More from ecologists to support natural history museums

Going, Going, Gone The Diminishing Capacity of Museum Specimen Collections to Address Global Change Research: A Case Study on Urban Reptiles

It has been increasingly popular to use natural history specimens to examine environmental changes. As the current functionality of museum specimens has extended beyond their traditional taxonomic role, there has been a renewed focus on the completeness of biological collections to provide data for current and future research. We used the collections of the Western Australian Museum to answer questions about the change in occurrence of five common reptile species due to the rapid urbanization of Perth. We recorded a significant decline in collection effort from the year 2000 onwards (F = 7.65, p < 0.01) compared to the period 1990–1999. Spatial analysis revealed that only 0.5% of our study region was well sampled, 8.5% were moderately sampled and the majority of the regions (91%) were poorly sampled. By analysing the trend of specimen acquisition from 1950 to 2010, we discovered a significant inconsistency in specimen sampling effort for 13 common reptile species across time and space. A large proportion of past specimens lacked information including the place and time of collection. An increase in investment to museums and an increase in geographically and temporally systematic collecting is advocated to ensure that collections can answer questions about environmental change.

Using a Collection Heath Index to prioritise access and activities in the New Zealand Arthropod Collection

A Collection Health Index (CHI) is a useful approach to help scope new activities, prioritise curation and accelerate digitisation within taxonomic collections. We use a Collection Health Index (CHI), based on McGinley (1993), to profile the curation levels in the New Zealand Arthropod Collection for major insect groups. There are several highly curated and well known groups (Hemiptera, Lepidoptera, ‘Other Insects’). However, three major issues were identified: 1) curation becoming increasingly outdated in sections with large numbers of, particularly older, specimens (Coleoptera, Diptera); 2) historically poorer curation, with no resident expertise or resource (Diptera); and 3) high levels of family and genus-only material that needs further identification and a significant amount of alpha level taxonomy (parts of Coleoptera, parts of Diptera and Hymenoptera). Assessment using the CHI is simple and fast, allows future planning and is based on common issues for collection management, such as care, accessibility, organisation and data capture.

Museomics and the holotype of a critically endangered cricetid rodent provide key evidence of an undescribed genus

Historical DNA obtained from voucher specimens housed in natural history museums worldwide have allowed the study of elusive, rare or even extinct species that in many cases are solely represented by museum holdings. This has resulted in the increase of taxonomic representation of many taxa, has led to the discovery of new species, and has yielded stunning novel insights into the evolutionary history of cryptic or even undescribed species. Peromyscus mekisturus, is a critically endangered cricetid rodent endemic to Mexico and is only known from two museum specimens collected in 1898 and 1947. Intensive field work efforts to attempt to determine if viable populations still exist have failed, suggesting that this species is extinct or is nearing extinction. In addition, a recent study using mitogenomes demonstrated that P. mekisturus forms a well-supported clade outside the genus Peromyscus and hypothesized that this taxon is the sister group of the genus Reithrodontomys. Here, we used target enrichment and high-throughput sequencing of several thousand nuclear ultraconserved elements and mitogenomes to reconstruct dated phylogenies to test the previous phylogenetic hypothesis. We analyzed the holotype and the only other known specimen of P. mekisturus and museum samples from other peromyscine rodents to test the phylogenetic position of the species. Our results confirm that the only two specimens known to science of P. mekisturus belong to the same species and support the hypothesis that this species belongs to an undescribed genus of cricetid rodents that is sister to the genus Reithrodontomys. We dated the origin of P. mekisturus together with other speciation events in peromyscines during the late Pliocene – early Pleistocene and related these events with the Pleistocene climatic cycles. In light of our results, we recommend a taxonomic re-evaluation of this enigmatic species to properly recognize its taxonomic status as a new genus. We also acknowledge the relevance of generating genomic data from type specimens and highlight the need and importance of continuing to build the scientific heritage of the collections to study and better understand past, present, and future biodiversity.

Natural history collections are critical resources for contemporary and future studies of urban evolution

Urban environments are among the fastest changing habitats on the planet, and this change has evolutionary implications for the organisms inhabiting them. Herein, we demonstrate that natural history collections are critical resources for urban evolution studies. The specimens housed in these collections provide great potential for diverse types of urban evolution research, and strategic deposition of specimens and other materials from contemporary studies will determine the resources and research questions available to future urban evolutionary biologists. As natural history collections are windows into the past, they provide a crucial historical timescale for urban evolution research. While the importance of museum collections for research is generally appreciated, their utility in the study of urban evolution has not been explicitly evaluated. Here, we: (a) demonstrate that museum collections can greatly enhance urban evolution studies, (b) review patterns of specimen use and deposition in the urban evolution literature, (c) analyze how urban versus rural and native versus nonnative vertebrate species are being deposited in museum collections, and (d) make recommendations to researchers, museum professionals, scientific journal editors, funding agencies, permitting agencies, and professional societies to improve archiving policies. Our analyses of recent urban evolution studies reveal that museum specimens can be used for diverse research questions, but they are used infrequently. Further, although nearly all studies we analyzed generated resources that could be deposited in natural history collections (e.g., collected specimens), a minority (12%) of studies actually did so. Depositing such resources in collections is crucial to allow the scientific community to verify, replicate, and/or re-visit prior research. Therefore, to ensure that adequate museum resources are available for future urban evolutionary biology research, the research community-from practicing biologists to funding agencies and professional societies-must make adjustments that prioritize the collection and deposition of urban specimens.

The Open-Specimen Movement

The open-science movement seeks to increase transparency, reproducibility, and access to scientific data. As primary data, preserved biological specimens represent records of global biodiversity critical to research, conservation, national security, and public health. However, a recent decrease in specimen preservation in public biorepositories is a major barrier to open biological science. As such, there is an urgent need for a cultural shift in the life sciences that normalizes specimen deposition in museum collections. Museums embody an open-science ethos and provide long-term research infrastructure through curation, data management and security, and community-wide access to samples and data, thereby ensuring scientific reproducibility and extension. We propose that a paradigm shift from specimen ownership to specimen stewardship can be achieved through increased open-data requirements among scientific journals and institutional requirements for specimen deposition by funding and permitting agencies, and through explicit integration of specimens into existing data management plan guidelines and annual reporting.

Global Patterns and Drivers of Bee Distribution

Insects are the focus of many recent studies suggesting population declines, but even invaluable pollination service providers such as bees lack a modern distributional synthesis. Here, we combine a uniquely comprehensive checklist of bee species distributions and >5,800,000 public bee occurrence records to describe global patterns of bee biodiversity. Publicly accessible records are sparse, especially from developing countries, and are frequently inaccurate throughout much of the world, consequently suggesting different biodiversity patterns from checklist data. Global analyses reveal hotspots of species richness, together generating a rare bimodal latitudinal richness gradient, and further analyses suggest that xeric areas, solar radiation, and non-forest plant productivity are among the most important global drivers of bee biodiversity. Together, our results provide a new baseline and best practices for studies on bees and other understudied invertebrates.

Natural history collections as a basis for sound biodiversity assessments: Plexauridae (Octocorallia, Holaxonia) of the Naturalis CANCAP and Tyro Mauritania II expeditions

Mapping biodiversity is the marathon of the 21^st Century as an answer to the present extinction crisis. A century in which science is also characterised by large scientific datasets collected through new technologies aiming to fill gaps in our knowledge of species distributions. However, most species records rely on observations that are not linked to specimens, which does not allow verification of species hypotheses by other scientists. Natural history museums form a verifiable source of biodiversity records which were made by taxonomists. Nonetheless, these museums seem to be forgotten by biologists in scientific fields other than taxonomy or systematics. Naturalis Biodiversity Center (NBC) in Leiden is care keeper of large collections of marine organisms, which were sampled in the Northeast Atlantic during the CANCAP and Tyro Mauritania II expeditions (1976–1988). Many octocorals were sampled and deposited in the NBC collection, where they became available for study and were partially identified by the senior author (M.G.) in the 1980s. Nonetheless, no checklist or taxonomic revision was published so far with the complete results. In 2016 the first author visited NBC to examine NE Atlantic Plexauridae octocorals. Plexauridae octocoral-vouchered records were listed and mapped to reveal high standard primary biodiversity records unreported so far for the NE Atlantic Ocean. Twenty-four Plexauridae species with ~ six putative new species to science were discovered and eleven new biogeographical records were made from distinct Macaronesian archipelagos. Finally, new depth range records were found for three species at sea basin level and for eight species at a regional scale.

Historical collections as a tool for assessing the global pollination crisis

There is increasing concern about the decline of pollinators worldwide. However, despite reports that pollinator declines are widespread, data are scarce and often geographically and taxonomically biased. These biases limit robust inference about any potential pollinator crisis. Non-structured and opportunistic historical specimen collection data provide the only source of historical information which can serve as a baseline for identifying pollinator declines. Specimens historically collected and preserved in museums not only provide information on where and when species were collected, but also contain other ecological information such as species interactions and morphological traits. Here, we provide a synthesis of how researchers have used historical data to identify long-term changes in biodiversity, species abundances, morphology and pollination services. Despite recent advances, we show that information on the status and trends of most pollinators is absent. We highlight opportunities and limitations to progress the assessment of pollinator declines globally. Finally, we demonstrate different approaches to analysing museum collection data using two contrasting case studies from distinct geographical regions (New Zealand and Spain) for which long-term pollinator declines have never been assessed. There is immense potential for museum specimens to play a central role in assessing the extent of the global pollination crisis.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.

Museum specimens of terrestrial vertebrates are sensitive indicators of environmental change in the Anthropocene

Natural history museums and the specimen collections they curate are vital scientific infrastructure, a fact as true today as it was when biologists began collecting and preserving specimens over 200 years ago. The importance of museum specimens in studies of taxonomy, systematics, ecology and evolutionary biology is evidenced by a rich and abundant literature, yet creative and novel uses of specimens are constantly broadening the impact of natural history collections on biodiversity science and global sustainability. Excellent examples of the critical importance of specimens come from their use in documenting the consequences of environmental change, which is particularly relevant considering the alarming rate at which we now modify our planet in the Anthropocene. In this review, we highlight the important role of bird, mammal and amphibian specimens in documenting the Anthropocene and provide examples that underscore the need for continued collection of museum specimens.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.

Herbarium data: Global biodiversity and societal botanical needs for novel research

Building on centuries of research based on herbarium specimens gathered through time and around the globe, a new era of discovery, synthesis, and prediction using digitized collections data has begun. This paper provides an overview of how aggregated, open access botanical and associated biological, environmental, and ecological data sets, from genes to the ecosystem, can be used to document the impacts of global change on communities, organisms, and society; predict future impacts; and help to drive the remediation of change. Advocacy for botanical collections and their expansion is needed, including ongoing digitization and online publishing. The addition of non-traditional digitized data fields, user annotation capability, and born-digital field data collection enables the rapid access of rich, digitally available data sets for research, education, informed decision-making, and other scholarly and creative activities. Researchers are receiving enormous benefits from data aggregators including the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), the Atlas of Living Australia (ALA), and the Biodiversity Heritage Library (BHL), but effective collaboration around data infrastructures is needed when working with large and disparate data sets. Tools for data discovery, visualization, analysis, and skills training are increasingly important for inspiring novel research that improves the intrinsic value of physical and digital botanical collections.

Maximising Synergy among Tropical Plant Systematists, Ecologists, and Evolutionary Biologists

Closer collaboration among ecologists, systematists, and evolutionary biologists working in tropical forests, centred on studies within long-term permanent plots, would be highly beneficial for their respective fields. With a key unifying theme of the importance of vouchered collection and precise identification of species, especially rare ones, we identify four priority areas where improving links between these communities could achieve significant progress in biodiversity and conservation science: (i) increasing the pace of species discovery; (ii) documenting species turnover across space and time; (iii) improving models of ecosystem change; and (iv) understanding the evolutionary assembly of communities and biomes.