Natural History Collections Research Articles

GridDER: Grid Detection and Evaluation in R

Observations and collections of organisms form the basis of our understanding of Earth's biodiversity and are an indispensable resource for global change studies. Geographic information is key, serving as the link between organisms and the environments they reside in. However, the geographic information associated with these records is often inaccurate, thus limiting their efficacy for research. While some tools for identifying erroneous coordinates have been developed, a prominent but less discussed source of inaccuracies arises from the use of gridded survey systems in many regions of the world. Here we present GridDER, a tool for identifying biodiversity records that have been designated locations based on widely used grid systems. Our tool also estimates the degree of environmental heterogeneity associated with grid systems, allowing users to make informed decisions about how to use such occurrence data in their research. We show that a significant proportion (∼13.5%; 261 million) of records on GBIF, the largest aggregator of natural history collection data, have potentially been assigned the centroid coordinates of grid cells of varying size, and demonstrate that our tool can reliably identify such records and quantify the associated uncertainties. GridDER can serve as a tool to not only screen for gridded points, but to quantify the geographic and environmental uncertainties associated with these records, which can be used to inform models and analyses that utilize these data, including those pertaining to global change.

Ecological disturbance reduces genomic diversity across an Alpine whitefish adaptive radiation.

Genomic diversity is associated with the adaptive potential of a population and thereby impacts the extinction risk of a species during environmental change. However, empirical data on genomic diversity of populations before environmental perturbations are rare and hence our understanding of the impact of perturbation on diversity is often limited. We here assess genomic diversity utilising whole-genome resequencing data from all four species of the Lake Constance Alpine whitefish radiation. Our data covers a period of strong but transient anthropogenic environmental change and permits us to track changes in genomic diversity in all species over time. Genomic diversity became strongly reduced during the period of anthropogenic disturbance and has not recovered yet. The decrease in genomic diversity varies between 18% and 30%, depending on the species. Interspecific allele frequency differences of SNPs located in potentially ecologically relevant genes were homogenized over time. This suggests that in addition to the reduction of genome-wide genetic variation, the differentiation that evolved in the process of adaptation to alternative ecologies between species might have been lost during the ecological disturbance. The erosion of substantial amounts of genomic variation within just a few generations in combination with the loss of potentially adaptive genomic differentiation, both of which had evolved over thousands of years, demonstrates the sensitivity of biodiversity in evolutionary young adaptive radiations towards environmental disturbance. Natural history collections, such as the one used for this study, are instrumental in the assessment of genomic consequences of anthropogenic environmental change. Historical samples enable us to document biodiversity loss against the shifting baseline syndrome and advance our understanding of the need for efficient biodiversity conservation on a global scale.

Freshwater decapod crustaceans from the state of Minas Gerais, Brazil: species composition and distribution.

Brazil contains about 5% (~120 spp.) of the total known species of freshwater decapods. Information on the occurrence of freshwater decapod species in the state of Minas Gerais is dispersed and much of this remains unpublished. We hereby propose to present the first inventory of freshwater decapods from the state, based on data compiled from publications and scientific collections and obtained from fieldwork in the state. Eleven species of freshwater decapods were recorded in Minas Gerais, including three species of crabs (Trichodactylidae), seven of shrimps (Palaemonidae) and one species of freshwater squat lobster (Aeglidae), classified into three infraorders, three families, and four genera. The genus Macrobrachium C.S. Bate, 1868 comprised most of the decapod records. The reduced number of species in relation to coastal states is related, at least in part, to the absence of amphidromic species. Environmental degradation and the construction of dams in several watersheds may be possible causes of this absence. The records obtained from surveys carried out in national parks situated in Minas Gerais and its surroundings indicate the importance of these areas for the conservation of decapod fauna in the state.

The Book by J. P. Eberhard on Applied Mathematics from the Book Collection of Kolyvan-Voskresensk Mining Plants

The purpose of the article is to consider the book by J. P. Eberhard (Johann Peter Eberhard, 1727– 1779) “Beiträge zur Mathesi Applicata...” (1757) in the context of the reconstruction of the composition of the foreign part of the book collection of Kolyvan Voznesensk mining plants. The edition is a collection of articles on applied mathematics, devoted to the issues of mechanics, optics and gnomonics and intended, according to Eberhard,“for students attending his lectures, for other teachers to prepare and conduct classes, and for those who want to help themselves in the study of applied mathematics”. The article defines the affiliation of the book to the library collections of the Kolyvan Voznesensk mining plants on the basis of service marks, reflecting the earliest stages of the use of the copy as a part of the Altai state libraries collections, attention is paid to thepersonality of the German author, whose works undoubtedly were a part of the scientific and technical thought of Europe in the second half of the XVIII century, the content of the articles composing the book and their compliance with the tasks of the Altai mining industry are revealed. The work “Beiträge zur Mathesi Applicata...” is considered in the context of other works, the continuation of which, according to the author's definition, it is and which, according to our assessment, are also presented in the book collection of the Kolyvan-Voskresensk mining plants. The results of the study expand the idea of the scale of J. P. Eberhard's personality and the relevance of his work for professional mining education and ensuring the production process in the Altai Mining District in the XVIII century, also add to the history of creation of the first in Siberia scientific technical library collection.

Distributed Team Working - Approaches for DiSSCo

As a highly decentralised research infrastructure, the Distributed System of Scientific Collections (DiSSCo) will need to develop cross-institutional teams, adopting work practices where individual staff are intensively working collectively on common tasks in a distributed environment. These flexible and distributed working practices will be essential to the delivery of the research infrastructure across a wide range of delivery partners and a geographically dispersed set of scarce resources and skills, particularly in more technical roles. Since work to consider secondment and distributed working in DiSSCo was first envisaged, there has been a step change in distributed working owing to the Covid-19 pandemic and lockdowns or other restrictions to where work could take place. This report examines distributed team working practices and how they have changed, through interviews with a range of key roles across DiSSCo Prepare institutions. It briefly examines key project management and technical team delivery techniques. It documents how some of these approaches have been piloted within DiSSCo Prepare for the development, testing and delivery of DiSSCo Policy and Digital Maturity tools. Finally, bringing this together with previous work on secondment policies and practices for DiSSCo, we make recommendations about how secondment and distributed team working can be approached to enhance DiSSCo capabilities and the likelihood of successful implementation of the research infrastructure.

Animal collection of Metropolitаn Josyf Slipy in the founds of the State natural-historical museum of the NAS of Ukraine

On the basis of literary and own research on the history of natural history collections of the State Natural History Museum of the National Academy of Sciences of Ukraine, the animal collection of Metropolitan Yosyf Slipy, which he collected during his exile in Siberia and donated to the museum, was analyzed. The obtained results will be taken into account in the further completion of the «Virtual collections» section of the information resource of the «Biodiversity of Ukraine» museum.

Outlining the aims and format of the project «Digitisation of natural history collections damaged as a result of hostilities and related factors: development of protocols and implementation based on the State Museum of Natural History of the National Academy of Sciences of Ukraine»

This article presents the format and outlines the goals and objectives of the project: "Digitisation of natural collections damaged by hostilities and associated factors: development of protocols and implementation based on the State Museum of Natural History of the National Academy of Sciences of Ukraine." This project, financed by the National Research Fund of Ukraine as part of the competition "Science for the Reconstruction of Ukraine in the War and Post-War Periods", involves the development of protocols and testing of digitisation technologies for vulnerable natural history museum collections and will be implemented in 2023-2024. The State Museum of Natural History of the National Academy of Sciences of Ukraine collections will be used to develop the protocols. Still, in general, the project has broader tasks. It is primarily aimed at the digitisation and virtual availability of natural collections that have already been damaged due to hostilities and related factors or may be damaged or lost shortly. Among the most vulnerable collections are those that require careful observance of the storage regime and are the first to undergo destruction or can be easily lost due to direct damage (for example, fire). Among such collections of the State Museum of Natural History of the National Academy of Sciences of Ukraine, the collections of invertebrate animals and herbarium funds, which were formed in 1870 and today constitute the object of the national heritage of Ukraine, have been identified. These collections are unique regarding the representativeness of the western region of Ukraine, although they are not limited to it. If these collections are lost, restoring or replacing damaged samples with equivalent ones is impossible. The consequence of the loss or damage of these collections will be the formation of a significant gap in the documentation of the history of the flora and fauna of the western region of Ukraine, which will be impossible to fill with existing data or cover with other, including foreign, collections. That is why, in martial law conditions, it is essential to develop protocols for the rapid digitisation of the most valuable and most vulnerable samples that have already suffered or may potentially suffer damage due to hostilities.

Scientific and educational potential of the malacological collection of the State Museum of Natural History of the National Academy of Sciences of Ukraine

The importance of the malacological collection of the State Museum of Natural History of the National Academy of Sciences of Ukraine in Lviv for the history and further development of malacological research in Ukraine is considered. The scientific potential of stock malacological materials, accumulated in the museum since the second half of the 19th century and significantly supplemented during the last decades, was analyzed in temporal and geographical aspects, as well as taking into account the taxonomic diversity and intraspecific conchological variability of the molluscs of Ukraine, the presence of typical materials, etc. It was found that the main (scientific) part of the malacological collection well represents the present land and freshwater mollusc fauna of Ukraine and its western part. Not represented in the museum's malacological collection are still some species that are mainly locally distributed in Ukraine and often have small sizes, which further complicates their sampling. Among the more recent additions to the malacological collection, we can especially mention the samples related to the study of the land mollusc fauna of the steppe zone of Ukraine, which remained poorly studied until the end of the 20th and even the beginning of the 21st century, as well as to the shell color and banding polymorphism in the Eastern European populations of two introduced species, Cepaea nemoralis and C. hortensis. Among the auxiliary part of the malacological collection, a large block of materials that can be used for exhibition purposes is selected. They allow demonstrating a wide range of topics from the taxonomic and morphological diversity of molluscs of Ukraine and the world to conchological adaptations. It can be useful when studying corresponding sections of a school biology course, as well as for students of biological specialties, amateur naturalists, etc. Various forms of virtual exhibiting allow to shown the public also numerous materials of the main (scientific) part of the malacological collection, which became possible within the framework of the Educational online program “Molluscs”. This allows us to talk about the gradual transformation of the main part of the malacological collection from a classical scientific collection to a scientific and educational one with virtual access.

Unlocking the genomes of formalin‐fixed freshwater fish specimens: An assessment of factors influencing DNA extraction quantity and quality

AbstractObjectiveRecent technological developments may facilitate the description of evolutionary relationships and population genetic structure as well as other information relevant to fisheries management by using readily available natural history collections. Contemporary sequence capture and short‐read sequencing methods offer opportunities to analyze highly fragmented DNA from formalin‐fixed specimens so long as enough DNA of sufficient quality is recovered.MethodsWe compared two protocols developed to extract DNA from formalin‐fixed tissues using specimens of three freshwater fishes: the Southern Brook Lamprey Ichthyomyzon gagei, Slimy Sculpin Cottus cognatus, and Brown Trout Salmo trutta. Extractions were attempted using hot alkali digestion with and without buffer wash pretreatments to compare the DNA concentration, purity, and fragment length of DNA recovered between extraction protocols, tissue types (muscle and caudal fin tissue for Brown Trout and Slimy Sculpin), and preservation periods (5 or 7 years for Southern Brook Lamprey).ResultLikelihood models generally did not detect DNA quantity differences between extraction protocols nor tissue types; however, 6.0–8.7× more DNA was recovered from Slimy Sculpin caudal fins than from muscle tissue. Extraction protocol had mixed effects on DNA purity; the wash protocol outperformed the no‐wash protocol for Slimy Sculpin and Brown Trout, but the reverse was true for the lamprey. Purer DNA was recovered from the caudal fins; however, fragment lengths were generally greater from muscle tissue for both ray‐finned species.ConclusionOur results suggest that the best tissue for sampling may depend on the quality metric considered most important for a study's objectives and that omitting time‐consuming tissue wash steps can yield DNA of quantity and quality comparable to DNA from more complex methods. Regardless of species, the DNA extracted from most samples using both protocols met quantity and quality thresholds that are likely to result in short‐read sequencing success. These results provide optimism for unlocking the wealth of genetic information in natural history collections for use in fisheries management and conservation genomics.

Digitisation of natural history collections: criteria for prioritisation

There are approximately 1.5 billion specimens kept in European Natural History Collections. The mission for the Distributed System of Scientific Collections (DiSSCo) is to unite all these specimens into a one-stop e-science infrastructure of digital specimens. This is a monumental digitisation task and criteria for how to prioritise this effort are, therefore, crucial for the success of the project. In this report, we have reviewed the literature and designed and conducted surveys of the digitisation plans and criteria used by DiSSCo Partners to understand the prioritisation criteria used in the digitisation of natural history collections. As an attempt to provide some guidance for the digitisation of specimens, we suggest that an organisation (e.g. DiSSCo or an individual institution) that is planning to digitise natural history collections considers four categories of prioritisation criteria: Relevance, Data quality, Cost and Feasibility.

Preproject 'Swiss Virtual Natural History Collection'.

The initiative 'Swiss Natural History Collection Network' (SwissCollNet) aims to improve the accessibility of the Swiss natural history collections for research, education and the wider public. In the 2021-24 funding period, SwissCollNet is identifying, prioritizing and digitizing as many collections as possible and building an online portal called the 'Swiss Virtual Natural History Collection' (hereafter SVNHC) to provide open access to harmonized sample data from Swiss collections. The University of Applied Sciences of the Grisons developed scenarios for the technical implementation of the SVNHC portal in a preliminary study on behalf of SwissCollNet and based on the requirements of collections and data centres.

Nuevos registros de la tijereta rayada Labidura riparia (Pallas, 1773) (Insecta: Dermaptera: Labiduridae) en México

The striped earwig Labidura riparia (Pallas, 1773) is a cosmopolitan species and the sole representative of the family Labiduridae in North America. In Mexico, this species has been previously mentioned for the states of Baja California, Oaxaca, Sonora, Tamaulipas, and Veracruz. In this contribution, it is reported for the first time for the states of Baja California Sur, Colima, Durango, Guerrero, Jalisco, Michoacán, Morelos, Nuevo León, Puebla, Quintana Roo, Sinaloa, and Yucatán, via the examination of vouchered specimens deposited in scientific collections. Additionally, records from the citizen science platform iNaturalist were consulted, confirming the presence of this species in the states of Aguascalientes, Chihuahua, Ciudad de México, Coahuila, Guanajuato, Hidalgo, Nayarit, Querétaro, San Luis Potosí, Tabasco, and Zacatecas. A brief diagnosis is provided for the family, genus, and species.

ON THE NEED FOR A COMPREHENSIVE GEOECOLOGICAL ASSESSMENT OF LANDS DISTURBED BY MINING

Link for citation: Gavrilov V.L., Nemova N.A., Reznik A.V., Kosarev N.S., Kolesnikov A.A. On the need for a comprehensive geoecological assessment of lands disturbed by mining. Bulletin of the Tomsk Polytechnic University. Geo Аssets Engineering, 2023, vol. 334, no. 10, рр. 76-87. In Rus. The relevance of the study is caused by the need to systematize information on the methods and procedure for obtaining data for a comprehensive geoecological assessment of territories disturbed by mining, based on the initial state of natural and modified components of the environment with the processes and phenomena occurring in it. This enables us to obtain information about the territories required for the development of methods and techniques for the subsequent reclamation of lands disturbed by mining. Objective: using various methods and techniques, to analyze methodological approaches that allow generating the necessary and sufficient volume of primary and required information synthesized on its basis, to proceed from a general to a comprehensive and detailed geoecological assessment of territories and areas disturbed and/or planned to be disturbed by mining operations. Objects: territories of Russia in mining regions disturbed by mining operations. Methods. Pre-selection of materials published in various publications since 2000 was carried out. Russian (E-library, VINITI RAS) and international (Scopus, GeoRef) information systems, websites of specialized and general scientific journals, library collections, and authors’ materials were used. When querying, the following basic terms and phrases were used in various combinations: «geoecological assessment», «assessment methods», «territories disturbed by mining», «remote sensing», «environmental condition». Of more than 1000 pre-identified publications, mostly Russian, devoted to various aspects of collecting and obtaining information on assessing the environmental condition in mining areas, more than 150 were selected. Publications were analyzed taking into account the most complete representation by region and publication. Additionally, materials published by federal and regional management and control authorities were used. The most important and representative ones were included in the review. Results. Existing and promising methods for collecting various data used in the geoecological assessment of territories disturbed by mining are considered. If required, these data will be further processed. Environmental, economic and social problems caused by the influence of mining operations are identified, the solution of these problems requires the generation of various information. The role of reliable and representative primary data measured on various scales is formulated to make a correct assessment of their impact on basic environmental components. The influence of the conditions of mining coal and ore deposits on environmental situation of the territories is considered. The necessity of using a set of methods for collecting and processing information, selected with regard to peculiarities of each mining area and mining specifics of various mineral deposits, is shown.

Nuevos registros estatales de la araña jorobada Zosis geniculata (Olivier, 1789) (Araneae: Uloboridae) en México

The humped spider Zosis geniculata (Olivier, 1789) is a tropicopolitan spider of the venomless family Uloboridae (Araneae). This species has been recorded for Mexico without a specific locality or state being mentioned, hereby being recorded for the states of Chiapas, Coahuila, Jalisco, Nuevo León, Tamaulipas and Yucatán either via the study of vouchered specimens, the revision of photographic records from the citizen science platform iNaturalist or digital records of scientific collections. A brief diagnosis is provided for the family and the species.

Het dagboek en alba amicorum van Sámuel Cseh-Szombathy

In this paper I have analysed the itinerary of Sámuel Cseh-Szombathy, a former studentof the Reformed College of Debrecen. After having finished his studies in Göttingen andVienna, he started with a journey in 1790 through Southern German cities, the DutchRepublic, England and finally France. During his journey he wrote an itinerary where hemade a record of his costs and what he as a medical doctor found interesting: hospitals,madhouses, natural history collections and of course the most important medicalpersonalities of his time. My main questions are: How unique is this itinerary and howwell does it fit in the Hungarian tradition of itineraries of the Early Modern Time?

To the 125th anniversary of the birth of Ivan Nikitich Matochkin

Ivan Nikitich Matochkin (18991973) is a prominent anatomist of the Soviet era, whose life story, as well as scientific and organizational work, should not be forgotten. The list of his merits should include the development of the department headed by him, participation in the organization of the Arkhangelsk branch of the All-Russian Scientific Society of Anatomists, Histologists and Embryologists, the Society Knowledge, numerous scientific works on neuromorphology and angiology, the publication of scientific collections on research topics, management of Arkhangelsk State Medical Institute, defense of dissertations by many students of Professor Matochkin, which opened the way for them to a bright scientific future.
 In this article, in addition to the main milestones in the life of Professor I. N. Matochkin, previously unknown archival data are presented that complement the pages of the biography of the scientist.

Andrew Carnegie’s museum of evolution

Abstract Carnegie Institute was established in Pittsburgh, Pennsylvania, during the great age of museum building in the United States. The institute took shape over two building programmes completed in 1895 and 1907. It comprised not only a natural history museum and art gallery but also a library and a music hall. Financed solely by Andrew Carnegie, it stood as an oddity in having no founder’s collection. Carnegie’s role has been interpreted as that of a silent financial partner who turned over creative control to others. Instead, and from the start, the natural history collection and art gallery were ideologically driven to accord with their founder’s idiosyncratic values. Carnegie Institute symbolized the thinking of philosopher Herbert Spencer and educational reformer Matthew Arnold, as absorbed and interpreted by Carnegie. The collections of palaeontology, casts, reproductions, paintings and drawings were displayed to reflect both Spencer’s concept of evolution and Arnold’s concept of anti-materialism.

Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections.

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.

Research on the Comprehensive Evaluation Method of Driving Behavior of Mining Truck Drivers in an Open-Pit Mine

Trucking is an important production link in most open-pit mines, and its transportation cost accounts for more than 50% of the total production cost of open-pit mines. The quality of the driver’s driving behavior plays a crucial role in the fine control of the production cost of transportation. Different from the previous evaluation studies of drivers’ driving behavior in open-pit mines, which mainly took safety driving behavior index as a factor variable, this paper puts forward a comprehensive evaluation method of driving behavior of mining truck drivers, which takes both safety driving and transportation cost as factor variables. Taking the mining truck as the research object, firstly, a scientific and reasonable data collection scheme is established, and the data information characterizing the transport state of the mining truck is obtained through data collection and analysis. Secondly, the RKNN algorithm of time series prediction and the wavelet analysis method are used to achieve noise reduction and missing processing of the original data so as to obtain accurate sample data. Then, taking the principal component analysis method as the entry point, through constructing the principal component analysis theory model, the key index system representing safe driving behavior and transportation cost is established to realize the comprehensive evaluation of the driving behavior of mining truck drivers, and the evaluation system of “standard driving”, “prudent driving” and “aggressive driving” of mining truck drivers is formulated. The results show that after noise reduction, the accuracy of mining car operation data can be improved by 7~12%, and the transportation cost can be reduced by about 5% after the driver’s operation behavior is standardized.

The temporary exhibition as a tool for communication and relationship between science and society: the case study of the Darwin-Dohrn Museum in Naples (Italy)

ABSTRACT The temporary exhibition ‘Sharks of the Mediterranean sea’ features scientific and artistic collections. Priority focus is the knowledge of the biodiversity of the selachians of the Mediterranean sea and the Gulf of Naples (Italy), through a museum itinerary that illustrates their biology, ecology, vulnerability, protection, and scientific research. The aim here is to describe the scientific communication strategies used to inform/educate the public but above all to promote a reflection that stimulates the latter to be a protagonist of a concrete action of care and custody of the selachians through a paradigm shift of the person-sea and person-shark relationship. The result is an exhibition set up in the graphic/photographic, videographic, and scenographic/museographic aspects, focusing on the visitor’s experience, his or her psychology, emotional and aesthetic relationships with the museum spaces as well as the solicitations of curiosity triggered by the interaction with the collections.