University of Florida (2015)

Digitizing Southwestern-African Herpetological Collections

Project Details

Grantee Organization: University of Florida
Grant Amount: $139,150
Contact: David Blackburn
Contact Email: DBlackburn 'atsign'
Funding Dates: 8/7/15-2/6/17

This project was originally based at the California Academy of Sciences, but migrated with the PI, Dr. David Blackburn, to the University of Florida in 2015. You can find the original grant page here.

BackgroundGNT60402 UFL Logo

Angola and Namibia form a hotspot for amphibian and reptile diversity, together encompassing a complete shift from arid to equatorial African communities of species. Most primary biodiversity data for species in these countries remain inaccessible. Decades of civil war in Angola coupled with a lack, in both countries, of expertise in biodiversity informatics means that much of the scientific collections that document the diversity and distribution of this unique fauna remain unknown.

Biodiversity data associated with specimens in scientific research collections underlies this project’s ability to investigate spatial patterns of biodiversity (including richness and endemism) as well as to make informed conservation decisions. A significant challenge facing students, biodiversity scientists, and conservationists working in Africa is the lack of access to information and primary data. By facilitating access to biodiversity data through digitizing existing scientific collections in countries, such as Angola and Namibia, and providing training to build in-country capacity in informatics, both basic science and conservation can be advanced for species and landscapes that have been changing rapidly and are likely to continue to do so.

Key Objectives and Activities

In partnership with African institutions, this project will collaboratively:

  • Digitize and geocode (to locality name) data from the principal herpetological collections for Angola and Namibia and distribute these globally under a Creative Commons license via VertNet
  • Georeference digitized data for amphibian and reptile specimens from Angola and Namibia in other collections in South Africa, Europe, and the United States
  • Train in-country students and collaborators via on-site sessions in biodiversity informatics
  • Update conservation assessments for reptile and amphibian species with data generated from this digitization, many of which have not yet been assessed or are currently assessed as “Data Deficient” because primary data are lacking
  • Provide in-country training focused on database creation, maintenance, use, and downstream conservation applications to colleagues in governmental and non-governmental institutions interested in the biodiversity of Angola and Namibia; and facilitate current priorities in these countries for biodiversity documentation.

Planned Outputs

  • Literature records of Angolan and Namibian amphibians and reptiles will be gathered, standardized, and annotated
  • Training sessions in georeferencing standards will be held for in-country partners
  • All unique localities for collated records will be georeferenced and proofed and all records will be formatted to Darwin Core standards
  • In collaboration with local partners, the postdoc, PIs, and co-investigator will personally verify all museum records in U.S., European, and African museum collections
  • A specialized training session in biodiversity informatics will be held in the region for 15 to 20 colleagues from Angola and Namibia
  • The fully verified data for Angolan and Namibian scientific collections will be published to GBIF (with sponsorship by VertNet) and updated georeferenced records will be redistributed to data providers
  • Technical syntheses will be distributed to appropriate conservation and governmental organizations for immediate use in threat assessment, while non-technical syntheses intended for broad dissemination are distributed to Angolan and Namibian governmental ministries, NGOs, and educational institutions

Planned Outcomes

The most significant results from this project will include the digitization and dissemination of more than 40,000 specimen records of approximately 440 reptile and 115 amphibian species from Angolan and Namibian museum collections and the capacity building of in-country collaborators in biodiversity informatics. This project will globally distribute data on historical localities for poorly known species that are of conservation concern. By providing staff at Angolan and Namibian institutions with equipment, software, and technical skills, this work will facilitate the further digitization of existing collections at these institutions.

These data will also be used in technical publications and non-technical syntheses including gazetteers of localities and summary documents on the conservation status of Angolan and Namibian amphibians and reptiles that will serve a broad audience including NGOs, ministries, and policy makers.

Last Updated: November 20th, 2017

Primary Software Platforms

  • VertNet to publish data
  • GBIF Integrated Publishing Toolkit

Results to Date

  • Comprehensively assembled specimen collections data for amphibians and reptiles of both Namibia (~37,000 records) and Angola (~9,460) from 53 scientific collections in 19 countries. In addition, members of the group have personally visited many of the museum collections to verify records and identifications, ensuring high data quality.
  • Geo-coded ~350 of ~850 collections localities so that the associated records can be geo-referenced.
  • Completed planning of a workshop to be held in Namibia in May 2106, which will include participants from partner institutions in both Angola and Namibia.
  • Published two papers and two short notes related to scientific collections from Angola as well as new species records from Namibia.
  • Used JRS funding to leverage additional support for the project from the National Science Foundation. The forthcoming project will use the data digitize here to determine and address geographic gaps in reptile and amphibian records. Field surveys in those areas will contribute to a more complete knowledge base of the status of reptiles and amphibians in Africa.

Lessons Learned

Generalism, blind faith, and not a small dose of luck, can be major assets to a multi-national project. The team was hoping to locate a famous collection believed to have been destroyed in civil unrest. They fortuitously discovered a reference to the collection made in 1948, and learned that the collection was intact at the Royal Museum of Central Africa in Belgium. The discovery of this reference was lucky because the reference was located in a Portuguese language report, a language in which Dr. Ceríaco is fluent. The group has unearthed many widely dispersed collections all over the world that will help build this dataset. While this has the benefit of bringing to light a great deal of previously unknown records, the existence of numerous small collections distributed all over the world makes it impossible for the investigators to personally visit each one and verify identifications, necessitating prioritization of some museum visits over others.

The group has found that the georeferencing of collection localities in Namibia is taking more time than expected, largely due to large number of localities, as well as some confusion of named locations with nearby farms. In this digital age, they are finding that the most valuable resource for tackling this challenge is Dr. Bauer’s collection of paper maps.

Related Publications

  • Bauer, AM; LMP Ceríaco; MP Heinicke; DC Blackburn (2015) Geographic Distribution. Pachydactylus barnardi FitzSimons, 1941, Barnard’s Rough Gecko. African Herp News. 62: 35-37.
  • Ceríaco, LMP; DC Blackburn; MP Marques; and FM Calado (2014) Catalogue of the amphibian and reptile type specimens of the Natural History Museum of the University of Porto in Portugal, with some comments on problematic taxa. Alytes.  31: 13-36. (link)
  • Ceríaco, LMP; AM Bauer; DC Blackburn; and A Lavres (2014) The herpetofauna of the Capanda Dam Region, Malanje, Angola. Herpetological Review. 45(4): 667–674 (link)
  • Ceríaco, LMP; SAC de Sá; S Bandeira; H Valério; EL Stanley; AL Kuhn; MP Marques; JV Vindum; DC Blackburn; AM Bauer. 2016. Herpetological survey of Iona National Park and Namibe Regional Natural Park, with a synoptic list of the amphibians and reptiles of Namibe Province, southwestern Angola. 2016. Proceedings of the California Academy of Sciences 63: 15–61 (link)
  • Stanley, E.L; LM Ceríaco; S Bandeira; H Valerio; MF Bates; WR Branch (2016). A review of Cordylus machadoi (Squamata: Cordylidae) in southwestern Angola, with the description of a new species from the Pro-Namib desert. Zootaxa, 4061(3), 201-226. (link)

Project Director Biography

While this project is awarded by JRS to the University of Florida, it is collaborative effort among four key researchers; project director David Blackburn, Luis Ceríaco in Portugal, Aaron Bauer at Villanova, and Matt Heinicke at the University of Michigan-Dearborn. David Blackburn is the Curator of Amphibians and Reptiles at the California Academy of Sciences. His research focuses on the evolution, diversity, and conservation of amphibians, particularly frogs in Africa. Since 2000, Dr. Blackburn has worked in many different countries and landscapes across Africa, ranging from the Sahara to montane forests.

Notes from JRS

One year in, the project based at the California Academy of Sciences is progressing well and we look forward to the acceleration of the curatorial and digitization activities as well as the greater partnership with local institutions in the coming year.

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