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Wu R, Zou Y, Liao S, Shi K, Nan X, Yan H, Luo J, Xiang Z, Bao Z. Shall we promote natural history collection today?-Answered by reviewing Ernest Henry Wilson's plant collection process in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170179. [PMID: 38246391 DOI: 10.1016/j.scitotenv.2024.170179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/20/2023] [Accepted: 01/13/2024] [Indexed: 01/23/2024]
Abstract
Plant diversity exploration needs to be accelerated because many species will go extinct before their discovery and description, and many species-rich regions remain poorly studied. However, most contemporary plant collections prefer to focus on a specific group, which hinders the exploration and conservation of plant diversity. Therefore, we need an alternative approach to the dilemma at hand. The comprehensive Natural History Collection (NHC), which existed throughout the pinnacle of biodiversity exploration in the 20th century could be considered. We explore Ernest Henry Wilson's (one of the most successful naturalists in the 20th) plant collections in China as a case to illustrate the advantages of NHC and discuss whether NHC deserves to be promoted again today. From multiple sources, we gathered 19,218 available specimen records of 11,884 collecting numbers assigned and analyzed the collected species, the collection's nature, and restored four routes of his explorations. Results reveal that Wilson's specimens were collected from 28 prefecture-level cities and 38 county-level regions of 7 provinces or municipalities, they belong to 200 families, 1046 genera, 3794 species, and 342 infraspecific taxa, approximately 41 %, 22 %, 10 %, 5 % of Chinese plant families, genera, species, and infraspecific taxa respectively. The Wilson case study shows that NHC is particularly effective in emphasizing species discovery and conservation, recording ecological information, understanding a region's flora, and developing landscape applications. Therefore, we strongly advocate for the expansion of natural history collections in species-rich regions. Furthermore, we recommend the employment of specialized collectors, the enlistment of international cooperation, and the standardization of guidelines for future NHCs.
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Affiliation(s)
- Renwu Wu
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China.
| | - Yongxi Zou
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Shuai Liao
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ke Shi
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xinge Nan
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Hai Yan
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Jifan Luo
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhoubing Xiang
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhiyi Bao
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
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2
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Braker EM. Phototank setup and focus stack imaging method for reptile and amphibian specimens (Amphibia, Reptilia). Zookeys 2022; 1134:185-210. [PMID: 36761107 PMCID: PMC9836466 DOI: 10.3897/zookeys.1134.96103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Fluid-preserved reptile and amphibian specimens are challenging to photograph with traditional methods due to their complex three-dimensional forms and reflective surfaces when removed from solution. An effective approach to counteract these issues involves combining focus stack photography with the use of a photo immersion tank. Imaging specimens beneath a layer of preservative fluid eliminates glare and risk of specimen desiccation, while focus stacking produces sharp detail through merging multiple photographs taken at successive focal steps to create a composite image with an extended depth of field. This paper describes the wet imaging components and focus stack photography workflow developed while conducting a large-scale digitization project for targeted reptile and amphibian specimens housed in the University of Colorado Museum of Natural History Herpetology Collection. This methodology can be implemented in other collections settings and adapted for use with fluid-preserved specimen types across the Tree of Life to generate high-quality, taxonomically informative images for use in documenting biodiversity, remote examination of fine traits, inclusion in publications, and educational applications.
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Affiliation(s)
- Emily M. Braker
- Vertebrate Zoology, University of Colorado Museum of Natural History, UCB 265, Boulder CO 80309, USAUniversity of Colorado Museum of Natural HistoryBoulderUnited States of America
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3
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Hardisty AR, Ellwood ER, Nelson G, Zimkus B, Buschbom J, Addink W, Rabeler RK, Bates J, Bentley A, Fortes JAB, Hansen S, Macklin JA, Mast AR, Miller JT, Monfils AK, Paul DL, Wallis E, Webster M. Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet. Bioscience 2022; 72:978-987. [PMID: 36196222 PMCID: PMC9525127 DOI: 10.1093/biosci/biac060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecological, environmental, climatological, and biological collections data, these initiatives have resulted in a plethora of mostly disconnected and siloed data, leaving to researchers the tedious and time-consuming manual task of finding and connecting them in usable ways, integrating them into coherent data sets, and making them interoperable. The focus to date has been on elevating analog and physical records to digital replicas in local databases prior to elevating them to ever-growing aggregations of essentially disconnected discipline-specific information. In the present article, we propose a new interconnected network of digital objects on the Internet—the Digital Extended Specimen (DES) network—that transcends existing aggregator technology, augments the DES with third-party data through machine algorithms, and provides a platform for more efficient research and robust interdisciplinary discovery.
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Affiliation(s)
| | | | - Gil Nelson
- Florida Museum of Natural History , Gainesville, Florida, United States
| | - Breda Zimkus
- Museum of Comparative Zoology , Cambridge, Massachusetts, United States
| | | | | | - Richard K Rabeler
- University of Michigan Herbarium , Ann Arbor, Michigan, United States
| | - John Bates
- Field Museum of Natural History , Chicago, Illinois, United States
| | - Andrew Bentley
- Biodiversity Institute, University of Kansas , Lawrence, Kansas, United States
| | | | - Sara Hansen
- Central Michigan University Herbarium, Central Michigan University , Mt. Pleasant, Michigan, United States
| | | | - Austin R Mast
- Department of Biological Science, Florida State University , Tallahassee, Florida, United States
| | - Joseph T Miller
- Global Biodiversity Information Facility Secretariat , Copenhagen, Denmark
| | - Anna K Monfils
- Central Michigan University Herbarium, Central Michigan University , Mt. Pleasant, Michigan, United States
| | - Deborah L Paul
- University of Illinois Urbana Champaign , Champaign, Illinois, United States
| | - Elycia Wallis
- Atlas of Living Australia, CSIRO , Melbourne, Australia
| | - Michael Webster
- Macaulay Library, Cornell Lab of Ornithology , Ithaca, New York, United States
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4
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Larson JG, Crowell HL, Walsh LL, Davis Rabosky AR. The Batrachian Barf Bowl: An authentic research experience using ecological data from frog diets. Ecol Evol 2022; 12:e9095. [PMID: 35866014 PMCID: PMC9288929 DOI: 10.1002/ece3.9095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/17/2022] [Accepted: 06/22/2022] [Indexed: 11/22/2022] Open
Abstract
Authentic research experiences (AREs) are a powerful strategy for inspiring and retaining students in science, technology, engineering, and math (STEM) fields. However, recent demand for virtual learning has emphasized the need for remote AREs that also foster a sense of community and interpersonal connections among participants. Here, we describe an ARE activity that leverages digitized diet data from natural history collections to provide students with collaborative research experience across any learning environment. Using magnified photographs of frog stomach contents collected in the Peruvian Amazon, we designed an open‐source “bowl game” competition that challenges students to identify, measure, and compare diet items across vouchered frog specimens (“Batrachian Barf Bowl”). To demonstrate learning outcomes, we ran this activity with 39 herpetology class students from the University of Notre Dame and the University of Michigan. We used pre‐ and post‐activity assessments to evaluate effectiveness, scientific accuracy of results, and impact on student well‐being. With minimal preparation and training in invertebrate identification, students were successful in identifying hundreds of frog diet items to taxonomic order, although accuracy varied among clades (global accuracy ~70%). While we found no difference in science identity, community, or self‐efficacy between the two institutions at either time point (pre‐ and post‐activity), we found that well‐being was significantly higher for both sets of students after the activity. Overall, this approach offers a model for combining active learning with museum collections to provide experiential research opportunities that highlight the power of scientific collaboration.
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Affiliation(s)
- Joanna G Larson
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor Michigan USA
- Department of Biological Sciences University of Notre Dame Notre Dame Indiana USA
| | - Hayley L Crowell
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor Michigan USA
| | - Lisa L Walsh
- Education Research & Outreach Donald Danforth Plant Science Center St. Louis Missouri USA
| | - Alison R Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor Michigan USA
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5
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Teixeira‐Costa L, Heberling JM, Wilson CA, Davis CC. Parasitic flowering plant collections embody the extended specimen. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Luiza Teixeira‐Costa
- Harvard University Herbaria Cambridge MA USA
- Hanse‐Wissenschaftskolleg – Institute for Advanced Study, Lehmkuhlenbusch 4, 27753 Delmenhorst Germany
| | | | - Carol A. Wilson
- University and Jepson Herbaria University of California, Berkeley, 1001 Valley Life Sciences Building Berkeley CA USA
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6
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Monfils AK, Krimmel ER, Linton DL, Marsico TD, Morris AB, Ruhfel BR. Collections Education: The Extended Specimen and Data Acumen. Bioscience 2021; 72:177-188. [PMID: 35145351 PMCID: PMC8824687 DOI: 10.1093/biosci/biab109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Biodiversity scientists must be fluent across disciplines; they must possess the quantitative, computational, and data skills necessary for working with large, complex data sets, and they must have foundational skills and content knowledge from ecology, evolution, taxonomy, and systematics. To effectively train the emerging workforce, we must teach science as we conduct science and embrace emerging concepts of data acumen alongside the knowledge, tools, and techniques foundational to organismal biology. We present an open education resource that updates the traditional plant collection exercise to incorporate best practices in twenty-first century collecting and to contextualize the activities that build data acumen. Students exposed to this resource gained skills and content knowledge in plant taxonomy and systematics, as well as a nuanced understanding of collections-based data resources. We discuss the importance of the extended specimen in fostering scientific discovery and reinforcing foundational concepts in biodiversity science, taxonomy, and systematics.
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Affiliation(s)
- Anna K Monfils
- Central Michigan University, Mount Pleasant, Michigan, United States
| | - Erica R Krimmel
- Florida State University, Tallahassee, Florida, United States
| | - Debra L Linton
- Central Michigan University, Mount Pleasant, Michigan, United States
| | | | - Ashley B Morris
- Furman University, Greenville, South Carolina, United States
| | - Brad R Ruhfel
- University of Michigan, Ann Arbor, Michigan, United States
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7
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Sheehan MJ, Miller SE. The promises and challenges of archiving insect behavior and natural history in a changing world. CURRENT OPINION IN INSECT SCIENCE 2021; 45:115-120. [PMID: 33857642 PMCID: PMC8316380 DOI: 10.1016/j.cois.2021.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/21/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Insect behavioral ecologists are not routinely archiving their behavioral media files and natural history observations. This is especially problematic because most behaviors are not preserved by the physical specimens stored in typical natural history collections. Improving the reporting and archiving of insect behavior and natural history data holds the promise of allowing scientists to track real-time responses of animals to global change and will preserve aspects of natural history that might otherwise be lost due to extinctions. Here we argue that behavioral ecologists should work to preserve and archive raw media files and field notes related to behavior and natural history of their study organisms. One major mechanism to incentivize archiving of such data would be for journals to develop policies for archiving of natural history data that is the focus of the paper or ancillary information collected about study subjects. Buy in from researchers, journals, and funding agencies will be needed to make substantial changes in data archiving.
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Affiliation(s)
- Michael J Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, United States.
| | - Sara E Miller
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, United States
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8
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Herrera Mesías F, Weigand AM. Updates to the checklist of the wild bee fauna of Luxembourg as inferred from revised natural history collection data and fieldwork. Biodivers Data J 2021; 9:e64027. [PMID: 34040491 PMCID: PMC8139942 DOI: 10.3897/bdj.9.e64027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/16/2021] [Indexed: 11/28/2022] Open
Abstract
Background Museums and other institutions curating natural history collections (NHCs) are fundamental entities to many scientific disciplines, as they house data and reference material for varied research projects. As such, biological specimens preserved in NHCs represent accessible physical records of the living world's history. They provide useful information regarding the presence and distribution of different taxonomic groups through space and time. Despite the importance of biological museum specimens, their potential to answer scientific questions, pertinent to the necessities of our current historical context, is often under-explored. The currently-known wild bee fauna of Luxembourg comprises 341 registered species distributed amongst 38 different genera. However, specimens stored in the archives of local NHCs represent an untapped resource to update taxonomic lists, including potentially overlooked findings relevant to the development of national conservation strategies. New information We re-investigated the wild bee collection of the Zoology Department of the National Museum of Natural History Luxembourg by using morphotaxonomy and DNA barcoding. The collection revision led to the discovery of four species so far not described for the country: Andrenalagopus (Latreille, 1809), Nomadafurva (Panzer, 1798), Hoplitispapaveris (Latreille, 1799) and Sphecodesmajalis (Pérez, 1903). Additionally, the presence of Nomadasexfasciata (Panzer, 1799), which inexplicably had been omitted by the most current species list, can be re-confirmed. Altogether, our findings increase the number of recorded wild bee species in Luxembourg to 346. Moreover, the results highlight the crucial role of NHCs as repositories of our knowledge of the natural world.
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Affiliation(s)
- Fernanda Herrera Mesías
- Department of Animal Ecology, Evolution and Biodiversity, Ruhr-Universität Bochum, Bochum, Germany Department of Animal Ecology, Evolution and Biodiversity, Ruhr-Universität Bochum Bochum Germany.,Musée national d'histoire naturelle de Luxembourg, Luxembourg, Luxembourg Musée national d'histoire naturelle de Luxembourg Luxembourg Luxembourg
| | - Alexander M Weigand
- Musée national d'histoire naturelle de Luxembourg, Luxembourg, Luxembourg Musée national d'histoire naturelle de Luxembourg Luxembourg Luxembourg
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9
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Pinou T, Pitzrick MS, Rahaman A, Young MA. Letters to the Editor. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2021; 22:jmbe-22-66. [PMID: 33953820 PMCID: PMC8060143 DOI: 10.1128/jmbe.v22i1.2199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Theodora Pinou
- Department of Biological and Environmental Sciences, Western Connecticut State University, Danbury, CT 06810;
| | - Michael S Pitzrick
- Center for Conservation Bioacoustics, Cornell University, Ithaca, NY 14850
| | - Ashakur Rahaman
- Center for Conservation Bioacoustics, Cornell University, Ithaca, NY 14850
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10
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Ferguson AW. On the role of (and threat to) natural history museums in mammal conservation: an African small mammal perspective. JOURNAL OF VERTEBRATE BIOLOGY 2020. [DOI: 10.25225/jvb.20028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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Csanády A. Hares and rabbits (Leporidae) in collection of the Šariš Museum, Bardejov (Slovakia). THERIOLOGIA UKRAINICA 2020. [DOI: 10.15407/tu1907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The Natural History Department of the Šariš Museum, Bardejov, Slovakia, was established in 1956 by PhMr. Tibor Weisz. The mammal collection consists of more than 5 000 specimens of 67 mammal species of the Slovakian fauna. The museum mostly represents the fauna of north-eastern Slovakia, i.e. the transition area between the Eastern and Western Carpathians and adjacent to the northernmost part of the Pannonian Basin. In the paper, data are presented on hare and rabbit specimens deposited in the collection of the Šariš Museum in Bardejov (SMB), Slovakia. In total, data were evaluated on 27 specimens of the brown hare (Lepus europaeus) from twelve sites of Slovakia (n = 19), one site of Czech Silesia (n = 1), and from unknow localities (n = 7). Individuals were acquired in 1958–1971, but mainly in 1965–1966 (n = 19, 70.4 %). Among them, one specimen had signs of „albinism“ and was collected from Zlaté village. The collection also includes a skull of a brown hare with anomalous dentition. Similarly, two skulls of the mountain hare (Lepus timidus) obtained from the Danish preparator N. H. Gustaffson were evaluated. Three rabit specimens were also found in the collection, including two skulls of the wild rabbit (Oryctolagus cuniculus) and a skin-mount and skull of a domestic rabbit (Oryctolagus cuniculus forma domestica). The collection contains 20 adult specimens (15 males and 5 females) with body size values recorded in the protocol cards. Mammalogical collections in the Šariš Museum in Bardejov represent an outstanding scientific time capsule. All stored specimens in this particular and other similar collections, including those in local museums, will largely be needed and used as datasets by ecologists and conservationists in the future. It is necesary to preserve the collections, to computerise and digitise their inventories and the wealth of information they represent. At present, most of these data are not accessible electronically or online. Therefore, such collections, including that in Bardejov, must be sustained for a long term, which will require increased funding for their physical and scientific preservation.
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12
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Miller SE, Barrow LN, Ehlman SM, Goodheart JA, Greiman SE, Lutz HL, Misiewicz TM, Smith SM, Tan M, Thawley CJ, Cook JA, Light JE. Building Natural History Collections for the Twenty-First Century and Beyond. Bioscience 2020. [DOI: 10.1093/biosci/biaa069] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Abstract
Natural history collections (NHCs) are important resources for a diverse array of scientific fields. Recent digitization initiatives have broadened the user base of NHCs, and new technological innovations are using materials generated from collections to address novel scientific questions. Simultaneously, NHCs are increasingly imperiled by reductions in funding and resources. Ensuring that NHCs continue to serve as a valuable resource for future generations will require the scientific community to increase their contribution to and acknowledgement of collections. We provide recommendations and guidelines for scientists to support NHCs, focusing particularly on new users that may be unfamiliar with collections. We hope that this perspective will motivate debate on the future of NHCs and the role of the scientific community in maintaining and improving biological collections.
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Affiliation(s)
- Sara E Miller
- Cornell University Department of Neurobiology and Behavior, Ithaca, New York
| | - Lisa N Barrow
- Museum of Southwestern Biology and with the Biology Department, University of New Mexico, Albuquerque
| | - Sean M Ehlman
- Ecology, Evolution, and Behavior Department, University of Minnesota—Twin Cities, Saint Paul
| | - Jessica A Goodheart
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, in Santa Barbara, California
- Scripps Institution of Oceanography, University of California San Diego, La Jolla
| | - Stephen E Greiman
- Department of Biology, Georgia Southern University, Statesboro Georgia
| | - Holly L Lutz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois
| | - Tracy M Misiewicz
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman
| | - Stephanie M Smith
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois
| | - Milton Tan
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Urbana–Champaign, Champaign
| | - Christopher J Thawley
- Department of Biological Sciences, University of Rhode Island, Kingston
- Department of Mathematics and Sciences, Neumann University, Aston, Pennsylvania
| | - Joseph A Cook
- Museum of Southwestern Biology and with the Biology Department, University of New Mexico, Albuquerque
| | - Jessica E Light
- Department of Ecology and Conservation Biology, Texas A&M University, College Station
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13
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Patzold F, Zilli A, Hundsdoerfer AK. Advantages of an easy-to-use DNA extraction method for minimal-destructive analysis of collection specimens. PLoS One 2020; 15:e0235222. [PMID: 32639972 PMCID: PMC7343169 DOI: 10.1371/journal.pone.0235222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/10/2020] [Indexed: 11/19/2022] Open
Abstract
Here we present and justify an approach for minimal-destructive DNA extraction from historic insect specimens for next generation sequencing applications. An increasing number of studies use insects from museum collections for biodiversity research. However, the availability of specimens for molecular analyses has been limited by the degraded nature of the DNA gained from century-old museum material and the consumptive nature of most DNA extraction procedures. The method described in this manuscript enabled us to successfully extract DNA from specimens as old as 241 years using a minimal-destructive approach. The direct comparison of the DNeasy extraction Kit and the Monarch® PCR & DNA Clean-up Kit showed a significant increase of 17.3-fold higher DNA yield extracted with the Monarch Oligo protocol on average. By using an extraction protocol originally designed for oligonucleotide clean-up, we were able to combine overcoming the restrictions by target fragment size and strand state, with minimising time consumption and labour-intensity. The type specimens used for the minimal-destructive DNA extraction exhibited no significant external change or post-extraction damage, while sufficient DNA was retrieved for analyses.
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Affiliation(s)
- Franziska Patzold
- Museum of Zoology (Museum für Tierkunde), Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Alberto Zilli
- Division Insects, Department Life Sciences, Natural History Museum, London, United Kingdom
| | - Anna K. Hundsdoerfer
- Museum of Zoology (Museum für Tierkunde), Senckenberg Natural History Collections Dresden, Dresden, Germany
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14
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Singer RA, Ellis S, Page LM. Awareness and use of biodiversity collections by fish biologists. JOURNAL OF FISH BIOLOGY 2020; 96:297-306. [PMID: 31621077 DOI: 10.1111/jfb.14167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
A survey of 280 fish biologists from a diverse pool of disciplines was conducted in order to assess the use made of biodiversity collections and how collections can better collect, curate and share the data they have. From the responses, data for how fish biologists use collections, what data they find the most useful, what factors influence the decisions to use collections, how they access the data and explore why some fish biologists make the decision to not use biodiversity collections is collated and reported. The results of which could be used to formulate sustainability plans for collections administrators and staff who curate fish biodiversity collections, while also highlighting the diversity of data and uses to researchers.
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Affiliation(s)
- Randal A Singer
- University of Michigan Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | - Shari Ellis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Lawrence M Page
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
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15
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Ellwood ER, Sessa JA, Abraham JK, Budden AE, Douglas N, Guralnick R, Krimmel E, Langen T, Linton D, Phillips M, Soltis PS, Studer M, White LD, Williams J, Monfils AK. Biodiversity Science and the Twenty-First Century Workforce. Bioscience 2020; 70:119-121. [PMID: 32063647 PMCID: PMC7012771 DOI: 10.1093/biosci/biz147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Elizabeth R Ellwood
- Natural History Museum of Los Angeles County, La Brea Tar Pits, Los Angeles, California.,Contributed equally production of the manuscript
| | - Jocelyn Anne Sessa
- Department of Biodiversity, Earth, and Environmental Science, Academy of Natural Sciences of Drexel University, Philadelphia, Pennsylvania
| | - Joel K Abraham
- Department of Biological Science, California State University, Fullerton
| | - Amber E Budden
- National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara
| | - Natalie Douglas
- Department of Communication Sciences and Disorders, Central Michigan University, Mt. Pleasant
| | - Robert Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville
| | - Erica Krimmel
- Institute for Digital Information and Scientific Communication, Florida State University, Tallahassee
| | - Tom Langen
- Department of Biology, Clarkson University, Potsdam, New York
| | - Debra Linton
- Department of Biology, Central Michigan University, Mt. Pleasant
| | - Molly Phillips
- Florida Museum of Natural History, University of Florida, Gainesville
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville
| | - Marie Studer
- Biodiversity education consultant, Stow, Massachusetts
| | - Lisa D White
- Museum of Paleontology, University of California, Berkeley
| | - Jason Williams
- Cold Spring Harbor Laboratory's DNA Learning Center, Cold Spring Harbor, New York
| | - Anna K Monfils
- Department of Biology, Central Michigan University, Mt. Pleasant.,Contributed equally production of the manuscript
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16
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Cobb NS, Gall LF, Zaspel JM, Dowdy NJ, McCabe LM, Kawahara AY. Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research. PeerJ 2019; 7:e8086. [PMID: 31788358 PMCID: PMC6882419 DOI: 10.7717/peerj.8086] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/23/2019] [Indexed: 12/21/2022] Open
Abstract
Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a "vast hidden treasure trove" of biodiversity -95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation's decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number of specimens in collections has increased by approximately 1% per year over the past 30 years. We propose that this rate of increase is insufficient to provide enough data to address biodiversity research needs, and that arthropod collections should aim to triple their rate of new specimen acquisition. (4) The collections we surveyed in the United States vary broadly in a number of indicators. Collectively, there is depth and breadth, with smaller collections providing regional depth and larger collections providing greater global coverage. (5) Increased coordination across museums is needed for digitization efforts to target taxa for research and conservation goals and address long-term data needs. Two key recommendations emerge: collections should significantly increase both their specimen holdings and their digitization efforts to empower continental and global biodiversity data pipelines, and stimulate downstream research.
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Affiliation(s)
- Neil S. Cobb
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Lawrence F. Gall
- Entomology Division, Yale Peabody Museum of Natural History, New Haven, CT, United States of America
| | - Jennifer M. Zaspel
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States of America
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
| | - Nicolas J. Dowdy
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States of America
- Department of Biology, Wake Forest University, Winston-Salem, NC, United States of America
| | - Lindsie M. McCabe
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Akito Y. Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
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17
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Lendemer J, Thiers B, Monfils AK, Zaspel J, Ellwood ER, Bentley A, LeVan K, Bates J, Jennings D, Contreras D, Lagomarsino L, Mabee P, Ford LS, Guralnick R, Gropp RE, Revelez M, Cobb N, Seltmann K, Aime MC. The Extended Specimen Network: A Strategy to Enhance US Biodiversity Collections, Promote Research and Education. Bioscience 2019; 70:23-30. [PMID: 31949317 PMCID: PMC6956879 DOI: 10.1093/biosci/biz140] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
| | - Barbara Thiers
- Biodiversity Collections Network Advisory Committee.,New York Botanical Garden, Bronx, New York
| | - Anna K Monfils
- Biodiversity Collections Network Advisory Committee.,Central Michigan University, Mt. Pleasant, Michigan
| | - Jennifer Zaspel
- Biodiversity Collections Network Advisory Committee.,Milwaukee Public Museum, Milwaukee, Wisconsin
| | - Elizabeth R Ellwood
- La Brea Tar Pits and Museum, Natural History Museum of Los Angeles County, Los Angeles, California
| | - Andrew Bentley
- Biodiversity Collections Network Advisory Committee.,University of Kansas Natural History Museum, Lawrence, Kansas
| | - Katherine LeVan
- New York Botanical Garden, Bronx, New York.,National Ecological Observatory Network, Boulder, Colorado
| | - John Bates
- Biodiversity Collections Network Advisory Committee.,Integrative Research Center, Field Museum of Natural History, Chicago, Illinois
| | - David Jennings
- Biodiversity Collections Network Advisory Committee.,Florida Museum of Natural History, University of Florida, Gainesville, Florida
| | | | | | - Paula Mabee
- University of South Dakota, Vermillion, South Dakota
| | - Linda S Ford
- Biodiversity Collections Network Advisory Committee.,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts
| | - Robert Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, Florida
| | - Robert E Gropp
- Biodiversity Collections Network Advisory Committee.,American Institute of Biological Sciences, Washington, DC
| | | | - Neil Cobb
- Merriam-Powell Center, Northern Arizona University, Flagstaff, Arizona
| | - Katja Seltmann
- Cheadle Center for Biodiversity and Ecological Restoration, University of California, Santa Barbara
| | - M Catherine Aime
- Purdue University Herbaria, Purdue University, West Lafayette, Indiana
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18
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Heberling JM, Prather LA, Tonsor SJ. The Changing Uses of Herbarium Data in an Era of Global Change: An Overview Using Automated Content Analysis. Bioscience 2019. [DOI: 10.1093/biosci/biz094] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
Widespread specimen digitization has greatly enhanced the use of herbarium data in scientific research. Publications using herbarium data have increased exponentially over the last century. Here, we review changing uses of herbaria through time with a computational text analysis of 13,702 articles from 1923 to 2017 that quantitatively complements traditional review approaches. Although maintaining its core contribution to taxonomic knowledge, herbarium use has diversified from a few dominant research topics a century ago (e.g., taxonomic notes, botanical history, local observations), with many topics only recently emerging (e.g., biodiversity informatics, global change biology, DNA analyses). Specimens are now appreciated as temporally and spatially extensive sources of genotypic, phenotypic, and biogeographic data. Specimens are increasingly used in ways that influence our ability to steward future biodiversity. As we enter the Anthropocene, herbaria have likewise entered a new era with enhanced scientific, educational, and societal relevance.
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Affiliation(s)
| | - L Alan Prather
- Department of Plant Biology at Michigan State University
| | - Stephen J Tonsor
- Director of Science & Research, Carnegie Museum of Natural History
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19
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Hogan J, Bass AIH, Zhang YM, Sharanowski BJ. Integrating multiple sources of biodiversity information greatly expands the range of a rare species of Hymenoptera (Vanhorniidae). Biodivers Data J 2019; 7:e37569. [PMID: 31360098 PMCID: PMC6650442 DOI: 10.3897/bdj.7.e37569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 07/12/2019] [Indexed: 11/12/2022] Open
Abstract
Background Vanhorniaeucnemidarum Crawford is the only species of Vanhorniidae that occurs in North America. This species is rarely collected and thus the distribution is not well documented. Intending to uncover a more accurate range of this species, we assembled collection records from museums, personal collections and citizen science projects. Many of these records were non-digitised and had to be personally requested. New information Here we expand the known distribution of V.eucnemidarum to include nine new provinces and states: Manitoba, Connecticut, Oregon, Mississippi, Missouri, New Hampshire, New Jersey, Texas and Wisconsin. Although Quebec has been listed as a previous locality, the recorded province was mislabelled, so Quebec is now also officially a provincial record.
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Affiliation(s)
- Joshua Hogan
- University of Central Florida, Orlando, United States of America University of Central Florida Orlando United States of America
| | - Amber I H Bass
- University of Central Florida, Orlando, United States of America University of Central Florida Orlando United States of America
| | - Y Miles Zhang
- University of Florida, Gainesville, United States of America University of Florida Gainesville United States of America
| | - Barbara J Sharanowski
- University of Central Florida, Orlando, United States of America University of Central Florida Orlando United States of America
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20
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Affiliation(s)
- Joseph A Cook
- Biology Department and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Jessica E Light
- Department of Wildlife and Fisheries Sciences and Biodiversity Research and Teaching Collections, Texas A&M University, College Station, TX, USA
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21
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Yeung NW, Hayes KA. Biodiversity and Extinction of Hawaiian Land Snails: How Many Are Left Now and What Must We Do To Conserve Them—A Reply to Solem (1990). Integr Comp Biol 2018; 58:1157-1169. [DOI: 10.1093/icb/icy043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Norine W Yeung
- Bishop Museum, Honolulu, HI 96817, USA
- Pacific Biosciences Research Center, University of Hawaii at Manoa, 2500 Campus Road, Honolulu, HI 96822, USA
| | - Kenneth A Hayes
- Bishop Museum, Honolulu, HI 96817, USA
- Pacific Biosciences Research Center, University of Hawaii at Manoa, 2500 Campus Road, Honolulu, HI 96822, USA
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22
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Digitization of museum collections holds the potential to enhance researcher diversity. Nat Ecol Evol 2017; 1:1789-1790. [DOI: 10.1038/s41559-017-0401-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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