Towards a global virtual natural history collection: GBIF and access to entomological specimens

2016 ◽  
Author(s):  
Donald Hobern
Keyword(s):  
Natural History ◽  
Natural History Collection

scholarly journals Comparison of Automated Georeferencing Tools Using Insect Collection Data

2019 ◽  
Vol 3 ◽  
Author(s):  
Leonor Venceslau ◽  
Luis Lopes
Keyword(s):  
Natural History ◽  
Average Distance ◽  
Sampling Location ◽  
Reference Dataset ◽  
Global Biodiversity Information Facility ◽  
Google Maps ◽  
Reference Location ◽  
Natural History Collection ◽  
Collection Data ◽  
Insect Collection

Major efforts are being made to digitize natural history collections to make these data available online for retrieval and analysis (Beaman and Cellinese 2012). Georeferencing, an important part of the digitization process, consists of obtaining geographic coordinates from a locality description. In many natural history collection specimens, the coordinates of the sampling location are not recorded, rather they contain a description of the site. Inaccurate georeferencing of sampling locations negatively impacts data quality and the accuracy of any geographic analysis on those data. In addition to latitude and longitude, it is important to define a degree of uncertainty of the coordinates, since in most cases it is impossible to pinpoint the exact location retrospectively. This is usually done by defining an uncertainty value represented as a radius around the center of the locality where the sampling took place. Georeferencing is a time-consuming process requiring manual validation; as such, a significant part of all natural history collection data available online are not georeferenced. Of the 161 million records of preserved specimens currently available in the Global Biodiversity Information Facility (GBIF), only 86 million (53.4%) include coordinates. It is therefore important to develop and optimize automatic tools that allow a fast and accurate georeferencing. The objective of this work was to test existing automatic georeferencing services and evaluate their potential to accelerate georeferencing of large collection datasets. For this end, several open-source georeferencing services are currently available, which provide an application programming interface (API) for batch georeferencing. We evaluated five programs: Google Maps, MapQuest, GeoNames, OpenStreetMap, and GEOLocate. A test dataset of 100 records (reference dataset), which had been previously individually georreferenced following Chapman and Wieczorek 2006, was randomly selected from the Museu Nacional de História Natural e da Ciência, Universidade de Lisboa insect collection catalogue (Lopes et al. 2016). An R (R Core Team 2018) script was used to georeference these records using the five services. In cases where multiple results were returned, only the first one was considered and compared with the manually obtained coordinates of the reference dataset. Two factors were considered in evaluating accuracy: Total number of results obtained and Distance to the original location in the reference dataset. Total number of results obtained and Distance to the original location in the reference dataset. Of the five programs tested, Google Maps yielded the most results (99) and was the most accurate with 57 results < 1000 m from the reference location and 79 within the uncertainty radius. GEOLocate provided results for 87 locations, of which 47 were within 1000 m of the correct location, and 57 were within the uncertainty radius. The other 3 services tested all had less than 35 results within 1000 m from the reference location, and less than 50 results within the uncertainty radius. Google Maps and Open Street Map had the lowest average distance from the reference location, both around 5500 m. Google Maps has a usage limit of around 40000 free georeferencing requests per month, beyond which the service is paid, while GEOLocate is free with no usage limit. For large collections, this may be a factor to take into account. In the future, we hope to optimize these methods and test them with larger datasets.

scholarly journals Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution

2019 ◽  
Vol 374 (1777) ◽  
pp. 20180248 ◽  
Author(s):  
Sangeet Lamichhaney ◽  
Daren C. Card ◽  
Phil Grayson ◽  
João F. R. Tonini ◽  
Gustavo A. Bravo ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Natural History ◽  
Convergent Evolution ◽  
Phenotypic Diversity ◽  
Taxonomic Diversity ◽  
Gold Rush ◽  
Phenotypic Data ◽  
Natural History Collections ◽  
Natural History Collection ◽  
Genomic Studies

Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current ‘genomics gold rush’ in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep ‘vertical’, natural history knowledge with ‘horizontal’ knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.

Marble Busts and Fish Fossils

Nuncius ◽  
2016 ◽  
Vol 31 (2) ◽  
pp. 439-483
Author(s):  
Elena Canadelli
Keyword(s):  
Eighteenth Century ◽  
Natural History ◽  
18Th Century ◽  
Museum Collections ◽  
The Public ◽  
Additional Information ◽  
Natural History Collection ◽  
Late 18Th Century ◽  
University Of Padua ◽  
The University

The historical catalogs of the museum collections contain a wealth of information for historians seeking to reconstruct their contents, how they were displayed and the ways in which they were used. This paper will present the complete transcription of a draft catalog that was prepared in 1797 for the Museum of Natural History and Antiquities of the University of Padua. Conserved in the university’s Museum of Geology and Paleontology, the catalog was the first to be compiled of the museum, which was established in 1733 thanks to the donation by Antonio Vallisneri Jr. of his father Antonio Vallisneri Sr.’s collection of antiquities and natural history. The catalog was compiled by the custodian of the museum, the herbalist and amateur naturalist Bartolomeo Fabris. It is of great interest because it provides a record of the number and nature of the pieces conserved in the museum at a time when natural history and archeology collections were still undivided. It also provides indications as to how such collections were arranged for display in the public halls of a university at the end of the eighteenth century. Based on this catalog, with additional information drawn from other manuscript and published sources and museum catalogs from the 1830s conserved in various institutes at the University of Padua, it is possible to reconstruct the contents and layout of a significant late 18th-century natural history collection.

Spend time now, save time later: IPM lessons learned from the National Museum of Natural History, Smithsonian Institution

2015 ◽  
Vol 29 (1-2) ◽  
pp. 61-66
Author(s):  
Amanda N. Lawrence ◽  
Jennifer Strotman
Keyword(s):  
Natural History ◽  
Pest Management ◽  
Smithsonian Institution ◽  
Lessons Learned ◽  
National Museum ◽  
Pest Infestation ◽  
Knowing That ◽  
Natural History Collection ◽  
New Pest

Abstract A case study involving a comprehensive inspection to discriminate between old and active pest infestations is described. Integrated pest management (IPM) processes within the National Museum of Natural History (NMNH), Smithsonian Institution, Division of Mammals (DOM) are challenging because of the size and composition of the collection, the age of storage equipment, and a low staffing to specimen ratio. Each specimen cabinet was inspected by IPM technicians during a 6-week period in late 2012. Following that inspection, two members of the NMNH collections program technician team began a 9-week project to clean 5,925 incidents in the affected cabinets in DOM storage areas in the Natural History Building downtown. The results of this project show that cleaning up a pest infestation in any natural history collection can be done in a reasonable amount of time and will help ensure the preservation of collections in the future. Knowing that the collections have been fully inspected and cleaned will allow staff in the DOM to easily and rapidly address future IPM issues in a structured way. Such efforts facilitate future IPM inspections because evidence of any new pest activity is no longer at risk of being overlooked due to debris from past infestations.

scholarly journals Art. XIX.—The Arabic, Syriac, and Hebrew Manuscripts in the Hunterian Library in the University of Glasgow

1899 ◽  
Vol 31 (4) ◽  
pp. 739-756
Author(s):  
T. H. Weir
Keyword(s):  
Natural History ◽  
Printed Books ◽  
Natural History Collection ◽  
The University ◽  
William Hunter

Dr. William Hunter (d. 1783) bequeathed to the University of Glasgow, along with his Natural History Collection, a library containing about twelve thousand volumes of printed books and six hundred manuscripts. The latter were catalogued by G. Haenel, in his Catalogi Librorum Manuscriptorum, Leipzig, 1830, columns 786–798. In regard to the Oriental manuscripts, however, he frequently does no more than state in what languages they are written, and that not always correctly. Thanks to the courtesy of the Keeper of the Museum, who gave every facility of access to the cases, the following is an emended list of the Arabic, Syriac, and Hebrew manuscripts. With the exception of No. 7, none of these is written on vellum.

scholarly journals Imaging natural history museum collections from the bottom up: 3D print technology facilitates imaging of fluid-stored arthropods with flatbed scanners

ZooKeys ◽  
2018 ◽  
Vol 795 ◽  
pp. 49-65 ◽  
Author(s):  
Patina K. Mendez ◽  
Sangyeon Lee ◽  
Chris E. Venter
Keyword(s):  
Image Quality ◽  
Natural History ◽  
Imaging Techniques ◽  
Natural History Museum ◽  
Laboratory Equipment ◽  
History Museum ◽  
3D Print ◽  
Natural History Collection ◽  
3D Printed ◽  
Microscope Slides

Availability of 3D-printed laboratory equipment holds promise to improve arthropod digitization efforts. A 3D-printed specimen scanning box was designed to image fluid-based arthropod collections using a consumer-grade flatbed scanner. The design was customized to accommodate double-width microscope slides and printed in both Polylactic Acid (PLA) and nylon (Polyamide). The workflow with two or three technicians imaged Trichoptera lots in batches of six scanning boxes. Individual images were cropped from batch imagess using an R script. PLA and nylon both performed similarly with no noticeable breakdown of the plastic; however, dyed nylon leeched color into the ethanol. The total time for handling, imaging, and cropping was ~8 minutes per vial, including returning material to vials and replacing ethanol. Image quality at 2400 dpi was the best and revealed several diagnostic structures valuable for partial identifications with higher utility if structures of the genitalia were captured; however, lower resolution scans may be adequate for natural history collection imaging. Image quality from this technique is similar to other natural history museum imaging techniques; yet, the scanning approach may have wider applications to morphometrics because of lack of distortion. The approach can also be applied to image vouchering for biomonitoring and other ecological studies.

Introduction of a novel natural history collection: a model for global scientific collaboration and enhancement of biodiversity infrastructure with a focus on developing countries

2019 ◽  
Vol 28 (7) ◽  
pp. 1921-1931
Author(s):  
Cord B. Eversole ◽  
Randy L. Powell ◽  
Dennis E. Lizarro ◽  
Federico Moreno ◽  
Gonzalo Calderon Vaca ◽  
...  
Keyword(s):  
Developing Countries ◽  
Natural History ◽  
Scientific Collaboration ◽  
Natural History Collection
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