Collection Of Natural History Museum Research Articles

GoEnrich: creating high quality genomic DNA resources from limited voucher specimen tissues or museum specimens of at-risk species for conservation-friendly use in the validation of environmental DNA assays

ObjectiveEnvironmental DNA (eDNA) methods are crucial for monitoring populations, particularly rare and cryptic species. For confident eDNA application, rigorous assay validation is required including specificity testing with genomic DNA (gDNA). However, this critical step is often difficult to achieve as obtaining fresh tissue samples from at-risk species can be difficult, highly limited, or impossible. Natural history museum collections could serve as a valuable and ethical voucher specimen resource for eDNA assay validation. The present study demonstrates the effectiveness of whole genome amplification (WGA) in providing enough gDNA to assemble high quality mitogenomes from which robust targeted eDNA assays can be designed.ResultsUsing fresh and historical museum tissue samples from six species spanning fish, birds, and mammals, we successfully developed a WGA method with an average yield of 380 to 1,268 ng gDNA per 20 µL reaction. This gDNA was used for whole genome shotgun sequencing and subsequent assembly of high quality mitogenomes using mtGrasp. These mitogenomes were then used to develop six new robust, targeted quantitative real time polymerase chain reaction-based eDNA assays and 200 ng WGA-enriched yielded satisfactory Cq values and near 100% detection frequencies for all assays tested. This approach offers a cost-effective and non-invasive alternative, streamlining eDNA research processes and aiding in conservation efforts.

Network analysis to reveal the most commonly detected compounds in predator-prey pairs in freshwater and marine mammals and fish in Europe

Marine and freshwater mammalian predators and fish samples, retrieved from environmental specimen banks (ESBs), natural history museum (NHMs) and other scientific collections, were analysed by LIFE APEX partners for a wide range of legacy and emerging contaminants (2545 in total). Network analysis was used to visualize the chemical occurrence data and reveal the predominant chemical mixtures for the freshwater and marine environments. For this purpose, a web tool was created to explore these chemical mixtures in predator-prey pairs. Predominant chemicals, defined as the most prevalent substances detected in prey-predator pairs were identified through this innovative approach. The analysis established the most frequently co-occurring substances in chemical mixtures from AP&P in the marine and freshwater environments. Freshwater and marine environments shared 23 chemicals among their top 25 predominant chemicals. Legacy chemical, including perfluorooctanesulfonic acid (PFOS), brominated diphenyl ethers (BDEs), polychlorinated biphenyls (PCBs), hexachlorobenzene and mercury were dominant chemicals in both environments. Furthermore, N-acetylaminoantipyrine was a predominant pharmaceutical in both environments. The LIFE APEX chemical mixture application (https://norman-data.eu/LIFE_APEX_Mixtures) was proven to be useful to establish most prevalent compounds in terms of number of detected counts in prey-predator pairs. Nonetheless, further research is needed to establish food chain associations of the predominant chemicals.

Taxonomic house-keeping: redescriptions of three poorly known pseudoscorpions described in the 19th century (Pseudoscorpiones: Atemnidae, Chernetidae)

The holotypes of three taxa from the collection of the Hungarian Natural History Museum are redescribed and taxonomically revised: Chernes horvathii Daday, 1889 from Azerbaijan, which is is transferred from the subfamily Chernetinae to Lamprochernetinae, as a member of the genus Pselaphochernes Beier, 1932, and newly synonymised with P. scorpioides (Hermann, 1804). Additionally, Chernes armatus Tömösváry, 1884 from West Africa is transferred from the family Chernetidae to Atemnidae, and to the genus Tamenus Beier, 1932, and Chernes brasiliensis Daday, 1889 from Brazil is confirmed as a species of Lustrochernes Beier, 1932.

New additions to the North Korean fauna based on the tenthredinid sawflies (Hymenoptera) housed in the Hungarian Natural History Museum

The North Korean sawflies housed in the Hymenoptera Collection of the Hungarian Natural History Museum are studied, with a focus on the subfamilies Athaliinae and Allantinae. Five genera and 10 species including one subspecies of the two subfamilies are identified. Athalia indiana Benson is reported for the first time from East Asia (North Korea), and further eight species and one subspecies are discovered in the new country of North Korea: Allantus helanshanicus Wei, Li and Xiao, Apethymus kolthoffi (Forsius), A. sidorenkoi Sundukov, Athalia japonica (Klug), A.proxima (Klug), A.rosae ruficornis Jakowlew, Beleses satonis (Takeuchi), Taxonus carbonarius Takeuchi, and T.montanus Togashi. Additionally, Athalia infumata (Marlatt) and Allantus exitus Lee and Ryu, syn. nov. are considered a junior subjective synonym of Athaliaproxima (Klug) and Allantus luctifer (F. Smith), respectively. Diagnoses and photographs of the newly recorded species are provided, as well as new distributional records and brief notes on the new synonymy.

The stuff of memories: Planning hindsight in animal cryobanks.

Biobanks are becoming ubiquitous infrastructures in zoology and other non-human life sciences. They promise to store frozen research samples for the long term for future use. That use remains speculative but nevertheless needs to be anticipated. Following the establishment of a physical and digital infrastructure for frozen samples in an animal biobanking project, this article explores how the future is anticipated to remember the past, and how frozen objects are shaped accordingly. Situating the biobank between mundane freezing routines in a research lab and the 'dry' and 'wet' collections of natural history museums, I argue that frozen research objects need to be conserved in two separate ways. The unavailability of cryo-objects in cold storage forces researchers to store materials independently of metadata, while retaining a link between them that allows for their reunion after thawing. The result is a split object, leading a double life at sub-zero and room temperature, linked only through the surface of special plastic containers. Following the making of such split objects, this article offers an elaboration of Radin's 'planned hindsight' as well as a reflection on the universality and particularity of biobanks as standardized scientific memory.

Not all apparently gynandromorphic butterflies are gynandrous: The case of Polyommatus icarus and its relatives (Lepidoptera: Lycaenidae)

Beside the more than two thousand normal specimens of Polyommatus icarus (Rottemburg, 1775) yielded by rearing experiments, there was one perfectly bilateral dichromatic individual first considered to be gynandrous. On the basis of analysing genitalia traits, wing surface covering scale micromorphology, and the spectral characteristics of the blue colour generated by the cover scales, the gender of the specimen has been identified as female. This exemplar was investigated in comparison with gynandrous specimens from the collections of the Hungarian Natural History Museum exhibiting various degrees of intermixing of blue and brown coloration. Focus stacking microscopy for detailed scale morphology and UV–visible reflectance spectroscopy was used for the characterization of the optical properties. Inspecting literature references and the Lycaenidae collection of the museum, further examples have been found for female bilateral dichromatism in the closely related polyommatine lycaenid species Lysandra bellargus (Rottemburg, 1775) and Lysandra coridon (Poda, 1761) what suggests that polyommatine female dichromaticity may be displayed by the manner of bilaterality and mosaicism, phenomena hitherto solely connected to gynandromorphy.

Butterflies Dismorphiinae (Lepidoptera: Pieridae) of Entomology Collection of Natural History Museum of Cauca University, Popayan, Colombia

Las colecciones biológicas almacenan organismos e información valiosa que puede ser´usada en investigaciones sobre biodiversidad. La Colección de Entomología del Museo de Historia Natural de la Universidad del Cauca - MHNUC, Colombia, alberga una considerable cantidad de ejemplares pertenecientes a diversos órdenes de insectos, entre los cuales destaca el orden Lepidoptera. Los lepidópteros son un grupo megadiverso, considerado uno de los más llamativos e importantes a nivel mundial, y Colombia es uno de los países que cuenta con mayor diversidad de este taxón. Teniendo en cuenta el potencial de las colecciones y la necesidad de organizar y poner a disposición la información sobre los lepidópteros, se realizó la revisión, organización y clasificación de los ejemplares de la subfamilia Dismorphiinae de la Colección de Entomología del MHNUC. Se encontraron 161 ejemplares de cuatro géneros, 14 especies y 18 subespecies pertenecientes a esta subfamilia de Pieridae, a partir de los cuales se realizaron análisis sobre abundancia, distribución geográfica y salud de la colección. El análisis de la calidad del inventario estableció una riqueza potencial para el departamento del Cauca de 21 especies, una pendiente de la curva de 0,12, y una proporción de especies observadas del 40,44%, que corresponde a un esfuerzo de muestreo estimado del 60,95%. Estos datos indican que el inventario no es totalmente aceptable, y que se requiere un mayor esfuerzo de muestreo para conocer los Dismorphiinae de la región suroccidental del país.

Collecting whales: processes and biases in Nordic museum collections.

Whales are unique museum objects that have entered collections in many ways and for different reasons. This work studies three Nordic natural history museum collections in Norway and Denmark with more than 2,500 whale specimens in total, and gathers the available biological and collection data on the specimens, which include skeletal elements, foetuses and organs preserved in ethanol or formalin, and a few dry-preserved organs. It finds that influx of specimens, which were mainly locally common species that were hunted, to the collections, mainly happened in the latest 1800s and earliest 1900s, fuelled by research trends, nation building, local whaling, and colonial mechanisms. Norway was a major whaling nation, but the largest hunt for whales in the Southern Ocean in the mid-1900s is not reflected in the Norwegian museum collections, probably because of the commercial focus of the whaling industry and logistical challenges, combined with limited research interest in zoological specimens at that time. The results demonstrate that it is important to understand these processes and the resulting biases for future research, outreach, and conservation.

Striped Ichthyophis Fitzinger, 1826 (Amphibia: Gymnophiona: Ichthyophiidae) from the Western Ghats of peninsular India in the collection of London's Natural History Museum and their implications for taxonomy and distribution

Striped Ichthyophis Fitzinger, 1826 (Amphibia: Gymnophiona: Ichthyophiidae) from the Western Ghats of peninsular India in the collection of London's Natural History Museum and their implications for taxonomy and distribution

Diplopod types in the Hungarian Natural History Museum, II. (Arthropoda: Myriapoda: Diplopoda)

After forty years, the type specimens kept in the Myriapoda Collection of the Hungarian Natural History Museum are revisited, a current catalogue is provided, and the status of the old names are updated and reevaluated. A total of 239 nominal taxa (species, subspecies, varietas and forma) are listed which is an almost fivefold increase compared to the number (35) of the previous catalogue from 1983. Two collections of old type specimens arrived to the museum after 1983: a set of Daday’s types from the Muséum d’Histoire Naturelle Genève in 2004, and another collection containing Loksa’s material from the Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, in 2017. Thorough search in the collection revealed type material of 66 species-group taxa originally considered lost. 53 type specimens that were supposedly deposited in the Hungarian Natural History Museum are missing, and the possible reason for that is discussed. In addition, a comprehensive bibliography is given along with the names of all type taxa dealt in those publications. With 43 figures, 8 tables, and an appendix.

Urban Beetle Diversity in Natural History Collections—A Hundred-Year Perspective

Natural history museum collections are essential for understanding biodiversity and environmental changes, especially in large cities with rapid urbanization. While the collaboration between curators and taxonomists with ecologists becomes more frequent, the museum collections still are not used to their full potential. This study aimed to digitize beetle specimens from Zagreb, which are kept in the Croatian Natural History Museum collections, provide recent nomenclature, analyse the proportion of currently endangered species, georeference, and compare the sampling locations with today’s iNaturalist citizen science records, as well as land cover changes between the time of collection creation and now. Comparing the sampling locations of collection specimens and citizen science records, it is possible to track the city’s expansion. Beetle family composition is more similar in the city centre than on the outskirts of Zagreb, where land cover changes are more pronounced. The districts in the northern part of Zagreb held higher numbers of threatened saproxylic beetles in both museum collections and citizen science records, highlighting the importance of urban parks and forests and providing insights into potential conservation threats. Museum collections have proved to be a valuable source of biodiversity records frozen in time, helping us track the urban beetle fauna decline.

Scanning electron microscopy study of Lars Silns cheilostome bryozoan type specimens in the historical collections of natural history museums in Sweden.

The type specimens of 42 cheilostome bryozoan species introduced by Lars Siln between 1938 and 1954 and housed at three different Swedish institutions (the Swedish Museum of Natural History in Stockholm, the Biological Museum in Lund and the Museum of Evolution in Uppsala) are here revised using scanning electron microscopy, with two exceptions, for the first time. As a result of this revision, new morphological observations were made for some species, such as ooecia in Antropora erecta, a costal pseudopore in Jullienula hippocrepis, intracolonial variation in the number of intracostal windows in Costaticella gisleni, and oral spines in Triphyllozoon mauritzoni. Some other observations confirmed the presence of structures/polymorphs in type material that had previously only been noted in non-type specimens, such as spinose interzooidal kenozooids in Retevirgula triangulata and putative brooding zooids in Bugulina kiuschiuensis. Structures originally interpreted as hydroid tube openings on the dorsal side of Triphyllozoon microstigmatum were confirmed to be avicularia, while the supposed kenozooidal attachment rootlet of Fedora nodosa might be the polypide tube of a coronate scyphozoan. In addition, the original combination Heliodoma goesi is here reinstated after Lagaaij assigned the species to Setosellina in 1963. The following new combinations are also proposed: Labioporella aviculifera for Siphonoporella aviculifera; Mangana canui and Mangana incrustata for Callopora canui and Tegella incrustata, respectively; Sphaerulobryozoon ovum for Fedora ovum. Lectotypes were selected when appropriate. This work clarifies the exact identity of some species that have never been recorded after their first description, such as Stylopoma magnovicellata and three species of Triphyllozoon, and contributes to the current increasing effort to digitize historical key specimens in natural history museum collections.

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.

Hidden shifts in allometry scaling between sound production and perception in anurans.

Animal communication consists of signal production and perception, which are crucial for social interactions. The main form used by anurans is auditory communication, in most cases produced as advertisement calls. Furthermore, sound perception happens mainly through an external tympanic membrane, and plays an important role in social behavior. In this study, we evaluated the influence of body and tympanic membrane sizes on call frequency across the phylogeny of anurans. We use data on snout-vent length, tympanic membrane diameter, and dominant frequency of the advertisement call from the literature and from natural history museum collections. We mapped these traits across the anuran phylogeny and tested different models of diversification. Our final dataset includes data on body size, tympanic membrane size, and call dominant frequency of 735 anuran species. The best explanatory model includes body and tympanum size with no interaction term. Although our results show that call frequency is strongly constrained by body and tympanum size, we identify five evolutionary shifts in allometry from that ancestral constraint. We relate these evolutionary shifts to the background noise experienced by populations. Body size is important for myriad ecological interactions and tympanum size is strongly associated with female call frequency preferences. Thus, allometric escape in frog calls might arise through environmental selection such as breeding in fast flowing or soundscape competition, as well as sexual selection linked to tympanum size.

Rediscovery of a lost semi-aquatic Leaf Beetle in the Hula Valley, Israel (Coleoptera, Chrysomelidae, Donaciinae).

Between 1951-1958, most of the Hula Lake and its surrounding swamps in the Upper Jordan River (Rift) Valley of Israel were drained with the supposed purposes to eliminate malaria and to reclaim land for agriculture; both reasons later proved to be unnecessary decisions. With the paucity of biological knowledge of the Hula region, especially its aquatic invertebrates, accurate assessment of the environmental damage from this drainage is still being realized. Based on natural history museum collection specimen records, the pre-drainage presence of some aquatic insect species has been verified. Among these was Donaciabicolora, a member of a semi-aquatic subfamily (Donaciinae) of Leaf Beetles (Chrysomelidae) and whose Israeli populations were thought to have gone extinct because of the drainage of the Hula and other locations. Recently this species was rediscovered in two populations. However, the molecular identification of two of these recently collected specimens from one population revealed that the identity of this species is actually Donaciasimplex. In this work, the re-discovery of this species is detailed, and its conservation importance discussed.

Taxonomy, phylogeny, and biodiversity of Lumbrineridae (Annelida, Polychaeta) from the Central Pacific Clarion-Clipperton Zone.

The DNA taxonomy of six species of the annelid family Lumbrineridae collected from the Clarion-Clipperton Zone (CCZ) in the Central Pacific, an area of potential mining interest for polymetallic nodules, is presented. Lumbrinerids are an ecologically important and understudied annelid family within the deep sea, with many species still undescribed. This study aims to document the taxonomy and biodiversity of the CCZ using specimens collected from the UK-1, OMS, and NORI-D exploration contract areas and Areas of Particular Environmental Interest. Species were identified through a combination of morphological and molecular phylogenetic analysis. We present informal species descriptions associated with voucher specimens, accessible through the Natural History Museum (London) collections, to improve future taxonomic and biodiversity studies of this region. Five taxa in this study had no morphological or genetic matches within the literature and therefore are possibly new to science, but their suboptimal morphological preservation prevented the formalisation of new species. The most abundant taxon Lumbrineridescf.laubieri (NHM_0020) was compared with the holotype of Lumbrinerideslaubieri Miura, 1980 from the deep Northeast Atlantic. Currently no reliable morphological characters separating the Pacific and Atlantic specimens have been found and molecular data from the Atlantic specimens was not available.

Historical RNA expression profiles from the extinct Tasmanian tiger.

Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.

The man‐eaters of Tsavo and the untapped potential of natural history collections

AbstractOne of the best‐known exhibits at Chicago's Field Museum of Natural History features the man‐eating lions of Tsavo. Over a period of nine months in 1898, this pair of lions systematically hunted, killed and consumed railroad workers engaged in building a bridge over the Tsavo River in East Africa. The lions were eventually killed by an engineer, J. H. Patterson, who afterwards wrote a best‐selling book about the episode. His dramatic story has been retold in countless articles, books, and motion pictures, each more sensational and gory than the last. What parts are true? Fortunately, the lions' skins and skulls offer an independent and verifiable chronicle of events that actually transpired. These two specimens effectively re‐wrote their own history through the scientific research sparked by their notoriety, reminding us that the collections of natural history museums hold almost limitless potential to illuminate the world around us and its history.

Digitization of natural history collections: A guideline and nationwide capacity building workshop in Malaysia.

Natural history museum collections are the most important sources of information on the present and past biodiversity of our planet. Most of the information is primarily stored in analogue form, and digitization of the collections can provide further open access to the images and specimen data to address the many global challenges. However, many museums do not digitize their collections because of constraints on budgets, human resources, and technologies. To encourage the digitization process, we present a guideline that offers low-cost and technical knowledge solutions yet balances the quality of the work and outcomes. The guideline describes three phases of digitization, namely preproduction, production, and postproduction. The preproduction phase includes human resource planning and selecting the highest priority collections for digitization. In the preproduction phase, a worksheet is provided for the digitizer to document the metadata, as well as a list of equipment needed to set up a digitizer station to image the specimens and associated labels. In the production phase, we place special emphasis on the light and color calibrations, as well as the guidelines for ISO/shutter speed/aperture to ensure a satisfactory quality of the digitized output. Once the specimen and labels have been imaged in the production phase, we demonstrate an end-to-end pipeline that uses optical character recognition (OCR) to transfer the physical text on the labels into a digital form and document it in a worksheet cell. A nationwide capacity workshop is then conducted to impart the guideline, and pre- and postcourse surveys were conducted to assess the confidence and skills acquired by the participants. This paper also discusses the challenges and future work that need to be taken forward for proper digital biodiversity data management.