April, 2014
from http://www.iDigBio.org
Jueterbock, A., Tyberghein, L., Verbruggen, H. Coyer, J.A., Olsen, J. L., Hoarau, G. 2013. Ecology and Evolution. 3(5): 1356-1373.
Neefus, C.D. 2013. Award Abstract 1304924. Retrieved April 22, 2014 from
http://www.nsf.gov/awardsearch/showaward?AWD_ID=1304924&HistoricalAwards=false.
Neefus, C.D. 2014. Herbarium Digitization Project Documents. Retrieved April 19, 2014 from http://macroalgae.unh.edu
Nettleton, J., Mathieson, A.C., Thornber, C., Neefus, C.D., Yarish, C. 2013. Introduction of Gracilaria vermiculophylla (Rhodophyta, Gracilariales) to
New England, USA: Estimated Arrival Times and Current Distribution. Rhodora 115(961): 28-41.
Oxford University Herbaria. 2014. Oxford University Herbaria, Department of Plant Sciences. Retrieved April 22, 2014 from
http:..herbaria.plants.ox.ac.uk.bol/oxford.