Collection Of Natural History Museum Research Articles

Kemp, C. 2017. The Lost Species: Great Expeditions in the Collections of Natural History Museums

Christopher Kemp es un científico dedicado a la divulgación de la ciencia. Ha realizado dos libros, el ahora reseñado y otro sobre el ambergris, ambos publicados por la Universidad de Chicago. En su más reciente libro expande sus ideas presentadas en la revista Nature (Kemp C 2015, 518:292-294), en la que llamó la atención sobre la precaria condición presupuestal y de personal en algunos de los mayores museos de historia natural del mundo. El libro también apunta a la relevancia del trabajo taxonómico y, en el subtítulo, enfatiza la importancia de las colecciones y del cómo mediante estudios finos equivaldría a la realización de grandes expediciones como las de antaño, pero ahora entre los materiales depositados en dichas colecciones. Se refiere, por supuesto, a la pieza culminante del trabajo taxonómico: las revisiones. Porque parecen poco comprendidas entre los profesionales de las ciencias ambientales haré unos comentarios sobre las mismas.

Using Deep Learning in Collection Management to Reduce the Taxonomist’s Workload

The completeness and quality of the information in natural history museum collections is essential to support its use, such as in collection management. Currently, the accuracy of the taxonomic information largely depends on expert provided metadata, such as species identification. At present an increase in the use of digitization techniques coincides with a dwindling of the number of taxonomic specialists, creating a growing backlog in specimen identifications. We are investigating the role of artificial intelligence for automatic species identification in supporting collection management. When identifying collection specimens, common species are predominantly present, taking up a large amount of the expert’s time, who has to deal with a relatively easy, repetitive task. Therefore, one of our aims is to use human expertise where it is most needed, for complex tasks, and use properly validated computational methods for repetitive, less difficult identifications. To this end, we demonstrate the use of automatic species identification in digitization workflows, using deep learning based image recognition. We investigated potential gains in the identification process of a large digitization project of papered Lepidoptera (>500,000 specimens). In this ongoing project, volunteers unpack, register and photograph the unmounted butterflies and repack them sustainably, still unmounted. Using only the individual images made by volunteers, taxonomic experts identify the specimens. Considering that the speed of digitization currently exceeds that of identification, a growing backlog of yet-to-be-identified specimens has formed, limiting the speed of publication of this biodiversity information. The test case for image recognition concerns specimens of the families Papilionidae and Lycaenidae, mostly collected in Indonesia. By allowing the volunteers to provide an automatically generated identification with each image, we enable the taxonomic specialists to quickly validate the more easily identifiable specimens. This reduces their workload, allows them to focus on the more demanding specimens and increases the rate of specimen identification. We demonstrate how to combine computer and human decisions to ensure both high data quality standards and reduction of expert time.

The Biggest Museum Project in Czech History: The New Permanent Natural History Exhibitions in the National Museum Prague

In 2018 the National Museum Prague (NMP) is celebrating its 200th anniversary. Today the Museum is facing its most valuable development: brand new permanent exhibitions. Our monumental historic building was constructed in 1891 in the heart of Prague. After more than one hundred years we had to close the building and remove all exhibitions which were older than 40 years. The building has about 8,000m2 and is divided into two parts. One belongs to our Natural History Museum (NHM) collections with Zoology, Palaeontology, Mineralogy, Botany and Mycology exhibitions. Our new natural history galleries will open in autumn 2019. Housed all on one floor, the galleries will be full of animals like invertebrates, fishes, reptiles, birds and mammals. The second floor will focus on palaeontology spanning more than 500 million years of evolution covering the geographical area of the modern Czech Republic. At the beginning we had to ask ourselves a few simple questions. How do we develop permanent exhibitions that will last for decades? Is excluding modern technology the right thing to do? Should we focus on a more informative/education style or should the interpretation be more populist? And what about the display cases? Should we use old repaired ones or modern cases? It would be great to have answers to all these questions but we still have to deal with the vision and constraints of our curators, collections, budget, legislation, technology and construction of the building. The project has no similar equivalent in the history of the Czech Republic so it was an extraordinary challenge to create our own process of developments with ongoing improvements. Through these developments we have formed new cooperation with technological partners and the creative industries. We are defining a new modern approach to the development and preparation of exhibitions in the Czech Republic. Now that we have reached the half way point towards our vision, it is a good time to report on progress.

Annotated checklist of the fishes of the archipelago of Madeira (NE Atlantic): I-Chondrichthyes.

As part of an annotated checklist of fishes of the archipelago of Madeira, a list with all cartilaginous fishes recorded from the archipelago is presented. The list contains 67 species of sharks, rays and chimaeras, whose presence in the area the authors consider confirmed. Another 14 species previously referred for the area are now considered dubious records and five species are withdrawn from the list. Centrophorus uyato is here recorded for the first time from Madeira. Three species (Mitsukurina owstoni, Odontaspis noronhai and Chimaera opalescens) are so far only present in Madeira within Macaronesia. The 67 confirmed species are based on occurrences, substantiated by specimens in natural history museum collections or other published evidence. For all species, the first reference is given, as well as other relevant references for the archipelago and remaining Macaronesia.

Cryopreservation of Fish Spermatogonial Cells: The Future of Natural History Collections

As global biodiversity declines, the value of biological collections increases. Cryopreserved diploid spermatogonial cells meet two goals: to yield high-quality molecular sequence data; and to regenerate new individuals, hence potentially countering species extinction. Cryopreserved spermatogonial cells that allow for such mitigative measures are not currently in natural history museum collections because there are no standard protocols to collect them. Vertebrate specimens, especially fishes, are traditionally formalin-fixed and alcohol-preserved which makes them ideal for morphological studies and as museum vouchers, but inadequate for molecular sequence data. Molecular studies of fishes routinely use tissues preserved in ethanol; yet tissues preserved in this way may yield degraded sequences over time. As an alternative to tissue fixation methods, we assessed and compared previously published cryopreservation methods by gating and counting fish testicular cells with flow cytometry to identify presumptive spermatogonia A-type cells. Here we describe a protocol to cryopreserve tissues that yields a high percentage of viable spermatogonial cells from the testes of Asterropteryx semipunctata, a marine goby. Material cryopreserved using this protocol represents the first frozen and post-thaw viable spermatogonial cells of fishes archived in a natural history museum to provide better quality material for re-derivation of species and DNA preservation and analysis.

Giant jelly eaters on the line: Species distribution and bycatch of three dominant sunfishes in the Southwest Pacific

The ocean sunfishes have a long and confusing taxonomic legacy, clouding the global zoogeography of each species and hindering fisheries bycatch assessments. The traditional view of Mola mola as the most common sunfish species worldwide is challenged by our findings from Australia and New Zealand, revealing that three large sunfishes, Masturus lanceolatus, Mola alexandrini and Mola tecta, dominate the tropical/subtropical, warm-temperate and cold-temperate waters here, respectively, while Mola mola – both Pacific and Atlantic clades – is relatively rare. These findings were based on phylogenetic (mtDNA D-loop) and/or morphological species identification of sunfish from longline bycatches (n = 106), natural history museum collections (n = 45) and other sources (n = 12), informed by recent advances in the taxonomy of the genus Mola. Furthermore, separation in species distributions were seen when comparing sampling latitude and sea surface temperature. The findings imply that the longline fisheries observer sunfish data from Australia and New Zealand is a mix of species, and not dominated by M. mola as previously assumed. Mean catch per unit Effort (2001–13) in 1° latitude/longitude grids off Pacific Australia and New Zealand were predominantly < 1 sunfish.1000 hooks−1 (up to 6.5 in some areas) with no statistical significant upwards or downwards trends detected over time in four fishing ground subareas, each presumably dominated by either Masturus lanceolatus, Mola alexandrini or Mola tecta. Widespread specimen identification errors had previously obscured a more complex Molidae zoogeography in the area, highlighting that phylogenetic analyses of sunfish bycatch globally would benefit species-level conservation status evaluations.

Muricidae (Neogastropoda) assemblages from the Middle Miocene of the Făget Basin (Romania) in the collection of the Hungarian Natural History Museum, Budapest

Muricidae (Neogastropoda) assemblages from the Middle Miocene of the Făget Basin (Romania) in the collection of the Hungarian Natural History Museum, Budapest

Supporting the long‐term curation and migration of natural history museum collections databases

ABSTRACTMigration of data collections from one platform to another is an important component of data curation – yet, there is surprisingly little guidance for information professionals faced with this task. Data migration may be particularly challenging when these data collections are housed in relational databases, due to the complex ways that data, data schemas, and relational database management software become intertwined over time. Here we present results from a study of the maintenance, evolution and migration of research databases housed in Natural History Museums. We find that database migration is an on‐going – rather than occasional – process for many Collection managers, and that they creatively appropriate and innovate on many existing technologies in their migration work. This paper contributes descriptions of a preliminary set of common adaptations and “migration patterns” in the practices of database curators. It also outlines the strategies they use when facing collection‐level data migration and describes the limitations of existing tools in supporting LAM and “small science” research database migration. We conclude by outlining future research directions for the maintenance and migration of collections and complex digital objects.

Leaf insects from Luzon, Philippines, with descriptions of four new species, the new genus Pseudomicrophyllium, and redescription of Phyllium (Phyllium) geryon Gray, 1843, (Phasmida: Phylliidae).

Examination of unidentified Phylliidae specimens revealed a number of undescribed species from the island of Luzon, Philippines. Morphological and molecular study of specimens from the obscure phasmid genus Microphyllium Zompro, 2001, revealed a new species, which we describe as Microphyllium haskelli Cumming sp. nov.. It is here described and differentiated from the two other species in the genus, both currently only known from adults of a single sex. Pseudomicrophyllium Cumming gen. nov. is described as a new genus within Phylliidae with the type species Pseudomicrophyllium faulkneri Cumming gen. et sp. nov. as the sole known species in the genus. As is unfortunately often the case in the leaf-mimicking family Phylliidae, this new genus and species is only known from a single specimen. In addition to the new genus, two new Phyllium (Phyllium) species from the siccifolium species-group are named and described as Ph. (Ph.) antonkozlovi Cumming sp. nov. and Ph. (Ph.) bourquei Cumming Le Tirant sp. nov.. In addition to the newly described species, Phyllium (Phyllium) geryon Gray, 1843 is redescribed from a nearly perfect specimen, completing some of the morphological knowledge gaps currently missing because of the severely damaged holotype specimen. A key to all known species of Phylliidae from Luzon is included. Holotype specimens for all four new species will be deposited in the National Museum of the Philippines type collection and paratype specimens will be deposited into the San Diego Natural History Museum collection or retained within the first author's collection.

Dirty sparrows provide a historic look at soot

Evolutionary biologist Shane G. DuBay and art historian and photographer Carl C. Fuldner of the University of Chicago were studying bird specimens in natural history museum collections when they began noticing that birds collected more than 100 years ago are much dirtier than recently collected birds. That observation led them in a new direction to use the soot embedded in bird feathers to estimate past black carbon aerosol pollution stemming from burning wood and coal (Proc. Natl. Acad. Sci. USA 2017, DOI: 10.1073/pnas.1710239114). The team used electron microscopy to gather photometric reflectance data on feathers from more than 1,300 bird specimens collected from 1880 to 2015 in the U.S. manufacturing belt, which includes Chicago, Detroit, and Pittsburgh. The researchers used the data to estimate black carbon concentrations, finding that levels peaked between 1900 and 1910 and that levels before 1910 were higher than previously thought—estimates were inexact until the mid-1950s

Arctic science education using public museum collections from the University of Alaska Museum: an evolving and expanding landscape

Alaska faces unique challenges in STEM (science, technology, engineering, and mathematics) education, including limited accessibility to resources and learning opportunities, and a lack of place-based education resources. Museum education programs, traditionally focused on public outreach through docent-led tours, are playing an increasingly important role in both formal and informal aspects of STEM education to help address these challenges. The University of Alaska Museum (UAM) stands as a model in the Arctic region exemplifying how public natural history museum collections can be utilized to create active place-based learning experiences with the aim of increasing engagement in STEM literacy and building connections between museums and communities. These efforts take many forms, including the development of teaching materials involving physical objects and (or) online data from the open-access database ARCTOS, training preservice teachers, and implementing citizen science projects. Because many UAM specimens and objects are from Alaska, they are easily incorporated into place-based education, thereby demonstrating how the Arctic environment is unique at local and regional scales. Here, we showcase several programs that are either unique to UAM or part of larger national projects and include exemplar teaching modules in order to provide learning opportunities in the Arctic region and other rural settings.

A catalogue of Coleoptera specimens with potential forensic interest in the Goulandris Natural History Museum collection

This paper presents a catalogue of the Coleoptera specimens in the Goulandris Natural History Museum collection that have potential forensic interest. Forensic entomology can help to estimate the time elapsed since death by studying the necrophagous insects collected on a cadaver and its surroundings. In this paper forty eight species (369 specimens) are listed that belong to seven families: Silphidae (3 species), Staphylinidae (6 species), Histeridae (11 species), Anobiidae (4 species), Cleridae (6 species), Dermestidae (14 species), and Nitidulidae (4 species). The aim of this paper is to present this collection and its importance for studying forensic entomology.

Catalogue of type specimens of ants (Hymenoptera: Formicidae) deposited in Czech museums

Type specimens of ants (Hymenoptera: Formicidae) deposited in natural history museum collections in the Czech Republic are catalogued. Altogether, we list types of 19 extant taxa housed in the Department of Entomology, National Museum, Prague; the Department of Entomology, Moravian Museum, Brno; the Department of Natural History, Museum of the Highlands, Jihlava; and the Department of Natural History, Silesian Museum, Opava.

A hiányzó orr esete

The study of an ancient Egyptian mummified head with a prosthetic nose in the Anthropological Collection of the Hungarian Natural History Museum in Budapest, raised historical, cultural and medical questions. The cultural and legal implications of a missing nose is discussed from several points of view in various cultures. The article deals with the significance of the nose in ancient Egypt and elsewhere, the possible reasons of its lack, the history of rhinoplasty and reconstructive surgery concerning the nose and the prosthesis. Cases from ancient Egypt explained in the Smith papyrus (cases 11.-14.), in India described in the Susrata Samhita and later, and in Europe from the Middle Ages to modern history are reviewed

Erannis jacobsoni Djakonov, 1926: new for the fauna of Korea (Lepidoptera, Geometridae: Ennominae)

Erannis jacobsoni sichotenariaKurentzov, 1937 is recorded for the first time from the Korean Peninsula on the basis of one male specimen deposited in the collection of the Hungarian Natural History Museum, Budapest. A key to the males of the Siberian and Pacific species of ErannisHubner, 1825 are given. With 8 figures.

Complete mitochondrial genomes of eleven extinct or possibly extinct bird species.

Natural history museum collections represent a vast source of ancient and historical DNA samples from extinct taxa that can be utilized by high-throughput sequencing tools to reveal novel genetic and phylogenetic information about them. Here, we report on the successful sequencing of complete mitochondrial genome sequences (mitogenomes) from eleven extinct bird species, using de novo assembly of short sequences derived from toepad samples of degraded DNA from museum specimens. For two species (the Passenger Pigeon Ectopistes migratorius and the South Island Piopio Turnagra capensis), whole mitogenomes were already available from recent studies, whereas for five others (the Great Auk Pinguinis impennis, the Imperial Woodpecker Campehilus imperialis, the Huia Heteralocha acutirostris, the Kauai Oo Moho braccathus and the South Island Kokako Callaeas cinereus), there were partial mitochondrial sequences available for comparison. For all seven species, we found sequence similarities of >98%. For the remaining four species (the Kamao Myadestes myadestinus, the Paradise Parrot Psephotellus pulcherrimus, the Ou Psittirostra psittacea and the Lesser Akialoa Akialoa obscura), there was no sequence information available for comparison, so we conducted blast searches and phylogenetic analyses to determine their phylogenetic positions and identify their closest extant relatives. These mitogenomes will be valuable for future analyses of avian phylogenetics and illustrate the importance of museum collections as repositories for genomics resources.

Moorean and Tahitian Partula tree snail survival after a mass extinction: New genomic insights using museum specimens

Natural history museum collections provide a biodiversity window into the past and are of particular importance to the study of extinction-impacted clades such as the Pacific Island tree snail family Partulidae. Deliberate introduction of the predatory rosy wolf snail Euglandina rosea in the late 20th century led to the extinction/extirpation of 55/61 Society Island Partulidae species. In this study, we phylogenomically investigated the inter-relationships of the three surviving Society Island valley Partula species: P. taeniata (Moorea), P. clara and P. hyalina (Tahiti). All three formed a distinct clade in earlier mitochondrial phylogenies. Using Next Generation Sequencing (NGS) double digested Restriction Associated DNA sequencing (ddRADseq), we found that 46-year-old lyophilized museum specimens produced similar numbers of reads, sequencing depth, and loci as 10-year old ethanol-preserved collections. Phylogenomic trees indicated that Tahitian P. clara and P. hyalina are the result of a single founding lineage from Moorea, contrasting previous mitochondrial results and clarifying the enigmatic taxonomic status of P. c. incrassa. Our study highlights the utility and viability of NGS techniques for museum specimens and their increased resolution of evolutionary patterns. Sampling will be expanded to include the remaining Society Island partulid taxa to further explore the evolutionary history of this radiation.

Revealing Invisible Beauty, Ultra Detailed: The Influence of Low Cost UV Exposure on Natural History Specimens in 2D+ Digitization.

Digitization of the natural history specimens usually occurs by taking detailed pictures from different sides or producing 3D models. Additionally this is normally limited to imaging the specimen while exposed by light of the visual spectrum. However many specimens can see in or react to other spectra as well. Fluorescence is a well known reaction to the ultraviolet (UV) spectrum by animals, plants, minerals etc. but rarely taken into account while examining natural history specimens. Our tests show that museum specimens still fluoresce when exposed to UV light of 395 nm and 365 nm, even after many years of preservation. When the UV exposure is used in the digitization of specimens using our low cost focus stacking (2D+) setup, the resulting pictures reveal more detail than the conventional 2D+ images. Differences in fluorescence using 395 nm or 365 nm UV lights were noticed, however there isn’t a preferred wavelength as some specimens react more to the first, while others have better results with the latter exposure. Given the increased detail and the low cost of the system, UV exposure should be considered while digitizing natural history museum collections.

A new quality management perspective for biodiversity conservation and research: Investigating Biospecimen Reporting for Improved Study Quality (BRISQ) and the Standard PRE-analytical Code (SPREC) using Natural History Museum and culture collections as case studies

The aims of this paper are to debate and raise awareness about the use of systematic, interconnected approaches for biodiversity collection curation by exploring the multi-disciplinary relevance of quality management tools developed by clinical biobanks. An appraisal of their best practices indicated the need for improved sample and process chain annotation as a significant number of historical collections used in medical research were of inadequate quality. This stimulated the creation of a new discipline, biospecimen science to develop quality management tools for clinical biobanks, two of which, Biospecimen Reporting for Improved Study Quality (BRISQ) and the Standard PRE-analytical Code (SPREC) report critical information about samples and process chain variables. Unprecedented advances in molecular-genetic and in silico technologies applied across the tree of life require international conservation networks to generate and share knowledge. This is used in biodiversity and systematics research, and to address the accelerating loss of species, including the sustainable use of bioresources. This review investigates the application of BRISQ and SPREC for biodiversity research and conservation using natural history, museum and living culture collections as case studies. The distinction between preservation and conservation is discussed with regard to process and storage treatments and how they impact on the usability of biospecimens and cultures. We conclude: (i) more rigorous approaches are needed for the quality management of biospecimens, bioresources and their associated sample and processing data to assure their fitness-for-purpose; and (ii) biospecimen science tools developed by clinical biobanks can be adapted to future-proof the quality of biodiversity collections and the reliability of molecular data generated from their use.

Assessing migration patterns in Passerina ciris using the world's bird collections as an aggregated resource.

Natural history museum collections (NHCs) represent a rich and largely untapped source of data on demography and population movements. NHC specimen records can be corrected to a crude measure of collecting effort and reflect relative population densities with a method known as abundance indices. We plotted abundance index values from georeferenced NHC data in a 12-month series for the new world migratory passerine Passerina ciris across its molting and wintering range in Mexico and Central America. We illustrated a statistically significant change in abundance index values across regions and months that suggests a quasi-circular movement around its non-breeding range, and used enhanced vegetation index (EVI) analysis of remote sensing plots to demonstrate non-random association of specimen record abundance with areas of high primary productivity. We demonstrated how abundance indices from NHC specimen records can be applied to infer previously unknown migratory behavior, and be integrated with remote sensing data to provide a deeper understanding of demography and behavioral ecology across time and space.