1
|
Nelder MP, Schats R, Poinar HN, Cooke A, Brickley MB. Pathogen prospecting of museums: Reconstructing malaria epidemiology. Proc Natl Acad Sci U S A 2024; 121:e2310859121. [PMID: 38527214 PMCID: PMC11009618 DOI: 10.1073/pnas.2310859121] [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] [Indexed: 03/27/2024] Open
Abstract
Malaria is a disease of global significance. Ongoing changes to the earth's climate, antimalarial resistance, insecticide resistance, and socioeconomic decline test the resilience of malaria prevention programs. Museum insect specimens present an untapped resource for studying vector-borne pathogens, spurring the question: Do historical mosquito collections contain Plasmodium DNA, and, if so, can museum specimens be used to reconstruct the historical epidemiology of malaria? In this Perspective, we explore molecular techniques practical to pathogen prospecting, which, more broadly, we define as the science of screening entomological museum specimens for human, animal, or plant pathogens. Historical DNA and pathogen prospecting provide a means of describing the coevolution of human, vector, and parasite, informing the development of insecticides, diagnostics, therapeutics, and vaccines.
Collapse
Affiliation(s)
- Mark P. Nelder
- Enteric, Zoonotic and Vector-Borne Diseases, Health Protection, Public Health Ontario, Toronto, ONM5G 1M1, Canada
| | - Rachel Schats
- Laboratory for Human Osteoarchaeology, Faculty of Archaeology, Leiden University, 2333 CCLeiden, The Netherlands
| | - Hendrik N. Poinar
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
- Department of Biochemistry, McMaster University, Hamilton, ONL8S 4L9, Canada
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| | - Amanda Cooke
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| | - Megan B. Brickley
- Department of Anthropology, McMaster University, Hamilton, ONL8S 4L9, Canada
| |
Collapse
|
2
|
Ribeiro TM, Espíndola A. Integrated phylogenomic approaches in insect systematics. CURRENT OPINION IN INSECT SCIENCE 2024; 61:101150. [PMID: 38061460 DOI: 10.1016/j.cois.2023.101150] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 11/16/2023] [Accepted: 11/25/2023] [Indexed: 12/29/2023]
Abstract
The increased accessibility of genomic and imaging methods, and the improved access to ecological, spatial, and other natural history-related data is allowing for insect systematics to grow and find answers to central evolutionary and taxonomic questions. Today, integrated studies in insect phylogenomics and systematics are combining natural history, behavior, developmental biology, morphology, fossils, geographic range data, and ecological interactions. This integration is contributing to the clarification of evolutionary relationships, and the recognition of the role played by these factors on the evolution of insects. Future work should continue to build on these advances, seeking to further increase open-access databasing and support for natural history research, as well as expand its analytical palettes.
Collapse
Affiliation(s)
- Taís Ma Ribeiro
- Department of Entomology, University of Maryland, 4112 Plant Sciences Building, 4291 Fieldhouse Dr., College Park, MD 20742-4454, USA
| | - Anahí Espíndola
- Department of Entomology, University of Maryland, 4112 Plant Sciences Building, 4291 Fieldhouse Dr., College Park, MD 20742-4454, USA.
| |
Collapse
|
3
|
Lövei GL, Ferrante M. The Use and Prospects of Nonlethal Methods in Entomology. ANNUAL REVIEW OF ENTOMOLOGY 2024; 69:183-198. [PMID: 37669564 DOI: 10.1146/annurev-ento-120220-024402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Arthropods are declining globally, and entomologists ought to be in the forefront of protecting them. However, entomological study methods are typically lethal, and we argue that this makes the ethical status of the profession precarious. Lethal methods are used in most studies, even those that aim to support arthropod conservation. Additionally, almost all collecting methods result in bycatch, and a first step toward less destructive research practices is to minimize bycatch and/or ensure its proper storage and use. In this review, we describe the available suite of nonlethal methods with the aim of promoting their use. We classify nonlethal methods into (a) reuse of already collected material, (b) methods that are damaging but not lethal, (c) methods that modify behavior, and (d) true nonlethal methods. Artificial intelligence and miniaturization will help to extend the nonlethal methodological toolkit, but the need for further method development and testing remains.
Collapse
Affiliation(s)
- Gábor L Lövei
- Department of Agroecology, Flakkebjerg Research Centre, Aarhus University, Slagelse, Denmark;
- Hungarian Research Network Anthropocene Ecology Research Group, Debrecen University, Debrecen, Hungary
| | - Marco Ferrante
- Functional Agrobiodiversity, Department of Crop Sciences, University of Göttingen, Germany;
| |
Collapse
|
4
|
Ferrari G, Esselens L, Hart ML, Janssens S, Kidner C, Mascarello M, Peñalba JV, Pezzini F, von Rintelen T, Sonet G, Vangestel C, Virgilio M, Hollingsworth PM. Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections. Biodivers Data J 2023; 11:e102317. [PMID: 38327316 PMCID: PMC10848826 DOI: 10.3897/bdj.11.e102317] [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: 02/21/2023] [Accepted: 08/04/2023] [Indexed: 02/09/2024] Open
Abstract
Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.
Collapse
Affiliation(s)
- Giada Ferrari
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Lore Esselens
- Royal Museum for Central Africa, Tervuren, BelgiumRoyal Museum for Central AfricaTervurenBelgium
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Michelle L Hart
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Steven Janssens
- Meise Botanic Garden, Meise, BelgiumMeise Botanic GardenMeiseBelgium
- Leuven Plant Institute, Department of Biology, Leuven, BelgiumLeuven Plant Institute, Department of BiologyLeuvenBelgium
| | - Catherine Kidner
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | | | - Joshua V Peñalba
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Flávia Pezzini
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMuseum für Naturkunde, Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Gontran Sonet
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Massimiliano Virgilio
- Royal Museum for Central Africa, Department of African Zoology, Tervuren, BelgiumRoyal Museum for Central Africa, Department of African ZoologyTervurenBelgium
| | - Peter M Hollingsworth
- Royal Botanic Garden Edinburgh, Edinburgh, United KingdomRoyal Botanic Garden EdinburghEdinburghUnited Kingdom
| |
Collapse
|
5
|
Llano-Arias CA, Guevara G, Bartlett CR. The Genus Thionia Stål, 1859 (Hemiptera: Auchenorrhyncha: Issidae) in Colombia: Highlighting the Value of Entomological Collections. NEOTROPICAL ENTOMOLOGY 2023; 52:81-91. [PMID: 36401152 PMCID: PMC9886584 DOI: 10.1007/s13744-022-01002-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Entomological collections represent a key source of information about the biological heritage of a country. However, the taxonomy and knowledge of many arthropods from megadiverse countries are underrepresented in these natural history collections as is the case with several planthoppers of the suborder Auchenorrhyncha. Issidae are fulgoromorphs distributed worldwide, except the poles and Greenland. Despite this ubiquity, Colombian planthoppers remain very poorly known and studied. Our objective was to provide the first consolidated records and distributional data for Colombian Issidae. We used reports of the representative genus Thionia deposited in biological collections in Colombia. In addition, we linked voucher specimen information and Olson's life zones showing an inter-Andean valley and Eastern Andean Cordillera distribution within Colombia. Our survey of Colombian biological collections revealed 55 individuals of the genus Thionia Stål, 1859 (53 adults, 2 immatures [nymphs]), which were collected by different methods; however, many of those records may be opportunistic. This genus (and its species) needs further study, with systematic and ecological revision, as is the case with other terrestrial Colombian hemipterans. Our consolidated records represent an advance to the knowledge of Issidae (and Thionia specifically) for the Neotropics and Colombia in particular, and a baseline for further study of distributional and biogeographic patterns of the suborder Auchenorrhyncha.
Collapse
Affiliation(s)
- Camilo Andrés Llano-Arias
- Grupo de Investigación BioNat, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Giovany Guevara
- Grupo de Investigación en Zoología (GIZ), Departamento de Biología, Facultad de Ciencias, Universidad del Tolima, Ibagué, Colombia.
| | - Charles R Bartlett
- Associate Professor of Entomology, Department of Entomology and Wildlife Ecology, University of Delaware, Newark, Delaware, USA
| |
Collapse
|
6
|
Tong C, Avilés L, Rayor LS, Mikheyev AS, Linksvayer TA. Genomic signatures of recent convergent transitions to social life in spiders. Nat Commun 2022; 13:6967. [PMID: 36414623 PMCID: PMC9681848 DOI: 10.1038/s41467-022-34446-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 10/25/2022] [Indexed: 11/24/2022] Open
Abstract
The transition from solitary to social life is a major phenotypic innovation, but its genetic underpinnings are largely unknown. To identify genomic changes associated with this transition, we compare the genomes of 22 spider species representing eight recent and independent origins of sociality. Hundreds of genes tend to experience shifts in selection during the repeated transition to social life. These genes are associated with several key functions, such as neurogenesis, behavior, and metabolism, and include genes that previously have been implicated in animal social behavior and human behavioral disorders. In addition, social species have elevated genome-wide rates of molecular evolution associated with relaxed selection caused by reduced effective population size. Altogether, our study provides unprecedented insights into the genomic signatures of social evolution and the specific genetic changes that repeatedly underpin the evolution of sociality. Our study also highlights the heretofore unappreciated potential of transcriptomics using ethanol-preserved specimens for comparative genomics and phylotranscriptomics.
Collapse
Affiliation(s)
- Chao Tong
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Leticia Avilés
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Linda S Rayor
- Department of Entomology, Cornell University, Ithaca, NY, 14853, USA
| | - Alexander S Mikheyev
- Evolutionary Genomics Group, Research School of Biology, Australian National University, Canberra, 0200, Australia
| | - Timothy A Linksvayer
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA.
| |
Collapse
|
7
|
Montero‐Castaño A, Koch JBU, Lindsay TT, Love B, Mola JM, Newman K, Sharkey JK. Pursuing best practices for minimizing wild bee captures to support biological research. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
| | - Jonathan Berenguer Uhuad Koch
- U.S. Department of Agriculture‐Agricultural Research Service Pollinating Insect‐Biology, Management, and Systematics Research Unit Logan Utah USA
| | - Thuy‐Tien Thai Lindsay
- U.S. Department of Agriculture‐Agricultural Research Service Pollinating Insect‐Biology, Management, and Systematics Research Unit Logan Utah USA
| | - Byron Love
- U.S. Department of Agriculture‐Agricultural Research Service Pollinating Insect‐Biology, Management, and Systematics Research Unit Logan Utah USA
| | - John M. Mola
- U.S. Geological Survey Fort Collins Science Center Fort Collins Colorado USA
| | - Kiera Newman
- School of Environmental Sciences University of Guelph Guelph Ontario Canada
| | - Janean K. Sharkey
- School of Environmental Sciences University of Guelph Guelph Ontario Canada
| |
Collapse
|
8
|
Doré M, Willmott K, Leroy B, Chazot N, Mallet J, Freitas AVL, Hall JPW, Lamas G, Dasmahapatra KK, Fontaine C, Elias M. Anthropogenic pressures coincide with Neotropical biodiversity hotspots in a flagship butterfly group. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Maël Doré
- Institut de Systématique, Evolution, Biodiversité MNHN‐CNRS‐Sorbonne Université‐EPHE‐Université des AntillesMuséum national d’Histoire naturelle de Paris Paris France
- Centre d’Ecologie et des Sciences de la Conservation UMR 7204 MNHN‐CNRS‐Sorbonne Université Muséum national d’Histoire naturelle de Paris Paris France
| | - Keith Willmott
- McGuire Center for Lepidoptera and Biodiversity Florida Museum of Natural History University of Florida Gainesville Florida USA
| | - Boris Leroy
- Unité Biologie des Organismes et Ecosystèmes Aquatiques (BOREA UMR 7208) Muséum National d’Histoire Naturelle Sorbonne UniversitésUniversité de Caen NormandieUniversité des AntillesCNRSIRD Paris France
| | - Nicolas Chazot
- Swedish University of Agricultural Sciences Uppsala Sweden
| | - James Mallet
- Dept of Organismic and Evolutionary Biology Harvard University Cambridge Massachusetts USA
| | - André V. L. Freitas
- Departamento de Biologia Animal and Museu da Biodiversidade Instituto de Biologia Universidade Estadual de Campinas São Paulo Brazil
| | - Jason P. W. Hall
- Department of Entomology National Museum of Natural History Smithsonian Institution Washington District of Columbia USA
| | - Gerardo Lamas
- Museo de Historia Natural Universidad Nacional Mayor de San Marcos Lima Peru
| | | | - Colin Fontaine
- Centre d’Ecologie et des Sciences de la Conservation UMR 7204 MNHN‐CNRS‐Sorbonne Université Muséum national d’Histoire naturelle de Paris Paris France
| | - Marianne Elias
- Institut de Systématique, Evolution, Biodiversité MNHN‐CNRS‐Sorbonne Université‐EPHE‐Université des AntillesMuséum national d’Histoire naturelle de Paris Paris France
| |
Collapse
|
9
|
Old Brains in Alcohol: The Usability of Legacy Collection Material to Study the Spider Neuroarchitecture. DIVERSITY 2021. [DOI: 10.3390/d13110601] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Natural history collections include rare and significant taxa that might otherwise be unavailable for comparative studies. However, curators must balance the needs of current and long-term research. Methods of data extraction that minimize the impact on specimens are therefore favored. Micro-CT has the potential to expose new character systems based on internal anatomy to taxonomic and phylogenetic analysis without dissection or thin sectioning for histology. However, commonly applied micro-CT protocols involve critical point drying, which permanently changes the specimen. Here, we apply a minimally destructive method of specimen preparation for micro-CT investigation of spider neuroanatomy suitable for application to legacy specimens in natural history collections. We used two groups of female spiders of the common species Araneus diadematus—freshly captured (n = 11) vs. legacy material between 70 and 90 years old (n = 10)—to qualitatively and quantitatively assess the viability of micro-CT scanning and the impact of aging on their neuroarchitecture. We statistically compared the volumes of the supraesophageal ganglion (syncerebrum) and used 2D geometric morphometrics to analyze variations in the gross shape of the brain. We found no significant differences in the brain shape or the brain volume relative to the cephalothorax size. Nonetheless, a significant difference was observed in the spider size. We considered such differences to be explained by environmental factors rather than preservation artifacts. Comparison between legacy and freshly collected specimens indicates that museum specimens do not degrade over time in a way that might bias the study results, as long as the basic preservation conditions are consistently maintained, and where lapses in preservation have occurred, these can be identified. This, together with the relatively low-impact nature of the micro-CT protocol applied here, could facilitate the use of old, rare, and valuable material from collections in studies of internal morphology.
Collapse
|
10
|
Grewe F, Kronforst MR, Pierce NE, Moreau CS. Museum genomics reveals the Xerces blue butterfly ( Glaucopsyche xerces) was a distinct species driven to extinction. Biol Lett 2021; 17:20210123. [PMID: 34283930 PMCID: PMC8292013 DOI: 10.1098/rsbl.2021.0123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The last Xerces blue butterfly was seen in the early 1940s, and its extinction is credited to human urban development. This butterfly has become a North American icon for insect conservation, but some have questioned whether it was truly a distinct species, or simply an isolated population of another living species. To address this question, we leveraged next-generation sequencing using a 93-year-old museum specimen. We applied a genome skimming strategy that aimed for the organellar genome and high-copy fractions of the nuclear genome by a shallow sequencing approach. From these data, we were able to recover over 200 million nucleotides, which assembled into several phylogenetically informative markers and the near-complete mitochondrial genome. From our phylogenetic analyses and haplotype network analysis we conclude that the Xerces blue butterfly was a distinct species driven to extinction.
Collapse
Affiliation(s)
- Felix Grewe
- Grainger Bioinformatics Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - Marcus R Kronforst
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Corrie S Moreau
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
11
|
Sheehan MJ, Miller SE. The promises and challenges of archiving insect behavior and natural history in a changing world. CURRENT OPINION IN INSECT SCIENCE 2021; 45:115-120. [PMID: 33857642 PMCID: PMC8316380 DOI: 10.1016/j.cois.2021.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/21/2021] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
Insect behavioral ecologists are not routinely archiving their behavioral media files and natural history observations. This is especially problematic because most behaviors are not preserved by the physical specimens stored in typical natural history collections. Improving the reporting and archiving of insect behavior and natural history data holds the promise of allowing scientists to track real-time responses of animals to global change and will preserve aspects of natural history that might otherwise be lost due to extinctions. Here we argue that behavioral ecologists should work to preserve and archive raw media files and field notes related to behavior and natural history of their study organisms. One major mechanism to incentivize archiving of such data would be for journals to develop policies for archiving of natural history data that is the focus of the paper or ancillary information collected about study subjects. Buy in from researchers, journals, and funding agencies will be needed to make substantial changes in data archiving.
Collapse
Affiliation(s)
- Michael J Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, United States.
| | - Sara E Miller
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, United States
| |
Collapse
|
12
|
Gerovichev A, Sadeh A, Winter V, Bar-Massada A, Keasar T, Keasar C. High Throughput Data Acquisition and Deep Learning for Insect Ecoinformatics. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.600931] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ecology documents and interprets the abundance and distribution of organisms. Ecoinformatics addresses this challenge by analyzing databases of observational data. Ecoinformatics of insects has high scientific and applied importance, as insects are abundant, speciose, and involved in many ecosystem functions. They also crucially impact human well-being, and human activities dramatically affect insect demography and phenology. Hazards, such as pollinator declines, outbreaks of agricultural pests and the spread insect-borne diseases, raise an urgent need to develop ecoinformatics strategies for their study. Yet, insect databases are mostly focused on a small number of pest species, as data acquisition is labor-intensive and requires taxonomical expertise. Thus, despite decades of research, we have only a qualitative notion regarding fundamental questions of insect ecology, and only limited knowledge about the spatio-temporal distribution of insects. We describe a novel high throughput cost-effective approach for monitoring flying insects as an enabling step toward “big data” entomology. The proposed approach combines “high tech” deep learning with “low tech” sticky traps that sample flying insects in diverse locations. As a proof of concept we considered three recent insect invaders of Israel’s forest ecosystem: two hemipteran pests of eucalypts and a parasitoid wasp that attacks one of them. We developed software, based on deep learning, to identify the three species in images of sticky traps from Eucalyptus forests. These image processing tasks are quite difficult as the insects are small (<5 mm) and stick to the traps in random poses. The resulting deep learning model discriminated the three focal organisms from one another, as well as from other elements such as leaves and other insects, with high precision. We used the model to compare the abundances of these species among six sites, and validated the results by manually counting insects on the traps. Having demonstrated the power of the proposed approach, we started a more ambitious study that monitors these insects at larger spatial and temporal scales. We aim at building an ecoinformatics repository for trap images and generating data-driven models of the populations’ dynamics and morphological traits.
Collapse
|
13
|
Abstract
Most animal species on Earth are insects, and recent reports suggest that their abundance is in drastic decline. Although these reports come from a wide range of insect taxa and regions, the evidence to assess the extent of the phenomenon is sparse. Insect populations are challenging to study, and most monitoring methods are labor intensive and inefficient. Advances in computer vision and deep learning provide potential new solutions to this global challenge. Cameras and other sensors can effectively, continuously, and noninvasively perform entomological observations throughout diurnal and seasonal cycles. The physical appearance of specimens can also be captured by automated imaging in the laboratory. When trained on these data, deep learning models can provide estimates of insect abundance, biomass, and diversity. Further, deep learning models can quantify variation in phenotypic traits, behavior, and interactions. Here, we connect recent developments in deep learning and computer vision to the urgent demand for more cost-efficient monitoring of insects and other invertebrates. We present examples of sensor-based monitoring of insects. We show how deep learning tools can be applied to exceptionally large datasets to derive ecological information and discuss the challenges that lie ahead for the implementation of such solutions in entomology. We identify four focal areas, which will facilitate this transformation: 1) validation of image-based taxonomic identification; 2) generation of sufficient training data; 3) development of public, curated reference databases; and 4) solutions to integrate deep learning and molecular tools.
Collapse
|
14
|
Duffus NE, Christie CR, Morimoto J. Insect Cultural Services: How Insects Have Changed Our Lives and How Can We Do Better for Them. INSECTS 2021; 12:insects12050377. [PMID: 33921962 PMCID: PMC8143511 DOI: 10.3390/insects12050377] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 12/15/2022]
Abstract
Simple Summary Insects—as many other organisms—provide services for our societies, which are essential for our sustainable future. A classic example of an insect service is pollination, without which food production collapses. To date, though, there has often been a generalised misconception about the benefits of insects to our societies, and misunderstandings on how insects have revolutionised our cultures and thus our lives. This misunderstanding likely underpins the general avoidance, disregard for, or even deliberate attempts to exterminate insects from our daily lives. In this Perspective, we provide a different viewpoint, and highlight the key areas in which insects have changed our cultures, from culinary traditions to architecture to fashion and beyond. We then propose a general framework to help portray insects—and their benefits to our societies—under a positive light, and argue that this can help with long-term changes in people’s attitude towards insects. This change will in turn contribute to more appropriate conservation efforts aimed to protect insect biodiversity and the services it provides. Therefore, our ultimate goal in the paper is to raise awareness of the intricate and wonderful cultural relationships between people and insects that are fundamental to our long-term survival in our changing world. Abstract Societies have benefited directly and indirectly from ecosystem services provided by insects for centuries (e.g., pollination by bees and waste recycling by beetles). The relationship between people and insect ecosystem services has evolved and influenced how societies perceive and relate to nature and with each other, for example, by shaping cultural values (‘cultural ecosystem services’). Thus, better understanding the significance of insect cultural services can change societies’ motivations underpinning conservation efforts. To date, however, we still overlook the significance of many insect cultural services in shaping our societies, which in turn likely contributes to the generalised misconceptions and misrepresentations of insects in the media such as television and the internet. To address this gap, we have reviewed an identified list of insect cultural services that influence our societies on a daily basis, including cultural services related to art, recreation, and the development of traditional belief systems. This list allowed us to formulate a multi-level framework which aims to serve as a compass to guide societies to better appreciate and potentially change the perception of insect cultural services from individual to global levels. This framework can become an important tool for gaining public support for conservation interventions targeting insects and the services that they provide. More broadly, this framework highlights the importance of considering cultural ecosystems services—for which values can be difficult to quantify in traditional terms—in shaping the relationship between people and nature.
Collapse
|
15
|
Bernaola L, Darlington M, Britt K, Prade P, Roth M, Pekarcik A, Boone M, Ricke D, Tran A, King J, Carruthers K, Thompson M, Ternest JJ, Anderson SE, Gula SW, Hauri KC, Pecenka JR, Grover S, Puri H, Vakil SG. Technological Advances to Address Current Issues in Entomology: 2020 Student Debates. JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:18. [PMID: 33908604 PMCID: PMC8080135 DOI: 10.1093/jisesa/ieab025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Indexed: 06/12/2023]
Abstract
The 2020 Student Debates of the Entomological Society of America (ESA) were live-streamed during the Virtual Annual Meeting to debate current, prominent entomological issues of interest to members. The Student Debates Subcommittee of the National ESA Student Affairs Committee coordinated the student efforts throughout the year and hosted the live event. This year, four unbiased introductory speakers provided background for each debate topic while four multi-university teams were each assigned a debate topic under the theme 'Technological Advances to Address Current Issues in Entomology'. The two debate topics selected were as follows: 1) What is the best taxonomic approach to identify and classify insects? and 2) What is the best current technology to address the locust swarms worldwide? Unbiased introduction speakers and debate teams began preparing approximately six months before the live event. During the live event, teams shared their critical thinking and practiced communication skills by defending their positions on either taxonomical identification and classification of insects or managing the damaging outbreaks of locusts in crops.
Collapse
Affiliation(s)
- Lina Bernaola
- Department of Entomology, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Molly Darlington
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Kadie Britt
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Patricia Prade
- Department of Entomology and Nematology, University of Florida, Fort Pierce, FL 34945, USA
| | - Morgan Roth
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Adrian Pekarcik
- Department of Entomology, The Ohio State University, Wooster, OH 44691, USA
| | - Michelle Boone
- Department of Entomology, University of Minnesota, St. Paul, MN 55108, USA
| | - Dylan Ricke
- Department of Entomology, The Ohio State University, Wooster, OH 44691, USA
| | - Anh Tran
- Department of Entomology, University of Minnesota, St. Paul, MN 55108, USA
| | - Joanie King
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Kelly Carruthers
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32608, USA
| | - Morgan Thompson
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - John J Ternest
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32608, USA
| | - Sarah E Anderson
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32608, USA
| | - Scott W Gula
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
| | - Kayleigh C Hauri
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Jacob R Pecenka
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA
| | - Sajjan Grover
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Heena Puri
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Surabhi Gupta Vakil
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| |
Collapse
|
16
|
Fischer EE, Cobb NS, Kawahara AY, Zaspel JM, Cognato AI. Decline of Amateur Lepidoptera Collectors Threatens the Future of Specimen-Based Research. Bioscience 2021. [DOI: 10.1093/biosci/biaa152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Abstract
Amateur butterfly and moth collectors in the United States have procured more Lepidoptera specimens than professional scientists. The advent of large government-supported database efforts has made a quantitative examination of the impact of amateur collecting of these insects possible. We reviewed trends in Lepidoptera collecting since 1800, using more than 1 million United States lepidopteran specimens that have been collected into public databases. Our findings show a steep rise in the collection of specimens after World War II, followed by a short plateau and sharp decline in the late 1990s. In contrast, the rate of observations submitted to database groups dramatically increased around 2005. Declining acquisition of Lepidoptera specimens may compromise critically important testing of contemporary and future ecological, conservation, and evolutionary hypotheses on a grand scale, particularly given documented declines in insect populations. We suggest that increasing collaboration between professional and community-based scientists could alleviate the decline in amateur-collected specimens.
Collapse
Affiliation(s)
- Erica E Fischer
- Department of Entomology, Michigan State University, East Lansing, Michigan, in the United States
| | - Neil S Cobb
- Northern Arizona University, Flagstaff, Arizona, United States
| | - Akito Y Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States
| | | | - Anthony I Cognato
- Department of Entomology, Michigan State University, East Lansing, Michigan, in the United States
| |
Collapse
|
17
|
Mason SC, Betancourt IS, Gelhaus JK. Importance of building a digital species index (spindex) for entomology collections: A case study, results and recommendations. Biodivers Data J 2021; 8:e58310. [PMID: 33390759 PMCID: PMC7773715 DOI: 10.3897/bdj.8.e58310] [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: 09/04/2020] [Accepted: 12/05/2020] [Indexed: 11/12/2022] Open
Abstract
The Entomology Collection at the Academy of Natural Sciences of Drexel University (ANSP) contains approximately four million insect specimens including some of the oldest in the Western Hemisphere. Like most large entomology collections, no complete inventory of the species represented in the collection was available and even a physical search for a species could not ensure that all available specimens would be recovered for study. Between 2010 and 2014, we created a species-level index (called here spindex) of all species and their specimen counts at ANSP, along with each species’ location in the collection. Additional data captured during the project included the higher level classification of each species and type of specimen preparation. The spindex is searchable online: http://symbiont.ansp.org/entomology/. The spindex project documented 96,126 species in the ANSP Entomology Collection, representing about 10% of the described insect fauna. Additionally, over 900 putative primary types were discovered outside the Primary Type Collection. The completion of this project has improved access to the collection by enabling scientists and other users worldwide to search these collection holdings remotely and has facilitated staff in curation, research, collection management and funding proposals. A spindex is an important tool that is overlooked for planning and carrying out specimen level digitisation. This project is a case study for building a species-level index. A detailed protocol is provided, along with recommendations for other collections, including cost estimates and strategies for tracking progress and avoiding common obstacles.
Collapse
Affiliation(s)
- Stephen C Mason
- Academy of Natural Sciences of Drexel University, Philadelphia, United States of America Academy of Natural Sciences of Drexel University Philadelphia United States of America.,Drexel University, Philadelphia, PA, United States of America Drexel University Philadelphia, PA United States of America
| | - Isabelle S Betancourt
- Academy of Natural Sciences of Drexel University, Philadelphia, United States of America Academy of Natural Sciences of Drexel University Philadelphia United States of America.,Drexel University, Philadelphia, PA, United States of America Drexel University Philadelphia, PA United States of America
| | - Jon K Gelhaus
- Academy of Natural Sciences of Drexel University, Philadelphia, United States of America Academy of Natural Sciences of Drexel University Philadelphia United States of America.,Drexel University, Philadelphia, PA, United States of America Drexel University Philadelphia, PA United States of America
| |
Collapse
|
18
|
Weigand AM, Desquiotz N, Weigand H, Szucsich N. Application of propylene glycol in DNA-based studies of invertebrates. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.57278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
High-throughput sequencing (HTS) studies on invertebrates commonly use ethanol as the main sample fixative (upon collection) and preservative (for storage and curation). However, alternative agents exists, which should not be automatically neglected when studies are newly designed. This review provides an overview of the application of propylene glycol (PG) in DNA-based studies of invertebrates, thus to stimulate an evidence-based discussion.
The use of PG in DNA-based studies of invertebrates is still limited (n = 79), but a steady increase has been visible since 2011. Most studies used PG as a fixative for passive trapping (73%) and performed Sanger sequencing (66%; e.g. DNA barcoding). More recently, HTS setups joined the field (11%). Terrestrial Coleoptera (30%) and Diptera (20%) were the most studied groups. Very often, information on the grade of PG used (75%) or storage conditions (duration, temperature) were lacking. This rendered direct comparisons of study results difficult, and highlight the need for further systematic studies on these subjects.
When compared to absolute ethanol, PG can be more widely and cheaply acquired (e.g. as an antifreeze, 13% of studies). It also enables longer trapping intervals, being especially relevant at remote or hard-to-reach places. Shipping of PG-conserved samples is regarded as risk-free and is authorised, pinpointing its potential for larger trapping programs or citizen science projects. Its property to retain flexibility of morphological characters as well as to lead to a reduced shrinkage effect was especially appraised by integrative study designs. Finally, the so far limited application of PG in the context of HTS showed promising results for short read amplicon sequencing and reduced representation methods. Knowledge of the influence of PG fixation and storage for long(er) read HTS setups is currently unavailable.
Given our review results and taking difficulties of direct methodological comparisons into account, future DNA-based studies of invertebrates should on a case-by-case basis critically scrutinise if the application of PG in their anticipated study design can be of benefit.
Collapse
|
19
|
Orr RJS, Sannum MM, Boessenkool S, Di Martino E, Gordon DP, Mello HL, Obst M, Ramsfjell MH, Smith AM, Liow LH. A molecular phylogeny of historical and contemporary specimens of an under-studied micro-invertebrate group. Ecol Evol 2021; 11:309-320. [PMID: 33437431 PMCID: PMC7790615 DOI: 10.1002/ece3.7042] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/08/2020] [Accepted: 10/28/2020] [Indexed: 11/06/2022] Open
Abstract
Resolution of relationships at lower taxonomic levels is crucial for answering many evolutionary questions, and as such, sufficiently varied species representation is vital. This latter goal is not always achievable with relatively fresh samples. To alleviate the difficulties in procuring rarer taxa, we have seen increasing utilization of historical specimens in building molecular phylogenies using high throughput sequencing. This effort, however, has mainly focused on large-bodied or well-studied groups, with small-bodied and under-studied taxa under-prioritized. Here, we utilize both historical and contemporary specimens, to increase the resolution of phylogenetic relationships among a group of under-studied and small-bodied metazoans, namely, cheilostome bryozoans. In this study, we pioneer the sequencing of air-dried cheilostomes, utilizing a recently developed library preparation method for low DNA input. We evaluate a de novo mitogenome assembly and two iterative methods, using the sequenced target specimen as a reference for mapping, for our sequences. In doing so, we present mitochondrial and ribosomal RNA sequences of 43 cheilostomes representing 37 species, including 14 from historical samples ranging from 50 to 149 years old. The inferred phylogenetic relationships of these samples, analyzed together with publicly available sequence data, are shown in a statistically well-supported 65 taxa and 17 genes cheilostome tree, which is also the most broadly sampled and largest to date. The robust phylogenetic placement of historical samples whose contemporary conspecifics and/or congenerics have been sequenced verifies the appropriateness of our workflow and gives confidence in the phylogenetic placement of those historical samples for which there are no close relatives sequenced. The success of our workflow is highlighted by the circularization of a total of 27 mitogenomes, seven from historical cheilostome samples. Our study highlights the potential of utilizing DNA from micro-invertebrate specimens stored in natural history collections for resolving phylogenetic relationships among species.
Collapse
Affiliation(s)
| | | | - Sanne Boessenkool
- Department of BiosciencesCentre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | | | - Dennis P. Gordon
- National Institute of Water and Atmospheric ResearchWellingtonNew Zealand
| | - Hannah L. Mello
- Department of Marine ScienceUniversity of OtagoDunedinNew Zealand
| | - Matthias Obst
- Department of Marine SciencesUniversity of GothenburgGothenburgSweden
| | | | - Abigail M. Smith
- Department of Marine ScienceUniversity of OtagoDunedinNew Zealand
| | - Lee Hsiang Liow
- Natural History MuseumUniversity of OsloOsloNorway
- Department of BiosciencesCentre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| |
Collapse
|
20
|
Miralles A, Bruy T, Wolcott K, Scherz MD, Begerow D, Beszteri B, Bonkowski M, Felden J, Gemeinholzer B, Glaw F, Glöckner FO, Hawlitschek O, Kostadinov I, Nattkemper TW, Printzen C, Renz J, Rybalka N, Stadler M, Weibulat T, Wilke T, Renner SS, Vences M. Repositories for Taxonomic Data: Where We Are and What is Missing. Syst Biol 2020; 69:1231-1253. [PMID: 32298457 PMCID: PMC7584136 DOI: 10.1093/sysbio/syaa026] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 02/20/2020] [Accepted: 03/24/2020] [Indexed: 12/05/2022] Open
Abstract
Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000-20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term-ideally perpetual-data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach-linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $ \le $2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000-40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.].
Collapse
Affiliation(s)
- Aurélien Miralles
- Departement Origins and Evolution, Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Teddy Bruy
- Departement Origins and Evolution, Institut Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, 57 rue Cuvier, CP50, 75005 Paris, France
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Katherine Wolcott
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Mark D Scherz
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
- Department of Biology, Universität Konstanz, Universitätstraße 10, 78464 Konstanz, Germany
| | - Dominik Begerow
- Department of Geobotany, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Bank Beszteri
- Department of Phycology, Faculty of Biology, University of Duisburg-Essen, Universitätsstraße 2, 45141 Essen, Germany
| | - Michael Bonkowski
- Department of Terrestrial Ecology, Center of Excellence in Plant Sciences (CEPLAS), Terrestrial Ecology, Institute of Zoology, University of Cologne, 50674 Köln, Germany
| | - Janine Felden
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Leobenerstraße 8, 28359 Bremen, Germany
- Alfred Wegener Institute - Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Birgit Gemeinholzer
- Department of Systematic Botany, Justus Liebig University Gießen, Heinrich-Buff Ring 38, 35392 Giessen, Germany
| | - Frank Glaw
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
| | - Frank Oliver Glöckner
- Alfred Wegener Institute - Helmholtz Center for Polar- and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Oliver Hawlitschek
- Department of Herpetology, Zoologische Staatssammlung München (ZSM-SNSB), Münchhausenstraße 21, 81247 München, Germany
- Department of Scientific Infrastructure, Centrum für Naturkunde (CeNak), Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Ivaylo Kostadinov
- GFBio - Gesellschaft für Biologische Daten e.V., c/o Research II, Campus Ring 1, 28759 Bremen, Germany
| | - Tim W Nattkemper
- Biodata Mining Group, Center of Biotechnology (CeBiTec), Bielefeld University, PO Box 100131, 33501 Bielefeld, Germany
| | - Christian Printzen
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, 60325 Frankfurt/Main, Germany
| | - Jasmin Renz
- Zooplankton Research Group, DZMB – Senckenberg am Meer, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Nataliya Rybalka
- Department of Experimental Phycology and Culture Collection of Algae, University Göttingen, Nikolausberger-Weg 18, 37073 Göttingen, Germany
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Tanja Weibulat
- GFBio - Gesellschaft für Biologische Daten e.V., c/o Research II, Campus Ring 1, 28759 Bremen, Germany
| | - Thomas Wilke
- Department of Animal Ecology and Systematics, Justus Liebig University Gießen, Heinrich-Buff Ring 26, 35392 Giessen, Germany
| | - Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzingerstraße 67, 80638 Munich, Germany
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany
| |
Collapse
|
21
|
Rosas-Ramos N, Mas-Peinado P, Gil-Tapetado D, Recuero E, Ruiz JL, García-París M. Catalogue, distribution, taxonomic notes, and conservation of the Western Palearctic endemic hunchback beetles (Tenebrionidae, Misolampus). Zookeys 2020; 963:81-129. [PMID: 32922132 PMCID: PMC7458947 DOI: 10.3897/zookeys.963.53500] [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: 04/21/2020] [Accepted: 07/10/2020] [Indexed: 11/12/2022] Open
Abstract
Hunchback darkling beetles of the Ibero-Maghrebian genus Misolampus Latreille, 1807 (Tenebrionidae, Stenochiinae) encompass six species: M. gibbulus (Herbst, 1799), M. goudotii Guérin-Méneville, 1834, M. lusitanicus Brême, 1842, M. ramburii Brême, 1842, M. scabricollis Graells, 1849, and M. subglaber Rosenhauer, 1856. Previously known distribution ranges of the species were delineated using many old records, the persistence of such populations being questionable under the current situation of global biodiversity loss. Additionally, the status of geographically isolated populations of the genus have been the subject of taxonomic controversy. An exhaustive bibliographical revision and field search was undertaken, and the Misolampus collection of the Museo Nacional de Ciencias Naturales (MNCN-CSIC) was revised. The aims are to (i) provide an updated geographic distribution range for the species of Misolampus; (ii) to determine the taxonomic status of controversial populations; (iii) to provide a catalogue for Misolampus; and (iv) to discuss the conservation status of these saproxylic beetles. As a result, a catalogue including synonymies and type localities, geographical records, diagnoses, and information on natural history for all species of Misolampus is presented. The results reveal that the distribution ranges of the species of Misolampus have not undergone a reduction in the last century, and indicate the presence of the genus in areas where it had never been recorded before. The morphological variability of M. goudotii drove the proposal of different taxa that are here formally synonymised as follows: M. goudotii Guérin-Méneville, 1834 = M. erichsoni Vauloger de Beaupré, 1900, syn. nov. = M. peyerimhoffi Antoine, 1926, syn. nov.
Collapse
Affiliation(s)
- Natalia Rosas-Ramos
- Departamento de Biología Animal (Área de Zoología), Facultad de Biología (Edificio de Farmacia, planta 5), Universidad de Salamanca, Campus Miguel de Unamuno s/n, 37007 Salamanca, SpainMuseo Nacional de Ciencias NaturalesMadridSpain
- Departamento de Biodiversidad y Biología Evolutiva. Museo Nacional de Ciencias Naturales, MNCN-CSIC. c/ José Gutiérrez Abascal, 2. 28006, Madrid, SpainUniversidad de SalamancaSalamancaSpain
| | - Paloma Mas-Peinado
- Departamento de Biodiversidad y Biología Evolutiva. Museo Nacional de Ciencias Naturales, MNCN-CSIC. c/ José Gutiérrez Abascal, 2. 28006, Madrid, SpainUniversidad de SalamancaSalamancaSpain
- Centro de Investigación en Biodiversidad y Cambio Global CIBC-UAM, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin 2, 28049-Madrid, SpainUniversidad Autónoma de MadridMadridSpain
| | - Diego Gil-Tapetado
- Departamento de Biodiversidad y Biología Evolutiva. Museo Nacional de Ciencias Naturales, MNCN-CSIC. c/ José Gutiérrez Abascal, 2. 28006, Madrid, SpainUniversidad de SalamancaSalamancaSpain
- Departamento de Biología, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, c/ José Antonio Novais, 12, 28040-Madrid, SpainUniversidad Complutense de MadridMadridSpain
| | - Ernesto Recuero
- Departamento de Biodiversidad y Biología Evolutiva. Museo Nacional de Ciencias Naturales, MNCN-CSIC. c/ José Gutiérrez Abascal, 2. 28006, Madrid, SpainUniversidad de SalamancaSalamancaSpain
| | - José L. Ruiz
- Instituto de Estudios Ceutíes. Paseo del Revellín, 30. 51001 Ceuta, SpainInstituto de Estudios CeutíesCeutaSpain
| | - Mario García-París
- Departamento de Biodiversidad y Biología Evolutiva. Museo Nacional de Ciencias Naturales, MNCN-CSIC. c/ José Gutiérrez Abascal, 2. 28006, Madrid, SpainUniversidad de SalamancaSalamancaSpain
| |
Collapse
|
22
|
Miller SE, Barrow LN, Ehlman SM, Goodheart JA, Greiman SE, Lutz HL, Misiewicz TM, Smith SM, Tan M, Thawley CJ, Cook JA, Light JE. Building Natural History Collections for the Twenty-First Century and Beyond. Bioscience 2020. [DOI: 10.1093/biosci/biaa069] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Abstract
Natural history collections (NHCs) are important resources for a diverse array of scientific fields. Recent digitization initiatives have broadened the user base of NHCs, and new technological innovations are using materials generated from collections to address novel scientific questions. Simultaneously, NHCs are increasingly imperiled by reductions in funding and resources. Ensuring that NHCs continue to serve as a valuable resource for future generations will require the scientific community to increase their contribution to and acknowledgement of collections. We provide recommendations and guidelines for scientists to support NHCs, focusing particularly on new users that may be unfamiliar with collections. We hope that this perspective will motivate debate on the future of NHCs and the role of the scientific community in maintaining and improving biological collections.
Collapse
Affiliation(s)
- Sara E Miller
- Cornell University Department of Neurobiology and Behavior, Ithaca, New York
| | - Lisa N Barrow
- Museum of Southwestern Biology and with the Biology Department, University of New Mexico, Albuquerque
| | - Sean M Ehlman
- Ecology, Evolution, and Behavior Department, University of Minnesota—Twin Cities, Saint Paul
| | - Jessica A Goodheart
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, in Santa Barbara, California
- Scripps Institution of Oceanography, University of California San Diego, La Jolla
| | - Stephen E Greiman
- Department of Biology, Georgia Southern University, Statesboro Georgia
| | - Holly L Lutz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois
| | - Tracy M Misiewicz
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman
| | - Stephanie M Smith
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, Illinois
| | - Milton Tan
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Urbana–Champaign, Champaign
| | - Christopher J Thawley
- Department of Biological Sciences, University of Rhode Island, Kingston
- Department of Mathematics and Sciences, Neumann University, Aston, Pennsylvania
| | - Joseph A Cook
- Museum of Southwestern Biology and with the Biology Department, University of New Mexico, Albuquerque
| | - Jessica E Light
- Department of Ecology and Conservation Biology, Texas A&M University, College Station
| |
Collapse
|
23
|
Gemeinholzer B, Vences M, Beszteri B, Bruy T, Felden J, Kostadinov I, Miralles A, Nattkemper TW, Printzen C, Renz J, Rybalka N, Schuster T, Weibulat T, Wilke T, Renner SS. Data storage and data re-use in taxonomy—the need for improved storage and accessibility of heterogeneous data. ORG DIVERS EVOL 2020. [DOI: 10.1007/s13127-019-00428-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractThe ability to rapidly generate and share molecular, visual, and acoustic data, and to compare them with existing information, and thereby to detect and name biological entities is fundamentally changing our understanding of evolutionary relationships among organisms and is also impacting taxonomy. Harnessing taxonomic data for rapid, automated species identification by machine learning tools or DNA metabarcoding techniques has great potential but will require their review, accessible storage, comprehensive comparison, and integration with prior knowledge and information. Currently, data production, management, and sharing in taxonomic studies are not keeping pace with these needs. Indeed, a survey of recent taxonomic publications provides evidence that few species descriptions in zoology and botany incorporate DNA sequence data. The use of modern high-throughput (-omics) data is so far the exception in alpha-taxonomy, although they are easily stored in GenBank and similar databases. By contrast, for the more routinely used image data, the problem is that they are rarely made available in openly accessible repositories. Improved sharing and re-using of both types of data requires institutions that maintain long-term data storage and capacity with workable, user-friendly but highly automated pipelines. Top priority should be given to standardization and pipeline development for the easy submission and storage of machine-readable data (e.g., images, audio files, videos, tables of measurements). The taxonomic community in Germany and the German Federation for Biological Data are researching options for a higher level of automation, improved linking among data submission and storage platforms, and for making existing taxonomic information more readily accessible.
Collapse
|
24
|
Cobb NS, Gall LF, Zaspel JM, Dowdy NJ, McCabe LM, Kawahara AY. Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research. PeerJ 2019; 7:e8086. [PMID: 31788358 PMCID: PMC6882419 DOI: 10.7717/peerj.8086] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/23/2019] [Indexed: 12/21/2022] Open
Abstract
Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a "vast hidden treasure trove" of biodiversity -95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation's decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number of specimens in collections has increased by approximately 1% per year over the past 30 years. We propose that this rate of increase is insufficient to provide enough data to address biodiversity research needs, and that arthropod collections should aim to triple their rate of new specimen acquisition. (4) The collections we surveyed in the United States vary broadly in a number of indicators. Collectively, there is depth and breadth, with smaller collections providing regional depth and larger collections providing greater global coverage. (5) Increased coordination across museums is needed for digitization efforts to target taxa for research and conservation goals and address long-term data needs. Two key recommendations emerge: collections should significantly increase both their specimen holdings and their digitization efforts to empower continental and global biodiversity data pipelines, and stimulate downstream research.
Collapse
Affiliation(s)
- Neil S. Cobb
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Lawrence F. Gall
- Entomology Division, Yale Peabody Museum of Natural History, New Haven, CT, United States of America
| | - Jennifer M. Zaspel
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States of America
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
| | - Nicolas J. Dowdy
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States of America
- Department of Biology, Wake Forest University, Winston-Salem, NC, United States of America
| | - Lindsie M. McCabe
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, United States of America
| | - Akito Y. Kawahara
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America
| |
Collapse
|
25
|
Derkarabetian S, Benavides LR, Giribet G. Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault. Mol Ecol Resour 2019; 19:1531-1544. [DOI: 10.1111/1755-0998.13072] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Shahan Derkarabetian
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Ligia R. Benavides
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| | - Gonzalo Giribet
- Museum of Comparative Zoology Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
| |
Collapse
|
26
|
Wong MKL, Guénard B, Lewis OT. Trait-based ecology of terrestrial arthropods. Biol Rev Camb Philos Soc 2019; 94:999-1022. [PMID: 30548743 PMCID: PMC6849530 DOI: 10.1111/brv.12488] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 12/11/2022]
Abstract
In focusing on how organisms' generalizable functional properties (traits) interact mechanistically with environments across spatial scales and levels of biological organization, trait-based approaches provide a powerful framework for attaining synthesis, generality and prediction. Trait-based research has considerably improved understanding of the assembly, structure and functioning of plant communities. Further advances in ecology may be achieved by exploring the trait-environment relationships of non-sessile, heterotrophic organisms such as terrestrial arthropods, which are geographically ubiquitous, ecologically diverse, and often important functional components of ecosystems. Trait-based studies and trait databases have recently been compiled for groups such as ants, bees, beetles, butterflies, spiders and many others; however, the explicit justification, conceptual framework, and primary-evidence base for the burgeoning field of 'terrestrial arthropod trait-based ecology' have not been well established. Consequently, there is some confusion over the scope and relevance of this field, as well as a tendency for studies to overlook important assumptions of the trait-based approach. Here we aim to provide a broad and accessible overview of the trait-based ecology of terrestrial arthropods. We first define and illustrate foundational concepts in trait-based ecology with respect to terrestrial arthropods, and justify the application of trait-based approaches to the study of their ecology. Next, we review studies in community ecology where trait-based approaches have been used to elucidate how assembly processes for terrestrial arthropod communities are influenced by niche filtering along environmental gradients (e.g. climatic, structural, and land-use gradients) and by abiotic and biotic disturbances (e.g. fire, floods, and biological invasions). We also review studies in ecosystem ecology where trait-based approaches have been used to investigate biodiversity-ecosystem function relationships: how the functional diversity of arthropod communities relates to a host of ecosystem functions and services that they mediate, such as decomposition, pollination and predation. We then suggest how future work can address fundamental assumptions and limitations by investigating trait functionality and the effects of intraspecific variation, assessing the potential for sampling methods to bias the traits and trait values observed, and enhancing the quality and consolidation of trait information in databases. A roadmap to guide observational trait-based studies is also presented. Lastly, we highlight new areas where trait-based studies on terrestrial arthropods are well positioned to advance ecological understanding and application. These include examining the roles of competitive, non-competitive and (multi-)trophic interactions in shaping coexistence, and macro-scaling trait-environment relationships to explain and predict patterns in biodiversity and ecosystem functions across space and time. We hope this review will spur and guide future applications of the trait-based framework to advance ecological insights from the most diverse eukaryotic organisms on Earth.
Collapse
Affiliation(s)
- Mark K. L. Wong
- Department of ZoologyUniversity of OxfordOxford, OX1 3PSU.K.
| | - Benoit Guénard
- School of Biological SciencesThe University of Hong Kong, Kadoorie Biological Sciences BuildingHong KongSARChina
| | - Owen T. Lewis
- Department of ZoologyUniversity of OxfordOxford, OX1 3PSU.K.
| |
Collapse
|
27
|
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
| |
Collapse
|
28
|
Matos-Maraví P, Duarte Ritter C, Barnes CJ, Nielsen M, Olsson U, Wahlberg N, Marquina D, Sääksjärvi I, Antonelli A. Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies. PeerJ 2019; 7:e6727. [PMID: 31106048 PMCID: PMC6499058 DOI: 10.7717/peerj.6727] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022] Open
Abstract
Massively parallel DNA sequencing opens up opportunities for bridging multiple temporal and spatial dimensions in biodiversity research, thanks to its efficiency to recover millions of nucleotide polymorphisms. Here, we identify the current status, discuss the main challenges, and look into future perspectives on biodiversity genomics focusing on insects, which arguably constitute the most diverse and ecologically important group among all animals. We suggest 10 simple rules that provide a succinct step-by-step guide and best-practices to anyone interested in biodiversity research through the study of insect genomics. To this end, we review relevant literature on biodiversity and evolutionary research in the field of entomology. Our compilation is targeted at researchers and students who may not yet be specialists in entomology or molecular biology. We foresee that the genomic revolution and its application to the study of non-model insect lineages will represent a major leap to our understanding of insect diversity.
Collapse
Affiliation(s)
- Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Institute of Entomology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Camila Duarte Ritter
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany
| | | | - Martin Nielsen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Section for Evolutionary Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Urban Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Daniel Marquina
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Royal Botanical Garden, Kew, Richmond, Surrey, UK
| |
Collapse
|
29
|
Rund SSC, Braak K, Cator L, Copas K, Emrich SJ, Giraldo-Calderón GI, Johansson MA, Heydari N, Hobern D, Kelly SA, Lawson D, Lord C, MacCallum RM, Roche DG, Ryan SJ, Schigel D, Vandegrift K, Watts M, Zaspel JM, Pawar S. MIReAD, a minimum information standard for reporting arthropod abundance data. Sci Data 2019; 6:40. [PMID: 31024009 PMCID: PMC6484025 DOI: 10.1038/s41597-019-0042-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/20/2019] [Indexed: 11/29/2022] Open
Abstract
Arthropods play a dominant role in natural and human-modified terrestrial ecosystem dynamics. Spatially-explicit arthropod population time-series data are crucial for statistical or mathematical models of these dynamics and assessment of their veterinary, medical, agricultural, and ecological impacts. Such data have been collected world-wide for over a century, but remain scattered and largely inaccessible. In particular, with the ever-present and growing threat of arthropod pests and vectors of infectious diseases, there are numerous historical and ongoing surveillance efforts, but the data are not reported in consistent formats and typically lack sufficient metadata to make reuse and re-analysis possible. Here, we present the first-ever minimum information standard for arthropod abundance, Minimum Information for Reusable Arthropod Abundance Data (MIReAD). Developed with broad stakeholder collaboration, it balances sufficiency for reuse with the practicality of preparing the data for submission. It is designed to optimize data (re)usability from the "FAIR," (Findable, Accessible, Interoperable, and Reusable) principles of public data archiving (PDA). This standard will facilitate data unification across research initiatives and communities dedicated to surveillance for detection and control of vector-borne diseases and pests.
Collapse
Affiliation(s)
- Samuel S C Rund
- VectorBase, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
| | - Kyle Braak
- Global Biodiversity Information Facility (GBIF) Secretariat, Copenhagen, Denmark
| | - Lauren Cator
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, United Kingdom
| | - Kyle Copas
- Global Biodiversity Information Facility (GBIF) Secretariat, Copenhagen, Denmark
| | - Scott J Emrich
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, USA
| | - Gloria I Giraldo-Calderón
- VectorBase, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
- Universidad Icesi, Facultad de Ciencias Naturales, Calle 18 No. 122-135, Cali, Colombia
| | - Michael A Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, 1324 Calle Cañada, San Juan, PR, USA
- Department of Epidemiology, Harvard School of Public Health, 677 Huntington Ave, Boston, MA, USA
| | - Naveed Heydari
- Center for Global Health and Translational Science, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Donald Hobern
- Global Biodiversity Information Facility (GBIF) Secretariat, Copenhagen, Denmark
| | - Sarah A Kelly
- VectorBase and Vector Immunogenomics and Infection Laboratory, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Daniel Lawson
- VectorBase and Vector Immunogenomics and Infection Laboratory, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Cynthia Lord
- Florida Medical Entomology Lab, University of Florida-IFAS, Vero Beach, FL, USA
| | - Robert M MacCallum
- VectorBase and Vector Immunogenomics and Infection Laboratory, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Dominique G Roche
- Institute of Biology, University of Neuchâtel, 2000, Neuchâtel, Switzerland
| | - Sadie J Ryan
- Quantitative Disease Ecology and Conservation Lab, Department of Geography, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- College of Life Sciences, University of Kwa-Zulu Natal, Durban, South Africa
| | - Dmitry Schigel
- Global Biodiversity Information Facility (GBIF) Secretariat, Copenhagen, Denmark
| | - Kurt Vandegrift
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Matthew Watts
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, United Kingdom
| | | | - Samraat Pawar
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, United Kingdom
| |
Collapse
|
30
|
Meineke EK, Davies TJ. Museum specimens provide novel insights into changing plant-herbivore interactions. Philos Trans R Soc Lond B Biol Sci 2018; 374:20170393. [PMID: 30455211 PMCID: PMC6282078 DOI: 10.1098/rstb.2017.0393] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 12/16/2022] Open
Abstract
Mounting evidence shows that species interactions may mediate how individual species respond to climate change. However, long-term anthropogenic effects on species interactions are poorly characterized owing to a lack of data. Insect herbivory is a major ecological process that represents the interaction between insect herbivores and their host plants, but historical data on insect damage to plants is particularly sparse. Here, we suggest that museum collections of insects and plants can fill key gaps in our knowledge on changing trophic interactions, including proximate mechanisms and the net outcomes of multiple global change drivers across diverse insect herbivore-plant associations. We outline theory on how global change may affect herbivores and their host plants and highlight the unique data that could be extracted from museum specimens to explore their shifting interactions. We aim to provide a framework for using museum specimens to explore how some of the most diverse co-evolved relationships are responding to climate and land use change.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.
Collapse
Affiliation(s)
- Emily K Meineke
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - T Jonathan Davies
- Departments of Botany, Forest, and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
- African Centre for DNA Barcoding, University of Johannesburg, Johannesburg 2006, South Africa
| |
Collapse
|
31
|
Decker P, Christian A, Xylander WER. VIRMISCO - The Virtual Microscope Slide Collection. Zookeys 2018:271-282. [PMID: 29706780 PMCID: PMC5904399 DOI: 10.3897/zookeys.741.22284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/08/2018] [Indexed: 11/22/2022] Open
Abstract
Digitisation allows scientists rapid access to research objects. For transparent to semi-transparent three-dimensional microscopic objects, such as microinvertebrates or small body parts of organisms, available databases are scarce. Most mounting media used for permanent microscope slides deteriorate after some years or decades, eventually leading to total damage and loss of the object. However, restoration is labour-intensive, and often the composition of the mounting media is not known. A digital preservation of important material, especially types, is important and an urgent need. The Virtual Microscope Slide Collection – VIRMISCO project has developed recommendations for taking microscopic image stacks of three-dimensional objects, depositing and presenting such series of digital image files or z-stacks as an online platform. The core of VIRMISCO is an online viewer, which enables the user to virtually focus through an object online as if using a real microscope. Additionally, VIRMISCO offers features such as search, rotating, zooming, measuring, changing brightness or contrast, taking snapshots, leaving feedback as well as downloading complete z-stacks as jpeg files or video file. The open source system can be installed by any institution and can be linked to common database or images can be sent to the Senckenberg Museum of Natural History Görlitz. The benefits of VIRMISCO are the preservation of important or fragile material, to avoid loan, to act as a digital archive for image files and to allow determination by experts from the distance, as well as providing reference libraries for taxonomic research or education and providing image series as online supplementary material for publications or digital vouchers of specimens of molecular investigations are relevant applications for VIRMISCO.
Collapse
Affiliation(s)
- Peter Decker
- Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Axel Christian
- Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | | |
Collapse
|