(2012 JMIH Symposium: Technology and Innovation in Herpetology and Ichthyology Collections)
Gregory Watkins-Colwell, Collections Manager of Herpetology and Ichthyology at the Yale Peabody Museum, and Mark Sabaj Pérez, Collections Manager of Fishes at the Academy of Natural Sciences, organized a successful full-day symposium for the 2012 Joint Meetings of Ichthyologists and Herpetologists (and 7th World Congress of Herpetology) held in Vancouver, British Columbia. The title of the symposium was: Technology and Innovation in Herpetology and Ichthyology Collections. A total of twenty-four speakers contributed twenty-two 15-minute (or longer) talks on a wide variety of collections-related topics including: historical perspectives, digitization and georeferencing, tissue/DNA storage and recovery, NextGen sequencing, collections of histological, zoo and project-based specimens, use of collections in conservation and pedagogy, rehydration of fluid-preserved specimens, regulatory compliance, NSF programs and initiatives, and the tragic loss of the Instituto Butantan collection to fire. The symposium was supported in part by the American Society of Ichthyologists and Herpetologists, the Society for the Study of Amphibians and Reptiles, the Herpetologists' League, and the Society for the Preservation of Natural History Collections. The maxim that collections are vital to research was roundly upheld.
Speakers & Abstracts
Fish collections as a resource for cyber-enabled discovery and innovation
Bart, Hank (Tulane University, Belle Chase)
Images of specimens from natural history collections are increasingly being used in scientific research. Some of this research (cybertaxonomy) aims to increase the traditionally slow pace of new species discovery and taxonomic description. A collaborative research project funded by the U.S. National Science Foundation is using 2-D and 3-D images of specimens from the Royal D. Suttkus Fish Collection to develop a computer-based species recognition and taxonomic diagnosis system. In one component of the project machine learning techniques are being used to train a computer algorithm to select features from images of specimens useful for distinguishing one collection of specimens from other known taxonomic groupings. A second component of the project involves using novelty (outlier) detection to distinguish unknown species from known species. This interdisciplinary research project is an example of technology and innovation at the crossroads of biology and computer science.
Specify 6: New innovative approaches to collection data entry and data storage
Bentley, Andrew; Beach, Jim (University of Kansas Biodiversity Institute, Lawrence)
Specify is a biological database application for museums and herbaria which processes specimen information for computerizing holdings, manages collection management transactions, and mobilizes species occurrence data to the web. Specify 6, is a wholly-new implementation coded in Java and designed to run identically on all three workstation environments--Windows, Mac OS X, and Linux. Specify versions for each platform (and the source code which is offered under an open source license agreement) are available at no cost from the Project web site –http://specifysoftware.org/. The Project is supported by the US NSF and the University of Kansas Biodiversity Institute. Specify 6 incorporates many significant changes, from its intuitive and highly-usable drag-and-drop user interface to many new functions and capabilities designed to streamline routine collections data tasks while preparing and validating data for biodiversity community networks. Specify 6 has numerous enhancements over previous versions, including support for using record sets as subsets of the complete catalog for various types of processing, such as: georeferencing, label and report production, and importing and exporting records. Specify 6‘s data model has been expanded and enriched to provide robust support for multiple collections within a single database, DNA information, field notebook information, file attachments, GUIDs, data entry and uploads through the Specify WorkBench and Excel, collecting trip data, repository agreements, accession logging, conservation treatments, collection object containers, and many more collections data issues. The Specify 6 form system is highly customizable, and Specify 6 comes with a robust label and report generator. The most important core advance with Specify 6 however, in addition to its long list of capability enhancements, is the program‘s modular architecture designed for functionality plug-ins and co-development collaborations. With the availability of specialized plug-in modules, Specify‘s research capabilities will be extended by online web-service links to other biodiversity data research community servers. Specify‘s soul as an open-source, internet-capable, integration platform will transform biological collections computing. This presentation will highlight Specify 6 and illustrate some of its innovative features.
The application of extant and museum genetic samples for investigating the genetic consequences of species recovery efforts from hybrid Giant Galapagos tortoises
Edwards, Danielle; Evans, Ben; Garrick, Ryan; Benavides, Edgar (Yale University); Tapia Aguilera, Washington (Galapagos National Park); Rusello, Mike (University of British Columbia); Gibbs, James (Syracuse University of New York); Caccone, Gisella (Yale University)
Repatriation of species that have become extinct either locally or in the wild can have important consequences for maintaining natural ecosystem processes. However, what are our options for repatriation when all that remains of a species are hybrids? For species with few or no individuals remaining historical DNA samples are vital for establishing background estimates of original allele frequencies and diversity. For Giant Galapagos tortoises, studies using historic genetic samples from museum specimens have been critical in clarifying the genetic architecture of extinct and endangered species. These data have also been combined with extant DNA samples to identify individuals from a population on northern Isabela Island that are hybrids containing ancestry in various Giant Galapagos tortoise species (e.g., Chelonoidis elephantopus, a species previously thought to be extinct). Historical interactions between humans and Giant Galapagos tortoises lead to the establishment of a hybrid population on Volcano Wolf (northern Isabela) containing the ancestry of many of the extant and some extinct species of tortoise. We use historic DNA samples taken from museum samples collected from Pinta to identify hybrids on Volcano Wolf with ancestry in C. abingdoni – typified by Lonesome George as the world‘s most endangered species that consists of a single individual. In order to explore the genetic outcomes that can be achieved using hybrid individuals in repatriation programs we use the genetic data from these hybrids in combination with demographic data taken from captive and wild tortoise populations to simulate the genetic outcome, relative to that previously observed on Pinta Island, of various repatriation strategies in a management and evolutionary perspective. Specifically, we sought to understand what the effects of long-term versus short-term backcrossing (i.e., for one to 5 generations) would have on the evolutionary trajectory (after 10 to 100 generations post repatriation) of the species under both unlimited and more economically realistic scenarios. Additionally, we analyze the effect of ―successfulness‖ of the breeding program on the future potential genetic architecture of the species. We present these results, in addition to discussing the challenges of species repatriation with limited genetic material and with only historical samples as a benchmark.
Regulatory compliance and permits for US borders: Developing a framework to comprehend, cope and comply
Ford, Linda S. (Museum of Comparative Zoology, Harvard University)
A steady and dramatic increase in regulatory responsibilities related to the collecting, transporting, and storage of animals and animal products have greatly affected natural history museums and educational institutions around the world. Ensuring compliance to the multitude of laws and regulations has become a major obligation for these institutions. The seriousness of this responsibility, especially in the US, stems from the broad application and potentially harsh legal consequences when these regulations are not followed. Compliance broadly applies whether the animal material is whole or just DNA, whether it‘s personally collected or an incoming/outgoing loan belonging to others, and whether the purpose is for scientific research or commerce. In many countries including the US, there is an added complexity in that regulations may involve multiple agencies within multiple governmental departments in both the sending and receiving countries. In the US, consequences for noncompliance generally fall under the Lacey Act, which can potentially include civil and/or criminal penalties for both the individual and institution. In addition, the Lacey Act not only enforces US laws but, also, any relevant laws of foreign countries within the borders of the US. With these various factors, scholars, who generally support regulations that serve to protect and conserve species in the wild, domesticated livestock, and the health and safety of people, frequently, find themselves at odds with these same laws. With a brief overview, a framework can be developed to help manage the legal expectations involved with moving amphibians, reptiles, and fish across the US borders.
The Herpetological Collection of Butantan Institute, São Paulo, Brazil: past, present, and future
Franco, Francisco Luís
The Herpetological Collection Alphonse Richard Hoge of Butantan Institute, São Paulo, Brazil was the biggest snake collection of the world, with more than 77.000 registered specimens and another 10.000 to be registered. It had the most important type‘s collection of Brazilian snakes; about 150 species or subspecies of snakes were included in this assemblage. This collection had world representativeness and was utilized by several researchers along the years. It is hard to find a Neotropical snake paper without the contribution of this collection. Tragically the fire on Saturday, May 15, 2010 destroyed about 80% of the preserved snakes. Fortunately, nobody was injured. Despite budget to buy fire prevention equipment, the fire happened few months before these acquisitions. The fire beginning about 07h00, and smoke were detected around 07h30, while the fire already destroyed the collection. At this same time the Engineering Department of the Butantan Institute (BI) began working in the maintenance of electric network of the BI. The experts of Fire Department explain that the fire must have started by an electric problem in a heating stone in a terrarium that was in the mezzanine beside the collection. In few hours the collection was almost all destroyed. Immediately a big wave of solidarity was begun. In a few minutes many people arrived at the IB to offer help. Brazilian and foreign people expressed solidarity in several and different ways. Thousands of emails pop up inboxes. We are deeply grateful with all. The rescue of the spared material began immediately and continued until June 04, when the procedures of demolition and removal of debris finished. Many actions to help the restructuring the collection as well as laboratories were made by individuals and private companies worldwide. Donations of books to recompose lost library, donation of much material for rescue and save provisionally the rescued specimens, rescue data of burned computer, creating Web sites offering support and solidarity, and donation of specimens to recompose the collection, etc. Also, multiple instances of the State and federal governments acted immediately to help the reconstruction of the collection of the BI and, even better, to try to help other Brazilian collections to get structure to prevent tragedies such this. There are a brand new build, safe and functional to BI collections, labs and offices. We must use this tragedy to prevent recurrences. We must not forget it.
Leveraging NextGen sequencing for Systematics
Li, Chenhong; Naylor, Gavin (College of Charleston); Hofreiter, Michi (York University, United Kingdom)
Next generation sequences affords opportunities to collect DNA sequence data on a genomic scale. However, the overhead associated with assembling and annotating genomes for downstream analyses is time consuming and currently represents a significant bottleneck to comparative genomics. Phylogenetic biologists are generally less interested in complete genomes than they are in obtaining multiple nuclear orthologous markers across a set of taxa of interest. To date, no procedures have been developed to facilitate the efficient collection of such data. We present a method that uses targeted gene capture in conjunction with next generation sequencing techniques to obtain sequence data from hundreds of orthologous protein coding sequences across multiple species in a single sequencing run. We demonstrate the efficacy of the approach with chondrichthyan fishes.
NSF Collections Programs: Advancing Digitization of Biological Collections (ADBC) and Collections in Support of Biological Research (CSBR)
Maglia, Anne (US National Science Foundation)
I will discuss two collections-relevant funding opportunities in the US National Science Foundation‘s Division of Biological Sciences---Advancing Digitization of Biological Collections (ADBC) and Collections in Support of Biological Research (CSBR). I will provide historical perspectives on the programs and updates on recent changes to the solicitations. Additional information may be found at: http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503559 (ADBC) and http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503651 (CSBR).
iDigBio, the National Resource for Advancing Digitization of Biological Collections (ADBC)
Page, Larry (Florida Museum of Natural History)
iDigBio, the National Resource for the NSF-funded "Advancing Digitization of Biological Collections" is working to build the teams and infrastructure that are required to successfully digitize information in biological collections throughout the U.S. iDigBio will provide core resources and coordination for the national digitization effort, oversee implementation of standards and best practices for digitization, provide a cloud computing environment for collections data, and plan for long-term sustainability of the national digitization effort. As the national repository grows, iDigBio will work to improve the understanding and appreciation of biodiversity, and of the collections that document biodiversity, by demonstrating the connection between biodiversity and scientific and societal benefits.
Value-added collections: Detection of parasites in herpetological museum specimens
Perkins, Susan (American Museum of Natural History)
It has been casually estimated that each vertebrate species is host to between one and ten "macro" parasite species and innumerable microbial symbionts and pathogens. Thus, each specimen in a collection may, in fact, be several specimens in one. Depending on the method of preservation, these parasites or symbionts may be preserved intact or may just have their genetic material preserved along with that of the host and can be detected and studied. Blood parasites may be particularly well captured in tissue collections given that their presence is not confined to a particular organ. The malaria parasites of lizards are extremely diverse, with over 100 described species from all over the planet. However, it is certain that this number is a gross underestimate of the true diversity of these parasites. The sampling of these taxa has also been largely opportunistic and so may result in skewed perceptions of biodiversity and evolution of the group. Here, I will present results from PCR-screening of lizard specimens from Vietnam and other areas as well as similar molecular detection work on other herpetological samples such as turtles and snakes, many of which indicate that several undiscovered taxa are present in these hosts. However, I will also offer a strong cautionary note about the reliance on PCR alone as a detection method and encourage all collectors to endeavor to take appropriate samples in the future to allow for proper parasite detection and description.
Collections in the 21st Century: an overview of issues in storing samples for genomic analysis with an emphasis on the AMNH collection
Perkins, Susan; Amato, George; Feinstein, Julie (American Museum of Natural History)
Repositories of frozen tissues and genetic isolates from the world's organisms represent an invaluable resource for the study of biodiversity and evolution. However, best practices for the establishment, organization, and maintenance are necessary if these collections are to have utility. The Ambrose Monell Cryo Collection for Molecular and Microbial Research was established at the American Museum of Natural History in New York in 2001 and quickly rose to prominence as one of the world's major frozen tissue collections. With a current holding of 70,000 tissues and a capacity for up to one million tissues, we are poised to continue to grow and expand this important resource. Critical to the value of this collection are the following attributes. The facility is a state of the art, passive, liquid nitrogen system ensuring best preservation of samples and protection against power failure. All of the samples are accessioned with complete collecting, metadata and permit information. Curation of the collection allows for retrieval of any sample within minutes and, facilitates the loaning of thousands of samples each year. In terms of herpetological diversity, this collection holds over 9,500 samples representing 1,231 species. Samples range from recent, comprehensive, population level, field collections numbering in hundreds of individuals to DNA samples extracted from the Museum‘s traditional, historical collections including 100 year-old type specimens. Examples from recent herpetological research on cryptic diversity in crocodilians, using recently collected and historical samples will be used to illustrate the value and importance of frozen tissue repositories for biodiversity and evolutionary studies.
Curating a different kind of collection: the use of zoo animals in research
Pramuk, Jennifer (Woodland Park Zoo)
Curating living specimens shares much in common with curating museum collections. Zoos and museums alike face the challenges of managing ever-larger databases while seeking funding and expertise necessary for managing these data. Of particular concern to those curating living collections and captive populations are data related to lineages (e.g., studbooks) and their management. Given the high visibility of individual animals housed in living institutions, zoos and aquariums also must adeptly manage issues related to animal welfare and potential fallout from visitor perceptions related to their use in research. For that reason it is especially critical for zoos and aquariums to form proficient committees for evaluating research proposals. Increasingly, institutions that manage living collections are partnering with universities and natural history museums for museum deposition, behavioral, and other studies. These partnerships can provide a unique synergy and new research opportunities related to conservation, improving animal husbandry and welfare, and understanding natural history. The challenges and benefits of developing partnerships between museums and living institutions will be discussed.
Using qPCR to detect the EIP, Batrachochytrium dendrobatidis, in fluid-preserved amphibian museum specimens
Richards-Hrdlicka, Katy (Yale University)
Batrachochytrium dendrobatidis is a fungal pathogen driving many amphibian species extinct. For some species, the only place they can be found is in natural history museum collections. Harnessing molecular tools to uncover this pathogen‘s date of arrival and movement throughout a region and through time will prove useful to broader B. dendrobatidis research. However, it has remained difficult to access B. dendrobatidis DNA from within preserved host tissues, especially specimens that were originally fixed in formalin. I describe two methods to extract and detect, via qPCR, B. dendrobatidis DNA in herpetological natural history collections. Both extraction methods use a DNA-binding matrix, either a magnetic bead resin or a silica-membrane, that retains and separates the extracted DNA from potentially qPCR-inhibiting contaminates. Nine positive control specimens enabled initial method optimizations, but coincidently limited empirical comparisons between each extraction method. Therefore to test each method, a pilot study involving 164 formalin-fixed amphibians from Connecticut, either having been originally fixed in the 1970‘s or 2000‘s, were swabbed and samples extracted by one of the two presented methods. Each method successfully extracted B. dendrobatidis DNA; of the 164 specimens tested, 37 were found Bd -positive, including 6 specimens (representing 3 caudate species) from 1968. The results suggest that these methods and qPCR are well suited to assess Bd presence but not to assign zoospore loads in preserved specimens. Further research would benefit from a comparison between the extraction methods to determine which yields more DNA or is more sensitive to low zoospore loads or degraded DNA. Recommendations for choosing and using these methods as well as sampling herpetological natural history collections for B. dendrobatidis DNA detection are provided.
BOSS, Biological Object Search Service: An Overview of the Architecture and Features of the FishNet2 Search Engine
Rios, Nelson; Bart, Henry (Tulane Univeristy, Belle Chasse); Bentley, Andy; Wiley, Edward (Kansas University Natural History Museum, Lawrence)
On April 22, 2010 an explosion on the British Petroleum Deepwater Horizon Oil Platform resulted in the release of large quantities of crude oil into the northern Gulf of Mexico. The ability of ecologists and other scientists to assess the impacts of the spill on the Gulf of Mexico ecosystem depends critically on the availability of baseline data on the composition and structure of biotic communities in the region under natural conditions. Natural history museums have the ability to provide much of this information as they contain data on biological resources spanning hundreds of years to the present. The FishNet2 network is a collaborative effort among fish collections around the world to share and distribute data on specimen holdings. Over the past year a number of developments have been made to address the needs of acquiring baseline data from FishNet2 in response to such temporally & geographically defined events as the BP Oil Spill. Specifically, we have improved upon the data harvesting architecture, added geospatial query capabilities, improved result summaries, made significant changes to the UI and produced an API to facilitate third party integration. The underlying architecture for FishNet2 has been generalized as the Biological Object Search Service allowing us to create instances applicable to other taxonomic networks. HerpNet2 is an example of such an instance utilizing the same architecture.
Can the Americas' oldest continuously operating natural history museum survive another 200 years?
Sabaj Pérez, Mark (Academy of Natural Sciences of Philadelphia) & Watkins-Colwell, Gregory (Yale Peabody Museum of Natural History)
In 1812, The Academy of Natural Sciences of Philadelphia was founded “for the encouragement and cultivation of the sciences, and the advancement of useful learning”. The not-for-profit Academy has been the architect of its own fortune (and misfortune) for nearly two centuries as the oldest standing natural history museum in the Western hemisphere. Despite a constant flow of biological specimens (now est. at 17 million), recent decades mark the ebb of annual budgets (deficits of 0.5–1 million for over a decade) and curatorial staff (down 50% from 14 in the 1990s). On the eve of its Bicentennial, the Academy affiliated with Drexel University, founded in 1891 and now the nation‘s 14th largest private university. The partnership is intended to enable the Academy “to grow and prosper into our 3rd century, enhancing our programs of scientific research and education with our combined resources”. The affiliation also joins Academy researchers with Drexel faculty into a new university department (Biodiversity, Earth & Environmental Sciences) that will accept its first students in Fall 2012. Many are optimistic that this alliance will expand successful Academy research programs and resuscitate those dormant, as well as promote the importance of natural history collections to a new populace of students and stakeholders. Long and passionately heralded by insiders, the irreplaceable nature of collections and their necessity to taxonomic and systematic research are in some ways gaining recognition beyond the museum community. In 2010, the US National Research Council identified “understanding biological diversity” among five “Grand Challenges” at the intersection of the biological and physical sciences. In response, NSF‘s Directorate for Biological Sciences will focus investments on research to address these challenges. Despite such prudence, anxious straits persist for many museums, and the FY 2013 budget request for NSF may add rocks to the waters (e.g., funding for Collections in Support of Biological Research may be effectively halved). The next century will be one of adaptation for The Academy and other museums, marked by many tests of putatively anodyne solutions to decidedly unsustainable futures. In addition to concluding remarks, this talk will identify models of university-museum alliances, explore the “Grand Challenges” facing natural history museums, and celebrate A Glorious Enterprise (1st complete history of the Academy by Peck & Stroud, 2012).
The Collection in the Classroom and Beyond
Sidlauskas, Brian (Oregon State University)
In addition to their well-documented role in catalyzing scientific discoveries, natural history collections provide exceptional resources with which to engage students in hands-on learning about biodiversity, evolution, ecology, morphology and geography. For example, it is one thing to tell a student about how fishes modify their fins for a variety of purposes (swimming, gliding, sucking, fishing!) and another to confront them with specimens showing those diverse adaptations, ask them to compare and contrast the fins that they see, and hypothesize how they might be used. University collections are well suited for collections-based education because they bring the specimens into close proximity with students ranging from grade school through the doctorate. During this talk, I‘ll highlight two programs at Oregon State University that draw on the diversity of students in order to teach the diversity of fishes. In the Discovery Units, undergraduate and graduate students design and lead hands-on sessions for groups of precollege students using the teaching collection. In the Systematics of Fishes course, undergraduates work in teams to compare and contrast specimens, discover diagnostic characteristics and learn how to identify fishes. We are in the early stages of developing an online version of this course based on a virtual teaching collection that will preserve the observational, group-learning environment as much as possible. Both programs are founded on the complementary ideas that active, hands-on engagement with collection objects strengthens learning by allowing students to make discoveries themselves, and that mastery of a subject is best achieved by helping others grasp the material in turn. While my examples are ichthyological in nature, these techniques translate easily to other taxa and represent some of the many ways that collections can impact education broadly.
Looking back at moving forward-an historic view of how new technologies and discoveries changed collections
Simmons, John (Museologica)
The first natural history collections contained only specimens that could be preserved dry. Individual specimens were rarely marked or labeled, and collections care was limited. Post-1600 advances in preservation technology included the introduction of glass and other stable containers; the use of embalming chemicals to dehydrate tissues; specimen preparation using wax injections; the application of arsenic and other pesticides; and the discovery of several fluid preservatives, most significantly ethyl alcohol. During the 1800s, improvements were made in containers and seals; cataloging and labeling of individual specimens became common; the concept of the study skin was developed; and formaldehyde fixation was introduced. Post-1975 collections grew increasingly larger and more complex, and the use of specimens and collection data extended beyond taxonomic uses. These larger, more heavily used collections required more care, resulting in the advent of the profession of collections management. The use of electronic databases greatly improved the management of collection records after 1980, but diverted significant time away from collection care. In 1985 the Society for the Preservation of Natural History Collections began promoting preventive conservation based collections management emphasizing collections storage environments and measures to prolong the useful life of specimens and associated data. With the widespread application of electronic database systems and digital imaging, collections and specimen data have become an international resource. To meet future research needs while properly managing collections, specimen preservation techniques should be diversified; more reliable means of DNA preservation must be developed; methods for cost-effective archival storage of collection information in electronic formats developed; and collection database systems must become comprehensive collections management tools that track specimen interactions with storage environments and individual specimen use histories.
Are Dehydrated Specimens A Lost Cause? A Case Study To Reclaim Dehydrated Fluid-Preserved Specimens
Singer, Randy (Florida Museum of Natural History)
Fluid-preserved specimens in collections persist only as long as their preservative is maintained. When preservatives evaporate due to neglect or container malfunction, collection managers are often forced to discard the specimens. Subjecting specimens to a rehydration process can be both time consuming and hazardous. A recent development in vertebrate specimen rehydration that mitigates these hazards and is relatively simple to conduct is discussed. Through the use of concentrated water vapor, and gradual staging in various concentrations of preservative, dehydrated museum specimens can be rehydrated. Similar techniques have been applied to invertebrates for decades, and more recently to herpetofauna. Herein a new technique is applied to both fishes and mammals and its efficacy for most other groups is indicated.
Curating and managing project-based collections of fishes
Snyder, Alexandra (University of New Mexico)
Fish specimens and data, curated by the Museum of Southwestern Biology (MSB), are typically used in studies conducted by state and federal agencies to monitor the status of New Mexico fish species and aquatic conditions. The MSB plays key research and conservation roles in providing agency biologists with important contemporary and historical data on New Mexico river basins and fish species. Agency biologists annually contribute specimens and data to the MSB while conducting rare species risk assessments, life history and ecological studies, and for “Chain of Custody” evidence. These collections, which are accessioned by the MSB at regular intervals throughout the year, present challenges in conserving such an abundance of material. The MSB has developed curatorial protocols for collections that have associated long-term aquatic microhabitat data, contain large numbers of specimens, tend to be redundant in species composition, and are sometimes preserved for analyses other than morphometric. This presentation will discuss deaccessioning cataloged specimens, techniques facilitating access to primary and ancillary collections yet meeting requirements for long-term conservation, and a database constructed for fish ecology studies.
Lessons Learned from HerpNET and VertNet: Collaborative Georeferencing and Data Quality Improvement in Natural History Collections
Spencer, Carol (Museum of Vertebrate Zoology); Cicero, Carla; Koo, Michelle (Museum of Vertebrate Zoology, UC Berkeley); Rios, Nelson (Tulane University); Bloom, David; Wieczorek, John (Museum of Vertebrate Zoology, UC Berkeley)
The main goal of VertNet and its associated projects (HerpNET, FishNet, MaNIS, ORNIS) is to make high quality biodiversity data available online. These data come from natural history collections all over the world, each with idiosyncratic database formats and textual-based locality information. Data have the potential to be used in ways that were unforeseen when they were originally collected. The value of these data is directly related to its fitness for a variety of uses, and as data becomes more accessible, many more uses become apparent. Georeferencing is one method to improve data quality. It is the process of translating textual locality descriptions into geographic coordinates with their associated uncertainty, while estimating the spatial extent of a locality. Through MaNIS, HerpNET and ORNIS, we developed georeferencing standards, now known as the Global Biodiversity Information Facility‘s “Guide to Best Practices in Georeferencing.” From projects and workshops, we refined these methods, and we developed and incorporated semi-automated tools, such as GEOLocate and BioGeomancer, into our best practices. In this talk, I will present the results of past georeferencing efforts from HerpNET and VertNet, give an overview of current collaborative automated georeferencing tools, and give our recommendations for management of future georeferencing projects.
Vertebrates in the Cloud: Are We There Yet?
Spencer, Carol (Museum of Vertebrate Zoology, Berkeley); Cicero, Carla; Koo, Michelle (Museum of Vertebrate Zoology, Berkeley); Rios, Nelson; Bart, Hank (Tulane University); Bloom, David (Museum of Vertebrate Zoology, Berkeley); Guralnick, Robert (University of Colorado, Boulder); Wieczorek, John (University of California, Berkeley); Vieglais, David (University of Kansas, Lawrence)
The NSF-funded VertNet project (vertnet.org) brings together FishNet2, MaNIS, HerpNET, and ORNIS into a single cloud-based platform for querying, visualizing, and annotating distributed vertebrate biodiversity data. VertNet will combine the four vertebrate data networks into a single portal, making it easier for researchers to aggregate and synthesize data across all vertebrates. VertNet will provide five new and improved features, including: 1 - sustainable solutions (no local servers and fewer IT problems); 2 - improved performance and reliability (faster searching, better visualization, more mapping features); 3 - ease of discoverability (creating a thesaurus of synonyms for taxonomy and geography); 4 - data improvement (enabling annotations from users, potential crowd-sourcing); and 5 - better integrations with other projects (including Specify, Arctos, Map of Life, Encyclopedia of Life, AmphibiaWeb, and iNaturalist). Development of VertNet APIs (Application Programming Interfaces) will be available to any online project for searching and visualizing VertNet data. For example, the Map of Life project will use VertNet APIs to display data points for species distribution maps while VertNet will display species range maps generated by Map of Life. In addition to infrastructure development, VertNet has been very active in outreach. Since January 2011, we have given six georeferencing workshops (in South Africa, Alabama, California, and North Carolina) that have trained 129 people from 13 countries. A Biodiversity Informatics Training Workshop held in June 2012 at Boulder, Colorado, trained an additional 25 students from 9 countries. We will work with institutions from existing networks over the next six months to put their data in the cloud, and the new prototype VertNet portal will be functional within the year.
Establishing and maintaining tissue collections for DNA
Walker, Jr., H.J. (Scripps Institution of Oceanography); Smith, W. Leo (Field Museum, Chicago)
Liquid nitrogen is currently the best method for the long-term preservation of tissues for DNA research. However, there are effective alternatives for those collections that do not have the space or funding for liquid nitrogen facilities. A brief survey of the some the largest repositories of fish tissues in the United States has revealed that the overwhelming majority of tissues has been preserved in ethanol, and that many of those tissues subsequently have been deposited into freezers of various kinds. We will discuss some of the advantages and disadvantages of liquid nitrogen, ethanol, dimethyl sulfoxide, standard and ultra-cold freezing, etc., with additional reference to both Sanger and next-generation DNA sequencing technologies.
Technology and Innovation in Herpetology and Ichthyology Collections: Symposium Opening Remarks and Collection Survey Results
Watkins-Colwell, Gregory (Yale Peabody Museum of Natural History); Sabaj Perez, Mark (The Academy of Natural Sciences, Philadelphia); Giermakowski, Tom (Museum of Southwestern Biology, Albuquerque)
Specimen collections have long been important to a wide variety of studies of natural history. Collections have always reflected changes in research techniques because they have been used as repositories for vouchers and additional research materials such as preserved materials, microscope slides and molecular samples. Furthermore, advances in data management systems, from innovations in archival paper production to computer databases, and advances in geographical information technologies have also lead to changes in collections and collection management practices. In a full day symposium we will explore some of the ways that technology has changed collections and lead to innovative ways to use collections for scientific exploration. We will also reflect upon the results of a survey of collections that indicate areas where improvements are needed.
The Harvard Embryology Collection: a case study on archival histology slides
Williston, Andrew (Museum Of Comparative Zoology)
Extensive embryology and histology slide collections are rare or unnoticed in natural history collections. Collections focused on keeping alcohol preserved and skeletal whole animals may overlook histological slides and other micro slides. Still, embryology and micro-slide collections have the potential to be valuable museum resources. The Harvard Embryology Collection (HEC) is an example of a historic, archival histological embryology collection available to researchers. The HEC was started in 1890 by notable American anatomist Charles Sedgewick Minot. The collection was designed to be broadly systematic, including 60 taxa—over half of which were fish (17), reptiles (15), and amphibians (5). The HEC was founded in a collaborative spirit as a cyclopedia to promote new research and reproducibility in comparative embryology. The HEC was successful in the early 1900s—being cited in more than 100 papers including two volumes of Keibel‘s Normal Tables. Bashford Dean‘s notable hagfish embryo slides were deposited in the collection. Fortunately, Minot (a former student of Louis Agassiz) had the insight to construct the collection according to strict archival standards so, as in other museum collections, HEC slides would act as permanent vouchers. Indeed, the slides have persisted to this day. Unfortunately the collection sank into obscurity as embryology research waned after the early 1900s. Still, the collection remained intact at the Warren Anatomical Museum at Harvard Medical School. Now, despite nearly a century of disuse, the collection is safely kept at the Museum of Comparative Zoology (MCZ) and is available to researchers. The collection‘s history stands as a reminder that even the most seemingly out of place collection objects can have great but unnoticed value. Curatioral improvements are now planned which will hopefully revive the collection‘s collaborative spirit and value in the research community. The collection may also serve as a model for researchers building modern, archival histology slide collections.