Project Description
1. Response to Previous Submission
This is a resubmission of a PEN proposal from 2012. While the prior panel recognized the
significant contribution that the BYU collection would make towards the Southwest Collections
of Arthropods Network (SCAN) TCN, a number of weaknesses were pointed out. We respond to
them briefly here, and elaborate on them in the body of the proposal.
(1) Insufficient documentation of collection use and publications. The BYU collection is actively
engaged in curation and outreach to the research community. Table 1 indicates that over the past
decade the collection has made 478 loans totaling 163,969 specimens, resulting in 220
publications.
(2) Inadequate articulation of the taxonomic spread of the collection. The BYU collection
consists of 2.5 million specimens from around the world, with an emphasis on western North
America. For the purposes of this PEN, we are focusing our cataloguing efforts on four families
(Acrididae, Carabidae, Tenebrionidae, and Formicidae). Our rationale is that (a) these are four of
the five groups which are the central focus of the SCAN TCN (the other being spiders) and (b) we
have exceptional strength in these holdings in terms of species diversity, specimen number, age of
specimens (100+ years old to recent), and degree of identification by specialists (Table 2).
(3) Absence of a compelling case for the urgency of digitization. For more than 50 years during
the early history of the collection (1902-1960), most of the collecting labels were produced on
photographic paper. Many of these BYU labels are already difficult to read, and they are all
quickly fading to black (Fig. 3). Without immediate digitization and replacement with archival
quality labels, a wealth of legacy data will be lost forever. Moreover, our collection enhances the
impact of the SCAN TCN by providing geographic coverage in the Great Basin that is largely
lacking in current digitization efforts.
(4) Broader Impacts were insufficiently detailed. We describe a clear strategy for recruiting and
mentoring undergraduate students and propose an exciting new interactive museum exhibit that
leverages the power of the NSF TCN to help educate the general public.
2. Introduction
A. Project Overview
SCAN (Southwest Collections of Arthropods
Network) connects collections to form a virtual
museum that will become a major component of
the iDigBio infrastructure and enable new kinds
of biodiversity science. SCAN already includes
ten small to large collections from the states of
Arizona, Colorado, New Mexico, and Texas (Fig.
1), plus Harvard University which has substantial
holdings of southwestern ants. However, there are
no collections from Utah and none that focus on
Figure 1 Collaborators in the SCAN TCN
the Great Basin region of the United States.
network. The southwestern United States as
defined by SCAN is indicated by the red line.
Participating institutions focus on digitizing
SCAN headquarters at Northern Arizona
specimens that are typically collected in pitfall
University is indicated by the large yellow and
trap studies, including spiders, orthopterans,
red marker. Other SCAN institutions are
ground-dwelling beetles, ants, and other terrestrial indicated by small yellow and orange markers.
arthropods, resulting in a database that includes
BYU is indicated by a large blue and yellow
marker. Note that BYU fills the large geographic
many thousands of species and over one million
gap in SCAN coverage in Utah, Nevada, and
specimens. Smaller collections in SCAN (e.g.,
western Colorado.
New Mexico State University and Northern
Arizona University) are funded to capture collecting and taxonomic information and to image
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many of their specimens. The larger collections (e.g., University of Arizona and Texas A&M) are
focused on cataloguing taxonomic and locality information and have a very limited imaging
component to their work. While SCAN is interested in all ground-dwelling arthropod species, it
has set as a priority five focal groups: ground beetles (Carabidae), darkling beetles
(Tenebrionidae), grasshoppers (Acrididae), ants (Formicidae), and spiders. BYU has extensive
and important holdings in the four insect families listed above. Due to the overwhelming numbers
of specimens in the BYU collection, we propose to catalogue specimens in these four highpriority groups, and limit our imaging to type specimens.
Figure 2. Examples of target taxa to be
digitized from the BYU collection. (a)
Dactylotum bicolor Charpentier (Acrididae);
(b) Chlaenius sericeus (Forster)
(Carabidae); (c) Eleodes parowana Blaisdell
(Tenebrionidae); (d) Pogonomyrmex
occidentalis (Cresson) (Formicidae).
B. Specific Goals of the BYU PEN to SCAN
Over three years of funding, we propose to:
(1) Capture collecting and identification data from 52,000 previously uncatalogued grounddwelling arthropod specimens from the BYU collection (Acrididae, Carabidae,
Tenebrionidae, and Formicidae). This reduces an enormous gap in SCAN’s geographic,
taxonomic, and temporal sampling. Overall, this will increase the total number of specimens
newly catalogued by SCAN from 525,349 to 577,349, an increase of 10%. To ensure superb
identification quality, taxonomic specialists will visit the collection before digitization.
(2) Georeference specimen localities contributed to SCAN, utilizing GEOLocate and other
resources, and upgrade fading locality labels on legacy specimens with archival quality
labels.
(3) Produce high-resolution images of type specimens of all ground-dwelling arthropod species
whose type material is housed at BYU (approximately 300 species), thereby augmenting the
image assemblage being contributed by other SCAN institutions.
(4) Contribute to SCAN’s synthetic regional database to promote accessible, well-structured,
taxonomically sound data for modeling climate change impacts on species distributions, and
thereby enhance SCAN’s remote specimen annotation and identification workflows.
(5) Provide three undergraduate students with an excellent mentored research experience as they
build an interactive museum exhibit that highlights arthropods in the southwestern United
States while leveraging the power of the SCAN TCN to better understand the species that are
around them.
C. Project Challenge
The southwestern United States encompasses an exceptionally rich diversity of taxa and
ecosystems that span the four major North American deserts, the southern Rocky Mountains, and
the Great Basin, for which BYU has important specimen coverage (Fig. 2). The Southwest region
is approximately 1.6 million km2 in area, comprising more than 20% of the contiguous United
States. Historically, the wide geographic spacing of arthropod collections and museums has made
cross-institutional integration of interests and projects difficult, and instead has led to most
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collections developing unique profiles of uneven coverage. For instance, more than 80-90% of
specimens at Arizona State University are identified to the level of species (see ledger at
franz.lab.asu.edu/collection.html); however, this collection has experienced very limited growth
in recent years. In contrast, the similarly scoped collection at Northern Arizona University has
amassed tens of thousands of specimens in recent years through structured sampling efforts that
offer valuable ecological insights; yet so far, only 12% of these specimens have been expertidentified to the level of species. BYU adds approximately 60,000 specimens annually, with
about half of them being identified by taxonomic authorities, and the collection has the
strength of holding both legacy material and recently collected material.
Once the accumulated holdings of southwestern arthropod collections are networked through a
unified e-portal, the aforementioned disparities between them will create a data environment
where specific requests for expert identifications of thousands of specimens will become feasible,
necessary, and likely very frequent. Finally, because of significant taxonomic overlap among the
regional collections, there will be a need to systematically and efficiently redistribute the "valueadded" species identification data among all collections; thus offering opportunities for implicit
identifications of specimens not directly examined by an expert but implied by the original
identification service.
3. Background
A. Creation of the Southwest Collections of Arthropods Network
SCAN began in 2006 as an informal association of insect and arthropod collections in the
southwestern United States. Group discussions identified the current lack of a unified, regional,
specimen-level database of arthropod taxa as the most critical impediment to future collaboration
and the potential centerpiece of a future collaborative group initiative. Two years ago, ten
institutions received NSF support. BYU was urged to be a participant, but due to conflicts with
other ongoing TCN proposals, we declined participation. We are now in a position to fully
collaborate as a PEN institution in the SCAN TCN.
B. Attributes of the BYU Collection
1. Historical Importance
The BYU arthropod collection has a rather long history, and it is therefore the repository for
voucher specimens and legacy data associated with numerous important studies. Although
Brigham Young Academy (the forerunner of BYU) was established in 1877, the oldest existing
arthropod specimens in the collection (apart from a few 19th century specimens obtained through
gifts or exchanges) are about 110 years old. From 1902 to 1904, Benjamin Cluff, principal of the
Academy, led a scientific expedition to explore parts of Latin America. Many of the biological
specimens collected are still at BYU. However, the arthropod collection did not begin in earnest
until the arrival of its first curator, Vasco M. Tanner, in 1925. The BYU collection preserves
legacy data from his numerous studies. He published prolifically over a career spanning more
than 50 years. Many of his articles dealt with Tenebrionidae, Carabidae, Curculionidae, and other
ground-dwelling arthropods targeted by SCAN (Allred & Tanner 1979; Tanner 1926, 1927a,
1927b, 1928, 1929, 1934a, 1934b, 1938, 1939, 1941a, 1941b, 1942, 1943, 1944, 1945, 1948,
1950, 1951, 1954, 1959, 1960, 1961, 1963, 1966, 1969, 1974, 1987; Tanner & Olsen 1929;
Tanner & Packham 1962, 1965).
Other researchers associated with BYU have also published on arthropods, including grounddwelling taxa, and vouchers for their investigations are also preserved here. Dorald M. Allred
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studied arachnids, isopods, myriapods, Formicidae, Mutillidae, and Scarabaeidae (Allred 1965,
1967, 1969, 1971, 1972, 1973a, 1973b, 1973c, 1973d, 1974, 1975, 1980, 1982; Allred & Beck
1965; Allred & Cole 1971, 1979; Allred & Gertsch 1976; Allred & Kaston 1983; Allred &
Mulaik 1965; Allred & Muma 1971; Allred & Tanner 1979; Beck et al. 1967; Gertsch & Allred
1965; Johnson & Allred 1972). Additionally, D. Elden Beck studied Formicidae and
Scarabaeidae (Beck et al. 1967; Allred & Beck 1965).
Numerous other entomologists have been associated with BYU and have added to our holdings.
They have included Richard W. Baumann, Gary M. Booth, Elias P. Brinton, Seth Bybee, Shawn
M. Clark, D. Elmo Hardy, Michael J. Hastriter, C. Lynn Hayward, C. Selby Herrin, Clive D.
Jorgensen, D. D. Jorgensen, Fred A. Mangum, Lucile Maughan, C. Riley Nelson, Mervin W.
Nielson, Robert V. Peterson, W. Levi Phillips, Vernon J. Tipton, Armand T. Whitehead, Michael
F. Whiting, Robert N. Winget, and Stephen L. Wood. Although most of their research did not
emphasize directly the targeted ground-dwelling taxa of SCAN, many of these workers were
prolific collectors of diverse arthropods, including ground-dwelling species. Their specimens are
housed in the BYU collection and form the basis for numerous published investigations by
scientists, both from BYU and elsewhere.
Arthropod research at BYU is ongoing. Major faunistic surveys have recently been conducted in
the Grand Staircase-Escalante National Monument in Southern Utah, Timpanogos Cave National
Monument in Central Utah, Lytle Preserve in the Mohave Desert, and Dugway Proving Ground
in Northern Utah. Although the collecting aspects of these investigations have been completed,
identification aspects continue. Moreover, studies of the collection are not limited to BYU
personnel, and specimens are extensively studied by scientists worldwide.
2. Museum Facilities
The BYU arthropod collection is housed in the Monte L. Bean Life Science Museum (MLBM) on
the campus of Brigham Young University (BYU) in Provo, Utah. The museum is ~88,000 ft²,
with ~25,000 ft² dedicated to research collections. The collections portion of the museum is
dedicated to scientific research and is inaccessible to the general public, except through special
arrangement. The museum as a whole has important roles in education and public outreach, with
several hundred thousand visitors each year. Exhibit planning is done with the advisement of the
Curators and curatorial staff. A significant expansion of the museum is scheduled for completion
in 2014 and will result in an increase of space across all collections by 50%. BYU has a clear and
long-term commitment to the ongoing support of the museum, and provides salary, supplies,
and other benefits to support permanent collections managers throughout the museum.
3. Collection Size
The BYU arthropod collection contains approximately 2.5 million specimens. It is the largest
arthropod collection west of the Great Plains and east of the Pacific Coast states. The
collection, with its associated offices and work areas, currently occupies more than 6,200 ft² on
the upper floor of the MLBM. The pinned portion of the collection is housed in steel cabinets
with approximately 4,300 Kansas drawers (20% larger than Cornell drawers). The exceptionally
large wet collection is currently housed in the same area as the pinned specimens, but it will soon
move to a newly constructed wet collections facility adjacent to the main museum building. Most
of the wet specimens are curated in patent-lip vials with neoprene stoppers, but some are in
cotton-plugged vials inside larger jars. Additionally, there are large collections of microscope
slides and odonates in envelopes. There are also ten ultralow freezers for storing arthropods
preserved in 100% ethanol (tissue collections). The arthropod tissue collection at BYU is among
4
the oldest, largest, and most diverse collection anywhere in the world. An expanded cryogenic
facility with liquid nitrogen storage is anticipated soon.
4. Taxonomic Emphases
The BYU collection is exceptional in that it has substantial, important holdings in almost all
arthropod groups, with a particular strength in beetles. During the collection’s history, beginning
in the early 1900s, there have been only four Head Curators, and two of them (Vasco Tanner and
Stephen Wood) were coleopterists. The current Collections Manager (Shawn Clark) is also a
coleopterist. Additionally, the collection is exceptionally strong in aquatic insects. Emeritus
Curator Richard Baumann and the current Assistant Curator Riley Nelson are both specialists on
stoneflies and other aquatic insects. As a result of their activities, BYU has the largest
Plecoptera collection in the world. There are additional major holdings in Diptera, Mecoptera,
Siphonaptera, Ephemeroptera, Odonata, and other groups. The Orthoptera collection is also
particularly noteworthy. Retired orthopterist Andrew Barnum donated his collection to BYU. It
fills more than 200 drawers, about half of these being grasshoppers (family Acrididae).
5. Geographic Emphases
The BYU collection is worldwide in coverage, with a principal emphasis in western North
America. The geographic location of BYU is important because it fills a major gap in the
geographic coverage of SCAN. As expected, the geographic strengths of current SCAN
collections are largely a reflection of the location of the museums. Whereas current SCAN
museums are from Arizona, Colorado, New Mexico, and Texas, none of them are located in the
central Rocky Mountains or in the Great Basin (areas within the scope of SCAN). BYU has major
holdings from these areas, as well as from throughout the Southwest. The only major collection
with a geographic focus similar to that of BYU is the Utah State University collection (not a
SCAN participant), and it does not have the same strengths in ground-dwelling arthropods. The
holdings of BYU are unique, important, and not duplicated elsewhere.
Among the many important studies conducted by BYU, the legacy data resulting from an
extensive biological survey of the Nevada Atomic Test Site (near Mercury, Nevada) is
noteworthy. During the 1950s and 1960s, massive collections were made resulting in numerous
publications on ground-dwelling arthropods (Allred 1965, 1967, 1973b, 1973d; Allred & Beck
1965; Allred & Mulaik 1965; Chamberlin 1962; Gertsch & Allred 1965; Tanner & Packham
1965). Much of the material from the study is deposited at BYU (Allred et al. 1963) and
represents one of the earliest comprehensive biological surveys within the Western United States.
More recently, BYU participated in an extensive survey of arthropods of the Grand StaircaseEscalante National Monument, a biologically very interesting part of the Colorado Plateau. This
resulted in 100,000 specimens, including many ground-dwelling species that were collected and
deposited in the BYU collection. An insect survey is also currently underway at the Lytle
Preserve in the Mohave Desert.
6. Collection Usage
The BYU arthropod collection is widely used by the scientific community. Each year on
average, more than 16,000 specimens are loaned to researchers from diverse institutions
(Table 1). Beyond loaned specimens, approximately 30 scientific researchers visit the collection
each year. We are aware of 220 scientific articles published in the last decade based on specimens
in the BYU arthropod collection, but suspect that the number is actually much greater since PIs
often neglect to send us reprints. We anticipate that as our collection records are made web-
5
accessible through SCAN, researchers will become more aware of our holdings, and loan requests
will become even more frequent.
Table 1 Activity in the BYU Collection as indicated by the number of specimen loans made over the past decade.
Year
Number
of loans
Number
of loaned
specimens
Taxa loaned
State or country of borrower
2012
42
12,912
AZ, CA, DC, IN, KS, MS, MT, NC, NE,
NM, OR, PA, SC, TX, UT, WI, Canada,
China, Mexico, Peru, Poland
2011
39
9,155
2010
37
11,446
2009
27
11,644
Blattodea, Coleoptera, Diptera,
Hemiptera, Hymenoptera, Lepidoptera,
Megaloptera, Orthoptera, Plecoptera,
Chilopoda, Diplopoda
Blattodea, Coleoptera, Diptera,
Hemiptera, Hymenoptera, Lepidoptera,
Neuroptera, Orthoptera, Plecoptera,
Trichoptera, Arachnida
Coleoptera, Diptera, Hemiptera,
Hymenoptera, Lepidoptera, Orthoptera,
Arachnida
Blattodea, Coleoptera, Diptera,
Hemiptera, Orthoptera, Trichoptera
2008
44
11,682
2007
46
17,068
2006
46
24,748
2005
60
20,885
2004
76
25,857
2003
61
18,572
Total 478
Coleoptera, Diptera, Hemiptera,
Hymenoptera, Lepidoptera, Neuroptera,
Orthoptera, Plecoptera, Trichoptera,
Arachnida
Coleoptera, Diptera, Ephemeroptera,
Hemiptera, Odonata, Orthoptera,
Plecoptera, Trichoptera
Coleoptera, Diptera, Ephemeroptera,
Hemiptera, Hymenoptera, Lepidoptera,
Neuroptera, Odonata, Orthoptera,
Plecoptera, Trichoptera, Arachnida
Coleoptera, Diptera, Ephemeroptera,
Hemiptera, Hymenoptera, Lepidoptera,
Orthoptera, Plecoptera, Trichoptera,
Arachnida, Diplopoda
Coleoptera, Diptera, Ephemeroptera,
Hemiptera, Hymenoptera, Lepidoptera,
Odonata, Orthoptera, Plecoptera,
Arachnida, Diplopoda
Coleoptera, Diptera, Hemiptera,
Hymenoptera, Lepidoptera, Mecoptera,
Megaloptera, Neuroptera, Odonata,
Orthoptera, Plecoptera, Rhaphidioptera,
Trichoptera, Chilopoda, Diplopoda
163,969
7. Current Personnel
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AZ, CA, DC, FL, IA, KS, MN, MS, MT,
NC, NV, NY, OR, PA, TX, UT,
Australia, Canada, Spain
AZ, CA, CO, DC, DE, FL, KS, KY, LA,
MT, NC, NY, PA, TX, UT, WV, Brazil,
Canada, Finland
AR, CO, CT, DC, KY, LA, MD, MS,
MT, OR, PA, SC, TX, UT, Brazil,
Canada, Czech Republic, Germany,
Italy, Spain
AZ, CA, CO, DC, MD, MI, MN, MS,
MT, ND, NM, OH, OR, PA, TX, UT,
Canada, Czech Republic, Germany, New
Zealand, Poland, South Korea, Ukraine
AZ, CA, CO, DC, FL, GA, HI, IL, KS,
KY, MD, MS, NM, NY, OH, OR, PA,
TX, UT, WA, Argentina, Australia,
Canada, Czech Republic, Finland,
Germany
AZ, CA, CO, DC, FL, GA, IL, LA, MD,
MO, MS, MT, NC, NH, NY, OR, PA,
TX, UT, VA, Canada, Latvia, Mexico
AR, AZ, CA, CO, DC, FL, HI, IN, MS,
MT, ND, NM, NY, OR, PA, SC, TX,
UT, WI, Canada, Germany, Slovenia
AR, AZ, CA, CO, CT, FL, IN, KY, MA,
MN, MS, MT, NC, ND, NH, NM, NY,
OH, OR, PA, TN, TX, UT, WA, WV,
Canada, Latvia
AK, AZ, CA, CO, DC, FL, IL, KY, MD,
MS, MT, NC, OH, OR, PA, TX, UT,
WA, Canada, Germany, Italy, Poland
Michael F. Whiting, a specialist on the higher-level phylogenetics of insects, is the Head Curator
and directs the BYU arthropod collection. Shawn M. Clark is the Senior Arthropod Collections
Manager who performs much of the routine curation, and he is a specialist in the systematics of
Chrysomelidae (leaf beetles). C. Riley Nelson is the Assistant Curator and specializes in
Plecoptera (stoneflies) and Diptera (particularly asilid flies). Richard W. Baumann is an Emeritus
Curator, and he remains very active in the study of Plecoptera. Michael W. Hastriter is an
Adjunct Curator and specializes in the systematics of Siphonaptera (fleas). Selby Herrin is a
Volunteer Curator of mites and Alan R. Myrup is a Volunteer Curator of Lepidoptera and
Odonata. Each year, approximately 20 student employees or volunteers also assist with curation.
C. Digital Contributions to SCAN
We have selected Specify as our databasing choice for capturing taxonomic, geographic, and
image data. This is because: (1) it is the standard databasing software used throughout our
museum; (2) it has built in error-checking and correcting capabilities for locality and taxonomic
information; (3) it has a controlled data entry environment whereby student workers can only
access a subset of the data during data entry; (4) it is equipped to handle images; and (5) it is the
databasing software being used by the majority of the SCAN participant institutions. To test our
workflow system (described below), we have already captured collecting and identification data
from nearly 5,000 arthropod specimens and passed these to SCAN
(http://symbiota1.acis.ufl.edu/scan/portal/collections/misc/collprofiles.php?collid=18). Similar to
the larger collections that participate in SCAN, we limit our imaging to only specimens from type
series (approximately 300 species). We have extensive experience imaging specimens, though
our current software and digital camera need updating (Olympus SZX12 microscope fitted with
mechanized focus, MTI 3CCD camera, Olympus MicroSuite montage software).
4. Rationale for Research Focus & Approach
A. Gap Analysis The participation of BYU in the SCAN TCN will fill the following gaps:
(1) Geographic gap. BYU is the largest arthropod collection east of the Great Plains and west of
the Pacific Coast states. We have substantial holdings from throughout the Southwest, and our
collection is especially replete with material from the central Rocky Mountains and the Great
Basin, regions that are moderately to poorly covered by the other SCAN participants. A search of
the SCAN database (http://symbiota1.acis.ufl.edu/scan/portal/collections/index.php) on October
16, 2013 revealed that, while a few records from the Great Basin and central Rockies are
included, most of these were apparently gleaned from already existing datasets and do not involve
the ground-dwelling taxa that are the emphasis of SCAN. BYU can offer many more records. As
a brief example of lack of current SCAN coverage, only three specimens are included for Morgan
County, Utah, and only eleven for Rich County, Utah. Collectors from BYU have visited these
counties hundreds of times and collected many thousands of specimens. Only 23 records are
included for Sanpete County, Utah. This is the area where early BYU entomologist Vasco Tanner
collected insects throughout his life. It is also the county containing family property of senior PI
Clark, where he has done extensive entomological sampling. Additionally, it is the home of
retired entomologist T. Blaine Moore, who donated nearly 8,000 specimens (mostly beetles) to
BYU. With regards to Utah County, Utah, the SCAN database includes a few specimen records
(189). However, as this is the home of BYU, there are thousands of specimens from this county
that BYU could offer. It is quite clear that we offer an extensive and geographically unique set
of specimens that will enhance the SCAN project.
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(2) Taxonomic gap. In view of the geographic focus of the BYU collection, it is not unexpected
that there are many species present in the BYU collection that are not well represented in other
collections, including many that form the basis of scientific publications. To test this assertion,
we randomly selected one dozen taxa from the collection that belong to the four families that we
will digitize. Four of the twelve taxa are represented in the SCAN database by fewer than 20
specimens. The SCAN database has only three records for Amblycheila schwarzi Horn
(Carabidae); the BYU collection has 29 specimens, including the holotype of the synonym A.
utahensis Tanner. The database has only 17 records for Eleodes dissimilis Blaisdell
(Tenebrionidae); there are 137 specimens in the BYU collection. The database has zero records
for Eleodes rotundipennis LeConte; the BYU collection has 220 specimens. The SCAN database
includes zero records for Melanoplus borealis utahensis Scudder (Acrididae); the BYU collection
has 74 specimens. Moreover, our holdings are particularly valuable because taxonomic
authorities have already identified ~ 95% of these specimens, including the types that are housed
at BYU. In addition, identifications will be verified and nomenclatural problems will be sorted
out by specialist collaborators prior to data entry (described below). BYU’s participation in
SCAN will fill many important taxonomic gaps.
(3) Temporal Gap. In contrast to some of the more recently established collections, BYU has
many historically important specimens, with their associated legacy data, dating back more than a
hundred years. This allows for study of changes in species distributions over time, with
implications related to habitat disturbance and climate change. In particular, the specimens that
came from the Nevada Test Site survey in 1950-1960 will provide important insights into
biogeographic patterns in this area.
B. Merits of SCAN
The importance of SCAN was well explained in the already funded SCAN TCN proposal.
Briefly, the project complements and synergizes other TCNs, it advances studies of community
ecology, it supplies critical data for investigations of climate change and arthropod distributions,
and it provides a framework for web-based identification of arthropods, incorporating Filtered
Push technology. For the first time, all significant collections within the Southwest will be tied
together within a unified framework allowing new and synergistic research activities. As an
added participant in the project, BYU will contribute to and enhance all of these activities.
C. How BYU Enhances the SCAN TCN
By adding records from 52,000 specimens from the four target families, the BYU collection will
supply a great deal of data, significantly increasing the magnitude and associated value of the
SCAN database. We will fill in the geographic, taxonomic, and temporal gaps as described above,
and will make these data widely available to the scientific community.
D. Urgency
There is particular urgency with respect to the BYU collection. For a period of more than 50
years during the early history of the collection, most of the collecting labels were produced on
photographic paper. Labels were initially made with a typewriter, then photographically reduced
with a camera. Photographs were afterwards cut into labels. Such labels darken over time, and
many of the BYU labels are already difficult to read (Fig. 3). Without immediate attention, these
labels will soon become completely unreadable, and a wealth of legacy data will be lost forever.
Our digitization of label information will preserve the data. Once specimens are databased, the
label printing feature of Specify will enable easy production of archival quality labels to be added
to the pins.
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Figure 3. Example of a photographically produced collecting label
that is darkening to black. We intend to transcribe and add
archival quality labels to these specimens as part of the digitization
process.
5. Management Plan
A. Organization & Responsibilities
BYU will work within the existing framework of the TCN. SCAN PI Neil Cobb (Northern
Arizona University) is responsible for overall SCAN performance, as well as collaborations with
other digitization efforts. PEN PI Clark will manage the BYU component, with the assistance of
Co-PIs Whiting and Nelson. He will be responsible for student recruitment, training, data entry,
curatorial work, and quality control.
B. Taxonomic Scope
Although SCAN has identified 100 ground-dwelling families to be digitized, not all of the
targeted families will be included at all of the institutions. As noted above, we will catalogue
locality and taxonomic information for material in the four highest priority insect families:
Carabidae (8,000 estimated specimens), Tenebrionidae (20,000 estimated specimens), Acrididae
(16,000 estimated specimens), and Formicidae (8,000 estimated specimens). While we will
certainly move on to other ground-dwelling groups as efficiency and budget allow, our primary
goal is to capture the data from these 52,000 specimens. Additionally, we will photograph type
specimens for ground-dwelling groups housed at BYU (approximately 300 species).
Table 2 Taxa targeted for digitization in the BYU collection. Note that we anticipate that the visiting specialists
will be able to determine many of our unidentified specimens, and these will be databased as well.
Family
Identifiers
Acrididae
(grasshoppers)
Andrew Barnum, Dan Otte,
Hojun Song
Carabidae
(ground beetles)
Michael Kippenhan, Barry
Knisley, Arvids Barsevskis,
Robert Acciavatti, Wendy
Moore, Terry Erwin, David
Maddison, Kipling Will,
Robert Davidson
Charles Triplehorn, Aaron
Smith, Stephanie Horne,
Warren Steiner, Kojun
Kanda, Ian Foley, Rolf
Aalbu, Vasco Tanner
Dorald Allred
Tenebrionidae
(darkling
beetles)
Formicidae
(ants)
Specimens Unident. Date Types
identified specimens range
by
authorities
16,300
1,300
1902- 0
2013
8,400
7,600
1885- 71
2013
Totals
9
19,700
9,800
19022013
49
7,600
7,700
19252013
19
52,000
26,400
C. Cataloguing New Specimen Data
BYU specimens will be catalogued using Specify, following the guidelines of SCAN. Data will
be periodically harvested by Symbiota. Cataloguing can operationally be divided into three
processes:
(1) Organizing specimens for ease in processing (“staging” the collection). Some curatorial work
is anticipated to increase efficiency and accuracy of data entry. For instance, taxonomic
specialists will visit the collection to scan for major identification and nomenclatural problems,
and may be able to provide quick identifications of obvious taxa. We anticipate that staging the
collection will require additional drawers and cabinets for storage requirements. There will be
extensive preparation of the database prior to entering data.
(2) Recording label data and accessory data. BYU will follow SCAN’s implementation of
multiple taxonomic nomenclatures as given in accepted catalogues and revisions. We will
georeference records through GEOLocate and other available resources. Additional habitat or
collection data not on specimen labels may also be recorded if they are readily available from
publications or field notes.
(3) Labeling. We will apply universally unique, barcoded, catalogue labels, consisting of an
alphanumeric catalogue number that includes the institution code and numeric code (e.g., BYUC0054321), plus a machine-readable matrix code. For specimens with fading labels, we will add
archival quality labels that include all of the information of the originals, and the original label
will be retained on the pin. Our intention is to minimize the size of labels, but not to the point of
hindering scanning for loans or inventory.
D. Incorporating Previously Catalogued Data
As a test of our digitization procedures and workflow, we catalogued nearly 5,000 specimens and
these data have already been successfully submitted to SCAN. This experience has allowed us to
refine our workflow and demonstrate our ability to capture these data and pass them to SCAN. In
conjunction with various past BYU surveys, we have an additional 20,000 records of arthropod
specimens that will also contributed to the TCN.
E. Imaging
There are approximately 300 ground-dwelling arthropod species that have at least part of their
type series deposited in the BYU collection. We will image all of these species using a system
that is already in place (Olympus SZX12 microscope fitted with mechanized focus, MTI 3CCD
camera, Olympus MicroSuite montage software), though we request funding to upgrade the
software and some of the imaging components. Using Specify, we will link images to the
catalogued type specimens and automate the delivery of new images to the SCAN image
repository. In addition, all images will be posted to Morphbank and other relevant portals
operated by taxon-specific user groups (e.g., BugGuide).
F. Training Plan
Clark will recruit and train students, and will be responsible for day-to-day student supervision.
Students will be recruited from BYU’s office of Multicultural Student Services to target
individuals who are underrepresented in the sciences. Clark has extensive experience in training
students in all aspects of curatorial work and has successfully recruited students from minority
groups. Before beginning digitization, students will be thoroughly instructed with regards to
scientific classification and nomenclature, and with regards to proper specimen handling and
museum protocol. During year 1 of the project, Clark will travel with students to Arizona where
they will observe firsthand the activities of institutions already participating in SCAN
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digitization. Clark will also travel to iDigBio for one week during the first year of the project, to
standardize and coordinate databasing activities. In order to facilitate the training of students and
standardize techniques, we will employ digital pamphlets and short “how-to” videos which can be
viewed on the SCAN website (http://scan1.acis.ufl.edu/content/protocols). A major goal of the
ADBC program is to promote increased efficiency in the digitization process. To that end, we
will continuously incorporate procedures used by other digitization projects that could
significantly increase our efficiency. As we note ways that lead to efficiency in workflow locally,
we will make those changes and will share them with the SCAN community for possible
incorporation elsewhere.
G. Plans for Integrating with iDigBio and sustaining PEN
As a collaborator with SCAN, BYU will adopt SCAN and iDigBio policies regarding workflows
of digital data. All BYU data will be shared in the format of other SCAN data and backed up and
maintained on BYU servers, as well as those of SCAN and iDigBio. Use of our data will be
tracked using functions in Specify as implemented at the SCAN servers. PI Clark will travel to
iDigBio in Florida during year 1 to work with the PIs there and to be certain that we are following
iDigBio policy and procedure. Clark will participate in all the iDigBio workshops and SCAN
workshops during the three years for funding. We have already attended an initial project meeting
of SCAN in Tempe, Arizona in August 2012 as preparation for this proposal.
H. Project Plan and Workflow: Our 12 Step Program
The following steps are listed in a rough, sequential order, although some of them will be
concurrent and ongoing. A timeline is given in Table 3 and a time analysis in Table 4.
Step 1 Specialist visits. Four taxonomic specialists have agreed to visit the BYU collection early
in the first year of funding (see letters of collaboration). These specialists are Kipling Will
(Carabidae), Aaron Smith (Tenebrionidae), Hojun Song (Acrididae), and John Longino
(Formicidae). The objective is not to have them identify a mass of previously undetermined
specimens, but rather to have them scan through the collection, correcting misidentifications and
taxonomic problems. We also anticipate that they will be able to quickly determine at least some
of the unidentified taxa. This will greatly improve the quality of data during the entry process and
reduce the amount of database editing required later.
Step 2 Imaging equipment. We will repair and upgrade imaging equipment.
Step 3 Employee recruitment. We will recruit three undergraduates through the BYU Office of
Multicultural Student Services.
Step 4 Mentoring and training. Clark will train undergraduates in specimen handling and
curatorial methods, in nomenclature and taxonomic hierarchy, in data entry using Specify, in
georeferencing, and in imaging. Early on in the project, students will visit SCAN institutions in
Arizona to learn firsthand from participants already involved in the project. They will also be
invited to observe and participate in diverse activities of the arthropod collection, including field
collecting, specimen preparation, identification, and participation at meetings (described in
Broader Impacts section).
Step 5 Collection staging. Before data capture for each section of the collection (usually for each
unit tray), students will rearrange specimens, placing those with similar data near each other (e.g.,
placing all specimens from the same locality together). This will speed data entry.
Step 6 Barcodes. Students will add a unique identifier to each specimen. We have opted to use
small labels that include both a human readable code (BYU acronym, plus number) and a
machine readable matrix.
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Step 7 Data entry. Students will digitize collecting and identification information, using Specify.
Clark will be responsible for quality control, frequently watching students as they work, and daily
checking at least ten entries selected randomly for each student.
Step 8 Archival labels. Subsequent to data entry, the label making feature of Specify will be used
to produce archival quality labels for those specimens currently labeled with photographic paper.
Undergraduates will add these labels to the specimens.
Step 9 Georeferencing. Following data entry, students will georeference specimens using
GEOLocate and other resources.
Step 10 Imaging. Students will image ground-dwelling specimens from the type collection.
Images will be appended to the Specify database.
Step 11 Database editing. Beyond daily spot-checks of the data digitized by students, Clark will
be responsible for thoroughly checking and editing the database before submission to SCAN. He
will carefully check both the taxonomic trees and the geography trees. He will employ the error
checking features of Specify.
Step 12 Data transfer. Periodically throughout the project, data will be submitted to the SCAN
portal (http://symbiota1.acis.ufl.edu/scan/portal/index.php).
I. Time Analysis, Cost Analysis, and Timeline
The time analysis is given in Table 3 below. Based on our prior experience of databasing 5,000
arthropod records and distributing them to SCAN, we estimate that it will take 8,130 student
hours to complete the databasing of the 52,000 target specimens. We typically pay students a
starting wage of $9.50/hour = $77,235 in student wages (direct costs) to database the 52,000
specimens = $1.49/specimen record. The actual direct cost will be a bit higher due to time that
will be needed for student training and the mentorship activities as described below. Again, we
emphasize that, based on our experience and our current workflow practice, we are highly
confidant that we can maintain this level of efficiency throughout the course of this project. Our
timeline for completing PEN activities is given in Table 4.
Table 3. Timeline of SCAN participation by BYU. The timeline chart reflects programing of key activities; dark
gray indicates times of strong focus.
Table 4 Time analysis for databasing activities
1. Cataloguing Pinned Specimens
TIMELINE
Summer
Year 1
FallSpring
Year 1
Visits from specialists
Hire and train database personnel
Catalogue Specimen Data
Georeference localities
Add archival labels
Upgrade imaging equipment
Image type specimens
Database editing
Symbiota Integration & Filtered Push
SCAN Image Repository (Web)
Data Sharing (GBIF, Morphbank)
Reports, Publications & Metadata
Student mentoring
Visit SCAN and iDigBio
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Summer
Year 2
Fall Spring
Year 2
Summer
Year 3
FallSpring
Year 3
Steps
1. Sort by taxonomy and label data
Mins/spec.
1.5
Number
Specimens
44,000
Total
(mins)
66,000
2. Produce barcode and add to pin
1
44,000
44,000
3. Enter collecting and taxonomic data
2
44,000
88,000
4. Georeference localities
2
44,000
88,000
1
44,000
44,000
44,000
Total
(min)
66,000
5. Error check and correction
6. Produce and add archival labels
1.5
396,000
2. Cataloguing ETOH Vial Specimens
Mins/vial
1.5
Number
Vials
8,000
Total
(mins)
12,000
2. Replace vials and fluid (if necessary)
1.5
8,000
12,000
3. Produce barcode and insert into vial
1
8,000
8,000
4. Enter collecting and taxonomic data
2
8,000
16,000
5. Georeference localities
2
8,000
16,000
6. Error check and correction
1
Steps
1. Sort by taxonomy and label data
8,000
Total
.
8,000
72,000
3. Digital Imaging of Type Specimens
Mins/image
Number
Images
Total
(mins)
5
300
15,000
2. Cleaning image with Photoshop
10
300
3,000
3. Transcribing data for each shot
4. Sizing, preparing, and uploading images to
database
3
300
900
Steps
1. Positioning specimen on stage, focusing, setting
top/bottom estimates, shooting and saving final
image
3
300
Total
900
19,800
7. Broader Impacts: Research, Mentoring & Outreach
As an affiliate with SCAN, BYU will provide a wide range of broader impacts, including genuine
conceptual and technological advances in web-based identifications, student mentoring, and
museum outreach.
A. Enhancing Virtual Capabilities
Virtual Specimen Examination. BYU will contribute to SCAN’s concentrated efforts on
developing the capacity for virtual research and education. There will be benefits to a broad range
of disciplines, including ecology, cyberinfrastructure, taxonomy, and especially species
exploration.
Trans-Border Impacts. At present, there are no suitable and actively maintained arthropod
collections located in the states of Sonora and Chihuahua, Mexico. However, BYU entomologists
conducted several expeditions to these areas in the 1980s and 1990s, and thousands of arthropod
specimens were collected. Utilizing SCAN’s cyberinfrastructure to manage specimen-level data,
BYU will support Mexican scientists in investigations of ground-dwelling arthropods and
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therefore enable international collaborations related to systematics, biogeography, and changing
distributions of these taxa.
eTaxonomy. SCAN, with BYU as a contributor, will have a potentially game-changing impact for
eTaxonomy. The ontology-based remote Filtered Push tools, as established by SCAN for
specimen identifications, will aid both the collections and systematics communities. The
taxonomic identification value associated with the SCAN data, including the data contributed by
BYU, will have positive impacts on derivative studies focusing on biodiversity, ecology, and
climate change.
B. Community Ecology Studies and Climate Change Impacts
A major SCAN outcome contributed by BYU will be the availability of data for ecologists and
climate change impact modelers interested in both species distributions and biodiversity models.
BYU’s participation in SCAN will help provide a more comprehensive data source on which
these studies will be based.
C. Student Mentoring
We plan to recruit three undergraduate students who will work ~20 hours a week during the three
years of funding to cover the 8,130 student hours required to complete data entry. Depending on
the schedule of these students, we may need to hire more students who will work fewer hours per
week. BYU has many students from groups underrepresented in the sciences, including Native
Americans, Native Hawaiians, and Pacific Islanders. Consequently, biology students will be
recruited through the BYU office of Multicultural Student Services. The PIs have successfully
recruited underrepresented students to work in the collection is the past, and we will target two of
the undergraduate slots to be for individuals from these groups.
The majority of the effort in this project consists of day-to-day supervision of undergraduate
students in data entry tasks. However, to make a more meaningful mentored research experience
for these students, we have budgeted time to give these students experiences in the various
aspects of collection work. We propose the following:
(1) Fieldwork Fridays. Every Friday afternoon during the spring and summer months, students
will go out in the field locally with the PI to collect insects, focusing on local, ground-dwelling
arthropods. As students are entering records into the database, we anticipate we will find many
cases were a local species was abundant in the past but has not been collected recently. Based on
these records, we will return to the same locality at a similar date and try to collect these species.
This will give the students an opportunity to see the species as something more than dead bugs on
a pin, while also emphasizing the importance of the work they are doing towards uncovering
historical distributional patterns.
(2) Specimen Preparation and Identification Activities. Students will prepare the specimens they
have collected by properly preserving them and making locality labels. Under the guidance of the
PIs, and through the use of the collection, taxonomic keys, and the SCAN remote Filtered Push
tools for specimen identification, they will attempt to identify the specimens they have collected.
This will give the students a basic understanding of insect taxonomy and a better view of the tools
of classification.
(3) Participation at the Entomological Collection Network (ECN) Meetings. Undergraduate
students will be invited to attend and participate at the ECN meetings during year three of
funding. These undergraduates will be expected to present a talk that focuses on BYU’s
participation in SCAN, and they will benefit by interacting with other PIs who are also actively
databasing collections.
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D. Museum Outreach
BYU’s Life Science Museum plays a prominent role in our community for expanding the public’s
understanding of organismal diversity and important environmental issues. Each year, the
museum hosts hundreds of thousands of patrons, the majority of whom are K-12 students, but
also includes university students and the general public. With the recent expansion of the
museum, we have received a commitment from the Museum Director, Dr. Larry St. Clair, for a
new display area and associated resources to highlight arthropods of the Southwest (see letter of
collaboration). In collaboration with the education staff of the museum, our plan is to create an
interactive display that leverages the power of the NSF TCN SCAN network for understanding
important historical patterns in Southwest arthropod species, with an emphasis on conservation.
Briefly, the display will consist of a variety of specimens (50-75) from the Southwest with their
common and scientific names. The specimens will include those that are widespread in their
distribution (e.g., Cicindela repanda Dejean) and those that are highly restricted in their
distribution (e.g., Cicindela limbata albissima Rumpp, a tiger beetle restricted to the Coral Pink
Sand Dunes in Utah). It will include old specimens, as well as new specimens. The front of the
display will have a touch screen computer that is linked to the SCAN website
(http://symbiota1.acis.ufl.edu/scan/portal/index.php). Patrons will be asked questions such as:
“What is the distribution of this species?” “What sort of environment do you think it lives in?”
“When was it last seen?” “Why do you think we have not seen it for 50 years?” Patrons will then
be prompted to enter the scientific name into the SCAN database, which will automatically
generate a distribution map in either Google Map or Google Earth format. They will then be able
to zoom in and see (for instance) that a certain species is no longer at a given locality because
someone built a Jiffy Lube on the type locality. We will work with museum staff to make this
exhibit highly interactive and anticipate that it will be wildly popular among children, while
highlighting the importance of the NSF TCN program to the general public.
Results from prior NSF Support for Shawn M. Clark (last 5 years)
Clark has had no NSF support in last 5 years.
Results from prior NSF Support for Michael F. Whiting (last 5 years)
NSF EF-0531665, Biocomplexity: Hexapod Phylogenomics, Bringing Supercomputing to the
Masses and DEB-0120718; AToL: Collaborative Research: Assembling the Beetle Tree of Life.
M. Whiting and collaborators. These two grants have thus far resulted in 79 publications directly
related to insect phylogenetics and evolution. On 16 of these publications, at least one
undergraduate student was an author, and on 14 of these the undergraduate was the senior author.
This funding has provided over 50 undergraduate students (including minority and disabled
students) with significant research experience, leading to publications and placement in excellent
graduate programs throughout the country.
Results from prior NSF Support for C. Riley Nelson (last 5 years)
DEB-BSI #0743732, Survey and Inventory of the Aquatic Insects of the Altai and Hangai
Mountains’ drainages, Mongolia. C. R. Nelson and co-principal investigators. This grant resulted
in uniformly sampling and databasing the aquatic insects of a large portion of western Mongolia,
with more than 500,000 specimens curated and deposited in major entomology museums around
the world. Over 55 undergraduates and graduate students from Mongolia have directly
participated in this program. The Mongolian Aquatic Insect Survey, with NSF funding, has
produced 141 presentations and 110 publications concerning systematics and aquatic ecology.
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