Consideration of sample source for establishing reliable genetic microsatellite data from mammalian carnivore specimens held in natural history collections

2019 ◽  
Vol 100 (5) ◽  
pp. 1678-1689 ◽  
Author(s):  
Robert C Lonsinger ◽  
David Daniel ◽  
Jennifer R Adams ◽  
Lisette P Waits
Keyword(s):  
Natural History ◽  
Large Scale ◽  
Environmental Changes ◽  
Error Rates ◽  
Reliable Data ◽  
Genotyping Error ◽  
Destructive Sampling ◽  
Term Care ◽  
Amplification Success ◽  
Natural History Collections

AbstractSpecimens from natural history collections (NHCs) are increasingly being used for genetic studies and can provide information on extinct populations, facilitate comparisons of historical and contemporary populations, produce baseline data before environmental changes, and elucidate patterns of change. Destructive sampling for DNA may be in disagreement with NHC goals of long-term care and maintenance. Differentiating quality among sample sources can direct destructive sampling to the source predicted to yield the highest quality DNA and most reliable data, potentially reducing damage to specimens, laboratory costs, and genotyping errors. We used the kit fox (Vulpes macrotis) as a model species and evaluated the quality and reliability of genetic data obtained from carnivoran specimens via three different sample sources: cranial bones, nasal bones, and toepads. We quantified variation in microsatellite amplification success and genotyping error rates and assessed the reliability of source-specific genic data. Toepads had the highest amplification success rates and lowest genotyping error rates. Shorter loci had higher amplification success and lower allelic dropout rates than longer loci. There were substantial differences in the reliability of resulting multilocus genotypes. Toepads produced the most reliable data, required the fewest replicates, and therefore, had the lowest costs to achieve reliable data. Our results demonstrate that the quality of DNA obtained from specimens varies by sample source and can inform NHCs when evaluating requests for destructive sampling. Our results suggest that prior to large-scale specimen sampling, researchers should conduct pilot studies to differentiate among source-specific data reliability, identify high performing loci, reduce costs of analyses, and minimize destructive sampling.

scholarly journals Digitization and the Future of Natural History Collections

BioScience ◽  
2020 ◽  
Vol 70 (3) ◽  
pp. 243-251 ◽  
Author(s):  
Brandon P Hedrick ◽  
J Mason Heberling ◽  
Emily K Meineke ◽  
Kathryn G Turner ◽  
Christopher J Grassa ◽  
...  
Keyword(s):  
Natural History ◽  
Global Change ◽  
Large Scale ◽  
Anthropogenic Impacts ◽  
Digital Content ◽  
Global Community ◽  
New Approaches ◽  
Natural History Collections ◽  
Data Links ◽  
Critical Issues

Abstract Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization—the conversion of specimen data into accessible digital content—has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0)—whereby specimens are digitized within NHCs—to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds on the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data links, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical issues of global change.

scholarly journals The development of a digitising service centre for natural history collections

ZooKeys ◽  
2012 ◽  
Vol 209 ◽  
pp. 75-86 ◽  
Author(s):  
Riitta Tegelberg ◽  
Jaana Haapala ◽  
Tero Mononen ◽  
Mika Pajari ◽  
Hannu Saarenmaa
Keyword(s):  
Natural History ◽  
Large Scale ◽  
Data Entry ◽  
Imaging Data ◽  
Long Term Storage ◽  
Service Centre ◽  
Natural History Collections ◽  
Darwin Core ◽  
The University

Digitarium is a joint initiative of the Finnish Museum of Natural History and the University of Eastern Finland. It was established in 2010 as a dedicated shop for the large-scale digitisation of natural history collections. Digitarium offers service packages based on the digitisation process, including tagging, imaging, data entry, georeferencing, filtering, and validation. During the process, all specimens are imaged, and distance workers take care of the data entry from the images. The customer receives the data in Darwin Core Archive format, as well as images of the specimens and their labels. Digitarium also offers the option of publishing images through Morphbank, sharing data through GBIF, and archiving data for long-term storage. Service packages can also be designed on demand to respond to the specific needs of the customer. The paper also discusses logistics, costs, and intellectual property rights (IPR) issues related to the work that Digitarium undertakes.

scholarly journals Digitization and the future of natural history collections

2019 ◽  
Author(s):  
Brandon Hedrick ◽  
Mason Heberling ◽  
Emily Meineke ◽  
Kathryn Turner ◽  
Christopher Grassa ◽  
...  
Keyword(s):  
Natural History ◽  
Global Change ◽  
Large Scale ◽  
Anthropogenic Impacts ◽  
Digital Content ◽  
Global Community ◽  
New Approaches ◽  
Natural History Collections ◽  
The Future ◽  
Data Linkages

Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization–the conversion of specimen data into accessible digital content–has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0)–whereby specimens are digitized within NHCs–to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds upon the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data linkages, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical modern issues of global change.

scholarly journals One World Collection: The state of the world’s natural history collections

2019 ◽  
Vol 3 ◽  
Author(s):  
Ian Owens ◽  
Kirk Johnson
Keyword(s):  
Decision Making ◽  
Natural History ◽  
Large Scale ◽  
Major Change ◽  
Global Strategy ◽  
Sources Of Information ◽  
Genomic Technologies ◽  
Natural History Collections ◽  
The World ◽  
Geographic Regions

The world's natural history collections represent a vast repository of information on the natural and cultural world, collected over 250 years of human exploration, and distributed across institutions on six continents. These collections provide a unique tool for answering fundamental questions about biological, geological and cultural diversity and how they interact to shape our changing planet. Recent advances in digital and genomic technologies promise to transform how natural history collections are used, especially with respect to addressing scientific and socio-economic challenges ranging from biodiversity loss, invasive species and food security, to climate change, scarce minerals, and emerging tropical diseases. It is not clear, however, how ready these collections are to meet this challenge because relatively little is known about their size, composition or geographical distribution. Similarly, relatively little is known about the extent, expertise or demography of their curatorial workforce. To address these questions, a large collaborative team of directors and scientists have collated a global database on natural history collections that comprises more than 70 of the world's largest institutions, including museums, botanic gardens, research institutes and universities. The institutions represented in the database span Africa, Asia, Australasia, Europe, and North and South America, with approximately one third of institutions from each of the Global South, Europe and North America. The database includes information on the number of specimens and experts with respect to both geographic regions and collection categories and geographic regions. Geographic regions include both the terrestrial and marine realms, and collection categories span anthropology, botany, entomology, geology, paleobiology, and vertebrate and invertebrate zoology. Analyses of this new database reveal that the global natural history collection represents one of the most extensive distributed scientific infrastructures in the world, comprising more than 1 billion specimens that are curated by a workforce of more than 7,000 individuals. The analyses also indicate, however, that a major change in approach is required for these collections to realize their potential to inform future decision making and stimulate the basic research that underpins future questions and knowledge. For instance, at a global scale the collection and expertise does indeed exist to map change in key groups and regions - but this requires large-scale coordination across institutions and countries. Similarly, cross-institution collaboration is required to fill strategic gaps in the collection, particularly for tropical, marine and polar regions. And finally, there is an urgent need for coordinated investment in digital and genomic technologies to make collections available to the global research community and link them with other sources of information. The vast majority of collection information currently exists as 'dark data'. We conclude that the global natueral history collection comprises one of the most extensive distributed scientific infrastructures in the world, but a major change in approach is required for them to realize their potential to inform future decision making. In particular, natural history collections need to work more effectively together to develop a global strategy, create a common data platform, accelerate the availability and use of specimen data and pursue major new collecting programs.

scholarly journals Leveraging the Benefits of Open Data Services for Natural History Collection Management

2018 ◽  
Vol 2 ◽  
pp. e25882
Author(s):  
Maarten Schermer ◽  
Daphne Duin
Keyword(s):  
Natural History ◽  
The Netherlands ◽  
Large Scale ◽  
Open Data ◽  
Collection Management ◽  
Collections Management ◽  
Biodiversity Data ◽  
Data Services ◽  
Natural History Collections ◽  
Digital Collection

The value of data present in natural history collections for research and collection management cannot be overstated. Naturalis Biodiversity Center, home to one of the largest natural history collections in the world, completed a large-scale digitisation project resulting in the registration of more than 38 million objects, many of them annotated with descriptive metadata, such as geographic coordinates and multimedia content. While digitisation is ongoing, we are now also looking for ways to leverage our digital collection, both for the benefit of collection management and that of networking with other natural history collections. To this end, we developed the Netherlands Biodiversity Data Services, providing centralized access to our collection data via state of the art, open access interfaces. Full, centralized access to the digital collection allows us to combine the data with other sources, such as collection scans focusing on the physical condition and accessibility of the collection. But also with data from external sources, such as the collection information of sister institutions, allowing for combining and comparing data, and exploring areas where collections can reinforce each other. Focusing on availability and accessibility, the services were deliberately designed as a versatile, low-level API to allow the use of our data with a broad variety of applications and services. These applications range from scientific research and remote mobile access to collection information, to “mash ups” with other data sources, apps and application in our own museum. We will demonstrate this range of applications through several examples, including the embedding of data in websites (example, Dutch Caribbean Species Register: http://www.dutchcaribbeanspecies.org/linnaeus_ng/app/views/species/nsr_taxon.php?id=177968&cat=165), use in the development of deep learning models, thematic portals (example, Naturalis meteorite collection: http://bioportal.naturalis.nl/result?theme=meteorites&language=en) and the development of Java- and R-clients. This presentation ties in with Max Caspers' presentation “Advancing collections management with the Netherlands Biodiversity Data Services“, in which he will demonstratie the potential of the services described in this presentation for the area of collections management, specifically.

scholarly journals Sex biases in bird and mammal natural history collections

2019 ◽  
Vol 286 (1913) ◽  
pp. 20192025 ◽  
Author(s):  
Natalie Cooper ◽  
Alexander L. Bond ◽  
Joshua L. Davis ◽  
Roberto Portela Miguez ◽  
Louise Tomsett ◽  
...  
Keyword(s):  
Body Size ◽  
Natural History ◽  
Evolutionary Biology ◽  
Large Scale ◽  
Sex Ratios ◽  
Museum Specimens ◽  
Male Bias ◽  
Biological Sex ◽  
Natural History Collections ◽  
Sex Biases

Natural history specimens are widely used across ecology, evolutionary biology and conservation. Although biological sex may influence all of these areas, it is often overlooked in large-scale studies using museum specimens. If collections are biased towards one sex, studies may not be representative of the species. Here, we investigate sex ratios in over two million bird and mammal specimen records from five large international museums. We found a slight bias towards males in birds (40% females) and mammals (48% females), but this varied among orders. The proportion of female specimens has not significantly changed in 130 years, but has decreased in species with showy male traits like colourful plumage and horns. Body size had little effect. Male bias was strongest in name-bearing types; only 27% of bird and 39% of mammal types were female. These results imply that previous studies may be impacted by undetected male bias, and vigilance is required when using specimen data, collecting new specimens and designating types.

scholarly journals Digitization and the future of natural history collections

2019 ◽  
Author(s):  
Brandon Hedrick ◽  
Mason Heberling ◽  
Emily Meineke ◽  
Kathryn Turner ◽  
Christopher Grassa ◽  
...  
Keyword(s):  
Natural History ◽  
Global Change ◽  
Large Scale ◽  
Anthropogenic Impacts ◽  
Digital Content ◽  
Global Community ◽  
New Approaches ◽  
Natural History Collections ◽  
The Future ◽  
Data Linkages

Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization–the conversion of specimen data into accessible digital content–has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0)–whereby specimens are digitized within NHCs–to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds upon the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data linkages, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical modern issues of global change.

scholarly journals Towards a Global Collection Description Standard

2019 ◽  
Vol 3 ◽  
Author(s):  
Niels Raes ◽  
Emily van Egmond ◽  
Ana Casino ◽  
Matt Woodburn ◽  
Deborah L Paul
Keyword(s):  
Natural History ◽  
Large Scale ◽  
The United States ◽  
Fragmented Landscape ◽  
Global Biodiversity Information Facility ◽  
Classification Schemes ◽  
Natural History Collections ◽  
Natural History Collection ◽  
World Collection ◽  
Scientific Collections

With digitisation of natural history collections over the past decades, their traditional roles — for taxonomic studies and public education — have been greatly expanded into the fields of biodiversity assessments, climate change impact studies, trait analyses, sequencing, 3D object analyses etc. (Nelson and Ellis 2019; Watanabe 2019). Initial estimates of the global natural history collection range between 1.2 and 2.1 billion specimens (Ariño 2010), of which 169 million (8-14% - as of April 2019) are available at some level of digitisation through the Global Biodiversity Information Facility (GBIF). With iDigBio (Integrated Digitized Biocollections) established in the United States and with the European DiSSCo (Distributed Systems of Scientific Collections) accepted on the ESFRI roadmap, it has become a priority to digitize natural history collections at an industrialized scale. Both iDigBio and DiSSCo aim at mobilising, unifying and delivering bio- and geo-diversity information at the scale, form and precision required by scientific communities, and thereby transform a fragmented landscape into a coherent and responsive research infrastructure. In order to prioritise digitisation based on scientific demand, and efficiency using industrial digitisation pipelines, it is required to arrive at a uniform and unambiguously accepted collection description standard that would allow comparing, grouping and analysing natural history collections at diverse levels. Several initiatives attempt to unambiguously describe natural history collections using taxonomic and storage classification schemes. These initiatives include One World Collection, Global Registry of Scientific Collections (GRSciColl), TDWG (Taxonomic Databases Working Group) Natural Collection Descriptions (NCD) and CETAF (Consortium of European Taxonomy Facilities) passports, among others. In a collaborative effort of DiSSCo, ICEDIG (Innovation and consolidation for large scale digitisation of natural heritage), iDigBio, TDWG and the Task Group Collection Digitisation Dashboards, the various schemes were compared in a cross-walk analysis to propose a preliminary natural collection description standard that is supported by the wider community. In the process, two main user groups of collection descriptions standards were identified; scientists and collection managers. The classification produced intends to meet requirements from them both, resulting in three classification schemes that exist in parallel to each other (van Egmond et al. 2019). For scientific purposes a ‘Taxonomic’ and ‘Stratigraphic’ classification were defined, and for management purposes a ‘Storage’ classification. The latter is derived from specimen preservation types (e.g. dried, liquid preserved) defining storage requirements and the physical location of specimens in collection holding facilities. The three parallel collection classifications can be cross-sectioned with a ‘Geographic’ classification to assign sub-collections to major terrestrial and marine regions, which allow scientists to identify particular taxonomic or stratigraphic (sub-)collections from major geographical or marine regions of interest. Finally, to measure the level of digitisation of institutional collections and progress of digitisation through time, the number of digitised specimens for each geographically cross-sectioned (sub-)collection can be derived from institutional collection management systems (CMS). As digitisation has different levels of completeness a ‘Digitisation’ scheme has been adopted to quantify the level of digitisation of a collection from Saarenmaa et al. 2019, ranging from ‘not digitised’ to extensively digitised, recorded in a progressive scale of MIDS (Minimal Information for Digital Specimen). The applicability of this preliminary classification will be discussed and visualized in a Collection Digitisation Dashboards (CDD) to demonstrate how the implementation of a collection description standard allows the identification of existing gaps in taxonomic and geographic coverage and levels of digitisation of natural history collections. This set of common classification schemes and dashboard design (van Egmond et al. 2019) will be contributed to the TDWG Collection Description interest group to ultimately arrive at the common goal of a 'World Collection Catalogue'.

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