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Astudillo-Clavijo V, Varella H, Mankis T, López-Fernández H. Historical Field Records Reveal Habitat as an Ecological Correlate of Locomotor Phenotypic Diversity in the Radiation of Neotropical Geophagini Fishes. Am Nat 2024; 204:147-164. [PMID: 39008839 DOI: 10.1086/730783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
AbstractPhenotypic macroevolutionary studies provide insight into how ecological processes shape biodiversity. However, the complexity of phenotype-ecology relationships underscores the importance of also validating phenotype-based ecological inference with direct evidence of resource use. Unfortunately, macroevolutionary-scale ecological studies are often hindered by the challenges of acquiring taxonomically and spatially representative ecological data for large and widely distributed clades. The South American cichlid fish tribe Geophagini represents a continentally distributed radiation whose early locomotor morphological divergence suggests habitat as one ecological correlate of diversification, but an association between locomotor traits and habitat preference has not been corroborated. Field notes accumulated over decades of collecting across South America provide firsthand environmental records that can be mined for habitat data in support of macroevolutionary ecological research. In this study, we applied a newly developed method to transform descriptive field note information into quantitative habitat data and used it to assess habitat preference and its relationship to locomotor morphology in Geophagini. Field note-derived data shed light on geophagine habitat use patterns and reinforced habitat as an ecological correlate of locomotor morphological diversity. Our work emphasizes the rich data potential of museum collections, including often-overlooked material such as field notes, for evolutionary and ecological research.
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Astudillo-Clavijo V, Mankis T, López-Fernández H. Opening the Museum's Vault: Historical Field Records Preserve Reliable Ecological Data. Am Nat 2024; 203:305-322. [PMID: 38358812 DOI: 10.1086/728422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
AbstractMuseum specimens have long served as foundational data sources for ecological, evolutionary, and environmental research. Continued reimagining of museum collections is now also generating new types of data associated with but beyond physical specimens, a concept known as "extended specimens." Field notes penned by generations of naturalists contain firsthand ecological observations associated with museum collections and comprise a form of extended specimens with the potential to provide novel ecological data spanning broad geographic and temporal scales. Despite their data-yielding potential, however, field notes remain underutilized in research because of their heterogeneous, unstandardized, and qualitative nature. We introduce an approach for transforming descriptive ecological notes into quantitative data suitable for statistical analysis. Tests with simulated and real-world published data show that field notes and our transformation approach retain reliable quantitative ecological information under a range of sample sizes and evolutionary scenarios. Unlocking the wealth of data contained within field records could facilitate investigations into the ecology of clades whose diversity, distribution, or other demographic features present challenges to traditional ecological studies, improve our understanding of long-term environmental and evolutionary change, and enhance predictions of future change.
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3
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Novikov A, Savytska A, Kuzyarin O, Nachychko V, Susulovska S, Rizun V, Susulovsky A, Hushtan H, Hushtan K, Leleka D. Data mobilisation in the LWS Herbarium: success and prospects. Biodivers Data J 2024; 12:e117292. [PMID: 38249570 PMCID: PMC10797612 DOI: 10.3897/bdj.12.e117292] [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: 12/13/2023] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
Background Digitisation of hosted specimens is a crucial task for all herbaria worldwide and is one of the main streams for today. By digitising their collections and publishing the datasets, the herbaria grant access to essential data to a wide research audience and, as a result, involve their collections in scientific work more actively. Digitisation also allows virtual preservation of the collections, which is especially important in conditions of hostilities, when the entire collection can be destroyed or damaged in one moment. This paper describes two datasets recently published in GBIF in the framework of the LWS herbarium digitisation initiative. It also contains some considerations about further digitisation priorities and plans in the LWS Herbarium in the context of complicated war conditions and limited facilities. New information In total, 2,419 occurrence records from Ukraine mobilised from LWS Herbarium were published. These datasets are planned to be dynamic with the addition of new records along with progress of digitisation work at LWS. At least 6,000 more records are planned to be published through these datasets in 2024.
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Affiliation(s)
- Andriy Novikov
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Anastasiia Savytska
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Oleksandr Kuzyarin
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Viktor Nachychko
- Ivan Franko National University of Lviv, Lviv, UkraineIvan Franko National University of LvivLvivUkraine
| | - Solomia Susulovska
- Ivan Franko National University of Lviv, Lviv, UkraineIvan Franko National University of LvivLvivUkraine
| | - Volodymyr Rizun
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Andrii Susulovsky
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Habriel Hushtan
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Kateryna Hushtan
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Dmytro Leleka
- Institute of Ecology of the Carpathians of the NAS of Ukraine, Lviv, UkraineInstitute of Ecology of the Carpathians of the NAS of UkraineLvivUkraine
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Kralick AE, Canington SL, Eller AR, McGrath K. Specimens as individuals: Four interventions and recommendations for great ape skeletal collections research and curation. Evol Anthropol 2023; 32:336-355. [PMID: 37750542 DOI: 10.1002/evan.22002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 04/14/2023] [Accepted: 08/01/2023] [Indexed: 09/27/2023]
Abstract
Extensive discourse surrounds the ethics of human skeletal research and curation, but there has yet to be a similar discussion of the treatment of great ape skeletal remains, despite the clear interest in their ethical treatment when alive. Here we trace the history of apes who were killed and collected for natural history museums during the early 20th century and showcase how the guiding research questions of the colonial era continue to influence scholarship. We discuss best practices for improving industry and academic standards of research on, and the curation of, ape remains. The suggested interventions involve restoring individual identity and narrative to great apes while engaging with contextual reflexivity and decolonial theory. The resulting recommendations include contextualizing the individual, piecing individuals back together, challenging/questioning the captive-wild dichotomy, and collaborative international conversations. Our objective is to encourage a conversation regarding ethical and theoretical considerations in great ape skeletal remains research.
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Affiliation(s)
- Alexandra E Kralick
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephanie L Canington
- Center for Functional Anatomy and Evolution, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Basic and Translational Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrea R Eller
- Department of Anthropology, Smithsonian National Museum of Natural History, Washington, District of Columbia, USA
| | - Kate McGrath
- Department of Anthropology, SUNY Oneonta, Oneonta, New York, USA
- Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, District of Columbia, USA
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5
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Nanglu K, de Carle D, Cullen TM, Anderson EB, Arif S, Castañeda RA, Chang LM, Iwama RE, Fellin E, Manglicmot RC, Massey MD, Astudillo‐Clavijo V. The nature of science: The fundamental role of natural history in ecology, evolution, conservation, and education. Ecol Evol 2023; 13:e10621. [PMID: 37877102 PMCID: PMC10591213 DOI: 10.1002/ece3.10621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
There is a contemporary trend in many major research institutions to de-emphasize the importance of natural history education in favor of theoretical, laboratory, or simulation-based research programs. This may take the form of removing biodiversity and field courses from the curriculum and the sometimes subtle maligning of natural history research as a "lesser" branch of science. Additional threats include massive funding cuts to natural history museums and the maintenance of their collections, the extirpation of taxonomists across disciplines, and a critical under-appreciation of the role that natural history data (and other forms of observational data, including Indigenous knowledge) play in the scientific process. In this paper, we demonstrate that natural history knowledge is integral to any competitive science program through a comprehensive review of the ways in which they continue to shape modern theory and the public perception of science. We do so by reviewing how natural history research has guided the disciplines of ecology, evolution, and conservation and how natural history data are crucial for effective education programs and public policy. We underscore these insights with contemporary case studies, including: how understanding the dynamics of evolutionary radiation relies on natural history data; methods for extracting novel data from museum specimens; insights provided by multi-decade natural history programs; and how natural history is the most logical venue for creating an informed and scientifically literate society. We conclude with recommendations aimed at students, university faculty, and administrators for integrating and supporting natural history in their mandates. Fundamentally, we are all interested in understanding the natural world, but we can often fall into the habit of abstracting our research away from its natural contexts and complexities. Doing so risks losing sight of entire vistas of new questions and insights in favor of an over-emphasis on simulated or overly controlled studies.
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Affiliation(s)
- Karma Nanglu
- Museum of Comparative Zoology and Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMassachusettsUSA
| | - Danielle de Carle
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of Invertebrate ZoologyRoyal Ontario MuseumTorontoOntarioCanada
| | - Thomas M. Cullen
- Department of GeosciencesAuburn UniversityAuburnAlabamaUSA
- Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Erika B. Anderson
- The HunterianUniversity of GlasgowGlasgowUK
- Department of Earth and SpaceRoyal Ontario MuseumTorontoOntarioCanada
| | - Suchinta Arif
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Rowshyra A. Castañeda
- Ecosystems and Ocean SciencesPacific Region, Fisheries and Oceans CanadaSidneyBritish ColumbiaCanada
| | | | - Rafael Eiji Iwama
- Departamento de Genética e Biologia Evolutiva, Instituto de BiociênciasUniversidade de São PauloSão PauloBrazil
| | - Erica Fellin
- Department of BiologyMcGill UniversityMontrealQuebecCanada
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Daru BH, Rodriguez J. Mass production of unvouchered records fails to represent global biodiversity patterns. Nat Ecol Evol 2023:10.1038/s41559-023-02047-3. [PMID: 37127769 DOI: 10.1038/s41559-023-02047-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/26/2023] [Indexed: 05/03/2023]
Abstract
The ever-increasing human footprint even in very remote places on Earth has inspired efforts to document biodiversity vigorously in case organisms go extinct. However, the data commonly gathered come from either primary voucher specimens in a natural history collection or from direct field observations that are not traceable to tangible material in a museum or herbarium. Although both datasets are crucial for assessing how anthropogenic drivers affect biodiversity, they have widespread coverage gaps and biases that may render them inefficient in representing patterns of biodiversity. Using a large global dataset of around 1.9 billion occurrence records of terrestrial plants, butterflies, amphibians, birds, reptiles and mammals, we quantify coverage and biases of expected biodiversity patterns by voucher and observation records. We show that the mass production of observation records does not lead to higher coverage of expected biodiversity patterns but is disproportionately biased toward certain regions, clades, functional traits and time periods. Such coverage patterns are driven by the ease of accessibility to air and ground transportation, level of security and extent of human modification at each sampling site. Conversely, voucher records are vastly infrequent in occurrence data but in the few places where they are sampled, showed relative congruence with expected biodiversity patterns for all dimensions. The differences in coverage and bias by voucher and observation records have important implications on the utility of these records for research in ecology, evolution and conservation research.
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Affiliation(s)
- Barnabas H Daru
- Department of Biology, Stanford University, Stanford, CA, USA.
| | - Jordan Rodriguez
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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7
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Museomics Provides Insights into Conservation and Education: The Instance of an African Lion Specimen from the Museum of Zoology “Pietro Doderlein”. DIVERSITY 2023. [DOI: 10.3390/d15010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Innovative technological approaches are crucial to enhance naturalistic museum collections and develop information repositories of relevant interest to science, such as threatened animal taxa. In this context, museomics is an emerging discipline that provides a novel approach to the enhancement and exploitation of these collections. In the present study, the discovery of a neglected lion skeleton in the Museum of Zoology “Pietro Doderlein” of the University of Palermo (Italy) offered the opportunity to undertake a multidisciplinary project. The aims of the study consisted of the following: (i) adding useful information for museographic strategies, (ii) obtaining a new genetic data repository from a vulnerable species, (iii) strengthening public awareness of wildlife conservation, and (iv) sharing new learning material. The remains of the lion were examined with a preliminary osteological survey, then they were restored by means of 3D printing of missing skeletal fragments. Phylogenetic analyses based on cytochrome b sequence clearly indicate that the specimen belongs to the Central Africa mitochondrial clade. At the end of the study, the complete and restored skeleton was exhibited, along with all of the information and data available from this project. This study shows a useful approach for the restoration and enhancement of a museum specimen, with important opportunities for preserving biodiversity and driving specific conservation policies, but also for providing Life Science learning material.
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Howard A, Monadjem A, MacFadyen D, Chimimba CT. Testing the efficacy of bat monitoring methods for identification and species surveys in KwaZulu-Natal province, South Africa. AFRICAN ZOOLOGY 2022. [DOI: 10.1080/15627020.2022.2138722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Alexandra Howard
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- Department of Zoology and Entomology, University of the Free State, Phuthaditjhaba, South Africa
| | - Ara Monadjem
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- Department of Biological Sciences, University of Eswatini, Kwaluseni, Eswatini
| | - Duncan MacFadyen
- Department of Research and Conservation, Oppenheimer Generations, Johannesburg, South Africa
| | - Christian T Chimimba
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- DSI-NRF Centre of Excellence for Invasion Biology (CIB), Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
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9
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Amarilla-Stevens HN, Stevens RD, Phillips CD, Bradley RD. Temporal rate of postmortem DNA degradation in archived tissue samples: evidence from liver and muscle. J Mammal 2022. [DOI: 10.1093/jmammal/gyac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Guidelines identifying best practices for harvesting tissues that lead to optimal DNA preservation are few but are important curatorial concerns for genetic resource collections. We conducted a temporal study to establish rate of DNA degradation of tissue samples extracted from field-caught museum specimens. Five individuals of Sigmodon hispidus were collected and their liver and muscle tissues were harvested. Each tissue type was sectioned into 15 subsamples, and each was preserved in liquid nitrogen at different time intervals (2, 4, 8, 16, and 32 min; 1, 2, 4, 8, and 16 h; and 1, 2, 4, 8, and 16 days) following death. DNA was extracted using an automated robotic instrument and molecular mass profiles were determined fluorometrically. Postmortem DNA degradation was continuous and dependent on time, but also was significantly affected by differences among individual cotton rats. DNA fragments of ≥10,000 base pairs in length were present in muscle samples across all time intervals, whereas DNA fragments of this size in liver samples were no longer present after 8–16 h postmortem. DNA molecular mass profiles showed that muscle samples retained 80% of their longest fragments (≥10,000 base pairs) until 1 day postmortem, whereas liver samples retained the same percentage only until 8 min after death. Although rates of decay were measured from samples in a laboratory (not field) setting, rates of decay presented here can guide field and museum workers in best practices. Results suggest that opportunistic samples, such as those from roadkill specimens, are more likely to be of use for a variety of molecular methods when muscle is preserved. Considerations of differences in rates of degradation may also guide selection of tissue types housed in genetic resource collections, especially under space-limited circumstances.
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Affiliation(s)
- Heidi N Amarilla-Stevens
- Natural Science Research Laboratory, Museum of Texas Tech University , Lubbock, Texas 79409-3131 , USA
| | - Richard D Stevens
- Natural Science Research Laboratory, Museum of Texas Tech University , Lubbock, Texas 79409-3131 , USA
- Department of Natural Resources Management, Texas Tech University , Lubbock, Texas 79409-3131 , USA
| | - Caleb D Phillips
- Natural Science Research Laboratory, Museum of Texas Tech University , Lubbock, Texas 79409-3131 , USA
- Department of Biological Sciences, Texas Tech University , Lubbock, Texas 79409-3131 , USA
| | - Robert D Bradley
- Natural Science Research Laboratory, Museum of Texas Tech University , Lubbock, Texas 79409-3131 , USA
- Department of Biological Sciences, Texas Tech University , Lubbock, Texas 79409-3131 , USA
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10
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Castañeda-Rico S, Edwards CW, Hawkins MTR, Maldonado JE. Museomics and the holotype of a critically endangered cricetid rodent provide key evidence of an undescribed genus. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.930356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Historical DNA obtained from voucher specimens housed in natural history museums worldwide have allowed the study of elusive, rare or even extinct species that in many cases are solely represented by museum holdings. This has resulted in the increase of taxonomic representation of many taxa, has led to the discovery of new species, and has yielded stunning novel insights into the evolutionary history of cryptic or even undescribed species. Peromyscus mekisturus, is a critically endangered cricetid rodent endemic to Mexico and is only known from two museum specimens collected in 1898 and 1947. Intensive field work efforts to attempt to determine if viable populations still exist have failed, suggesting that this species is extinct or is nearing extinction. In addition, a recent study using mitogenomes demonstrated that P. mekisturus forms a well-supported clade outside the genus Peromyscus and hypothesized that this taxon is the sister group of the genus Reithrodontomys. Here, we used target enrichment and high-throughput sequencing of several thousand nuclear ultraconserved elements and mitogenomes to reconstruct dated phylogenies to test the previous phylogenetic hypothesis. We analyzed the holotype and the only other known specimen of P. mekisturus and museum samples from other peromyscine rodents to test the phylogenetic position of the species. Our results confirm that the only two specimens known to science of P. mekisturus belong to the same species and support the hypothesis that this species belongs to an undescribed genus of cricetid rodents that is sister to the genus Reithrodontomys. We dated the origin of P. mekisturus together with other speciation events in peromyscines during the late Pliocene – early Pleistocene and related these events with the Pleistocene climatic cycles. In light of our results, we recommend a taxonomic re-evaluation of this enigmatic species to properly recognize its taxonomic status as a new genus. We also acknowledge the relevance of generating genomic data from type specimens and highlight the need and importance of continuing to build the scientific heritage of the collections to study and better understand past, present, and future biodiversity.
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11
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González-Toral C, Cires E. Relevance of DNA preservation for future botany and ecology. Mol Ecol 2022; 31:5125-5131. [PMID: 36214196 DOI: 10.1111/mec.16652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/20/2022] [Accepted: 08/03/2022] [Indexed: 12/15/2022]
Abstract
The use of molecular methods in plant systematics and taxonomy has increased during the last decades; however, the accessibility of curated genetic samples and their metadata is a bottleneck for DNA-based genetic studies in botany. Plant biodiversity DNA banks and DNA-friendly collections could be critical suppliers of curated genetic material for researchers in the current context of plant biodiversity loss. Here, we aimed to understand the potential of plant DNA banks and DNA-friendly collections to enhance the growth and openness of scientific knowledge. The preservation of genetic material should become part of a natural collection's process for the generation of extended specimens enabling the preservation of both the phenotype and genotype and contributing to the generation of data networks which cross-fertilize other fields. These curated collections are advantageous in endangered species research, detecting processes related to extinction, giving a genetic dimension to IUCN assessments or completing the Leipzig Catalogue of Vascular Plants. Therefore, DNA collections are fundamental in producing FAIR data, responsible research and innovation (RRI) and meeting the goals of international conservation programmes. The completion of natural collections is important for current research efforts and furthermore vital to support future research in an era of ongoing plant biodiversity loss.
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Affiliation(s)
| | - Eduardo Cires
- Department of Organisms and Systems Biology, University of Oviedo, Oviedo, Spain.,Institute of Natural Resources and Territorial Planning (INDUROT), Mieres, Spain
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12
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Halsey MK, Stuhler JD, Bayona-Vásquez NJ, Platt RN, Goetze JR, Martin RE, Matocha KG, Bradley RD, Stevens RD, Ray DA. Comparison of genetic variation between rare and common congeners of Dipodomys with estimates of contemporary and historical effective population size. PLoS One 2022; 17:e0274554. [PMID: 36099283 PMCID: PMC9469943 DOI: 10.1371/journal.pone.0274554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Species with low effective population sizes are at greater risk of extinction because of reduced genetic diversity. Such species are more vulnerable to chance events that decrease population sizes (e.g. demographic stochasticity). Dipodomys elator, (Texas kangaroo rat) is a kangaroo rat that is classified as threatened in Texas and field surveys from the past 50 years indicate that the distribution of this species has decreased. This suggests geographic range reductions that could have caused population fluctuations, potentially impacting effective population size. Conversely, the more common and widespread D. ordii (Ord’s kangaroo rat) is thought to exhibit relative geographic and demographic stability. We assessed the genetic variation of D. elator and D. ordii samples using 3RAD, a modified restriction site associated sequencing approach. We hypothesized that D. elator would show lower levels of nucleotide diversity, observed heterozygosity, and effective population size when compared to D. ordii. We were also interested in identifying population structure within contemporary samples of D. elator and detecting genetic variation between temporal samples to understand demographic dynamics. We analyzed up to 61,000 single nucleotide polymorphisms. We found that genetic variability and effective population size in contemporary D. elator populations is lower than that of D. ordii. There is slight, if any, population structure within contemporary D. elator samples, and we found low genetic differentiation between spatial or temporal historical samples. This indicates little change in nuclear genetic diversity over 30 years. Results suggest that genetic diversity of D. elator has remained stable despite reduced population size and/or abundance, which may indicate a metapopulation-like system, whose fluctuations might counteract species extinction.
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Affiliation(s)
- Michaela K. Halsey
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
- Department of Natural Resources Management, Texas Tech University, Lubbock, Texas, United States of America
| | - John D. Stuhler
- Department of Natural Resources Management, Texas Tech University, Lubbock, Texas, United States of America
| | - Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Roy N. Platt
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Jim R. Goetze
- Natural Sciences Department, Laredo College, Laredo, Texas, United States of America
| | - Robert E. Martin
- Department of Biology, McMurry University, Abilene, Texas, United States of America
| | - Kenneth G. Matocha
- Department of Biology, South Arkansas Community College, El Dorado, Arkansas, United States of America
| | - Robert D. Bradley
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
- Natural Science Research Laboratory, Museum of Texas Tech, Lubbock, Texas, United States of America
| | - Richard D. Stevens
- Department of Natural Resources Management, Texas Tech University, Lubbock, Texas, United States of America
- Natural Science Research Laboratory, Museum of Texas Tech, Lubbock, Texas, United States of America
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
- * E-mail:
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13
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Phillips LM, Leihy RI, Chown SL. Improving species-based area protection in Antarctica. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13885. [PMID: 35040183 DOI: 10.1111/cobi.13885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/13/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Area protection is a major mechanism deployed for environmental conservation in Antarctica. Yet, the Antarctic protected areas network is widely acknowledged as inadequate, in part because the criteria for area protection south of 60°S are not fully applied. The most poorly explored of these criteria is the type locality of species, which provides the primary legal means for Antarctic species-based area protection and a method for conserving species even if little is known about their habitat or distribution. The type locality criterion has not been systematically assessed since its incorporation into the Protocol on Environmental Protection to the Antarctic Treaty in 1991, so the extent to which the criterion is being met or might be useful for area protection is largely unknown. To address the matter, we created and analyzed a comprehensive database of Antarctic type localities of terrestrial and lacustrine lichens, plants, and animals. We compiled the database via a literature search of key taxonomic and geographic terms and then analyzed the distance between type localities identifiable to a ≤ 25km2 resolution and current Antarctic Specially Protected Areas (ASPAs) and human infrastructure. We used a distance-clustering approach for localities outside current ASPAs to determine candidate protected areas that could contain these unprotected localities. Of the 386 type localities analyzed, 108 were within or overlapped current ASPAs. Inclusion of the remaining 278 type localities in the ASPA network would require the designation of a further 105 protected areas. Twenty-four of these areas included human infrastructure disturbance. Given the slow rate of ASPA designation, growing pace of human impacts on the continent, and the management burden associated with ASPAs, we propose ways in which the type locality criterion might best be deployed. These include a comprehensive, systematic conservation planning approach and an alternative emphasis on the habitat of species, rather than on a single locality.
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Affiliation(s)
- Laura M Phillips
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Rachel I Leihy
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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14
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Irschick DJ, Christiansen F, Hammerschlag N, Martin J, Madsen P, Wyneken J, Brooks A, Gleiss A, Fossette S, Siler C, Gamble T, Fish F, Siebert U, Patel J, Xu Z, Kalogerakis E, Medina J, Mukherji A, Mandica M, Zotos S, Detwiler J, Perot B, Lauder G. 3D Visualization Processes for Recreating and Studying Organismal Form. iScience 2022; 25:104867. [PMID: 36060053 PMCID: PMC9437858 DOI: 10.1016/j.isci.2022.104867] [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: 11/20/2022] Open
Abstract
The study of biological form is a vital goal of evolutionary biology and functional morphology. We review an emerging set of methods that allow scientists to create and study accurate 3D models of living organisms and animate those models for biomechanical and fluid dynamic analyses. The methods for creating such models include 3D photogrammetry, laser and CT scanning, and 3D software. New multi-camera devices can be used to create accurate 3D models of living animals in the wild and captivity. New websites and virtual reality/augmented reality devices now enable the visualization and sharing of these data. We provide examples of these approaches for animals ranging from large whales to lizards and show applications for several areas: Natural history collections; body condition/scaling, bioinspired robotics, computational fluids dynamics (CFD), machine learning, and education. We provide two datasets to demonstrate the efficacy of CFD and machine learning approaches and conclude with a prospectus.
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15
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Bernstein JM, Ruane S. Maximizing Molecular Data From Low-Quality Fluid-Preserved Specimens in Natural History Collections. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.893088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Over the past decade, museum genomics studies have focused on obtaining DNA of sufficient quality and quantity for sequencing from fluid-preserved natural history specimens, primarily to be used in systematic studies. While these studies have opened windows to evolutionary and biodiversity knowledge of many species worldwide, published works often focus on the success of these DNA sequencing efforts, which is undoubtedly less common than obtaining minimal or sometimes no DNA or unusable sequence data from specimens in natural history collections. Here, we attempt to obtain and sequence DNA extracts from 115 fresh and 41 degraded samples of homalopsid snakes, as well as from two degraded samples of a poorly known snake, Hydrablabes periops. Hydrablabes has been suggested to belong to at least two different families (Natricidae and Homalopsidae) and with no fresh tissues known to be available, intractable museum specimens currently provide the only opportunity to determine this snake’s taxonomic affinity. Although our aim was to generate a target-capture dataset for these samples, to be included in a broader phylogenetic study, results were less than ideal due to large amounts of missing data, especially using the same downstream methods as with standard, high-quality samples. However, rather than discount results entirely, we used mapping methods with references and pseudoreferences, along with phylogenetic analyses, to maximize any usable molecular data from our sequencing efforts, identify the taxonomic affinity of H. periops, and compare sequencing success between fresh and degraded tissue samples. This resulted in largely complete mitochondrial genomes for five specimens and hundreds to thousands of nuclear loci (ultra-conserved loci, anchored-hybrid enrichment loci, and a variety of loci frequently used in squamate phylogenetic studies) from fluid-preserved snakes, including a specimen of H. periops from the Field Museum of Natural History collection. We combined our H. periops data with previously published genomic and Sanger-sequenced datasets to confirm the familial designation of this taxon, reject previous taxonomic hypotheses, and make biogeographic inferences for Hydrablabes. A second H. periops specimen, despite being seemingly similar for initial raw sequencing results and after being put through the same protocols, resulted in little usable molecular data. We discuss the successes and failures of using different pipelines and methods to maximize the products from these data and provide expectations for others who are looking to use DNA sequencing efforts on specimens that likely have degraded DNA.Life Science Identifier (Hydrablabes periops)urn:lsid:zoobank.org:pub:F2AA44 E2-D2EF-4747-972A-652C34C2C09D.
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16
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Hamer M, Behr K, Engelbrecht I, Richards L. Permit requirements, associated challenges and recommendations for biodiversity collections and research in South Africa. S AFR J SCI 2021. [DOI: 10.17159/sajs.2021/11765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Michelle Hamer
- Natural Science Collections Facility, South African National Biodiversity Institute, Pretoria, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Karin Behr
- Foundational Biodiversity Science, South African National Biodiversity Institute, Pretoria, South Africa
| | - Ian Engelbrecht
- Natural Science Collections Facility, South African National Biodiversity Institute, Pretoria, South Africa
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17
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Zacho CM, Bager MA, Margaryan A, Gravlund P, Galatius A, Rasmussen AR, Allentoft ME. Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes. PLoS One 2021; 16:e0256353. [PMID: 34424926 PMCID: PMC8382189 DOI: 10.1371/journal.pone.0256353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/04/2021] [Indexed: 11/19/2022] Open
Abstract
Natural history museum collections worldwide represent a tremendous resource of information on past and present biodiversity. Fish, reptiles, amphibians and many invertebrate collections have often been preserved in ethanol for decades or centuries and our knowledge on the genomic and metagenomic research potential of such material is limited. Here, we use ancient DNA protocols, combined with shotgun sequencing to test the molecular preservation in liver, skin and bone tissue from five old (1842 to 1964) museum specimens of the common garter snake (Thamnophis sirtalis). When mapping reads to a T. sirtalis reference genome, we find that the DNA molecules are highly damaged with short average sequence lengths (38-64 bp) and high C-T deamination, ranging from 9% to 21% at the first position. Despite this, the samples displayed relatively high endogenous DNA content, ranging from 26% to 56%, revealing that genome-scale analyses are indeed possible from all specimens and tissues included here. Of the three tested types of tissue, bone shows marginally but significantly higher DNA quality in these metrics. Though at least one of the snakes had been exposed to formalin, neither the concentration nor the quality of the obtained DNA was affected. Lastly, we demonstrate that these specimens display a diverse and tissue-specific microbial genetic profile, thus offering authentic metagenomic data despite being submerged in ethanol for many years. Our results emphasize that historical museum collections continue to offer an invaluable source of information in the era of genomics.
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Affiliation(s)
- Claus M. Zacho
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Martina A. Bager
- Section for EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Section for EvoGenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Anders Galatius
- Department of Bioscience, Aarhus University, Roskilde, Denmark
| | - Arne R. Rasmussen
- Institute of Conservation, Royal Danish Academy—Architecture, Design, Conservation, Copenhagen, Denmark
| | - Morten E. Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Australia
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18
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Buckner JC, Sanders RC, Faircloth BC, Chakrabarty P. The critical importance of vouchers in genomics. eLife 2021; 10:68264. [PMID: 34061026 PMCID: PMC8186901 DOI: 10.7554/elife.68264] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/26/2021] [Indexed: 12/16/2022] Open
Abstract
A voucher is a permanently preserved specimen that is maintained in an accessible collection. In genomics, vouchers serve as the physical evidence for the taxonomic identification of genome assemblies. Unfortunately, the vast majority of vertebrate genomes stored in the GenBank database do not refer to voucher specimens. Here, we urge researchers generating new genome assemblies to deposit voucher specimens in accessible, permanent research collections, and to link these vouchers to publications, public databases, and repositories. We also encourage scientists to deposit voucher specimens in order to recognize the work of local field biologists and promote a diverse and inclusive knowledge base, and we recommend best practices for voucher deposition to prevent taxonomic errors and ensure reproducibility and legality in genetic studies.
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Affiliation(s)
- Janet C Buckner
- Museum of Natural Science, Louisiana State University, Baton Rouge, United States
| | - Robert C Sanders
- Museum of Natural Science, Louisiana State University, Baton Rouge, United States
| | - Brant C Faircloth
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, United States
| | - Prosanta Chakrabarty
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, United States.,Carleton University, Ottawa, Canada.,American Museum of Natural History, New York, United States
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19
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Hilton EJ, Watkins-Colwell GJ, Huber SK. The Expanding Role of Natural History Collections. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/t2020018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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20
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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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21
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Ewers-Saucedo C, Allspach A, Barilaro C, Bick A, Brandt A, Fiege D, Füting S, Hausdorf B, Hayer S, Husemann M, Joger U, Kamcke C, Küster M, Lohrmann V, Martin I, Michalik P, Reinicke GB, Schwentner M, Stiller M, Brandis D. Natural history collections recapitulate 200 years of faunal change. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201983. [PMID: 33996123 PMCID: PMC8059531 DOI: 10.1098/rsos.201983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Changing species assemblages represent major challenges to ecosystems around the world. Retracing these changes is limited by our knowledge of past biodiversity. Natural history collections represent archives of biodiversity and are therefore an unparalleled source to study biodiversity changes. In the present study, we tested the value of natural history collections for reconstructing changes in the abundance and presence of species over time. In total, we scrutinized 17 080 quality-checked records for 242 epibenthic invertebrate species from the North and Baltic Seas collected throughout the last 200 years. Our approaches identified eight previously reported species introductions, 10 range expansions, six of which are new to science, as well as the long-term decline of 51 marine invertebrate species. The cross-validation of our results with published accounts of endangered species and neozoa of the area confirmed the results for two of the approaches for 49 to 55% of the identified species, and contradicted our results for 9 to 10%. The results based on relative record trends were less validated. We conclude that, with the proper approaches, natural history collections are an unmatched resource for recovering early species introductions and declines.
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Affiliation(s)
- Christine Ewers-Saucedo
- Zoologisches Museum, Christian-Albrechts-Universität zu Kiel, Hegewischstraße 3, 24105 Kiel, Germany
| | - Andreas Allspach
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Christina Barilaro
- Landesmuseum Natur und Mensch Oldenburg, Damm 38-44, 26135 Oldenburg, Germany
| | - Andreas Bick
- Zoological Collections of the University of Rostock, Institute for Biological Sciences, General and Systematic Zoology, Universitätsplatz 2, 18055 Rostock, Germany
| | - Angelika Brandt
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Goethe-University of Frankfurt, FB 15, Institute for Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60439 Frankfurt am Main, Germany
| | - Dieter Fiege
- Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Susanne Füting
- Museum für Natur und Umwelt Lübeck, Musterbahn 8, 23552 Lübeck, Germany
| | - Bernhard Hausdorf
- Centrum für Naturkunde (CeNak), Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Sarah Hayer
- Zoologisches Museum, Christian-Albrechts-Universität zu Kiel, Hegewischstraße 3, 24105 Kiel, Germany
| | - Martin Husemann
- Centrum für Naturkunde (CeNak), Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Ulrich Joger
- Staatliches Naturhistorisches Museum, Pockelsstraße 10, 38106 Braunschweig, Germany
| | - Claudia Kamcke
- Staatliches Naturhistorisches Museum, Pockelsstraße 10, 38106 Braunschweig, Germany
| | - Mathias Küster
- Müritzeum, Zur Steinmole 1, 17192 Waren (Müritz), Germany
| | - Volker Lohrmann
- Übersee-Museum Bremen, Bahnhofsplatz 13, 28195 Bremen, Germany
| | - Ines Martin
- Deutsches Meeresmuseum, Katharinenberg 14-20, 18439 Stralsund, Germany
| | - Peter Michalik
- Zoologisches Museum der Universität Greifswald, Loitzer Straße 26, 17489 Greifswald, Germany
| | | | - Martin Schwentner
- Centrum für Naturkunde (CeNak), Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
- Naturhistorisches Museum Wien, Burgring 7, 1140 Wien, Austria
| | - Michael Stiller
- Übersee-Museum Bremen, Bahnhofsplatz 13, 28195 Bremen, Germany
| | - Dirk Brandis
- Zoologisches Museum, Christian-Albrechts-Universität zu Kiel, Hegewischstraße 3, 24105 Kiel, Germany
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22
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Méndez M, Cortés-Fossati F. Relative Contribution of Citizen Science, Museum Data and Publications in Delineating the Distribution of the Stag Beetle in Spain. INSECTS 2021; 12:insects12030202. [PMID: 33673533 PMCID: PMC7997236 DOI: 10.3390/insects12030202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/17/2021] [Accepted: 02/23/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Conservation of insects requires a reliable knowledge of their distribution. Such knowledge is hard to obtain in many cases, due to lack of human power and funding for extensive surveys. Three ways out of this problem have been suggested: (1) data already available in museum collections, (2) data already available in the entomological literature and (3) use of citizen science projects as a cheap, efficient way to survey extensive territories. We assessed the contribution of each of these sources of information in delineating the Spanish distribution of the European stag beetle. Although citizen science quickly contributed more grid cells than the other sources, some grid cells were uniquely contributed by museum and publication data. Thus, the three sources of information need to be combined when targeting endangered species in a broad, heterogenous, sparsely populated territory such as Spain. Abstract Reliable distribution maps are in the basis of insect conservation, but detailed chorological information is lacking for many insects of conservation concern (the Wallacean shortfall). Museum collections, entomological publications and citizen science projects can contribute to solve this Wallacean shortfall. Their relative contribution to the knowledge on the distribution of threatened insects has been scarcely explored, but it is important given that each of these three sources of information has its own biases and costs. Here we explore the contribution of museum data, entomological publications and citizen science in delineating the distribution of the European stag beetle in Spain. Citizen science contributed the highest number of records and grid cells occupied, as well as the highest number of grid cells not contributed by any other information source (unique grid cells). Nevertheless, both museum data and publications contributed almost 25% of all unique grid cells. Furthermore, the relative contribution of each source of information differed in importance among Spanish provinces. Given the pros and cons of museum data, publications and citizen science, we advise their combined use in cases, such as the European stag beetle in Spain, in which a broad, heterogeneous, sparsely populated territory has to be prospected.
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23
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Thompson CW, Phelps KL, Allard MW, Cook JA, Dunnum JL, Ferguson AW, Gelang M, Khan FAA, Paul DL, Reeder DM, Simmons NB, Vanhove MPM, Webala PW, Weksler M, Kilpatrick CW. Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies. mBio 2021; 12:e02698-20. [PMID: 33436435 PMCID: PMC7844540 DOI: 10.1128/mbio.02698-20] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.
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Affiliation(s)
- Cody W Thompson
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Museum of Zoology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Marc W Allard
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, Maryland, USA
| | - Joseph A Cook
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Jonathan L Dunnum
- Museum of Southwestern Biology, Biology Department, University of New Mexico, Albuquerque, New Mexico, USA
| | - Adam W Ferguson
- Gantz Family Collections Center, Field Museum of Natural History, Chicago, Illinois, USA
| | - Magnus Gelang
- Gothenburg Natural History Museum, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Deborah L Paul
- Florida State University, Tallahassee, Florida, USA
- Species File Group, University of Illinois, Urbana-Champaign, Illinois, USA
| | | | - Nancy B Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Maarten P M Vanhove
- Hasselt University, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Diepenbeek, Belgium
| | - Paul W Webala
- Department of Forestry and Wildlife Management, Maasai Mara University, Narok, Kenya
| | - Marcelo Weksler
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Shultz AJ, Adams BJ, Bell KC, Ludt WB, Pauly GB, Vendetti JE. Natural history collections are critical resources for contemporary and future studies of urban evolution. Evol Appl 2021; 14:233-247. [PMID: 33519967 PMCID: PMC7819571 DOI: 10.1111/eva.13045] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 12/30/2022] Open
Abstract
Urban environments are among the fastest changing habitats on the planet, and this change has evolutionary implications for the organisms inhabiting them. Herein, we demonstrate that natural history collections are critical resources for urban evolution studies. The specimens housed in these collections provide great potential for diverse types of urban evolution research, and strategic deposition of specimens and other materials from contemporary studies will determine the resources and research questions available to future urban evolutionary biologists. As natural history collections are windows into the past, they provide a crucial historical timescale for urban evolution research. While the importance of museum collections for research is generally appreciated, their utility in the study of urban evolution has not been explicitly evaluated. Here, we: (a) demonstrate that museum collections can greatly enhance urban evolution studies, (b) review patterns of specimen use and deposition in the urban evolution literature, (c) analyze how urban versus rural and native versus nonnative vertebrate species are being deposited in museum collections, and (d) make recommendations to researchers, museum professionals, scientific journal editors, funding agencies, permitting agencies, and professional societies to improve archiving policies. Our analyses of recent urban evolution studies reveal that museum specimens can be used for diverse research questions, but they are used infrequently. Further, although nearly all studies we analyzed generated resources that could be deposited in natural history collections (e.g., collected specimens), a minority (12%) of studies actually did so. Depositing such resources in collections is crucial to allow the scientific community to verify, replicate, and/or re-visit prior research. Therefore, to ensure that adequate museum resources are available for future urban evolutionary biology research, the research community-from practicing biologists to funding agencies and professional societies-must make adjustments that prioritize the collection and deposition of urban specimens.
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Affiliation(s)
- Allison J. Shultz
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Ornithology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - Benjamin J. Adams
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Entomology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Department of Biological SciencesGeorge Washington UniversityWashingtonDCUSA
| | - Kayce C. Bell
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Mammalogy DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - William B. Ludt
- Ichthyology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - Gregory B. Pauly
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Herpetology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - Jann E. Vendetti
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Malacology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
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25
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Colella JP, Stephens RB, Campbell ML, Kohli BA, Parsons DJ, Mclean BS. The Open-Specimen Movement. Bioscience 2020. [DOI: 10.1093/biosci/biaa146] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Abstract
The open-science movement seeks to increase transparency, reproducibility, and access to scientific data. As primary data, preserved biological specimens represent records of global biodiversity critical to research, conservation, national security, and public health. However, a recent decrease in specimen preservation in public biorepositories is a major barrier to open biological science. As such, there is an urgent need for a cultural shift in the life sciences that normalizes specimen deposition in museum collections. Museums embody an open-science ethos and provide long-term research infrastructure through curation, data management and security, and community-wide access to samples and data, thereby ensuring scientific reproducibility and extension. We propose that a paradigm shift from specimen ownership to specimen stewardship can be achieved through increased open-data requirements among scientific journals and institutional requirements for specimen deposition by funding and permitting agencies, and through explicit integration of specimens into existing data management plan guidelines and annual reporting.
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Affiliation(s)
| | - Ryan B Stephens
- Department of Natural Resources and the Environment, University of New Hampshire, Durham
| | - Mariel L Campbell
- Museum of Southwestern Biology, Division of Genomic Resources, University of New Mexico, Albuquerque
| | - Brooks A Kohli
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus
| | - Danielle J Parsons
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus
| | - Bryan S Mclean
- Department of Biology, University of North Carolina, Greensboro
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26
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Bell RC, Mulcahy DG, Gotte SW, Maley AJ, Mendoza C, Steffensen G, Barron II JC, Hyman O, Flint W, Wynn A, Mcdiarmid RW, Mcleod DS. The Type Locality Project: collecting genomic-quality, topotypic vouchers and training the next generation of specimen-based researchers. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1769224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Rayna C. Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Daniel G. Mulcahy
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Steve W. Gotte
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- U. S. Geological Survey, Patuxent Wildlife Research Center, National Museum of Natural History, Museum Support Center, Suitland, MD 20746, USA
| | - Abigail J. Maley
- Biology Department, Eastern Mennonite University, Harrisonburg, VA 22802, USA
- Division of Integrated Sciences, Wilson College, Chambersburg, PA 17201, USA
| | - Cerrie Mendoza
- Biology Department, Eastern Mennonite University, Harrisonburg, VA 22802, USA
| | - Gregory Steffensen
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Joseph C. Barron II
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24060, USA
| | - Oliver Hyman
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - William Flint
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
| | - Addison Wynn
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Roy W. Mcdiarmid
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
- U. S. Geological Survey, Patuxent Wildlife Research Center, National Museum of Natural History, Museum Support Center, Suitland, MD 20746, USA
| | - David S. Mcleod
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
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27
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Strijk JS, Binh HT, Ngoc NV, Pereira JT, Slik JWF, Sukri RS, Suyama Y, Tagane S, Wieringa JJ, Yahara T, Hinsinger DD. Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea. PLoS One 2020; 15:e0232936. [PMID: 32442164 PMCID: PMC7244142 DOI: 10.1371/journal.pone.0232936] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 04/24/2020] [Indexed: 11/21/2022] Open
Abstract
Natural history collections and tropical tree diversity are both treasure troves of biological and evolutionary information, but their accessibility for scientific study is impeded by a number of properties. DNA in historical specimens is generally highly fragmented, complicating the recovery of high-grade genetic material. Furthermore, our understanding of hyperdiverse, wide-spread tree assemblages is obstructed by extensive species ranges, fragmented knowledge of tropical tree diversity and phenology, and a widespread lack of species-level diagnostic characters, prohibiting the collecting of readily identifiable specimens which can be used to build, revise or strengthen taxonomic frameworks. This, in turn, delays the application of downstream conservation action. A sizable component of botanical collections are sterile-thus eluding identification and are slowing down progress in systematic treatments of tropical biodiversity. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections that have been built up over centuries. Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci, for both freshly collected materials and museum specimens (aged >100 years) of Lithocarpus-a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from historical and recently collected samples was not affected by sample age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach. Phylogenomic inference and biogeographic reconstruction across insular Asia, highlights repeated migration and diversification patterns between continental regions and islands. Results indicate that co-occurring insular species at the extremity of the distribution range are not monophyletic, raising the possibility of multiple independent dispersals along the outer edge of Wallacea. This suggests that dispersal of large seeded tree genera throughout Malesia and across Wallacea may have been less affected by large geographic distances and the presence of marine barriers than generally assumed. We demonstrate the utility of MIGseq in museomic studies using non-model taxa, presenting the first range-wide genomic assessment of Lithocarpus and tropical Fagaceae as a proof-of-concept. Our study shows the potential for developing innovative genomic approaches to improve the capture of novel evolutionary signals using valuable natural history collections of hyperdiverse taxa.
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Affiliation(s)
- Joeri S. Strijk
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, China
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
- Alliance for Conservation Tree Genomics, Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
| | | | | | - Joan T. Pereira
- Sabah Forestry Department, Forest Research Centre, Sandakan, Sabah, Malaysia
| | - J. W. Ferry Slik
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Rahayu S. Sukri
- Environmental and Life Sciences Programme, Faculty of Science, Universiti Brunei Darussalam, Gadong, Brunei Darussalam
| | - Yoshihisa Suyama
- Kawatabi Field Science Centre, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Shuichiro Tagane
- The Kagoshima University Museum, Kagoshima University, Kagoshima, Japan
| | | | - Tetsukazu Yahara
- Center for Asian Conservation Ecology, Kyushu University, Fukuoka, Japan
| | - Damien D. Hinsinger
- Biodiversity Genomics Team, Plant Ecophysiology & Evolution Group, Guangxi Key Laboratory of Forest Ecology and Conservation, College of Forestry, Guangxi University, Nanning, Guangxi, China
- Alliance for Conservation Tree Genomics, Alliance for Conservation Tree Genomics, Pha Tad Ke Botanical Garden, Luang Prabang, Laos
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l′Énergie Atomique (CEA), CNRS, Université Évry, Université Paris-Saclay, Évry, France
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28
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Henningsen M, Peitzner G, Peitzner P, Husemann M. An updated checklist of type material of dragonflies and damselflies (Odonata) housed in the Zoological Museum Hamburg (ZMH), Germany. EVOLUTIONARY SYSTEMATICS 2020. [DOI: 10.3897/evolsyst.4.48407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We present an updated checklist of type specimens of dragonflies (Odonata: Anisoptera) and damselflies (Odonata: Zygoptera) housed in the collection of the Zoological Museum of Hamburg (ZMH), part of the Centrum für Naturkunde (CeNak), Hamburg, Germany. We list all types currently housed in the dry and wet collections of the museum and compare the current holdings to the previous catalogues provided by Weidner (1962, 1977). In total, the collection of the ZMH currently houses 84 type specimens belonging to 44 species (38 of which are still valid species); these include 17 holotypes, 7 syntypes, 4 lectotypes, 33 paratypes, and 23 paralectotypes. We here provide an updated list of Odonata types in the ZMH, which includes any changes in taxonomy, but also corrects mistakes of previous catalogues.
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29
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Arbeláez-Cortés E, Villamizar-Escalante D, Rondón-González F. On birds of Santander-Bio Expeditions, quantifying the cost of collecting voucher specimens in Colombia. ACTA BIOLÓGICA COLOMBIANA 2020. [DOI: 10.15446/abc.v25n1.77442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Several scientific reasons support continuing bird collection in Colombia, a megadiverse country with modest science financing. Despite the recognized value of biological collections for the rigorous study of biodiversity, there is scarce information on the monetary costs of specimens. We present results for three expeditions conducted in Santander (municipalities of Cimitarra, El Carmen de Chucurí, and Santa Barbara), Colombia, during 2018 to collect bird voucher specimens, quantifying the costs of obtaining such material. After a sampling effort of 1290 mist net hours and occasional collection using an airgun, we collected 300 bird voucher specimens, representing 117 species from 30 families. Such collection represents one of the largest series obtained during the historical ornithological exploration of Santander. We report differences among expeditions regarding the capture rate in mist nets, as well as differences in the sizes of taxa collected by mist nets and airgun. We discuss results in the context of previous ornithological expeditions in Colombia, commenting issues on the biology of some species, particularly those considered as noteworthy records (e.g., Red-legged Tinamou [Crypturellus erythropus], Cinnamon Screech Owl [Megascops petersoni], Saffron-headed Parrot [Pyrilia pyrilia], Black Inca [Coeligena prunellei], and Chestnut-crowned Gnateater [Conopophaga castaneiceps]). We calculated that the costs of obtaining and curating a specimen in Colombia, including tissues for molecular analysis, was ~US$60.4 (~$196 176 COP), which is among published costs of obtaining voucher specimens in other taxa and countries. These costs must be considered an investment in scientific capital because voucher specimens will provide biological information for hundreds of years.
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30
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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: 75] [Impact Index Per Article: 15.0] [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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31
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Muñoz-Rodríguez P, Carruthers T, Wood JRI, Williams BRM, Weitemier K, Kronmiller B, Goodwin Z, Sumadijaya A, Anglin NL, Filer D, Harris D, Rausher MD, Kelly S, Liston A, Scotland RW. A taxonomic monograph of Ipomoea integrated across phylogenetic scales. NATURE PLANTS 2019; 5:1136-1144. [PMID: 31712754 DOI: 10.1038/s41477-019-0535-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/23/2019] [Indexed: 05/21/2023]
Abstract
Taxonomic monographs have the potential to make a unique contribution to the understanding of global biodiversity. However, such studies, now rare, are often considered too daunting to undertake within a realistic time frame, especially as the world's collections have doubled in size in recent times. Here, we report a global-scale monographic study of morning glories (Ipomoea) that integrated DNA barcodes and high-throughput sequencing with the morphological study of herbarium specimens. Our approach overhauled the taxonomy of this megadiverse group, described 63 new species and uncovered significant increases in net diversification rates comparable to the most iconic evolutionary radiations in the plant kingdom. Finally, we show that more than 60 species of Ipomoea, including sweet potato, independently evolved storage roots in pre-human times, indicating that the storage root is not solely a product of human domestication but a trait that predisposed the species for cultivation. This study demonstrates how the world's natural history collections can contribute to global challenges in the Anthropocene.
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Affiliation(s)
| | - Tom Carruthers
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - John R I Wood
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Royal Botanic Gardens, Kew, Richmond, UK
| | | | - Kevin Weitemier
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Brent Kronmiller
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, USA
| | - Zoë Goodwin
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Alex Sumadijaya
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | - Denis Filer
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | - Mark D Rausher
- French Family Science Center, Duke University, Durham, NC, USA
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
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32
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Guevara L. Paleodistribution modelling for planning the growth of natural history collections. REV MEX BIODIVERS 2019. [DOI: 10.22201/ib.20078706e.2019.90.2953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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33
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Phillips CD, Dunnum JL, Dowler RC, Bradley LC, Garner HJ, MacDonald KA, Lim BK, Revelez MA, Campbell ML, Lutz HL, Garza NO, Cook JA, Bradley RD, Alvarez-Castañeda ST, Bradley JE, Bradley RD, Carraway LN, Carrera-E JP, Conroy CJ, Coyner BS, Demboski JR, Dick CW, Dowler RC, Doyle K, Dunnum JL, Esselstyn JA, Gutiérrez E, Hanson JD, Holahan PM, Holmes T, Iudica CA, Leite RN, Lee TE, Lim BK, Malaney JL, McLean BS, McLaren SB, Moncrief ND, Olson L, Ordóñez-Garza N, Phillips CD, Revelez MA, Rickart EA, Rogers DS, Thompson CW, Upham NS, Velazco PM. Curatorial guidelines and standards of the American Society of Mammalogists for collections of genetic resources. J Mammal 2019. [DOI: 10.1093/jmammal/gyz111] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
The Systematic Collections Committee of the American Society of Mammalogists advises curators and other personnel affiliated with natural history collections in matters relating to administration, curation, and accreditation of mammal specimens and their associated data. The Systematic Collections Committee also maintains a list of curatorial standards for managing a collection-accreditation program under the auspices of the American Society of Mammalogists. To date, the Systematic Collections Committee has provided guidance for the more traditional specimen collections (skin, skeletal, fluid, etc.) and specimen data management. Given the rapidly expanding role of genetic resources in biological research, the Systematic Collections Committee herein presents a series of formal guidelines and standards designed to assist collections professionals in the current best practices for curation and maintenance of collections of genetic resources, to ensure long-term integrity of the archived material, and to address personnel safety and guidelines for researchers and curatorial staff. These guidelines and standards are intended to provide constructive guidance and a mechanism of accreditation for collections that vary in scale and infrastructure.
El Comité de Colecciones Sistemáticas de la Sociedad Americana de Mastozoólogos asesora a curadores y demás personal afiliado a colecciones de historia natural en asuntos relacionados a la administración, curación y acreditación de especímenes de mamíferos y su información pertinente. El Comité de Colecciones Sistemáticas mantiene también una lista de normas curatoriales para la gestión de un programa de acreditación de colecciones auspiciados por la Sociedad Americana de Mastozoólogos. A la fecha, el Comité de Colecciones Sistemáticas ha proporcionado una guía para las colecciones de muestras tradicionales (piel, esqueleto, líquido, etc.) y el manejo de datos asociados a estos especímenes. Dado el rápido crecimiento del papel que desempeñan los recursos genéticos en investigaciones biológicas, el Comité de Colecciones Sistemáticas presenta en esta publicación una serie de pautas y estándares formales diseñados para ayudar a los profesionales de colecciones científicas en las mejores prácticas actuales para la conservación y mantenimiento de colecciones de recursos genéticos, a modo de garantizar la integridad a largo plazo del material archivado, y tratar sobre la seguridad del personal y directrices para investigadores y personal curatorial. Estas pautas y estándares tienen como objetivo proporcionar una orientación constructiva y un mecanismo de acreditación para colecciones que varían en escala e infraestructura.
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Affiliation(s)
- Caleb D Phillips
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
- Museum of Texas Tech University, Lubbock, TX, USA
| | - Jonathan L Dunnum
- Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Robert C Dowler
- Department of Biology and Angelo State Natural History Collections, Angelo State University, San Angelo, TX, USA
| | | | | | | | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
| | | | - Mariel L Campbell
- Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Holly L Lutz
- Field Museum of Natural History, Chicago, IL, USA
| | | | - Joseph A Cook
- Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Robert D Bradley
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
- Museum of Texas Tech University, Lubbock, TX, USA
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34
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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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35
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Bradley RD, Dowler RC. A century of mammal research: changes in research paradigms and emphases. J Mammal 2019. [DOI: 10.1093/jmammal/gyy147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Robert D Bradley
- Department of Biological Sciences, Texas Tech University, Lubbock, USA
- Museum of Texas Tech University, Lubbock, TX, USA
| | - Robert C Dowler
- Department of Biology, Angelo State University, San Angelo, TX, USA
- Angelo State Natural History Collections, Angelo State University, San Angelo, TX, USA
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36
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Dunnum JL, McLean BS, Dowler RC. Mammal collections of the Western Hemisphere: a survey and directory of collections. J Mammal 2018; 99:1307-1322. [PMID: 30538340 PMCID: PMC6283736 DOI: 10.1093/jmammal/gyy151] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/07/2018] [Indexed: 01/13/2023] Open
Abstract
As a periodic assessment of the mammal collection resource, the Systematic Collections Committee (SCC) of the American Society of Mammalogists undertakes decadal surveys of the collections held in the Western Hemisphere. The SCC surveyed 429 collections and compiled a directory of 395 active collections containing 5,275,155 catalogued specimens. Over the past decade, 43 collections have been lost or transferred and 38 new or unsurveyed collections were added. Growth in number of total specimens, expansion of genomic resource collections, and substantial gains in digitization and web accessibility were documented, as well as slight shifts in proportional representation of taxonomic groups owing to increasingly balanced geographic representation of collections relative to previous surveys. While we find the overall health of Western Hemisphere collections to be adequate in some areas, gaps in spatial and temporal coverage and clear threats to long-term growth and vitality of these resources have also been identified. Major expansion of the collective mammal collection resource along with a recommitment to appropriate levels of funding will be required to meet the challenges ahead for mammalogists and other users, and to ensure samples are broad and varied enough that unanticipated future needs can be powerfully addressed.
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Affiliation(s)
- Jonathan L Dunnum
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Bryan S McLean
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Robert C Dowler
- Department of Biology, Angelo State University, San Angelo, TX, USA
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37
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Morrison SA, Sillett TS, Funk WC, Ghalambor CK, Rick TC. California Island Rediscovery: Building an Archive to Improve Conservation Today and Equip the Historical Ecologist of Tomorrow. WEST N AM NATURALIST 2018. [DOI: 10.3398/064.078.0423] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Scott A. Morrison
- The Nature Conservancy, 201 Mission St., 4th Floor, San Francisco, CA 94105
| | - T. Scott Sillett
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, MRC 5503, Washington, DC 20013
| | - W. Chris Funk
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523
| | - Cameron K. Ghalambor
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523
| | - Torben C. Rick
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013
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38
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Abdelkrim J, Aznar-Cormano L, Fedosov AE, Kantor YI, Lozouet P, Phuong MA, Zaharias P, Puillandre N. Exon-Capture-Based Phylogeny and Diversification of the Venomous Gastropods (Neogastropoda, Conoidea). Mol Biol Evol 2018; 35:2355-2374. [DOI: 10.1093/molbev/msy144] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Jawad Abdelkrim
- Outils et Méthodes de la Systématique Intégrative (OMSI) UMS 2700, Muséum National d’Histoire Naturelle, Paris, France
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Laetitia Aznar-Cormano
- Outils et Méthodes de la Systématique Intégrative (OMSI) UMS 2700, Muséum National d’Histoire Naturelle, Paris, France
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Alexander E Fedosov
- A.N. Severtzov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninski prospect 33, 119071 Moscow, Russian Federation
| | - Yuri I Kantor
- A.N. Severtzov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninski prospect 33, 119071 Moscow, Russian Federation
| | - Pierre Lozouet
- Muséum National d’Histoire Naturelle, Direction des Collections, 55, rue Buffon, 75005 Paris, France
| | - Mark A Phuong
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Paul Zaharias
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP 26, 75005 Paris, France
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39
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Thines M, Crous PW, Aime MC, Aoki T, Cai L, Hyde KD, Miller AN, Zhang N, Stadler M. Ten reasons why a sequence-based nomenclature is not useful for fungi anytime soon. IMA Fungus 2018; 9:177-183. [PMID: 30018878 PMCID: PMC6048572 DOI: 10.5598/imafungus.2018.09.01.11] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/23/2018] [Indexed: 11/08/2022] Open
Abstract
The large number of species still to be discovered in fungi, together with an exponentially growing number of environmental sequences that cannot be linked to known taxa, has fuelled the idea that it might be necessary to formally name fungi on the basis of sequence data only. Here we object to this idea due to several shortcomings of the approach, ranging from concerns regarding reproducibility and the violation of general scientific principles to ethical issues. We come to the conclusion that sequence-based nomenclature is potentially harmful for mycology as a discipline. Additionally, a classification based on sequences as types is not within reach anytime soon, because there is a lack of consensus regarding common standards due to the fast pace at which sequencing technologies develop.
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Affiliation(s)
- Marco Thines
- Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60483 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Pedro W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - M. Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Takayuki Aoki
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Kevin D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, 59 Dudley Road, Foran Hall 201, New Brunswick, New Jersey 08901, USA
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz-Zentrum für Infektionsforschung, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
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40
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Mayfield TJ, Olimpo JT, Floyd KW, Greenbaum E. Collaborative Posters Develop Students' Ability to Communicate about Undervalued Scientific Resources to Nonscientists. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2018; 19:jmbe-19-21. [PMID: 29904523 PMCID: PMC5969409 DOI: 10.1128/jmbe.v19i1.1442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/27/2017] [Indexed: 06/08/2023]
Abstract
Scientists are increasingly called upon to communicate with the public, yet most never receive formal training in this area. Public understanding is particularly critical to maintaining support for undervalued resources such as biological collections, research data repositories, and expensive equipment. We describe activities carried out in an inquiry-driven organismal biology laboratory course designed to engage a diverse student body using biological collections. The goals of this cooperative learning experience were to increase students' ability to locate and comprehend primary research articles, and to communicate the importance of an undervalued scientific resource to nonscientists. Our results indicate that collaboratively created, research-focused informational posters are an effective tool for achieving these goals and may be applied in other disciplines or classroom settings.
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Affiliation(s)
- Teresa J. Mayfield
- Biodiversity Collections, The University of Texas at El Paso, El Paso, TX 79968
| | - Jeffrey T. Olimpo
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968
| | - Kevin W. Floyd
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968
| | - Eli Greenbaum
- Biodiversity Collections, The University of Texas at El Paso, El Paso, TX 79968
- Department of Biological Sciences, The University of Texas at El Paso, El Paso, TX 79968
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Hope AG, Sandercock BK, Malaney JL. Collection of Scientific Specimens: Benefits for Biodiversity Sciences and Limited Impacts on Communities of Small Mammals. Bioscience 2018. [DOI: 10.1093/biosci/bix141] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Arbeláez-Cortés E, Acosta-Galvis AR, DoNascimiento C, Espitia-Reina D, González-Alvarado A, Medina CA. Knowledge linked to museum specimen vouchers: measuring scientific production from a major biological collection in Colombia. Scientometrics 2017. [DOI: 10.1007/s11192-017-2461-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Morrison SA, Sillett TS, Funk WC, Ghalambor CK, Rick TC. Equipping the 22nd-Century Historical Ecologist. Trends Ecol Evol 2017. [PMID: 28645487 DOI: 10.1016/j.tree.2017.05.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Historical ecology provides information needed to understand contemporary conditions and make science-based resource management decisions. Gaps in historical records, however, can limit inquiries and inference. Unfortunately, the patchiness of data that poses challenges for today's historical ecologist may be similarly problematic for those in the future seeking to understand what are currently present-day conditions and trends, in part because of societal underinvestment in systematic collection and curation. We therefore highlight the generational imperative that contemporary scientists and managers individually have - especially in this era of tremendous global change - to ensure sufficient documentation of the past and current conditions of the places and resources to which they have access.
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Affiliation(s)
- Scott A Morrison
- The Nature Conservancy, 201 Mission St., 4th Floor, San Francisco, CA 94105, USA.
| | - T Scott Sillett
- Migratory Bird Center, Smithsonian Conservation Biology Institute, National Zoological Park, MRC 5503, Washington, DC 20013, USA
| | - W Chris Funk
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Cameron K Ghalambor
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - Torben C Rick
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, MRC 112, Washington, DC 20013, USA
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Meyer C, Weigelt P, Kreft H. Multidimensional biases, gaps and uncertainties in global plant occurrence information. Ecol Lett 2016; 19:992-1006. [DOI: 10.1111/ele.12624] [Citation(s) in RCA: 261] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/17/2016] [Accepted: 04/14/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Carsten Meyer
- Biodiversity, Macroecology and Conservation Biogeography Group; Faculty of Forest Sciences; University of Göttingen; Büsgenweg 1 37077 Göttingen Germany
- Synthesis Centre (sDiv); German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e 04103 Leipzig Germany
| | - Patrick Weigelt
- Biodiversity, Macroecology and Conservation Biogeography Group; Faculty of Forest Sciences; University of Göttingen; Büsgenweg 1 37077 Göttingen Germany
| | - Holger Kreft
- Biodiversity, Macroecology and Conservation Biogeography Group; Faculty of Forest Sciences; University of Göttingen; Büsgenweg 1 37077 Göttingen Germany
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Srivathsan A, Ang A, Vogler AP, Meier R. Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate. Front Zool 2016; 13:17. [PMID: 27103937 PMCID: PMC4839110 DOI: 10.1186/s12983-016-0150-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/14/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Rapid habitat loss and degradation are responsible for population decline in a growing number of species. Understanding the natural history of these species is important for designing conservation strategies, such as habitat enhancements or ex-situ conservation. The acquisition of observational data may be difficult for rare and declining species, but metagenomics and metabarcoding can provide novel kinds of information. Here we use these methods for analysing fecal samples from an endangered population of a colobine primate, the banded leaf monkey (Presbytis femoralis). RESULTS We conducted metagenomics via shotgun sequencing on six fecal samples obtained from a remnant population of P. femoralis in a species-rich rainforest patch in Singapore. Shotgun sequencing and identification against a plant barcode reference database reveals a broad dietary profile consisting of at least 53 plant species from 33 families. The diet includes exotic plant species and is broadly consistent with > 2 years of observational data. Metagenomics identified 15 of the 24 plant genera for which there is observational data, but also revealed at least 36 additional species. DNA traces for the diet species were recovered and identifiable in the feces despite long digestion times and a large number of potential food plants within the rainforest habitat (>700 species). We also demonstrate that metagenomics provides greater taxonomic resolution of food plant species by utilizing multiple genetic markers as compared to single-marker metabarcoding. In addition, full mitochondrial genomes of P. femoralis individuals were reconstructed from fecal metagenomic shotgun reads, showing very low levels of genetic diversity in the focal population, and the presence of gut parasites could also be confirmed. Metagenomics thus allows for the simultaneous assessment of diet, population genetics and gut parasites based on fecal samples. CONCLUSIONS Our study demonstrates that metagenomic shotgun sequencing of fecal samples can be successfully used to rapidly obtain natural history data for understudied species with a complex diet. We predict that metagenomics will become a routinely used tool in conservation biology once the cost per sample reduces to ~100 USD within the next few years.
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Affiliation(s)
- Amrita Srivathsan
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543 Singapore ; Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY UK ; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Andie Ang
- Department of Anthropology, University of Colorado Boulder, Boulder, CO 80302 USA
| | - Alfried P Vogler
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY UK ; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Rudolf Meier
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543 Singapore ; Lee Kong Chian Natural History Museum, 2 Conservatory Drive, Singapore, 117377 Singapore
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McLean BS, Bell KC, Dunnum JL, Abrahamson B, Colella JP, Deardorff ER, Weber JA, Jones AK, Salazar-Miralles F, Cook JA. Natural history collections-based research: progress, promise, and best practices. J Mammal 2016; 97:287-297. [PMID: 26989266 PMCID: PMC4794611 DOI: 10.1093/jmammal/gyv178] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 12/20/2022] Open
Abstract
Specimens and associated data in natural history collections (NHCs) foster substantial scientific progress. In this paper, we explore recent contributions of NHCs to the study of systematics and biogeography, genomics, morphology, stable isotope ecology, and parasites and pathogens of mammals. To begin to assess the magnitude and scope of these contributions, we analyzed publications in the Journal of Mammalogy over the last decade, as well as recent research supported by a single university mammal collection (Museum of Southwestern Biology, Division of Mammals). Using these datasets, we also identify weak links that may be hindering the development of crucial NHC infrastructure. Maintaining the vitality and growth of this foundation of mammalogy depends on broader engagement and support from across the scientific community and is both an ethical and scientific imperative given the rapidly changing environmental conditions on our planet.
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Affiliation(s)
- Bryan S. McLean
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA (BSM, KCB, JLD, BA, JPC, ERD, JAW, AKJ, FS-M, JAC)
| | - Kayce C. Bell
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA (BSM, KCB, JLD, BA, JPC, ERD, JAW, AKJ, FS-M, JAC)
| | - Jonathan L. Dunnum
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA (BSM, KCB, JLD, BA, JPC, ERD, JAW, AKJ, FS-M, JAC)
| | - Bethany Abrahamson
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA (BSM, KCB, JLD, BA, JPC, ERD, JAW, AKJ, FS-M, JAC)
| | - Jocelyn P. Colella
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA (BSM, KCB, JLD, BA, JPC, ERD, JAW, AKJ, FS-M, JAC)
| | - Eleanor R. Deardorff
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA (BSM, KCB, JLD, BA, JPC, ERD, JAW, AKJ, FS-M, JAC)
| | - Jessica A. Weber
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA (BSM, KCB, JLD, BA, JPC, ERD, JAW, AKJ, FS-M, JAC)
| | - Amanda K. Jones
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA (BSM, KCB, JLD, BA, JPC, ERD, JAW, AKJ, FS-M, JAC)
| | - Fernando Salazar-Miralles
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA (BSM, KCB, JLD, BA, JPC, ERD, JAW, AKJ, FS-M, JAC)
| | - Joseph A. Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA (BSM, KCB, JLD, BA, JPC, ERD, JAW, AKJ, FS-M, JAC)
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