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Stothut M, Mahla L, Backes L, Weber S, Avazzadeh A, Moradmand M, Krehenwinkel H. Recovering plant-associated arthropod communities by eDNA metabarcoding historical herbarium specimens. Curr Biol 2024; 34:4318-4324.e6. [PMID: 39197459 DOI: 10.1016/j.cub.2024.07.100] [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: 03/18/2024] [Revised: 06/01/2024] [Accepted: 07/30/2024] [Indexed: 09/01/2024]
Abstract
Natural history collections are a priceless resource for understanding patterns and processes of biodiversity change in the Anthropocene.1 Herbaria, which house millions of historical plant records from all over the globe, are particularly valuable to study population genetics of the plants themselves and to understand the assembly of plant-associated microbial communities.2 Here we test if herbaria can serve yet another essential purpose, namely to provide information on the historical assembly of plant-arthropod interactions. The specificity and temporal stability of these associations are poorly known.3 Considering their pivotal role in the assembly of terrestrial food webs,4 this knowledge is paramount to understanding the consequences of global change. We use environmental DNA (eDNA) metabarcoding to characterize communities of plant-associated arthropods from archived herbarium specimens of different ages and origins. The herbarium specimens yield arthropod DNA across various ecological guilds and trophic levels over multiple decades. In an experiment, we also show that the typical dry storage of plants in herbaria does not alter the recovered arthropod diversity and community composition. By analyzing a time series of leaf samples from a forest monitoring project, we then characterize changes in arthropod biodiversity over two decades, showing that archived plants can also provide the time series data that are urgently needed to understand arthropod declines.5 This use of herbaria and plant archives promises unprecedented insights into plant-arthropod interactions and revolutionizes our ability to monitor spatiotemporal changes in interaction diversity.
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Affiliation(s)
- Manuel Stothut
- Department of Biogeography, Trier University, Universitätsring 15, 54296 Trier, Rhineland-Palatinate, Germany
| | - Lisa Mahla
- Department of Biogeography, Trier University, Universitätsring 15, 54296 Trier, Rhineland-Palatinate, Germany
| | - Lennart Backes
- Department of Biogeography, Trier University, Universitätsring 15, 54296 Trier, Rhineland-Palatinate, Germany
| | - Sven Weber
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, 130 Mulford Hall #3114, Berkeley, CA 94720, USA
| | - Amirmohammad Avazzadeh
- Department of Plant and Animal Biology, University of Isfahan, Hezarjerib Avenue, 81746-73441 Isfahan, Iran
| | - Majid Moradmand
- Department of Biogeography, Trier University, Universitätsring 15, 54296 Trier, Rhineland-Palatinate, Germany; Department of Plant and Animal Biology, University of Isfahan, Hezarjerib Avenue, 81746-73441 Isfahan, Iran.
| | - Henrik Krehenwinkel
- Department of Biogeography, Trier University, Universitätsring 15, 54296 Trier, Rhineland-Palatinate, Germany.
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2
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Guedes JJM, Diniz-Filho JAF, Moura MR. Macroecological correlates of Darwinian shortfalls across terrestrial vertebrates. Biol Lett 2024; 20:20240216. [PMID: 39046287 PMCID: PMC11268159 DOI: 10.1098/rsbl.2024.0216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/25/2024] Open
Abstract
Most described species have not been explicitly included in phylogenetic trees-a problem named the Darwinian shortfall-owing to a lack of molecular and/or morphological data, thus hampering the explicit incorporation of evolution into large-scale biodiversity analyses. We investigate potential drivers of the Darwinian shortfall in tetrapods, a group in which at least one-third of described species still lack phylogenetic data, thus necessitating the imputation of their evolutionary relationships in fully sampled phylogenies. We show that the number of preserved specimens in scientific collections is the main driver of phylogenetic knowledge accumulation, highlighting the major role of biological collections in unveiling novel biodiversity data and the importance of continued sampling efforts to reduce knowledge gaps. Additionally, large-bodied and wide-ranged species, as well as terrestrial and aquatic amphibians and reptiles, are phylogenetically better known. Future efforts should prioritize phylogenetic research on organisms that are narrow-ranged, small-bodied and underrepresented in scientific collections, such as fossorial species. Addressing the Darwinian shortfall will be imperative for advancing our understanding of evolutionary drivers shaping biodiversity patterns and implementing comprehensive conservation strategies.
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Affiliation(s)
- Jhonny J. M. Guedes
- Departamento de Ecologia, Programa de Pós-Graduação em Ecologia e Evolução, Universidade Federal de Goiás—Campus Samambaia, Goiânia, GO74690-900, Brazil
| | - José Alexandre F. Diniz-Filho
- Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás — Campus Samambaia, Goiânia, GO74690-900, Brazil
| | - Mario R. Moura
- Departamento de Biologia Animal, Universidade Federal de Campinas, Campinas, SP13083-970, Brazil
- Departamento de Biociências, Universidade Federal da Paraíba, Areia, PB58397-000, Brazil
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3
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Albano PG, Hong Y, Steger J, Yasuhara M, Bartolini S, Bogi C, Bošnjak M, Chiappi M, Fossati V, Huseyinoglu MF, Jiménez C, Lubinevsky H, Morov AR, Noè S, Papatheodoulou M, Resaikos V, Zuschin M, Guy-Haim T. New records of non-indigenous species from the eastern Mediterranean Sea (Crustacea, Mollusca), with a revision of genus Isognomon (Mollusca: Bivalvia). PeerJ 2024; 12:e17425. [PMID: 38832036 PMCID: PMC11146324 DOI: 10.7717/peerj.17425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/28/2024] [Indexed: 06/05/2024] Open
Abstract
We report new data on non-indigenous invertebrates from the Mediterranean Sea (four ostracods and 20 molluscs), including five new records for the basin: the ostracods Neomonoceratina iniqua, Neomonoceratina aff. mediterranea, Neomonoceratina cf. entomon, Loxoconcha cf. gisellae (Arthropoda: Crustacea)-the first records of non-indigenous ostracods in the Mediterranean-and the bivalve Striarca aff. symmetrica (Mollusca). Additionally, we report for the first time Electroma vexillum from Israel, and Euthymella colzumensis, Joculator problematicus, Hemiliostraca clandestina, Pyrgulina nana, Pyrgulina microtuber, Turbonilla cangeyrani, Musculus aff. viridulus and Isognomon bicolor from Cyprus. We also report the second record of Fossarus sp. and of Cerithiopsis sp. cf. pulvis in the Mediterranean Sea, the first live collected specimens of Oscilla galilae from Cyprus and the northernmost record of Gari pallida in Israel (and the Mediterranean). Moreover, we report the earliest records of Rugalucina angela, Ervilia scaliola and Alveinus miliaceus in the Mediterranean Sea, backdating their first occurrence in the basin by 3, 5 and 7 years, respectively. We provide new data on the presence of Spondylus nicobaricus and Nudiscintilla aff. glabra in Israel. Finally, yet importantly, we use both morphological and molecular approaches to revise the systematics of the non-indigenous genus Isognomon in the Mediterranean Sea, showing that two species currently co-occur in the basin: the Caribbean I. bicolor, distributed in the central and eastern Mediterranean, and the Indo-Pacific I. aff. legumen, at present reported only from the eastern Mediterranean and whose identity requires a more in-depth taxonomic study. Our work shows the need of taxonomic expertise and investigation, the necessity to avoid the unfounded sense of confidence given by names in closed nomenclature when the NIS belong to taxa that have not enjoyed ample taxonomic work, and the necessity to continue collecting samples-rather than relying on visual censuses and bio-blitzes-to enable accurate detection of non-indigenous species.
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Affiliation(s)
- Paolo G. Albano
- Department of Marine Animal Conservation and Public Engagement, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Yuanyuan Hong
- School of Biological Sciences, Area of Ecology and Biodiversity, Swire Institute of Marine Science, Institute for Climate and Carbon Neutrality, and Musketeers Foundation Institute of Data Science, The University of Hong Kong, Hong Kong SAR, China
| | - Jan Steger
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Moriaki Yasuhara
- School of Biological Sciences, Area of Ecology and Biodiversity, Swire Institute of Marine Science, Institute for Climate and Carbon Neutrality, and Musketeers Foundation Institute of Data Science, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
| | | | - Cesare Bogi
- Gruppo Malacologico Livornese, Livorno, Italy
| | | | - Marina Chiappi
- Enalia Physis Environmental Research Centre, Nicosia, Cyprus
| | | | | | - Carlos Jiménez
- Enalia Physis Environmental Research Centre, Nicosia, Cyprus
| | | | | | - Simona Noè
- Department of Marine Animal Conservation and Public Engagement, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- National Biodiversity Future Center, Palermo, Italy
| | | | | | - Martin Zuschin
- Department of Palaeontology, University of Vienna, Vienna, Austria
| | - Tamar Guy-Haim
- Israel Oceanographic and Limnological Research, Haifa, Israel
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4
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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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Krishnan A. The global butterfly effect of wing pattern convergence. Proc Natl Acad Sci U S A 2023; 120:e2314443120. [PMID: 37729172 PMCID: PMC10556623 DOI: 10.1073/pnas.2314443120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023] Open
Affiliation(s)
- Anand Krishnan
- Evolutionary and Organismal Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru560064, India
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6
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Keinath S, Frisch J, Müller J, Mayer F, Struck U, Rödel M. Species- and sex-dependent changes in body size between 1892 and 2017, and recent biochemical signatures in rural and urban populations of two ground beetle species. Ecol Evol 2023; 13:e10329. [PMID: 37484935 PMCID: PMC10361362 DOI: 10.1002/ece3.10329] [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: 01/27/2023] [Revised: 07/02/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023] Open
Abstract
Increasing urbanisation and intensified agriculture lead to rapid transitions of ecosystems. Species that persist throughout rapid transitions may respond to environmental changes across space and/or time, for instance by altering morphological and/or biochemical traits. We used natural history museum specimens, covering the Anthropocene epoch, to obtain long-term data combined with recent samples. We tested whether rural and urban populations of two ground beetle species, Harpalus affinis and H. rufipes, exhibit spatio-temporal intraspecific differences in body size. On a spatial scale, we tested signatures of nitrogen and carbon stable isotopes enrichments in different tissues and body components in recent populations of both species from urban and agricultural habitats. For body size examinations, we used beetles, collected from the early 20th century until 2017 in the Berlin-Brandenburg region, Germany, where urbanisation and agriculture have intensified throughout the last century. For stable isotope examinations, we used recent beetles from urban and agricultural habitats. Our results revealed no spatio-temporal changes in body size in both species' females. Body size of H. rufipes males decreased in the city but remained constant in rural areas over time. We discuss our findings with respect to habitat quality, urban heat and interspecific differences in activity pattern. Although nitrogen isotope ratios were mostly higher in specimens from agricultural habitats, some urban beetles reached equal enrichments. Carbon signatures of both species did not differ between habitats, detecting no differences in energy sources. Our results indicate that increasing urbanisation and intensified agriculture are influencing species' morphology and/or biochemistry. However, changes may be species- and sex-specific.
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Affiliation(s)
- Silvia Keinath
- Museum für Naturkunde, Berlin – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research – BBIBBerlinGermany
| | - Johannes Frisch
- Museum für Naturkunde, Berlin – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Johannes Müller
- Museum für Naturkunde, Berlin – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research – BBIBBerlinGermany
| | - Frieder Mayer
- Museum für Naturkunde, Berlin – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research – BBIBBerlinGermany
| | - Ulrich Struck
- Museum für Naturkunde, Berlin – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
- Department of Earth ScienceFreie Universität BerlinBerlinGermany
| | - Mark‐Oliver Rödel
- Museum für Naturkunde, Berlin – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research – BBIBBerlinGermany
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7
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Ceríaco LMP, Marques MP, de Sousa ACA, Veríssimo J, Beja P, Ferreira S. Illustrated keys and a DNA barcode reference library of the amphibians and terrestrial reptiles (Amphibia, Reptilia) of São Tomé and Príncipe (Gulf of Guinea, West Africa). Zookeys 2023; 1168:41-75. [PMID: 37415718 PMCID: PMC10320720 DOI: 10.3897/zookeys.1168.101334] [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: 02/03/2023] [Accepted: 04/18/2023] [Indexed: 07/08/2023] Open
Abstract
The herpetofauna of São Tomé and Príncipe consists of nine species of amphibians, all endemic, and 21 species of terrestrial reptiles, of which 17 are endemic. Our current knowledge regarding its natural history, ecology, and distribution is limited. Here two important tools are provided to support researchers, conservationists, and local authorities in the identification of the country's herpetofauna: an illustrated key to the herpetofauna of the two islands and surroundings islets and a DNA barcode reference library. The keys allow a rapid and unambiguous morphological identification of all occurring species. The DNA barcodes for the entire herpetofauna of the country were produced from 79 specimens, all of which are deposited in museum collections. The barcodes generated are available in online repositories and can be used to provide unambiguous molecular identification of most of the species. Future applications and use of these tools are briefly discussed.
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Affiliation(s)
- Luis Miguel Pires Ceríaco
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência & Instituto de Investigação Científica Tropical (IICT), Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, Portugal
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Av. Bartolomeu de Gusmão 875, São Cristóvão, 20941-160 Rio de Janeiro, Brasil
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Mariana Pimentel Marques
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência & Instituto de Investigação Científica Tropical (IICT), Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
| | | | - Joana Veríssimo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021, 4169-007 Porto, Portugal
| | - Pedro Beja
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência & Instituto de Investigação Científica Tropical (IICT), Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Sónia Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
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8
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Lund MC, Larsen BB, Rowsey DM, Otto HW, Gryseels S, Kraberger S, Custer JM, Steger L, Yule KM, Harris RE, Worobey M, Van Doorslaer K, Upham NS, Varsani A. Using archived and biocollection samples towards deciphering the DNA virus diversity associated with rodent species in the families cricetidae and heteromyidae. Virology 2023; 585:42-60. [PMID: 37276766 DOI: 10.1016/j.virol.2023.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/07/2023]
Abstract
Rodentia is the most speciose order of mammals, and they are known to harbor a wide range of viruses. Although there has been significant research on zoonotic viruses in rodents, research on the diversity of other viruses has been limited, especially for rodents in the families Cricetidae and Heteromyidae. In fecal and liver samples of nine species of rodents, we identify 346 distinct circular DNA viral genomes. Of these, a large portion are circular, single-stranded DNA viruses in the families Anelloviridae (n = 3), Circoviridae (n = 5), Genomoviridae (n = 7), Microviridae (n = 297), Naryaviridae (n = 4), Vilyaviridae (n = 15) and in the phylum Cressdnaviricota (n = 13) that cannot be assigned established families. We also identified two large bacteriophages of 36 and 50 kb that are part of the class Caudoviricetes. Some of these viruses are clearly those that infect rodents, however, most of these likely infect various organisms associated with rodents, their environment or their diet.
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Affiliation(s)
- Michael C Lund
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98102, USA
| | - Dakota M Rowsey
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Hans W Otto
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Sophie Gryseels
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium; Department of Biology, University of Antwerp, 2000, Antwerp, Belgium; OD Taxonomy and Phylogeny, Royal Belgian Museum of Natural Sciences, 1000, Brussels, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA
| | - Laura Steger
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Kelsey M Yule
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Robin E Harris
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, AZ, 85724, USA
| | - Nathan S Upham
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; Biodiversity Knowledge Integration Center, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA; The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7701, South Africa.
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9
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Stebbins TD, Wetzer R. Review and guide to the isopods (Crustacea, Isopoda) of littoral and sublittoral marine habitats in the Southern California Bight. Zookeys 2023; 1162:1-167. [PMID: 37235199 PMCID: PMC10206732 DOI: 10.3897/zookeys.1162.100390] [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: 01/11/2023] [Accepted: 03/14/2023] [Indexed: 05/28/2023] Open
Abstract
The isopod crustaceans reported from or expected to occur in littoral and sublittoral marine habitats of the Southern California Bight (SCB) in the northeastern Pacific Ocean are reviewed. A total of 190 species, representing 105 genera in 42 families and six suborders are covered. Approximately 84% of these isopods represent described species with the remaining 16% comprising well-documented "provisional" but undescribed species. Cymothoida and Asellota are the most diverse of the six suborders, accounting for ca. 36% and 29% of the species, respectively. Valvifera and Sphaeromatidea are the next most speciose suborders with between 13-15% of the species each, while the suborder Limnorioidea represents fewer than 2% of the SCB isopod fauna. Finally, the mostly terrestrial suborder Oniscidea accounts for ca. 5% of the species treated herein, each which occurs at or above the high tide mark in intertidal habitats. A key to the suborders and superfamilies is presented followed by nine keys to the SCB species within each of the resultant groups. Figures are provided for most species. Bathymetric range, geographic distribution, type locality, habitat, body size, and a comprehensive list of references are included for most species.
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Affiliation(s)
- Timothy D. Stebbins
- Research and Collections Branch, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USANatural History Museum of Los Angeles CountyLos AngelesUnited States of America
- City of San Diego Marine Biology Laboratory (retired), Public Utilities Department, San Diego, California 92101, USACity of San Diego Marine Biology LaboratorySan DiegoUnited States of America
| | - Regina Wetzer
- Research and Collections Branch, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USANatural History Museum of Los Angeles CountyLos AngelesUnited States of America
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10
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Byrne AQ. Reimagining the future of natural history museums with compassionate collection. PLoS Biol 2023; 21:e3002101. [PMID: 37141192 PMCID: PMC10159148 DOI: 10.1371/journal.pbio.3002101] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
Compassionate collection involves minimizing harm while collecting museum data in the field. By adopting this practice, natural history museums could better maintain existing collections, accommodate more nonlethal specimens and data, and foster an inclusive community.
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Affiliation(s)
- Allison Q Byrne
- Department of Environmental Science, Policy & Management, University of California, Berkeley, California, United States of America
- Museum of Vertebrate Zoology, University of California, Berkeley, California, Unites States of America
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11
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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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12
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Pizarro AK, DeRaad DA, McCormack JE. Temporal stability of the hybrid zone between Calocitta magpie-jays revealed through comparison of museum specimens and iNaturalist photos. Ecol Evol 2023; 13:e9863. [PMID: 36937059 PMCID: PMC10017314 DOI: 10.1002/ece3.9863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/01/2023] [Accepted: 02/10/2023] [Indexed: 03/18/2023] Open
Abstract
Hybrid zones are natural experiments for the study of avian evolution. Hybrid zones can be dynamic, moving as species adjust to new climates and habitats, with unknown implications for species and speciation. There are relatively few studies that have comparable modern and historic sampling to assess change in hybrid zone location and width over time, and those studies have generally found mixed results, with many hybrid zones showing change over time, but others showing stability. The white-throated magpie-jay (Calocitta formosa) and black-throated magpie-jay (Calocitta colliei) occur along the western coast of Mexico and Central America. The two species differ markedly in throat color and tail length, and prior observation suggests a narrow hybrid zone in southern Jalisco where individuals have mixed throat color. This study aims to assess the existence and temporal stability of this putative hybrid zone by comparing throat color between georeferenced historical museum specimens and modern photos from iNaturalist with precise locality information. Our results confirm the existence of a narrow hybrid zone in Jalisco, with modern throat scores gradually increasing from the parental ends of the cline toward the cline center in a sigmoidal curve characteristic of hybrid zones. Our temporal comparison suggests that the hybrid zone has not shifted its position between historical (pre-1973) and modern (post-2005) time periods-a surprising result given the grand scale of habitat change to the western Mexican lowlands during this time. An anomalous pocket of white-throated individuals in the northern range of the black-throated magpie-jay hints at the possibility of prehistorical long-distance introduction. Future genomic data will help disentangle the evolutionary history of these lineages and better characterize how secondary contact is affecting both the DNA and the phenotype of these species.
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Affiliation(s)
- Alana K. Pizarro
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
| | - Devon A. DeRaad
- Biodiversity Institute and Department of Ecology & Evolutionary BiologyKansas UniversityKansasLawrenceUSA
| | - John E. McCormack
- Moore Laboratory of ZoologyOccidental CollegeLos AngelesCaliforniaUSA
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13
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Rivera JD, Favila ME. Good news! Sampling intensity needed for accurate assessments of dung beetle diversity may be lower in the Neotropics. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.999488] [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
Ecological studies with Scarabaeinae dung beetles have increased exponentially over the past 30 years, using lethal pitfall traps baited with mammal feces or carrion as the preferred sampling method. Different studies have determined the distance between pitfall traps for effective sampling, but the number of traps is often subjective, leading to excessive or poor sampling. This study provides quantitative guidelines for establishing the sample size for optimal completeness of dung beetle diversity by systematically reviewing the relationship between sampling intensity and sampling coverage, habitat type, and the journal impact factor in peer-reviewed research. We gathered 94 studies covering a range from México to Argentina. Sampling was conducted mainly in forested habitats, followed by treeless agriculture and agroforestry systems, with a median value of 50 pitfall traps per sampled habitat. Sampling completeness was above 0.9 in 95% of the studies. Oversampling ranged from 1 to more than 96,000 individuals, and sampling deficit varied between 2 and 3,300 specimens. Sampling intensity and the journal impact factor were significantly and positively correlated with oversampling, but these variables did not explain the sampling deficit. The positive correlation between journal impact factor and oversampling may reflect a publication bias where high-impact journals and researchers seek more generalizable information obtained with a higher sampling intensity. Dung beetle oversampling was not homogeneous between habitats, being highest in old-growth forests and lowest in disturbed habitats such as pastures and forest edges. Our results show that the collection intensity used in dung beetle studies should be reconsidered carefully. By incorporating ethical principles used in animal science, we suggest sampling guidelines for a robust sampling scheme of dung beetle diversity, which would also prevent oversampling. Consciously reducing sampling intensity will make resource use more cost-effective. We suggest increasing the number of independent sampling units rather than intensifying subsampling, thereby increasing the predictive power of statistical models to obtain more robust evidence of the phenomena under study.
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14
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Villalobos R, Aylagas E, Pearman JK, Curdia J, Lozano-Cortés D, Coker DJ, Jones B, Berumen ML, Carvalho S. Inter-annual variability patterns of reef cryptobiota in the central Red Sea across a shelf gradient. Sci Rep 2022; 12:16944. [PMID: 36210380 PMCID: PMC9548503 DOI: 10.1038/s41598-022-21304-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 09/26/2022] [Indexed: 12/29/2022] Open
Abstract
The combination of molecular tools, standard surveying techniques, and long-term monitoring programs are relevant to understanding environmental and ecological changes in coral reef communities. Here we studied temporal variability in cryptobenthic coral reef communities across the continental shelf in the central Red Sea spanning 6 years (three sampling periods: 2013-2019) and including the 2015 mass bleaching event. We used a combination of molecular tools (barcoding and metabarcoding) to assess communities on Autonomous Reef Monitoring Structures (ARMS) as a standardized sampling approach. Community composition associated with ARMS for both methodologies (barcoding and metabarcoding) was statistically different across reefs (shelf position) and time periods. The partition of beta diversity showed a higher turnover and lower nestedness between pre-bleaching and post-bleaching samples than between the two post-bleaching periods, revealing a community shift from the bleaching event. However, a slight return to the pre-bleaching community composition was observed in 2019 suggesting a recovery trajectory. Given the predictions of decreasing time between bleaching events, it is concerning that cryptobenthic communities may not fully recover and communities with new characteristics will emerge. We observed a high turnover among reefs for all time periods, implying a homogenization of the cryptobiome did not occur across the cross shelf following the 2015 bleaching event. It is possible that dispersal limitations and the distinct environmental and benthic structures present across the shelf maintained the heterogeneity in communities among reefs. This study has to the best of our knowledge presented for the first time a temporal aspect into the analysis of ARMS cryptobenthic coral reef communities and encompasses a bleaching event. We show that these structures can detect cryptic changes associated with reef degradation and provides support for these being used as long-term monitoring tools.
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Affiliation(s)
- R Villalobos
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - E Aylagas
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
- The Red Sea Development Company, 5th Floor, MU04 Tower, ITCC Complex, AlRaidah Digital City, Al Nakhil District 3807, Riyadh, 12382-6726, Saudi Arabia
| | - J K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - J Curdia
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - D Lozano-Cortés
- Environmental Protection, Saudi Aramco, Dhahran, Saudi Arabia
| | - D J Coker
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - B Jones
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - M L Berumen
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia
| | - S Carvalho
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal, 23955-6900, Saudi Arabia.
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15
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Ramírez-Castañeda V, Westeen EP, Frederick J, Amini S, Wait DR, Achmadi AS, Andayani N, Arida E, Arifin U, Bernal MA, Bonaccorso E, Bonachita Sanguila M, Brown RM, Che J, Condori FP, Hartiningtias D, Hiller AE, Iskandar DT, Jiménez RA, Khelifa R, Márquez R, Martínez-Fonseca JG, Parra JL, Peñalba JV, Pinto-García L, Razafindratsima OH, Ron SR, Souza S, Supriatna J, Bowie RCK, Cicero C, McGuire JA, Tarvin RD. A set of principles and practical suggestions for equitable fieldwork in biology. Proc Natl Acad Sci U S A 2022; 119:e2122667119. [PMID: 35972961 PMCID: PMC9407469 DOI: 10.1073/pnas.2122667119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Field biology is an area of research that involves working directly with living organisms in situ through a practice known as "fieldwork." Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of the core team members. However, existing power imbalances stemming from geopolitical history, discrimination, and professional position, among other factors, perpetuate inequities when conducting these research endeavors. After reflecting on our own research programs, we propose four general principles to guide equitable, inclusive, ethical, and safe practices in field biology: be collaborative, be respectful, be legal, and be safe. Although many biologists already structure their field programs around these principles or similar values, executing equitable research practices can prove challenging and requires careful consideration, especially by those in positions with relatively greater privilege. Based on experiences and input from a diverse group of global collaborators, we provide suggestions for action-oriented approaches to make field biology more equitable, with particular attention to how those with greater privilege can contribute. While we acknowledge that not all suggestions will be applicable to every institution or program, we hope that they will generate discussions and provide a baseline for training in proactive, equitable fieldwork practices.
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Affiliation(s)
- Valeria Ramírez-Castañeda
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Erin P. Westeen
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Environmental, Science, Policy, and Management, University of California, Berkeley, CA, 94720
| | - Jeffrey Frederick
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Sina Amini
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Daniel R. Wait
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Anang S. Achmadi
- Research Center for Applied Zoology, National Research and Innovation Agency, Jawa Barat 16911, Indonesia
| | - Noviar Andayani
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Kampus UI Depok, Depok 16424, Indonesia
- Research Center for Climate Change, Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Evy Arida
- Research Center for Applied Zoology, National Research and Innovation Agency, Jawa Barat 16911, Indonesia
| | - Umilaela Arifin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Centre for Taxonomy and Morphology, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg 20146 Germany
| | - Moisés A. Bernal
- Department of Biological Sciences, Auburn University, Auburn, AL 36849
| | - Elisa Bonaccorso
- Laboratorio de Biología Evolutiva, Colegio de Ciencias Biológicas y Ambientales e Instituto Biósfera, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Marites Bonachita Sanguila
- Biodiversity Informatics and Research Center, Father Saturnino Urios University, Butuan City 8600, Philippines
| | - Rafe M. Brown
- Biodiversity Institute, University of Kansas, Lawrence, KS 66044
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66044
| | - Jing Che
- State Key Laboratory of Genetic Resource and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
| | - F. Peter Condori
- Museo de Biodiversidad del Perú, Cusco 08003, Perú
- Museo de Historia Natural de la Universidad Nacional de San Antonio Abad del Cusco, Cusco 08002, Perú
| | | | - Anna E. Hiller
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Djoko T. Iskandar
- Basic Sciences Commision, Indonesian Academy of Sciences, Jakarta 10110, Indonesia
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Rosa Alicia Jiménez
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Escuela de Biología, Facultad de Ciencias Químicas y Farmacia, Universidad de San Carlos de Guatemala, Ciudad de Guatemala 01012, Guatemala
| | - Rassim Khelifa
- Institute for Resources, Environment and Sustainability, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Biology Department, Condordia University, Montreal, Quebec H4B 1R6, Canada
| | - Roberto Márquez
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Michigan Society of Fellows, University of Michigan, Ann Arbor, MI 48109
| | - José G. Martínez-Fonseca
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86011
- Nicaraguan Bat Conservation Program, Carazo, Nicaragua
| | - Juan L. Parra
- Grupo de Ecología y Evolución de Vertebrados, Instituto de Biología, Universidad de Antioquia, Medellín 050010, Colombia
| | - Joshua V. Peñalba
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin 10115, Germany
| | - Lina Pinto-García
- Centro Interdisciplinario de Estudios sobre el Desarrollo, Universidad de los Andes, Bogotá 111711, Colombia
- Institute for Science, Innovation and Society, University of Oxford, Oxford OX2 6PN, United Kingdom
| | - Onja H. Razafindratsima
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
- Mention Zoologie et Biodiversité Animale, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Santiago R. Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito 170525, Ecuador
| | - Sara Souza
- Environment, Health & Safety, University of California, Berkeley, CA 94720
| | - Jatna Supriatna
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Kampus UI Depok, Depok 16424, Indonesia
- Research Center for Climate Change, Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Rebecca D. Tarvin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
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16
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Andreone F, Boero F, Bologna MA, Carpaneto GM, Castiglia R, Gippoliti S, Massa B, Minelli A. Reconnecting research and natural history museums in Italy and the need of a national collection biorepository. Zookeys 2022; 1104:55-68. [PMID: 36761931 PMCID: PMC9848790 DOI: 10.3897/zookeys.1104.79823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/18/2022] [Indexed: 11/12/2022] Open
Abstract
In Italy, differently from other countries, a national museum of natural history is not present. This absence is due, among other reasons, to its historical political fragmentation up to 1870, which led to the establishment of medium-sized museums, mostly managed by local administrations or universities. Moreover, a change of paradigm in biological research, at the beginning of the 20th century, contributed to privilege experimental studies in universities and facilitated the dismissal of descriptive and exploratory biology, which formed the basis of the taxonomic research carried out by natural history museums. Consequently, only a few museums have a provision of curatorial staff, space and material resources adequate to maintain their original mission of discovering the natural world, by conducting a regular research activity accompanied by field campaigns. The creation of a national research centre for the study of biodiversity, facilitating interconnections among the existing natural history museums could be a solution and is here supported, together with a centralised biorepository to host collections and vouchers, to the benefit of current and future taxonomic research and environmental conservation. Such an institution should find place and realisation within the recently proposed National Biodiversity Future Center (NBFC) planned within the National Plan of Recovery and Resilience (PNRR). Pending upon the creation of this new national centre, a network among the existing museums should coordinate their activities.
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Affiliation(s)
- Franco Andreone
- Museo Regionale di Scienze Naturali, Via G. Giolitti, 36, I-10123 Torino, ItalyMuseo Regionale di Scienze NaturaliTorinoItaly
| | - Ferdinando Boero
- Università di Napoli Federico II, CNR-IAS, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, ItalyUniversità di Napoli Federico IINapoliItaly
| | - Marco A. Bologna
- Dipartimento di Scienze, Università Roma Tre, Viale G. Marconi, 446, I-00146 Roma, ItalyUniversità Roma TreRomaItaly
| | - Giuseppe M. Carpaneto
- Dipartimento di Scienze, Università Roma Tre, Viale G. Marconi, 446, I-00146 Roma, ItalyUniversità Roma TreRomaItaly
| | - Riccardo Castiglia
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Università “La Sapienza” di Roma, Via A. Borelli, 50, I-00161 Roma, ItalyUniversità “La Sapienza” di RomaRomaItaly
| | - Spartaco Gippoliti
- Società Italiana per la Storia della Fauna “Giuseppe Altobello”, Viale Liegi, 48A, I-00198 Roma, ItalySocietà Italiana per la Storia della Fauna “Giuseppe Altobello”RomeItaly
| | - Bruno Massa
- Dipartimento di Scienze agrarie, alimentari e forestali, Università di Palermo, Viale Scienze, 13, I-90128 Palermo, ItalyUniversità di PalermoPalermoItaly
| | - Alessandro Minelli
- Dipartimento di Biologia, Università di Padova, Via Ugo Bassi, 58B, I-35131 Padova, ItalyUniversità di PadovaPadovaItaly
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17
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Mulcahy DG, Ibáñez R, Jaramillo CA, Crawford AJ, Ray JM, Gotte SW, Jacobs JF, Wynn AH, Gonzalez-Porter GP, McDiarmid RW, Crombie RI, Zug GR, de Queiroz K. DNA barcoding of the National Museum of Natural History reptile tissue holdings raises concerns about the use of natural history collections and the responsibilities of scientists in the molecular age. PLoS One 2022; 17:e0264930. [PMID: 35245325 PMCID: PMC8896674 DOI: 10.1371/journal.pone.0264930] [Citation(s) in RCA: 5] [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: 04/23/2021] [Accepted: 02/22/2022] [Indexed: 01/09/2023] Open
Abstract
Natural history collections are essential to a wide variety of studies in biology because they maintain large collections of specimens and associated data, including genetic material (e.g., tissues) for DNA sequence data, yet they are currently under-funded and collection staff have high workloads. With the advent of aggregate databases and advances in sequencing technologies, there is an increased demand on collection staff for access to tissue samples and associated data. Scientists are rapidly developing large DNA barcode libraries, DNA sequences of specific genes for species across the tree of life, in order to document and conserve biodiversity. In doing so, mistakes are made. For instance, inconsistent taxonomic information is commonly taken from different lending institutions and deposited in data repositories, such as the Barcode of Life Database (BOLD) and GenBank, despite explicit disclaimers regarding the need for taxonomic verification by the lending institutions. Such errors can have profound effects on subsequent research based on these mis-labelled sequences in data repositories. Here, we present the production of a large DNA barcode library of reptiles from the National Museum of Natural History tissue holdings. The library contains 2,758 sequences (2,205 COI and 553 16S) from 2260 specimens (four crocodilians, 37 turtles, and 2,219 lizards, including snakes), representing 583 named species, from 52 countries. In generating this library, we noticed several common mistakes made by scientists depositing DNA barcode data in public repositories (e.g., BOLD and GenBank). Our goal is to raise awareness of these concerns and offer advice to avoid such mistakes in the future to maintain accurate DNA barcode libraries to properly document Earth’s biodiversity.
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Affiliation(s)
- Daniel G. Mulcahy
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
- * E-mail:
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Sistema Nacional de Investigación, SENACYT, Panamá City, República de Panamá
- Departamento de Zoología, Universidad de Panamá, Panamá City, República de Panamá
| | - Cesar A. Jaramillo
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Departamento de Histología y Neuroanatomía, Facultad de Medicina, Universidad de Panamá, Panamá City, República de Panamá
| | - Andrew J. Crawford
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biological Sciences, Museo de Historia Natural C.J. Marinkelle, Universidad de los Andes, Bogotá, Colombia
| | - Julie M. Ray
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
| | - Steve W. Gotte
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | - Jeremy F. Jacobs
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | - Addison H. Wynn
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | | | - Roy W. McDiarmid
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | - Ronald I. Crombie
- Department of Herpetology, California Academy of Sciences, San Francisco, California, United States of America
| | - George R. Zug
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
| | - Kevin de Queiroz
- Division of Amphibians and Reptiles, Department of Vertebrate Zoology, National Museum of Natural History, Washington, DC, United States of America
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18
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Sun KH(M, Wong YT(H, Cheung KM(C, Yuen C(M, Chan YT(T, Lai WY(J, Chao C(D, Fan WS(K, Chow YK(K, Law MF, Tam HC(T. Update on Molecular Diagnosis in Extranodal NK/T-Cell Lymphoma and Its Role in the Era of Personalized Medicine. Diagnostics (Basel) 2022; 12:diagnostics12020409. [PMID: 35204500 PMCID: PMC8871212 DOI: 10.3390/diagnostics12020409] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 01/23/2022] [Accepted: 01/28/2022] [Indexed: 02/06/2023] Open
Abstract
Natural killer (NK)/T-cell lymphoma (NKTCL) is an aggressive malignancy with unique epidemiological, histological, molecular, and clinical characteristics. It occurs in two pathological forms, namely, extranodal NKTCL (ENKTCL) and aggressive NK leukemia, according to the latest World Health Organization (WHO) classification. Epstein–Barr virus (EBV) infection has long been proposed as the major etiology of lymphomagenesis. The adoption of high-throughput sequencing has allowed us to gain more insight into the molecular mechanisms of ENKTCL, which largely involve chromosome deletion and aberrations in Janus kinase (JAK)-signal transducer and activator of transcription (STAT), programmed cell death protein-1 (PD-1)/PD-ligand 1 (PD-L1) pathways, as well as mutations in tumor suppressor genes. The molecular findings could potentially influence the traditional chemoradiotherapy approach, which is known to be associated with significant toxicity. This article will review the latest molecular findings in NKTCL and recent advances in the field of molecular diagnosis in NKTCL. Issues of quality control and technical difficulties will also be discussed, along with future prospects in the molecular diagnosis and treatment of NKTCL.
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Affiliation(s)
- Ka-Hei (Murphy) Sun
- Division of Hematopathology, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Hong Kong; (K.-H.S.); (C.Y.)
| | | | - Ka-Man (Carmen) Cheung
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Carmen (Michelle) Yuen
- Division of Hematopathology, Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Hong Kong; (K.-H.S.); (C.Y.)
| | - Yun-Tat (Ted) Chan
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Wing-Yan (Jennifer) Lai
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Chun (David) Chao
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Wing-Sum (Katie) Fan
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Yuen-Kiu (Karen) Chow
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
| | - Man-Fai Law
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
- Correspondence:
| | - Ho-Chi (Tommy) Tam
- Department of Medicine and Therapeutics, Prince of Wales Hospital, Hong Kong; (K.-M.C.); (Y.-T.C.); (W.-Y.L.); (C.C.); (W.-S.F.); (Y.-K.C.); (H.-C.T.)
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19
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OUP accepted manuscript. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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20
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Wolfgramm H, Martens J, Töpfer T, Vamberger M, Pathak A, Stuckas H, Päckert M. Asymmetric allelic introgression across a hybrid zone of the coal tit ( Periparus ater) in the central Himalayas. Ecol Evol 2021; 11:17332-17351. [PMID: 34938512 PMCID: PMC8668783 DOI: 10.1002/ece3.8369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/07/2022] Open
Abstract
In the Himalayas, a number of secondary contact zones have been described for vicariant vertebrate taxa. However, analyses of genetic divergence and admixture are missing for most of these examples. In this study, we provide a population genetic analysis for the coal tit (Periparus ater) hybrid zone in Nepal. Intermediate phenotypes between the distinctive western "spot-winged tit" (P. a. melanolophus) and Eastern Himalayan coal tits (P. a. aemodius) occur across a narrow range of <100 km in western Nepal. As a peculiarity, another distinctive cinnamon-bellied form is known from a single population so far. Genetic admixture of western and eastern mitochondrial lineages was restricted to the narrow zone of phenotypically intermediate populations. The cline width was estimated 46 km only with a center close to the population of the cinnamon-bellied phenotype. In contrast, allelic introgression of microsatellite loci was asymmetrical from eastern P. a. aemodius into far western populations of phenotypic P. a. melanolophus but not vice versa. Accordingly, the microsatellite cline was about 3.7 times wider than the mitochondrial one.
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Affiliation(s)
- Hannes Wolfgramm
- Senckenberg Natural History Collections DresdenDresdenGermany
- Present address:
Department of Functional GenomicsInterfaculty Institute of Genetics and Functional GenomicsUniversity Medicine GreifswaldGreifswaldGermany
| | - Jochen Martens
- Institute of Organismic and Molecular Evolution (iomE)Johannes Gutenberg UniversityMainzGermany
| | - Till Töpfer
- Leibniz Institute for the Analysis of Biodiversity ChangeZoological Research Museum Alexander KoenigBonnGermany
| | | | - Abhinaya Pathak
- Department of National Parks and Wildlife ConservationKathmanduNepal
| | - Heiko Stuckas
- Senckenberg Natural History Collections DresdenDresdenGermany
| | - Martin Päckert
- Senckenberg Natural History Collections DresdenDresdenGermany
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21
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Abstract
Natural history collections are invaluable repositories of biological information that provide an unrivaled record of Earth's biodiversity. Museum genomics-genomics research using traditional museum and cryogenic collections and the infrastructure supporting these investigations-has particularly enhanced research in ecology and evolutionary biology, the study of extinct organisms, and the impact of anthropogenic activity on biodiversity. However, leveraging genomics in biological collections has exposed challenges, such as digitizing, integrating, and sharing collections data; updating practices to ensure broadly optimal data extraction from existing and new collections; and modernizing collections practices, infrastructure, and policies to ensure fair, sustainable, and genomically manifold uses of museum collections by increasingly diverse stakeholders. Museum genomics collections are poised to address these challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.
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Affiliation(s)
- Daren C Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, California 95064, USA
| | - Gonzalo Giribet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
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22
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Niza H, Bento M, Lopes LF, Cartaxana A, Correia AM. A picture is worth a thousand words: using digital tools to visualise marine invertebrate diversity data along the coasts of Mozambique and São Tomé & Príncipe. Biodivers Data J 2021; 9:e68817. [PMID: 34690514 PMCID: PMC8486733 DOI: 10.3897/bdj.9.e68817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/24/2021] [Indexed: 11/12/2022] Open
Abstract
The amount of biological data available in online repositories is increasing at an exponential rate. However, data on marine invertebrate biodiversity resources from Mozambique and São Tomé and Príncipe are still sparse and scattered. Online repositories are useful instruments for biodiversity research, as they provide a fast access to data from different sources. The use of interactive platforms comprising web mapping are becoming more important, not only for the scientific community, but also for conservation managers, decision-makers and the general public as they allow data presentation in simple and understandable visual schemes. The main goal of this study was to create an interactive online digital map (hosted and available at MARINBIODIV Atlas), through the collection of data from various sources, to visualise marine invertebrate occurrences and distribution across different habitats, namely mangroves, seagrasses, corals and other coastal areas, in Mozambique and São Tomé and Príncipe. The acquired biodiversity data were managed and structured to be displayed as spatial data and to be disseminated using the geographic information system ArcGIS, where data can be accessed, filtered and mapped. The ArcGIS web mapping design tools were used to produce interactive maps to visualise marine invertebrate diversity information along the coasts of Mozambique and São Tomé and Príncipe, through different habitats, offering the foundation for analysing species incidence and allocation information. Understanding the spatial occurrences and distribution of marine invertebrates in both countries can provide a valuable baseline, regarding information and trends on their coastal marine biodiversity.
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Affiliation(s)
- Henrique Niza
- Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal Faculdade de Ciências da Universidade de Lisboa Lisboa Portugal.,MARE - ULisboa, Lisboa, Portugal MARE - ULisboa Lisboa Portugal
| | - Marta Bento
- Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal Faculdade de Ciências da Universidade de Lisboa Lisboa Portugal.,MARE - ULisboa, Lisboa, Portugal MARE - ULisboa Lisboa Portugal
| | - Luis F Lopes
- Instituto de Investigação Científica e Tropical (IHMT) and Global Health and Tropical Medicine (GHTM), Lisboa, Portugal Instituto de Investigação Científica e Tropical (IHMT) and Global Health and Tropical Medicine (GHTM) Lisboa Portugal.,Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa Lisboa Portugal
| | - Alexandra Cartaxana
- MARE - ULisboa, Lisboa, Portugal MARE - ULisboa Lisboa Portugal.,Museu Nacional de História Natural e da Ciência (MNHNC), Lisboa, Portugal Museu Nacional de História Natural e da Ciência (MNHNC) Lisboa Portugal
| | - Alexandra M Correia
- Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal Faculdade de Ciências da Universidade de Lisboa Lisboa Portugal.,MARE - ULisboa, Lisboa, Portugal MARE - ULisboa Lisboa Portugal
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23
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Chandramouli S, R.S. Naveen, S. Sureshmarimuthu, S. Babu, P.V. Karunakaran, Honnavalli N. Kumara. Catalogue of herpetological specimens from Meghalaya, India at the Salim Ali Centre for Ornithology and Natural History. JOURNAL OF THREATENED TAXA 2021. [DOI: 10.11609/jott.7318.13.11.19603-19610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
We present a catalogue of herpetological specimens collected from select community reserves of Meghalaya, northeastern India. The collection comprises a total of 75 species of the herpetofauna, including 29 species of amphibians from 20 genera in seven families and 46 species of reptiles from 30 genera, in 10 families. We provide the details on number of examples, sex, museum numbers, and collection details including location and collector along with the relevant remarks where applicable. A total of five species of amphibians and four species of reptiles remain to be resolved systematically since no precise name could be attributed to them.
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24
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Pino Pérez R, Llucià-Pomares D, Pino Pérez JJ. Las especies del infraorden Gryllidea (Orthoptera, Ensifera) de la Colección Entomológica del Centro de Investigación Forestal de Lourizán (Pontevedra). GRAELLSIA 2021. [DOI: 10.3989/graellsia.2021.v77.302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Se presenta información específica de los ejemplares del infraorden Gryllidea depositados en la Colección Entomológica LOU-Arthr del Centro de Investigación Forestal de Lourizán y se revisa su estado de conocimiento en Galicia. Actualmente la colección cuenta con 450 ejemplares pertenecientes a cuatro de las cinco familias conocidas de la península ibérica (Gryllidae, Trigonidiidae, Mogoplistidae y Gryllotalpidae), seis subfamilias (Gryllinae, Oecanthinae, Trigonidiinae, Nemobiinae, Mogoplistinae y Gryllotalpinae), y 10 táxones [Eugryllodes escalerai (Bolívar, 1894), Gryllus (Gryllus) campestris Linnaeus, 1758, Gryllus (Gryllus) bimaculatus De Geer, 1773, Eumodicogryllus bordigalensis (Latreille, 1804), Oecanthus pellucens pellucens (Scopoli, 1763), Trigonidium (Trigonidium) cicindeloides Rambur, 1838, Nemobius sylvestris sylvestris (Bosc, 1792), Pteronemobius (Stilbonemobius) lineolatus (Brullé, 1835), Pseudomogoplistes vicentae Gorochov, 1996 y Gryllotalpa vineae Bennet-Clark, 1970]. Se citan por primera vez G. (G.) campestris para Lugo, O. pellucens pellucens para Lugo y Ourense, T. (T.) cicindeloides para A Coruña, Pt. (St.) lineolatus para Lugo, Ourense y Pontevedra, E. bordigalensis para Ourense y Pontevedra y G. vineae para Galicia.
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25
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Hyperspectral data as a biodiversity screening tool can differentiate among diverse Neotropical fishes. Sci Rep 2021; 11:16157. [PMID: 34373560 PMCID: PMC8352966 DOI: 10.1038/s41598-021-95713-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/13/2021] [Indexed: 11/08/2022] Open
Abstract
Hyperspectral data encode information from electromagnetic radiation (i.e., color) of any object in the form of a spectral signature; these data can then be used to distinguish among materials or even map whole landscapes. Although hyperspectral data have been mostly used to study landscape ecology, floral diversity and many other applications in the natural sciences, we propose that spectral signatures can be used for rapid assessment of faunal biodiversity, akin to DNA barcoding and metabarcoding. We demonstrate that spectral signatures of individual, live fish specimens can accurately capture species and clade-level differences in fish coloration, specifically among piranhas and pacus (Family Serrasalmidae), fishes with a long history of taxonomic confusion. We analyzed 47 serrasalmid species and could distinguish spectra among different species and clades, with the method sensitive enough to document changes in fish coloration over ontogeny. Herbivorous pacu spectra were more like one another than they were to piranhas; however, our method also documented interspecific variation in pacus that corresponds to cryptic lineages. While spectra do not serve as an alternative to the collection of curated specimens, hyperspectral data of fishes in the field should help clarify which specimens might be unique or undescribed, complementing existing molecular and morphological techniques.
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26
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Ceríaco LM, Parrinha D, Marques MP. Saving collections: taxonomic revision of the herpetological collection of the Instituto de Investigação Científica Tropical, Lisbon (Portugal) with a protocol to rescue abandoned collections. Zookeys 2021; 1052:85-156. [PMID: 34393554 PMCID: PMC8346433 DOI: 10.3897/zookeys.1052.64607] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022] Open
Abstract
The herpetological collections of the Instituto de Investigação Científica Tropical, Lisbon, are amongst the most important collections from the former Portuguese territories in Africa and Asia. The collection comprises more than 5000 preserved specimens, including type specimens of nine taxa, Trachylepis adamastor, Trachypelis thomensis, Panaspis thomensis, Naja peroescobari, Dalophia angolensis, Hemidactylus nzingae, Boaedon fradei, Platysaurus maculatus maculatus, and Platysaurus maculatus lineicauda. The collection was abandoned in the early years of 2000s and was at risk of being lost. In this paper the entire collection is reviewed, a catalogue provided of the extant specimens, and a brief account of the history of herpetological research at IICT given. Details are also provided on the recovery of the collection and a protocol to rescue abandoned collections.
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Affiliation(s)
- Luis M.P. Ceríaco
- Museu de História Natural e da Ciência da Universidade do Porto, Praça Gomes Teixeira 4099-002 Porto, PortugalUniversidade de LisboaLisboaPortugal
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, PortugalMuseu de História Natural e da Ciência da Universidade do PortoPortoPortugal
| | - Diogo Parrinha
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, PortugalMuseu de História Natural e da Ciência da Universidade do PortoPortoPortugal
| | - Mariana P. Marques
- Departamento de Zoologia e Antropologia (Museu Bocage), Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, PortugalMuseu de História Natural e da Ciência da Universidade do PortoPortoPortugal
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO, Universidade do Porto, Rua Padre Armando Quintas 7, Vairão, 4485-661 Porto, PortugalUniversidade do PortoPortoPortugal
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27
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Hammer MP, Taillebois L, King AJ, Crook DA, Wedd D, Adams M, Unmack PJ, Hoese DF, Bertozzi T. Unravelling the taxonomy and identification of a problematic group of benthic fishes from tropical rivers (Gobiidae: Glossogobius). JOURNAL OF FISH BIOLOGY 2021; 99:87-100. [PMID: 33583039 DOI: 10.1111/jfb.14701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/01/2021] [Accepted: 02/13/2021] [Indexed: 06/12/2023]
Abstract
Flathead gobies (genus Glossogobius) include c. 40 small- to medium-sized benthic fishes found primarily in freshwater habitats across the Indo-Pacific, having biodiversity value as well as cultural and economic value as food fishes, especially in developing countries. To help resolve considerable confusion regarding the identification of some of the larger-growing Glossogobius species, a systematic framework was established using nuclear genetic markers, mitochondrial DNA barcoding and phenotypic evidence for a geographically widespread collection of individuals from the waterways of tropical northern Australia. Species boundaries and distribution patterns were discordant with those previously reported, most notably for the tank goby Glossogobius giuris, which included a cryptic species. Genetic divergence was matched with accompanying unique visual characters that aid field identification. Additional taxonomic complexity was also evident, by comparison with DNA barcodes from international locations, suggesting that the specific names applicable for two of the candidate species in Australia remain unresolved due to confusion surrounding type specimens. Although flathead gobies are assumed to be widespread and common, this study demonstrates that unrealised taxonomic and ecological complexity is evident, and this will influence assessments of tropical biodiversity and species conservation. This study supports the need for taxonomic studies of freshwater fishes to underpin management in areas subject to significant environmental change.
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Affiliation(s)
- Michael P Hammer
- Museum and Art Gallery of the Northern Territory, Darwin, Northern Territory, Australia
| | - Laura Taillebois
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Alison J King
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - David A Crook
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Dion Wedd
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mark Adams
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - Peter J Unmack
- Centre of Applied Water Science, Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Doug F Hoese
- Australian Museum, Sydney, New South Wales, Australia
| | - Terry Bertozzi
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
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28
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Straube N, Lyra ML, Paijmans JLA, Preick M, Basler N, Penner J, Rödel MO, Westbury MV, Haddad CFB, Barlow A, Hofreiter M. Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens. Mol Ecol Resour 2021; 21:2299-2315. [PMID: 34036732 DOI: 10.1111/1755-0998.13433] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 01/02/2023]
Abstract
Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies.
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Affiliation(s)
- Nicolas Straube
- University Museum of Bergen, Bergen, Norway.,SNSB Bavarian State Collection of Zoology, München, Germany
| | - Mariana L Lyra
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil.,Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Johanna L A Paijmans
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michaela Preick
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Nikolas Basler
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Johannes Penner
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,Chair of Wildlife Ecology and Management, Albert Ludwigs University Freiburg, Freiburg, Germany
| | - Mark-Oliver Rödel
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Célio F B Haddad
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil
| | - Axel Barlow
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael Hofreiter
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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29
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García NC, Robinson WD. Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.622603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.
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30
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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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Eversole CB, Powell RL, Lizarro D, Crocker AV, Vaca GC, De La Quintana P. Herpetofauna of the Reserva de la Biósfera Estación Biológica del Beni and the Chimane Reserve Indigenous Territory, Bolivia. NEOTROPICAL BIODIVERSITY 2021. [DOI: 10.1080/23766808.2021.1920294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Cord B. Eversole
- Department of Biology and Chemistry, Texas A&M International University, Laredo, Texas, USA
| | - Randy L. Powell
- Department of Biology, Texas A&M University-Kingsville, Kingsville, Texas, USA
| | - Dennis Lizarro
- Department of Herpetology, Centro de Investigación de Recursos Acuáticos (CIRA), Trinidad, Beni, Bolivia
- Universidad Autónoma Del Beni “José Ballivián”, Trinidad, Beni, Bolivia
| | - Ashton V. Crocker
- Department of Biology, Texas A&M University-Kingsville, Kingsville, Texas, USA
| | | | - Paola De La Quintana
- Red de Investigadores en Herpetología, La Paz, Bolivia
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, Ilhéus, CEP 45662-900, Brasil
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França RC, Morais M, França FGR, Rödder D, Solé M. Snakes of the Pernambuco Endemism Center, Brazil: diversity, natural history and conservation. Zookeys 2020; 1002:115-158. [PMID: 33363430 PMCID: PMC7746674 DOI: 10.3897/zookeys.1002.50997] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/14/2020] [Indexed: 11/24/2022] Open
Abstract
The Atlantic Forest is one of the largest and richest tropical rainforests on the planet, being one of the 25 world priorities for conservation. The Atlantic Forest portion located north of the São Francisco River corresponds to the Pernambuco Endemism Center (PEC). We describe the snake composition of the PEC, providing information about the diversity, natural history and geographical distribution of the species, based on records from five scientific collections and additional information from the literature. A total of 78 species of snakes distributed in eight families was registered in the Pernambuco Endemism Center. The Caatinga is the Brazilian biome that most shares species with the PEC, followed by Cerrado. On the other hand, seven species are considered endemic of this region. Most of the snake species in the PEC have been registered in forest (94.8%), followed by “Brejos Nordestinos” (46.1%), Tabuleiros (43.5%), Restingas (14.1%) and Mangroves (5.1%). The PEC snake fauna includes mainly terrestrial species (60.2%) and cryptozoic and/or fossorial species (21.7%), but also presents a high richness of semi-arboreal and arboreal species (29.5%). Vertebrates are the main food item consumed by the species (78% of species), among the main prey are mammals, lizards, and amphibians. Most species show a strictly nocturnal activity period (50%), followed by strictly diurnal (38%). The PEC is the most degraded and least known region of the Atlantic Forest, yet it has revealed a high richness of snake species, including seven endemic species. It is emphasized that regional conservation efforts need to be intensified, because few forests in the region are formally protected, and the majority consist of small and poorly protected fragments, which means that many species in the region may be in risk of extinction.
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Affiliation(s)
- Rafaela C França
- Programa de Pós-graduação em Ecologia e Conservação da Biodiversidade, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, Km 16, CEP 45662-900 Ilhéus, Bahia, Brazil.,Herpetology Section, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Mayara Morais
- Programa de Pós-graduação em Zoologia, Universidade Estadual de Santa Cruz, 11 Rodovia Jorge Amado, Km 16, CEP 45662-900 Ilhéus, Bahia, Brazil
| | - Frederico G R França
- Departamento de Engenharia e Meio Ambiente, Centro de Ciências Aplicadas e Educação, Universidade Federal da Paraíba - UFPB, Av. Santa Elizabete, s/n - Centro. CEP 58297-000, Rio Tinto, PB, Brazil
| | - Dennis Rödder
- Herpetology Section, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Mirco Solé
- Herpetology Section, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany.,Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km,16, 45662-900 Ilhéus, Bahia, Brazil
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Pacheco MA, Ceríaco LMP, Matta NE, Vargas-Ramírez M, Bauer AM, Escalante AA. A phylogenetic study of Haemocystidium parasites and other Haemosporida using complete mitochondrial genome sequences. INFECTION GENETICS AND EVOLUTION 2020; 85:104576. [PMID: 33002605 DOI: 10.1016/j.meegid.2020.104576] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 11/26/2022]
Abstract
Haemosporida are diverse vector-borne parasites associated with terrestrial vertebrates. Driven by the interest in species causing malaria (genus Plasmodium), the diversity of avian and mammalian haemosporidian species has been extensively studied, relying mostly on mitochondrial genes, particularly cytochrome b. However, parasites from reptiles have been neglected in biodiversity surveys. Reptilian haemosporidian parasites include Haemocystidium, a genus that shares morphological features with Plasmodium and Haemoproteus. Here, the first complete Haemocystidium mitochondrial DNA (mtDNA) genomes are studied. In particular, three mtDNA genomes from Haemocystidium spp. sampled in Africa, Oceania, and South America, are described. The Haemocystidium mtDNA genomes showed a high A + T content and a gene organization, including an extreme fragmentation of the rRNAs, found in other Haemosporida. These Haemocystidium mtDNA genomes were incorporated in phylogenetic and molecular clock analyses together with a representative sample of haemosporidian parasites from birds, mammals, and reptiles. The recovered phylogeny supported Haemocystidium as a monophyletic group apart from Plasmodium and other Haemosporida. Both the phylogenetic and molecular clock analyses yielded results consistent with a scenario in which haemosporidian parasites radiated with modern birds. Haemocystidium, like mammalian parasite clades, seems to originate from host switches by avian Haemosporida that allowed for the colonization of new vertebrate hosts. This hypothesis can be tested by investigating additional parasite species from all vertebrate hosts, particularly from reptiles. The mtDNA genomes reported here provide baseline data that can be used to scale up studies in haemosporidian parasites of reptiles using barcode approaches.
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Affiliation(s)
- M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122-1801, USA
| | - Luis M P Ceríaco
- Museu de História Natural e da Ciência da Universidade do Porto, Praça de Gomes Teixeira, 4099-002 Porto, Portugal; Departamento de Zoologia e Antropología (Museu Bocage), Museu Nacional de História Natural e da Ciência, Universidade de Lisboa, Rua da Escola Politécnica, 58, 1269-102 Lisboa, Portugal
| | - Nubia E Matta
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Carrera 30 No 45-03, Bogotá, Colombia
| | - Mario Vargas-Ramírez
- Instituto de Genética, Universidad Nacional de Colombia, Sede Bogotá, Carrera 30 No 45-03, Bogotá, Colombia
| | - Aaron M Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085-1699, USA
| | - Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine (iGEM), Temple University, Philadelphia, PA 19122-1801, USA.
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O'Connell DP, Kelly DJ, Analuddin K, Karya A, Marples NM, Martin TE. Adapt taxonomy to conservation goals. Science 2020; 369:1172. [PMID: 32883855 DOI: 10.1126/science.abd7717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Darren P O'Connell
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK. darren.o'.,Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin D02 CX56, Ireland
| | - David J Kelly
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin D02 CX56, Ireland
| | - Kangkuso Analuddin
- Department of Biology and Biotechnology, Universitas Halu Oleo, Southeast Sulawesi, Indonesia
| | - Adi Karya
- Department of Biology and Biotechnology, Universitas Halu Oleo, Southeast Sulawesi, Indonesia
| | - Nicola M Marples
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin D02 CX56, Ireland
| | - Thomas E Martin
- Operation Wallacea Ltd, Wallace House, Old Bolingbroke, Spilsby, Lincolnshire, PE23 4EX, UK
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36
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Cocca W, Andreone F, Belluardo F, Rosa GM, Randrianirina JE, Glaw F, Crottini A. Resolving a taxonomic and nomenclatural puzzle in mantellid frogs: synonymization of Gephyromantis azzurrae with G. corvus, and description of Gephyromantis kintana sp. nov. from the Isalo Massif, western Madagascar. Zookeys 2020; 951:133-157. [PMID: 32774110 PMCID: PMC7390805 DOI: 10.3897/zookeys.951.51129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/09/2020] [Indexed: 11/30/2022] Open
Abstract
The genus Gephyromantis belongs to the species-rich family Mantellidae and is currently divided in six subgenera. Among these is the subgenus Phylacomantis, which currently includes four described species: Gephyromantispseudoasper, G.corvus, G.azzurrae, and G.atsingy. The latter three species are distributed in western Madagascar, and two of them (G.azzurrae and G.corvus) occur in the Isalo Massif. Based on the analysis of molecular data (a fragment of the 16S rRNA gene), morphological inspection of museum specimens, and photographic comparisons, G.azzurrae is synonymised with G.corvus and the second Phylacomantis lineage of Isalo is described as G.kintanasp. nov. This medium-sized frog species (adult snout-vent length 35–44 mm) is assigned to this subgenus according to genetic and morphological similarities to the other known species of Phylacomantis. Gephyromantiskintanasp. nov. is known only from the Isalo Massif, while new records for G.corvus extend its range to ca. 200 km off its currently known distribution. These two taxa seem to occur in syntopy in at least one locality in Isalo, and the easiest way to distinguish them is the inspection of the ventral colouration, dark in G.corvus and dirty white in G.kintana.
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Affiliation(s)
- Walter Cocca
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, No 7, 4485-661 Vairão, Portugal
| | - Franco Andreone
- Sezione di Zoologia, Museo Regionale di Scienze Naturali, Via G. Giolitti, 36, 10123 Torino, Italy
| | - Francesco Belluardo
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, No 7, 4485-661 Vairão, Portugal
| | - Gonçalo M Rosa
- Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY London, UK.,Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Bloco C2, Campo Grande, 1749-016 Lisboa, Portugal
| | | | - Frank Glaw
- Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
| | - Angelica Crottini
- CIBIO, Research Centre in Biodiversity and Genetic Resources, InBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, No 7, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre, s/n, 4169-007, Porto, Portugal
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37
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Leveraging legacy archaeological collections as proxies for climate and environmental research. Proc Natl Acad Sci U S A 2020; 117:8287-8294. [PMID: 32284414 DOI: 10.1073/pnas.1914154117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Understanding the causes and consequences of previous climate changes is essential for testing present-day climate models and projections. Archaeological sites are paleoenvironmental archives containing unique ecological baselines with data on paleoclimate transformations at a human timescale. Anthropogenic and nonanthropogenic forces have destroyed many sites, and others are under immediate threat. In the face of this loss, previously excavated collections from these sites-referred to as legacy collections-offer a source of climate and other paleoenvironmental information that may no longer exist elsewhere. Here, we 1) review obstacles to systematically using data from legacy archaeological collections, such as inconsistent or unreported field methods, inadequate records, unsatisfactory curation, and insufficient public knowledge of relevant collections; 2) suggest best practices for integrating archaeological data into climate and environmental research; and 3) summarize several studies to demonstrate the benefits and challenges of using legacy collections as archives of local and regional environmental proxies. Data from archaeological legacy collections contribute regional ecological baselines as well as serve to correct shifting baselines. They also enable regional climate reconstructions at various timescales and corroborate or refine radiocarbon dates. Such uses of legacy collections raise ethical concerns regarding ownership of and responsibility for cultural resources and highlight the importance of Indigenous involvement in planning and executing fieldwork and stewardship of cultural heritage. Finally, we discuss methodologies, practices, and policies pertaining to archaeological legacy collections and support calls for discipline-wide shifts in collections management to ensure their long-term utility in multidisciplinary research and public engagement.
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Zoantharia (Cnidaria: Hexacorallia) of the Dutch Caribbean and One New Species of Parazoanthus. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12050190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Species of the anthozoan order Zoantharia (=Zoanthidea) are common components of subtropical and tropical shallow water coral reefs. Despite a long history of research on their species diversity in the Caribbean, many regions within this sea remain underexamined. One such region is the Dutch Caribbean, including the islands of St. Eustatius, St. Maarten, Saba, Aruba, Bonaire, and Curaçao, as well as the Saba Bank, for which no definitive species list exists. Here, combining examinations of specimens housed in the Naturalis Biodiversity Center collection with new specimens and records from field expeditions, we provide a list of zoantharian species found within the Dutch Caribbean. Our results demonstrate the presence at least 16 described species, including the newly described Parazoanthus atlanticus, and the additional potential presence of up to four undescribed species. These records of new and undescribed species demonstrate that although the zoantharian research history of the Caribbean is long, further discoveries remain to be found. In light of biodiversity loss and increasing anthropogenic pressure on declining coral reefs, documenting the diversity of zoantharians and other coral reef species to provide baseline data takes on a new urgency.
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Salvador RB, Cunha CM. Natural history collections and the future legacy of ecological research. Oecologia 2020; 192:641-646. [PMID: 32056020 DOI: 10.1007/s00442-020-04620-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/07/2020] [Indexed: 11/29/2022]
Abstract
Natural history collections are now being championed as key to broad ecological studies, especially those involving human impacts in the Anthropocene. However, collections are going through a crisis that threatens their present and future value, going beyond underfunding/understaffing to a more damaging practice: current researchers are no longer depositing material. This seems to be especially true for ecological studies that now benefit from historical collections, as those researchers are not trained to think about voucher specimens. We investigated indexed journals in Ecology and Zoology to assess if they have guidelines concerning voucher specimens. Only 4% of ecological journals presently encourage (but mostly do not require) voucher deposition, while 15% of zoological journals encourage it. In the first place, this goes contrary to scientific standards of reproducibility, since specimens are primary data. Secondly, this erodes the legacy we will leave for future researchers, because if this trend goes on unchecked, it will leave a massive gap in collections' coverage, undermining the quality that is presently acclaimed. The scientific community needs a wakeup call to avoid impoverishing the future value of natural history collections. Training and changing researchers' mindsets is essential, but that takes time. For the moment, we propose a stopgap measure: at the minimum, academic journals should encourage authors to deposit specimens in open collections, such as museums and universities.
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Affiliation(s)
- Rodrigo B Salvador
- Museum of New Zealand Te Papa Tongarewa, 169 Tory Street, Wellington, 6011, New Zealand.
| | - Carlo M Cunha
- Universidade Metropolitana de Santos, Avenida Conselheiro Nébias 536, Santos, SP, 11045-002, Brazil
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40
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Miyazaki Y, Murase A. Fish rubbings, 'gyotaku', as a source of historical biodiversity data. Zookeys 2020; 904:89-101. [PMID: 32009831 PMCID: PMC6983646 DOI: 10.3897/zookeys.904.47721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/10/2019] [Indexed: 11/23/2022] Open
Abstract
Methods for obtaining historical biodiversity information are mostly limited to examining museum specimens or surveying past literature. Such materials are sometimes time limited due to degradation, discarding, or other loss. The Japanese cultural art of ‘gyotaku’, which means “fish impression” or “fish rubbing” in English, captures accurate images of fish specimens, and has been used by recreational fishermen and artists since the Edo Period (the oldest known ‘gyotaku’ was made in 1839). ‘Gyotaku’ images often include distributional information, i.e., locality and sampling date. To determine the extent and usefulness of these data, field and questionnaire surveys targeting leisure fishing and boating stores were conducted in the following regions where threatened or extinct fishing targets exist (four regions including the northernmost to the southernmost regions). As a result, 261 ‘gyotaku’ rubbings were digitally copied with their owners’ consents. From these, distributional data were extracted for 218 individuals, which roughly represented regional fish faunas and common fishing targets. The peak number of ‘gyotaku’ stocked at the surveyed shops was made in 2002, while ones made before 1985 were much fewer. The number of ‘gyotaku’ rubbings made in recent years shows a recovery trend after 2011–2012. The present study demonstrates the validity of examining ‘gyotaku’ for historical biodiversity information.
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Affiliation(s)
- Yusuke Miyazaki
- Department of Child Studies and Welfare, Shiraume Gakuen College, 1-830 Ogawa-chou, Kodaira, Tokyo 187-8570, Japan
| | - Atsunobu Murase
- Nobeoka Marine Science Station, Field Science Center, University of Miyazaki, 376-6 Akamizu, Nobeoka, Miyazaki 889-0517, Japan.,Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-Kibanadai-Nishi, Miyazaki 889-2192, Japan
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41
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Bakker FT, Antonelli A, Clarke JA, Cook JA, Edwards SV, Ericson PGP, Faurby S, Ferrand N, Gelang M, Gillespie RG, Irestedt M, Lundin K, Larsson E, Matos-Maraví P, Müller J, von Proschwitz T, Roderick GK, Schliep A, Wahlberg N, Wiedenhoeft J, Källersjö M. The Global Museum: natural history collections and the future of evolutionary science and public education. PeerJ 2020; 8:e8225. [PMID: 32025365 PMCID: PMC6993751 DOI: 10.7717/peerj.8225] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 11/15/2019] [Indexed: 12/27/2022] Open
Abstract
Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well as a locus for community engagement. At the same time, like a synthesis radio telescope, when joined together through emerging digital resources, the global community of museums (the ‘Global Museum’) is more than the sum of its parts, allowing insights and answers to diverse biological, environmental, and societal questions at the global scale, across eons of time, and spanning vast diversity across the Tree of Life. We argue that, whereas natural history collections and museums began with a focus on describing the diversity and peculiarities of species on Earth, they are now increasingly leveraged in new ways that significantly expand their impact and relevance. These new directions include the possibility to ask new, often interdisciplinary questions in basic and applied science, such as in biomimetic design, and by contributing to solutions to climate change, global health and food security challenges. As institutions, they have long been incubators for cutting-edge research in biology while simultaneously providing core infrastructure for research on present and future societal needs. Here we explore how the intersection between pressing issues in environmental and human health and rapid technological innovation have reinforced the relevance of museum collections. We do this by providing examples as food for thought for both the broader academic community and museum scientists on the evolving role of museums. We also identify challenges to the realization of the full potential of natural history collections and the Global Museum to science and society and discuss the critical need to grow these collections. We then focus on mapping and modelling of museum data (including place-based approaches and discovery), and explore the main projects, platforms and databases enabling this growth. Finally, we aim to improve relevant protocols for the long-term storage of specimens and tissues, ensuring proper connection with tomorrow’s technologies and hence further increasing the relevance of natural history museums.
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Affiliation(s)
- Freek T Bakker
- Biosystematics Group, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Julia A Clarke
- Jackson School of Geosciences, University of Texas at Austin, Austin, TX, United States of America
| | - Joseph A Cook
- Museum of Southwestern Biology, Department of Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America.,Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Nuno Ferrand
- Museu de História Natural e da Ciência, Universidade do Porto, Porto, Portugal
| | - Magnus Gelang
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Rosemary G Gillespie
- Essig Museum of Entomology, Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States of America
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Kennet Lundin
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Ellen Larsson
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - Pável Matos-Maraví
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czechia
| | - Johannes Müller
- Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
| | - Ted von Proschwitz
- Department of Zoology, Gothenburg Natural History Museum, Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden
| | - George K Roderick
- Essig Museum of Entomology, Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States of America
| | - Alexander Schliep
- Department of Computer Science and Engineering, University of Gothenburg, Göteborg, Sweden
| | | | - John Wiedenhoeft
- Department of Computer Science and Engineering, University of Gothenburg, Göteborg, Sweden
| | - Mari Källersjö
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, Sweden.,Gothenburg Botanical Garden, Göteborg, Sweden
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Keinath S, Frisch J, Müller J, Mayer F, Rödel MO. Spatio-Temporal Color Differences Between Urban and Rural Populations of a Ground Beetle During the Last 100 Years. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2019.00525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Heard J, Chen JP, Wen CKC. Citizen science yields first records of Hippocampus japapigu and Hippocampus denise (Syngnathidae) from Taiwan: A hotspot for pygmy seahorse diversity. Zookeys 2019; 883:83-90. [PMID: 31719774 PMCID: PMC6828823 DOI: 10.3897/zookeys.883.39662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 09/29/2019] [Indexed: 11/20/2022] Open
Abstract
Relatively very little is known about pygmy seahorses, and even basic information regarding their distributions is largely inconsistent and often based on unofficial reports. However, monitoring marine diversity, particularly for small and cryptic species, such as pygmy seahorses, can be both costly and time consuming. In such cases, the use of citizen science can offer an effective tool for addressing knowledge gaps caused by a lack of biodiversity-related data. Scuba divers and underwater photographers were engaged through social media in order to investigate pygmy seahorse diversity in Taiwan. Using this approach five species of pygmy seahorses were identified, including two new records for Taiwan: Hippocampusdenise and Hippocampusjapapigu, the latter of which is the first record of the species from outside of Japan. These new records mark Taiwan as one of the world’s pygmy seahorse diversity hotspots, matching that of Japan and Indonesia, as well as demonstrating the value of citizen science for marine biodiversity monitoring, particularly for small cryptic species.
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Affiliation(s)
- Joseph Heard
- Department of Life Science, Tunghai University, Taichung, Taiwan
| | - Jeng-Ping Chen
- Taiwan Ocean Research Institute, National Applied Research Laboratories, Taiwan
| | - Colin K C Wen
- Department of Life Science, Tunghai University, Taichung, Taiwan.,Center for Ecology and Environment, Tunghai University, Taiwan
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Hayman DTS. African Primates: Likely Victims, Not Reservoirs, of Ebolaviruses. J Infect Dis 2019; 220:1547-1550. [PMID: 30657949 PMCID: PMC7107455 DOI: 10.1093/infdis/jiz007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/14/2019] [Indexed: 12/19/2022] Open
Affiliation(s)
- David T S Hayman
- EpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
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Sampaio Í, Carreiro-Silva M, Freiwald A, Menezes G, Grasshoff M. Natural history collections as a basis for sound biodiversity assessments: Plexauridae (Octocorallia, Holaxonia) of the Naturalis CANCAP and Tyro Mauritania II expeditions. Zookeys 2019; 870:1-32. [PMID: 31417333 PMCID: PMC6692302 DOI: 10.3897/zookeys.870.35285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/02/2019] [Indexed: 12/05/2022] Open
Abstract
Mapping biodiversity is the marathon of the 21st Century as an answer to the present extinction crisis. A century in which science is also characterised by large scientific datasets collected through new technologies aiming to fill gaps in our knowledge of species distributions. However, most species records rely on observations that are not linked to specimens, which does not allow verification of species hypotheses by other scientists. Natural history museums form a verifiable source of biodiversity records which were made by taxonomists. Nonetheless, these museums seem to be forgotten by biologists in scientific fields other than taxonomy or systematics. Naturalis Biodiversity Center (NBC) in Leiden is care keeper of large collections of marine organisms, which were sampled in the Northeast Atlantic during the CANCAP and Tyro Mauritania II expeditions (1976–1988). Many octocorals were sampled and deposited in the NBC collection, where they became available for study and were partially identified by the senior author (M.G.) in the 1980s. Nonetheless, no checklist or taxonomic revision was published so far with the complete results. In 2016 the first author visited NBC to examine NE Atlantic Plexauridae octocorals. Plexauridae octocoral-vouchered records were listed and mapped to reveal high standard primary biodiversity records unreported so far for the NE Atlantic Ocean. Twenty-four Plexauridae species with ~ six putative new species to science were discovered and eleven new biogeographical records were made from distinct Macaronesian archipelagos. Finally, new depth range records were found for three species at sea basin level and for eight species at a regional scale.
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Affiliation(s)
- Íris Sampaio
- MARE - Marine and Environmental Sciences Centre of the Institute of Marine Research, Rua Prof. Dr. Frederico Machado 9901-862 Horta, Açores, Portugal.,IMAR - University of the Azores, Rua Prof. Dr. Frederico Machado 9901-862 Horta, Açores, Portugal.,Senckenberg am Meer, Abteilung Meeresforschung, Südstrand 40, 26382 Wilhelmshaven, Germany
| | - Marina Carreiro-Silva
- MARE - Marine and Environmental Sciences Centre of the Institute of Marine Research, Rua Prof. Dr. Frederico Machado 9901-862 Horta, Açores, Portugal.,IMAR - University of the Azores, Rua Prof. Dr. Frederico Machado 9901-862 Horta, Açores, Portugal.,OKEANOS Research Unit, Faculty of Science and Technology, University of the Azores, 9901-862 Horta, Açores, Portugal
| | - André Freiwald
- Senckenberg am Meer, Abteilung Meeresforschung, Südstrand 40, 26382 Wilhelmshaven, Germany
| | - Gui Menezes
- University of the Azores, Rua Prof. Dr. Frederico Machado 9901-862, Horta, Açores, Portugal
| | - Manfred Grasshoff
- Senckenberg Forschungsinstitut, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
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Theeten F, Adam M, Vandenberghe T, Dillen M, Semal P, Scory S, Herpers JM, Van den Spiegel D, Mergen P, Smirnova L, Engledow H, Casino A, Gödderz K. NaturalHeritage: Bridging Belgian natural history collections. ACTA ACUST UNITED AC 2019. [DOI: 10.3897/biss.3.37854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The Royal Belgian Institute of Natural Sciences (RBINS), the Royal Museum for Central Africa (RMCA) and Meise Botanic Garden house more than 50 million specimens covering all fields of natural history.
While many different research topics have their own specificities, throughout the years it became apparent that with regards to collection data management, data publication and exchange via community standards, collection holding institutions face similar challenges (James et al. 2018, Rocha et al. 2014). In the past, these have been tackled in different ways by Belgian natural history institutions. In addition to local and national collaborations, there is a great need for a joint structure to share data between scientific institutions in Europe and beyond. It is the aim of large networks and infrastructures such as the Global Biodiversity Information Facility (GBIF), the Biodiversity Information Standards (TDWG), the Distributed System of Scientific collections (DiSSCo) and the Consortium of European Taxonomic Facilities (CETAF) to further implement and improve these efforts, thereby gaining ever increasing efficiencies.
In this context, the three institutions mentioned above, submitted the NaturalHeritage project (http://www.belspo.be/belspo/brain-be/themes_3_HebrHistoScien_en.stm) granted in 2017 by the Belgian Science Policy Service, which runs from 2017 to 2020.
The project provides links among databases and services. The unique qualities of each database are maintained, while the information can be concentrated and exposed in a structured way via one access point. This approach aims also to link data that are unconnected at present (e.g. relationship between soil/substrate, vegetation and associated fauna) and to improve the cross-validation of data.
(1) The NaturalHeritage prototype (http://www.naturalheritage.be) is a shared research portal with an open access infrastructure, which is still in the development phase. Its backbone is an ElasticSearch catalogue, with Kibana, and a Python aggregator gathering several types of (re)sources: relational databases, REpresentational State Transfer (REST) services of objects databases and bibliographical data, collections metadata and the GBIF Internet Publishing Toolkit (IPT) for observational and taxonomical data. Semi-structured data in English are semantically analysed and linked to a rich autocomplete mechanism. Keywords and identifiers are indexed and grouped in four categories (“what”, “who”, “where”, “when”). The portal can act also as an Open Archives Initiatives Protocol for Metadata Harvesting (OAI-PMH) service and ease indexing of the original webpage on the internet with microdata enrichment.
(2) The collection data management system of DaRWIN (Data Research Warehouse Information Network) of RBINS and RMCA has been improved as well.
External (meta)data requirements, i.e. foremost publication into or according to the practices and standards of GBIF and OBIS (Ocean Biogeographic Information System: https://obis.org) for biodiversity data, and INSPIRE (https://inspire.ec.europa.eu) for geological data, have been identified and evaluated. New and extended data structures have been created to be compliant with these standards, as well as the necessary procedures developed to expose the data.
Quality control tools for taxonomic and geographic names have been developed. Geographic names can be hard to confirm as their lack of context often requires human validation. To address this a similarity measure is used to help map the result. Species, locations, sampling devices and other properties have been mapped to the World Register of Marine Species and DarwinCore (http://www.marinespecies.org), Marine Regions and GeoNames, the AGRO Agronomy and Vertebrate trait ontologies and the British Oceanographic Data Centre (BODC) vocabularies (http://www.obofoundry.org/ontology/agro.html). Extensive mapping is necessary to make use of the ExtendedMeasurementOrFact Extension of DarwinCore (https://tools.gbif.org/dwca-validator/extensions.do).
External (meta)data requirements, i.e. foremost publication into or according to the practices and standards of GBIF and OBIS (Ocean Biogeographic Information System: https://obis.org) for biodiversity data, and INSPIRE (https://inspire.ec.europa.eu) for geological data, have been identified and evaluated. New and extended data structures have been created to be compliant with these standards, as well as the necessary procedures developed to expose the data.
Quality control tools for taxonomic and geographic names have been developed. Geographic names can be hard to confirm as their lack of context often requires human validation. To address this a similarity measure is used to help map the result. Species, locations, sampling devices and other properties have been mapped to the World Register of Marine Species and DarwinCore (http://www.marinespecies.org), Marine Regions and GeoNames, the AGRO Agronomy and Vertebrate trait ontologies and the British Oceanographic Data Centre (BODC) vocabularies (http://www.obofoundry.org/ontology/agro.html). Extensive mapping is necessary to make use of the ExtendedMeasurementOrFact Extension of DarwinCore (https://tools.gbif.org/dwca-validator/extensions.do).
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D’Elía G, Fabre PH, Lessa EP. Rodent systematics in an age of discovery: recent advances and prospects. J Mammal 2019. [DOI: 10.1093/jmammal/gyy179] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pierre-Henri Fabre
- Institut des Sciences de l’Evolution (ISEM, UMR 5554 CNRS-UM2-IRD), Université Montpellier, Montpellier Cedex 5, France
| | - Enrique P Lessa
- Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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48
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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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50
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Troudet J, Vignes-Lebbe R, Grandcolas P, Legendre F. The Increasing Disconnection of Primary Biodiversity Data from Specimens: How Does It Happen and How to Handle It? Syst Biol 2018; 67:1110-1119. [PMID: 29893962 DOI: 10.1093/sysbio/syy044] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 06/02/2018] [Indexed: 02/04/2023] Open
Abstract
Primary biodiversity data represent the fundamental elements of any study in systematics and evolution. They are, however, no longer gathered as they used to be and the mass-production of observation-based (OB) occurrences is overthrowing the collection of specimen-based (SB) occurrences. Although this change in practice is a major upheaval with significant consequences in the study of biodiversity, it remains understudied and has not attracted yet the attention it deserves. Analyzing 536 million occurrences from the Global Biodiversity Information Facility (GBIF) mediated data, we show that this spectacular change affects the 24 eukaryote taxonomic classes we targeted: from 1970 to 2016 the proportion of occurrences marked as traceable to tangible material (i.e., SB occurrences) fell from 68% to 18%; moreover, most of those specimen based-occurrences cannot be readily traced back to a specimen because the necessary information is missing. Ethical, practical or legal reasons responsible for this shift are known, and this situation appears unlikely to be reversed. Still, we urge scholars to acknowledge this dramatic change, embrace it and actively deal with it. Specifically, we emphasize why SB occurrences must be gathered, as a warrant to allow both repeating evolutionary studies and conducting rich and diverse investigations. When impossible to secure, voucher specimens must be replaced with OB occurrences combined with ancillary data (e.g., pictures, recordings, samples, DNA sequences). Ancillary data are instrumental for the usefulness of biodiversity occurrences and we show that, despite improving technologies to collate them, they remain rarely shared. The consequences of such a change are not yet clear but we advocate collecting material evidence or ancillary data to ensure that primary biodiversity data collected lately do not partly become obsolete when doubtful.
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Affiliation(s)
- Julien Troudet
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
| | - Régine Vignes-Lebbe
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
| | - Philippe Grandcolas
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
| | - Frédéric Legendre
- Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
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