scholarly journals The Importance of Storing and Delivering Geochemical Data for Earth Science Collections

2019 ◽  
Vol 3 ◽  
Author(s):  
Giles Miller ◽  
Kerstin Lehnert
Keyword(s):  
Natural History ◽  
Hydrothermal Vents ◽  
Earth Science ◽  
Volcanic Eruptions ◽  
Geochemical Data ◽  
Mass Extinctions ◽  
Museum Collections ◽  
Natural History Collections ◽  
Wide Range ◽  
Biodiversity Changes

The composition and state of the earth’s lithosphere through time has had profound effect on past and present biodiversity and will continue to do so into the future. Environments ranging from deep sea hydrothermal vents to active continental volcanic centres provide a wide range of ecosystems that have shaped the planet we know. Catastrophic events relating to movements of the lithosphere and events deep in the mantle have also caused major biodiversity changes such as mass extinctions. Our museum collections contain rock and fossil specimens collected from many of these environments and suites of samples specifically collected in order to better understand the evolution of our planet. Requests to carry out geochemical investigations on these samples are common and a large amount of data is generated as a result. Currently there are no natural history collections management systems tailored towards recording and delivering these datasets and the result is that the data is recorded in various distributed systems and cannot be easily assessed and used. It is important for these analyses on our museum collections to be delivered in a standard way so that the importance and relevance of these collections can be demonstrated and large datasets generated to answer big questions regarding the geological evolution of our planet. Examples of these questions include “how and when will volcanic eruptions will occur?” and “what has been the role of volcanism during mass extinction?”. Other geochemical studies such as oxygen isotope studies have been carried out on museum collections in order to investigate past oceanic environments and the effects of changes in climate on our oceans. Geochemical data aggregators such as EarthChem have made great strides in working towards international data standards and providing portals for delivering this type of data. As we progress towards one European Collection (DiSSCo) it is vital that we recognise the importance of these natural history collections related geochemical datasets and include delivering them on the general roadmap.

scholarly journals Natural history collections recapitulate 200 years of faunal change

2021 ◽  
Vol 8 (4) ◽  
Author(s):  
Christine Ewers-Saucedo ◽  
Andreas Allspach ◽  
Christina Barilaro ◽  
Andreas Bick ◽  
Angelika Brandt ◽  
...  
Keyword(s):  
Natural History ◽  
Cross Validation ◽  
Marine Invertebrate ◽  
Species Introductions ◽  
Faunal Change ◽  
Invertebrate Species ◽  
The North ◽  
Natural History Collections ◽  
Biodiversity Changes

Changing species assemblages represent major challenges to ecosystems around the world. Retracing these changes is limited by our knowledge of past biodiversity. Natural history collections represent archives of biodiversity and are therefore an unparalleled source to study biodiversity changes. In the present study, we tested the value of natural history collections for reconstructing changes in the abundance and presence of species over time. In total, we scrutinized 17 080 quality-checked records for 242 epibenthic invertebrate species from the North and Baltic Seas collected throughout the last 200 years. Our approaches identified eight previously reported species introductions, 10 range expansions, six of which are new to science, as well as the long-term decline of 51 marine invertebrate species. The cross-validation of our results with published accounts of endangered species and neozoa of the area confirmed the results for two of the approaches for 49 to 55% of the identified species, and contradicted our results for 9 to 10%. The results based on relative record trends were less validated. We conclude that, with the proper approaches, natural history collections are an unmatched resource for recovering early species introductions and declines.

scholarly journals Uncertain Geo-Uncertainty: Ecological research and public biodiversity data repositories

2019 ◽  
Vol 3 ◽  
Author(s):  
Arnald Marcer ◽  
Elspeth Haston ◽  
Quentin Groom ◽  
F. Xavier Picó ◽  
Agustí Escobar ◽  
...  
Keyword(s):  
Natural History ◽  
Spatial Information ◽  
Species Distribution Modelling ◽  
Location Information ◽  
Ecological Research ◽  
Biodiversity Data ◽  
Data Repositories ◽  
Ecological Requirements ◽  
Natural History Collections ◽  
Wide Range

Natural history collections represent a vast and superb wealth of information gathered and curated across centuries by institutions such as natural history museums and botanical gardens around the world. The relatively recent advent and maturation of accessible computer technology has allowed the initiation of major digitization projects aimed at making the contents of these collections publicly available for education and research purposes. The final destinations of these newly digitized data are public biodiversity data repositories, of which, GBIF is the main one. These respositories are gateways where researchers can access and retrieve the data for use in a wide range of analyses. This unprecedented volume of information on biodiversity represents an extraordinary asset for research in ecology and evolution. A particularly important part of the digitized data for any given specimen is its collection location, as it indirectly gives information on the species’ habitat and thus, its ecological requirements. Many specimens in natural history collections come from a time where the collecting event, which includes the location information, was hand-written on physical tags attached to the specimen. This location information was given as a description of a place, e.g. a site name, and could be a rather precise or vague description. In order to convert this description of locality into a digitized research-grade georeferenced record, the research community has come up with a set of guidelines and recommendations; the most prominent one the point-radius method devised by Wieczorek et al. in 2004. However, and despite the public availability of this know-how, the end result is that the data available at the end of the pipeline, e.g. GBIF, often lacks georeferencing information with enough quality to be used for research purposes. Occurrence records from natural history collection datasets held at GBIF, often lack spatial coordinates and, if present, in most cases their precision and uncertainty fields are blank. The final consequence of this lack of complete georeferencing information is that the affected records are rendered useless for many kinds of research. For example, the flourishing field of species distribution modelling absolutely depends on accurate spatial information in order to be able to retrieve information on the environmental conditions in which the species live. The availability of global environmental and remote sensing datasets together with the sophisticated geospatial tools at the disposal of the researcher become powerless if no quality geoinformation is available. In this study, we perform a preliminary analysis on the status and availability of geoferencing information in datasets originated from specimens in natural history collections held at GBIF, discuss how the quality of this spatial info may affect ecological research, and conclude with some recommendations on how to better describe the georeferencing process within public digital biodiversity repositories.

scholarly journals GEOCHEMISTRY AND PETROGENESIS OF VOLCANIC ROCKS AND THEIR MANTLE SOURCE IN THE EAST VIETNAM SEA AND ADJACENT REGIONS IN THE CENOZOIC

2018 ◽  
Vol 17 (4) ◽  
pp. 406-426 ◽  
Author(s):  
Le Duc Anh ◽  
Nguyen Hoang ◽  
Phung Van Phach ◽  
Malinovskii A. I. ◽  
Kasatkin S. A. ◽  
...  
Keyword(s):  
Volcanic Rocks ◽  
Volcanic Eruptions ◽  
Geochemical Data ◽  
Central Type ◽  
Late Mesozoic ◽  
Melting Pressure ◽  
Marginal Seas ◽  
Wide Range ◽  
Primitive Magma ◽  
Continuous Range

The East Vietnam Sea is one of the largest marginal basins in western Pacific Ocenan, formed by breaking of continental margin in the Late Mesozoic. Geochemical data of the Miocene - Pleistocene bazanic samples collected in the East Sea and neighboring areas show two major eruption trends that reflect the formation and development of the region. The early eruption event is characterized by low alkaline, TiO2, Na2O, K2O and P2O5, and high SiO2 group, comprising olivine and tholeiitic bazans. The later eruption demonstrates high alkaline, TiO2, Na2O, K2O and P2O5, and low SiO2 group, mainly generated by central-type volcanic eruptions, consisting of alkaline olivine and olivine bazans. Distinctive geochemistry of the volcanic rocks within the East Vietnam Sea and adjacent areas is illustrated by wide range of Magnesium index (Mg#= 35-75). At the values of Mg#>65, the relation between Mg# and major oxides is unclear. In contrast, Mg#65 (Olivine differentiation) the isotope ratios start changing. The primitive components are computed based on the principle of olivine compensation. The computed results show that the critical pressure for Tholeiite melting was estimated from ~11.97-20.33 Kb (ca. 30 - 60 km deep) and the Alkaline melting pressure varies from ~16.87-34.93 Kb (corresponding to the depths of ~60 km to 100 km). The continuous range of melting pressures suggests two trends of tholeiitic and alkaline eruptions occurr at various depths in the same magmatic source. Hight temperature and melting pressure of the primitive magma are dependent on partial melting pressure. Possibly, this process was triggered by the asthenosphere intrusion resulted from the closure of the Neo-Tethys following the India - Eurasia collision. This event has not only made the mantle hotter and easily melted but also triggered the opening of the marginal seas, including the East Vietnam Sea.

scholarly journals Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives

2019 ◽  
Author(s):  
CA Hamilton ◽  
RA St Laurent ◽  
K Dexter ◽  
IJ Kitching ◽  
JW Breinholt ◽  
...  
Keyword(s):  
Natural History ◽  
Biological Data ◽  
Evolutionary Patterns ◽  
Natural History Collections ◽  
Preservation Method ◽  
Modified Dna ◽  
Wide Range ◽  
Anchored Hybrid Enrichment ◽  
Taxonomic Studies ◽  
Probe Set

AbstractBackgroundThe silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying some of the most spectacular forms and ecological traits among insects, relatively little attention has been given to understanding their evolution and the drivers of their diversity.ResultsTo begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, producing a well-supported phylogeny. The tree was overall consistent with prior morphological and molecular studies, although some taxa (e.g.,ArotrosSchaus) were misplaced in the Bombycidae and here formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths).ConclusionsWe postulate that these rate shifts are due to the well-documented bat-moth “arms race” and differences in selective pressures from insectivorous bats. The study establishes a backbone for future evolutionary, comparative, and taxonomic studies, and presents a modified DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections, succeeding in samples up to 30 years old. Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.

scholarly journals Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
C. A. Hamilton ◽  
R. A. St Laurent ◽  
K. Dexter ◽  
I. J. Kitching ◽  
J. W. Breinholt ◽  
...  
Keyword(s):  
Natural History ◽  
Biological Data ◽  
Ecological Traits ◽  
Evolutionary Patterns ◽  
Natural History Collections ◽  
Preservation Method ◽  
Wide Range ◽  
Anchored Hybrid Enrichment ◽  
Taxonomic Studies ◽  
Probe Set

Abstract Background Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections. Results The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa were misplaced. The bombycid Arotros Schaus was formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths). Conclusions Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth “arms race”. Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.

scholarly journals An annotated catalogue of the types of short-horned grasshoppers (Orthoptera, Caelifera) housed in the Zoological Museum Hamburg (ZMH)

2018 ◽  
Vol 2 (1) ◽  
pp. 21-30 ◽  
Author(s):  
Lara-Sophie Dey ◽  
Martin Husemann
Keyword(s):  
Natural History ◽  
Zoological Museum ◽  
Mass Extinctions ◽  
Museum Collections ◽  
Animal Life ◽  
Type Specimens ◽  
Essential Resource ◽  
Life On Earth ◽  
Formal Status ◽  
Original Reference

Zoological collections remain the main archive of animal life on earth, especially in times of mass extinctions. The most important animals of these collections are the type specimens, which represent the original reference for a species. While a full digitization of most museum collections currently remains utopic, lists of types are an essential resource for researchers to perform taxonomic revisions. Here, we provide an updated type catalogue of the short-horned grasshoppers (Caelifera) housed in the Zoological Museum of Hamburg (ZMH), now part of the Center for Natural History Hamburg (CeNak). This collection comprises 209 type specimens belonging to 128 species: 65 holotypes, three lectotypes, one syntype and a large number of paratypes. We also list topotypes of two species for reasons of completeness but note that they have no formal status. Overall, types of 13 species were added to the collection since the last catalogues in 1968 and 1977 and several corrections to the last catalogues were made. We provide a full bibliography for these species, aiming to provide a comprehensive taxonomic guide to this collection.

Joseph Sidebotham: vicissitudes of a Victorian collector

2015 ◽  
Vol 42 (2) ◽  
pp. 197-210 ◽  
Author(s):  
Laurence M. Cook
Keyword(s):  
Natural History ◽  
Species Limits ◽  
Clear Cut ◽  
Natural History Collections ◽  
As Species ◽  
Scientific World

Joseph Sidebotham (1824–1885) was a Manchester cotton baron whose natural history collections are now in the Manchester Museum. In addition to collecting he suggested a method for identifying and classifying Lepidoptera and investigated variation within species as well as species limits. With three close collaborators, he is credited with discovering many species new to Britain in both Lepidoptera and Coleoptera. A suspicion of fraud attaches to these claims. The evidence is not clear-cut in the Lepidoptera, but a possible reason is suggested why Sidebotham, as an amateur in the increasingly professional scientific world, might have engaged in deceit.

The Banksian natural history collections of the Endeavour voyage and their relevance to modern taxonomy

1981 ◽  
Vol 1981 (1) ◽  
pp. 61-70
Author(s):  
H. B. Carter ◽  
Judith A. Diment ◽  
C. J. Humphries ◽  
Alwyne Wheeler
Keyword(s):  
Natural History ◽  
Natural History Collections
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