Looking back to move forward – Impact of historical moss specimens on modern systematics

The Role of Natural History Institutions and Bioinformatics in Conservation Biology

Animal specimens in natural history collections are invaluable resources in examining the historical context of pathogen dynamics in wildlife and spillovers to humans. For example, natural history specimens may reveal new associations between bat species and coronaviruses. However, RNA viruses are difficult to study in historical specimens because protocols for extracting RNA from these specimens have not been optimized. Advances have been made in our ability to recover nucleic acids from formalin-fixed paraffin-embedded samples (FFPE) commonly used in human clinical studies, yet other types of formalin preserved samples have received less attention. Here, we optimize the recovery of RNA from formalin-fixed ethanol-preserved museum specimens in order to improve the usability of these specimens in surveys for zoonotic diseases. We provide RNA quality and quantity measures for replicate tissues subsamples of 22 bat specimens from five bat genera (Rhinolophus, Hipposideros, Megareops, Cynopterus, and Nyctalus) collected in China and Myanmar from 1886 to 2003. As tissues from a single bat specimen were preserved in a variety of ways, including formalin-fixed (8 bats), ethanol-preserved and frozen (13 bats), and flash frozen (2 bats), we were able to compare RNA quality and yield across different preservation methods. RNA extracted from historical museum specimens is highly fragmented, but usable for short-read sequencing and targeted amplification. Incubation of formalin-fixed samples with Proteinase-K following thorough homogenization improves RNA yield. This optimized protocol extends the types of data that can be derived from existing museum specimens and facilitates future examinations of host and pathogen RNA from specimens.

ABSTRACTWith the advent of high‐throughput sequencing techniques, natural history museums and herbaria have become new frontiers for genetic research. Genomic information from historical specimens has provided evidence to solve significant questions in broad research areas. However, access to such valuable genetic resources remains limited in lichens due to experimental challenges in extracting and amplifying highly degraded DNA in historical specimens. So far, only a handful of studies have reported successful sequencing of several short genetic markers from historical lichen specimens despite the increasing importance of genetic information in lichenology. Here, we aimed to establish an efficient method for sequencing the whole genome of historical lichen specimens. We modified a method used in ancient DNA studies and sequenced the whole genome of Usnea and Cladonia specimens, including lectotype and holotype. Our approach shows that 2.7%–23.3% and 3.0%–11.8% of the total sequenced reads originate from the genomes of fungal (mycobiont) and algal (photobiont) symbionts, respectively. The mycobiont‐ and photobiont‐derived reads are comprised of DNA fragments shorter than 46 bp, covering 73%–99% and 92%–99% of the mycobiont and photobiont reference genomes, respectively. We retrieved 792,245 and 410,705 Single Nucleotide Variant sites (SNVs) to perform phylogenetic analysis of the U. hakonensis and C. kurogawae mycobionts, respectively. We also demonstrated experimental modifications that improved proportions of symbiont‐derived reads within sequenced data. We believe that our method is applicable to lichen specimens in a broad range of ages and taxonomic groups, thereby potentially converting historical lichen specimens into resources of genome‐wide studies.

Natural history collections are unparalleled repositories of geographical and temporal variation in faunal conditions. Molecular studies offer an opportunity to uncover much of this variation; however, genetic studies of historical museum specimens typically rely on extracting highly degraded and chemically modified DNA samples from skins, skulls or other dried samples. Despite this limitation, obtaining short fragments of DNA sequences using traditional PCR amplification of DNA has been the primary method for genetic study of historical specimens. Few laboratories have succeeded in obtaining genome-scale sequences from historical specimens and then only with considerable effort and cost. Here, we describe a low-cost approach using high-throughput next-generation sequencing to obtain reliable genome-scale sequence data from a traditionally preserved mammal skin and skull using a simple extraction protocol. We show that single-nucleotide polymorphisms (SNPs) from the genome sequences obtained independently from the skin and from the skull are highly repeatable compared to a reference genome.

Population‐level, historical studies can provide insights on the distribution, abundance and demographic characteristics of imperiled species prior to human exploitation, habitat modification or climate change. These studies provide a baseline for contemporary data, which often shape successful management and recovery. The smalltooth sawfish (Pristis pectinata) occupies ~20% of its historical range due to declines driven primarily by mortalities in fisheries and coastal habitat loss over the last century. As a result, they are listed as Critically Endangered on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species and as Endangered federally in the United States (U.S.). Because P. pectinata grow to a large size and have a toothed rostrum, many historical photographs and specimens are archived in natural history collections. Metadata and morphometric data were collected and analysed from P. pectinata photographs (n = 84) and specimens (n = 429) to evaluate temporal changes in average size and historical distribution of five age classes in U.S. waters. Historically, smaller age classes were well‐distributed throughout the northern Gulf of Mexico, while only larger age classes were recorded on the U.S. east coast, north of Florida. All age classes were found in both Florida and Texas historically, but records from Texas decline after the 1980s and remain persistent in Florida, indicative of a strong‐hold for the U.S. population. Regardless of origin, individuals in three of the five age classes were larger on average historically than those observed today. Understanding which age classes used previously occupied areas will help direct habitat restoration efforts and support recovery, especially in the face of climate change. Non‐traditional data sources, such as those used here, may often be the only means of providing historical context to modern research on imperiled species, ultimately guiding restoration and conservation efforts.

The European honeybee (Apis mellifera) is a key pollinator and has in the last decades suffered significant population decline. A combination of factors, including decrease in genetic diversity and introduction of Varroa mites, have been suggested to be responsible for these losses, but no definitive cause has yet been appointed. In Europe not only have wild colonies been severely affected, but managed hives have had a massive decline in numbers. To test the hypothesis that honeybees’ genetic diversity has decreased in the recent past, we used reduced representation genome sequencing of 40 historical honeybee specimens collected in Natural History collections across Europe and compared them to genomic data from 40 individuals from extant populations (collected post 2006). Our results are consistent with the existence of five evolutionary lineages as previously described, and show a decrease in genetic diversity between historical and extant individuals of the same lineage, as well as high levels of admixture in historical specimens. Our data confirm that a loss of genetic diversity has occurred during the last century, potentially increasing honeybees’ vulnerability to contemporary ecological and anthropogenic stressors.

The 2011 Great East Japan Earthquake revealed that one of the reasons for the lack of effective and timely action to rescue and restore natural history collections is that the organizational laws and policies are insufficient and inapplicable under extreme circumstances. Laws and policies for collections are primarily concerned with designation and registration, preservation and management, financial assistance, government involvement and public awareness. The Cultural Property Protection System and the Act on Cultural Properties Preservation prioritized the rescue and restoration of cultural assets, both nationally and regionally, however, attention to the state of natural history collections was delayed and was primarily fueled by volunteers (Mawatari 2015). Earlier in the Meiji era (1868~1912), national emphasis on cultural assets, represented by Japanese art, contributed to the formation and spread of nationalism (Kanayama 2011). Consequently, the laws and policies in question were enacted, focusing on attaching importance to and preservervation of cultural assets. After a few attempts at national discussion on whether science specimens (in natural history collections) should be covered by the law, the problem remain unsolved. In the few cases, where natural history collections were designated by the law, the focus tended to be centered on the value to humanity. It is clear from the laws and policies that decision-makers lack an understanding of the importance of natural history collections. Further narrowing down the scope, operational rules and regulations are often based on the handling and practices of cultural history objects within the public museums, and descriptions of natural history collections are lacking in many practice guidelines for museums and textbooks on museum studies. Other than the need for better law and policy, the 2011 disaster has also left curators of natural history collections with a renewed sense of the importance of establishing theories on conservation science and other practice standards for natural history collections through networking and cooperation, not only under extreme circumstances but also for daily management and practical utility. However, the current lack of curators with expertise in natural history collections, the few chances to participate in skill-share programs, and insufficient financial and official support for pioneering research, remain challenging. To address this, it may be possible to propose methodologies and gather individuals with similar interests to deepen the debate on the importance of research and establishment of standards to give curators more chances, support and recognition to carry on conservation science research. Therefore, increasing connections within the natural history museum community is a feasible step to take in the near term. There are some actions in progress such as cross-museum collaboration to establish research projects and the skill-share projects organized by the Natural History Museum Network of Western Japan. What about the non-natural history museums and natural history collections with few or without specialized curators? The natural history curator community in Japan is small. In 2020, there were 228 museums in Japan holding biological specimens (geological and paleontology specimens were not counted in the research), fewer than half of which were assigned to natural history curators. In the natural history museums, the average number of natural history curators was 2.49; that of science museums, history museums and regional museums was less than 1, indicating that the natural history curator community is a minority in the museum sector of Japan (Fig. 1, Japanese Association of Museums 1986). Even those where there were assignments of natural history curators, the curators' specialized field may not be a perfect match with the collections, ending up with cases such as a curator of entomology having to take care of botanical specimens. In some regions, in 2020, there were only one or two natural history curators, indicating the unevenness in curator assignments across regions of Japan (Fig. 2, Japanese Association of Museums 1986). This makes it even harder to find other curators who can help when encountering problems beyond one’s expertise. All of this underlines the importance of creating a strong national network of natural history museum curators to share experiences, expertise, methodologies, and standards of care.

This study was carried out to gauge the current status of natural history collection centres in Malaysia, primarily focused on animal collections. Part of the research is reported here and it constituted objective one which is to compare the status of natural history collection between the various centres in Malaysia and also with three selected Southeast Asian tropical region museums in trying to understand need of the Malaysian public for a natural history museum. It maps out the locations, describes the number and kinds of specimens kept at each collection centre. Financial and governance aspects are also described. In total 11 centres were visited all over Malaysia. These collection centres and museums were managed by federal or state government or universities. Duration of visit at each location ranged from one to seven days. During the visit interviews were carried out with collection manager to obtained Questionnaire was also left behind for managers of centre to fill in and sent back to researchers. In addition, three natural history collection centres and museums in South East Asia tropical region were also visited: Bogor Zoological Museum, Indonesia; Lee Kong Chian Natural History Museum, Singapore and Mahachakri Sirindhorn Natural History Museum, Prince of Songkhla University, Thailand. Following the same protocol as with Malaysian centres, the information obtained enable researcher to make comparison between Malaysia and those in the region. This paper found that most of the natural history museums and collection centres were focused in the centre of peninsular Malaysia. However, natural history collections in Malaysia are still limited by state and national borders. Coordination and integration of these centres, currently runned separately by the federal, state governments, research institutions and institution of higher learning, is seen as the way forward to provide for a strong basis of understanding biodiversity among the Malaysian public.

In an era where digitization and networking technologies offer a new way for environmental and natural history institutions, like natural history museums and science centers, to promote their services to the general public, new challenges rise on the field on intellectual property rights. Natural Europe project aim is to make natural history knowledge accessible on an open access basis to a wide spectrum of end-users, through Europeana portal. The value the project delivers is not merely in making works available online, but in the open access terms under which the works are available. Therefore understanding Intellectual Property considerations is fundamental in achieving this goal. The aim of this paper is to enable a further discussion on issues concerning the intellectual property rights for environmental and natural history collections.

Natural history collections house an enormous amount of plant and animal specimens, which constitute a promising source for molecular analyses. Storage conditions differ among taxa and can have a dramatic effect on the success of DNA work. Here, we analyze the feasibility of DNA extraction from ethanol preserved spiders (Araneae). We tested genotyping success using several hundred specimens of the wasp spider, Argiope bruennichi, deposited in two large German natural history collections. We tested the influence of different factors on the utility of specimens for genotyping. Our results show that not the specimen’s age, but the museum collection is a major predictor of genotyping success. These results indicate that long term storage conditions should be optimized in natural history museums to assure the utility of collections for DNA work. Using historical material, we also traced historical genetic and morphological variation in the course of a poleward range expansion of A. bruennichi by comparing contemporary and historical specimens from a native and an invasive population in Germany. We show that the invasion of A. bruennichi is tightly correlated with an historical increase of genetic and phenotypic variation in the invasive population.

Several initiatives aim to map the diversity of Natural History (NH) collections and standardise their descriptions. The Global Registry of Biodiversity Repositories (GRBio) is the most recent global registry. Unfortunately the server has been down since mid-2018 but the Global Biodiversity Information Facility (GBIF) recently "rescued" this data. In addition to this, the One World Collection exercise is a set of high-level collection descriptors (size, group coverage and geographic distribution) supporting a common strategy between the largest world institutions. Despite these efforts, a large part of the NH collections remains digitally unavailable and digitisation at the specimen level will take several decades. A new NH collections dashboard is needed in order to harmonise the efforts of the institutions. The Consortium of European Taxonomic Facilities (CETAF) is a good place to introduce this excercise. CETAF’s members hold over half of the world’s NH collections, representing 80% of the world's bio- and geo-diversity. Most of these collections are now engaged in the preparation for the common process of the Distributed System of Scientific Collections (DiSSCo, European Strategy Forum on Research Infrastructure). Additionally in Belgium, the Royal Belgian Institute of Natural Sciences (RBINS), Royal Museum of Central Africa (RMCA), Meise Botanic Garden (MBG) and CETAF have joined efforts to set up a common research portal (Natural Heritage, BRAIN-be project). The goal is to link together several collection management systems (CMS) and to (re)create links between isolated collection items. The CETAF collections dashboard splits the information into small metadata units related to topics relevant to the collections (taxonomy, geographic distribution, digitisation strategy and coverage, stratigraphy, etc.). The model allows for the creation of new units without a complete modification of the database structure. All units are defined by the Dublin Core and by fields derived from the Innovation and consolidation for large scale digitisation of natural heritage (ICEDIG) d2.3 deliverable (van Egmond et al. 2019). The object hierarchy allows for the creation of sub-collections and preserves the unity of the information. The CMS has an internal object database with a full index and a faceted search interface. It also has web services and XLS (Microsoft® Excel®) import/export functionalities. The collection dashboard also includes a complete workflow and access rights management at the object level. This is important for the information that is protected by the EU General Data Protection Regulation (GDPR). The dashboard is now being evaluated with the collections hosted by the partners of Natural Heritage. The system will be proposed to CETAF members and connections will be established with the international portals such as the GBIF or the future DiSSCo portal.

<p>The Natural History Museum in London has embarked on an epic journey to digitise 80 million specimens from one of the world's most important natural history collections. Publishing this data to our open Data Portal will give the global scientific community access to unrivalled historical, geographic and taxonomic specimen data gathered over the last 250 years. We have been involving the public in this large task by asking digital volunteers to help transcribe information written on specimen labels, via an online crowdsourcing interface, such that anyone in the world can participate. In this talk we will share our experience with these projects over the past year. </p> <p>Within the Digital Collections Programme at the Natural History Museum London we have so far digitally imaged approximately 200,000 of our total holdings of around two million microscope slides, and from these have selected two discrete collections for crowdsourcing the transcription effort. Miniature Lives Magnified (now complete) contained 6,285 digitised Chalcidoidea slides from our Hymenoptera collection, and Miniature Fossils Magnified (not yet complete at time of writing) contains 2,000 Foraminifera slides from our Micropalaeontology collection. Both projects are hosted on the Notes from Nature platform, which has been built on the Zooniverse Panoptes open-project platform.</p> <p>As the lead partner of the Crowdsourcing task within SYNTHESYS3, an EC-funded project creating an integrated European infrastructure for natural history collections, we have partnered with our fellow consortium members to help them design and launch crowdsourcing projects of their own. These have included an Amaranthaceae collection with 444 specimens and a Primulaceae collection with 3,093 specimens hosted on Notes from Nature, and a Brachiopod collection with 1,810 specimens built directly on Panoptes. </p> <p>In this talk we will share the key insights gained through practical experience with this wide range of specimens, specimen data, and label-styles. In particular, we have gained insights into the design of the workflow and interface, such as the considerable reduction in human error when drop-down menu options are introduced where possible, rather than free data entry fields. </p> <p>These five projects provided us with a unique opportunity to compare the dedicated Notes from Nature platform, which has significant advantages due to the size and engagement-level of the existing community, to the open project-building Panoptes platform, which has storytelling advantages in terms of the capacity to provide more information about a specific collection, its subject, and its underlying scientific importance. </p> <p>A crucial element of running successful crowdsourcing projects is building an engaged community of digital volunteers. We compared the use of social media channels with more traditional Museum communication channels (such as e-newsletter and website), and found that the latter had the most reach in terms of raising awareness of the projects, but that the former enabled more frequent and varied engagement with a potential volunteer audience. However, when examining which metrics are the most important to track in assessing the success of various initiatives, we found that the highest impact on the ultimate volume of transcription were in-house volunteering days run in person, rather than online.</p> <p>In reaching out and engaging with a diverse range of volunteer audiences, we found evidence of the major sources of motivation that are described in the existing citizen science literature, but also more nuanced insight into behaviours such as pursuing independent learning, the desire to enter all of the information even when not requested, and preferring tasks that can be performed by rote. Our efforts to support and nurture the existing Notes from Nature community confirmed the importance of the principle of 'giving-back', and gave us insight into how to do this when research results emerge over a longer timeline than is typical of field-based citizen science projects.</p> <p>And finally, we will share our experience with the behind-the-scenes elements of crowdsourcing - the parts the 'crowd' doesn't see - such as data quality assessment, data ingestion, data publication, and the flow of data between internal systems.</p> <p>In conclusion we will propose some visions of the future, such as moving towards a global platform for specimen label transcription with a shared underlying database infrastructure, how to deepen the engagement of digital volunteers from transcription tasks to scientific observations, and ways to bring online crowdsourcing and field-based citizen science together in a more streamlined way.</p>

Biological specimens in natural history collections constitute a massive repository of genetic information. Many specimens have been collected in areas in which they no longer exist or in areas where present‐day collecting is not possible. There are also specimens in collections representing populations or species that have gone extinct. Furthermore, species or populations may have been sampled throughout an extensive time period, which is particularly valuable for studies of genetic change through time. With the advent of high‐throughput sequencing, natural history museum resources have become accessible for genomic research. Consequently, these unique resources are increasingly being used across many fields of natural history. In this paper, we summarize our experiences of resequencing hundreds of genomes from historical avian museum specimens. We publish the protocols we have used and discuss the entire workflow from sampling and laboratory procedures, to the bioinformatic processing of historical specimen data.

Drosophila and parasitic wasps in the genus Leptopilina have long been a model for understanding host-parasite interactions. Indeed, parasitic wasps are important drivers of ecological and evolutionary processes broadly, but we are generally lacking information about the diversity, natural history, and evolution of these relationships. We collected insects from the Caribbean Island of Saint Lucia, home to the eastern Caribbean ‘dunni’ subgroup of Drosophila: a clade long appreciated for its recent patterns of speciation and adaptation. Here we present an integrative approach that incorporates natural history, taxonomy, physiology, and genomics to describe Leptopilina n. sp. Buffington, Lue, Davis & Tracey sp. nov. (Hymenoptera: Figitidae), a virulent parasitoid of dunni group flies, especially Drosophila antillea. Leptopilina n. sp. is nested within an early-branching clade of Leptopilina, offering insights into the evolution of this important genus of Drosophila parasitoids. We present a high-quality assembly for this wasp’s 1Gbp genome, and for its bacterial endosymbiont: Wolbachia strain “wLmal”. Furthermore, we show that wLmal induces parthenogenesis in the wasp, and that these wasps are reliant upon their Wolbachia infections to produce female offspring. Finally, comparison to historical museum specimens indicate that Leptopilina n. sp. had been collected approximately 40 years prior from the nearby island of Guadeloupe and were also asexually reproducing. This work represents one of only a handful of studies in which field biology, taxonomy, systematics, genomics, and experimental biology are integrated into a species description: showcasing the possibilities for biodiversity research in the genomic era.

Drosophila and parasitic wasps in the genus Leptopilina have long been a model for understanding host-parasite interactions. Indeed, parasitic wasps are important drivers of ecological and evolutionary processes broadly, but we are generally lacking information about the diversity, natural history, and evolution of these relationships. We collected insects from the Caribbean Island of Saint Lucia, home to the eastern Caribbean dunni subgroup of Drosophila: a clade long appreciated for its recent patterns of speciation and adaptation. Here we present an integrative approach that incorporates natural history, taxonomy, physiology, and genomics to describe Leptopilina malgretoutensis Buffington, Lue, Davis & Tracey sp. nov. (Hymenoptera: Figitidae), a virulent parasitoid of dunni group flies, specifically Drosophila antillea. Leptopilina malgretoutensis is nested within an early-branching clade of Leptopilina, offering insights into the evolution of this important genus of Drosophila parasitoids. We present a high-quality assembly for this wasp's 1Gbp genome, and for its bacterial endosymbiont: Wolbachia strain "wLmal". Furthermore, we show that wLmal induces parthenogenesis in the wasp, and that these wasps are reliant upon their Wolbachia infections to produce female offspring. Finally, comparisons to historical museum specimens indicated that Leptopilina malgretoutensis had been collected approximately 40 years prior from the nearby island of Guadeloupe, and these wasps were also asexually reproducing. This work represents one of only a handful of studies in which field biology, taxonomy, systematics, genomics, and experimental biology are integrated into a species description: showcasing the possibilities for biodiversity research in the genomic era.