Digitization of museum collections holds the potential to enhance researcher diversity

The Megachilidae (Hymenoptera, Apoidea, Apiformes) of the Democratic Republic of Congo curated at the Royal Museum for Central Africa (RMCA, Belgium)

Natural history collections are a cornerstone of entomology, and the conservation of specimens is the essential prerequisite for the development of research into systematics, biogeography, ecology, evolution and other disciplines. Yet, specimens collected during decades of entomological research conducted in less developed countries across Sub-Saharan Africa on pests, beneficial insects and insect biodiversity in general have largely been exported to be permanently preserved in developed countries, mainly in Europe and the United States of America. This is particularly true for the Democratic Republic of the Congos (DRC) diverse wild bee fauna, which has been investigated throughout the colonial period by visiting or resident entomologists and missionaries who have then transferred their collected material primarily to Belgium as part of a wider legacy of scientific exploration and colonialism. Digitizing NHC is one way to mitigate this current bias, by making samples accessible to researchers from the target post-colonial countries as well as to the wider international scientific community. In this study, we compiled and digitized 6,490 specimens records relevant to 195 wild bee species grouped in 18 genera within the biodiverse family Megachilidae, essentially from the colonial era (i.e., mostly between 19051960, with additional records up to 1978), and curated at the Royal Museum for Central Africa in Belgium. We provide a detailed catalogue of all records with updated locality and province names, including 29 species only available as type specimens. We also explore the historical patterns of diversity and distribution across DRC, and we provide a list of the research entomologists involved. This study is an important first step that uses digital technologies to democratize and repatriate important aspects of DRCs natural heritage of insect biodiversity, to stimulate more contemporary field surveys and modern taxonomic revisions, as well as to identify and characterize research gaps and biodiversity shortfalls in some of the less-explored regions of Sub-Saharan Africa.

Assessing digital accessible botanical knowledge and priorities for exploration and discovery of plant diversity across Mesoamerica

Digital accessible biodiversity knowledge has the potential to greatly advance botanical research and guide conservation efforts. Evaluating its shortfalls is key to understanding its limits and prioritising regions in need of renewed survey efforts. We used the Royal Botanical Gardens Kew's World Checklist of Vascular Plants to parse publicly available occurrence data downloaded from the Global Biodiversity Information Facility and quantify the spatial distribution of spatial, phylogenetic, and temporal data shortfalls across Mesoamerica. After processing 3578 777 occurrence records for 32 522 species of vascular plants across Mesoamerica, we found evidence of poor data coverage: incomplete characterisation of species diversity, old occurrence records, and low phylogenetic representation. One-third of the region showed large gaps for at least one of these dimensions (hotspots) and < 15% had adequate data coverage across dimensions. Overall, the shortfalls we identified compromise the quality of digitally available occurrence data and hamper research on spatial phylogenetics and species dynamics under anthropogenic disturbances. Our analyses identified areas of opportunity for increased efforts in data digitisation, botanical exploration, sequencing, and biodiversity monitoring. These efforts would serve to increase and rejuvenate knowledge on the geographic distribution of vascular plants in Mesoamerica.

The colonial legacy of herbaria

Herbarium collections shape our understanding of Earth's flora and are crucial for addressing global change issues. Their formation, however, is not free from sociopolitical issues of immediate relevance. Despite increasing efforts addressing issues of representation and colonialism in natural history collections, herbaria have received comparatively less attention. While it has been noted that the majority of plant specimens are housed in the Global North, the extent and magnitude of this disparity have not been quantified. Here we examine the colonial legacy of botanical collections, analysing 85,621,930 specimen records and assessing survey responses from 92 herbarium collections across 39 countries. We find an inverse relationship between where plant diversity exists in nature and where it is housed in herbaria. Such disparities persist across physical and digital realms despite overt colonialism ending over half a century ago. We emphasize the need for acknowledging the colonial history of herbarium collections and implementing a more equitable global paradigm for their collection, curation and use.

The herbarium of the future

The ~400 million specimens deposited across ~3000 herbaria are essential for: (i) understanding where plants have lived in the past, (ii) forecasting where they may live in the future, and (iii) delineating their conservation status. An open access 'global metaherbarium' is emerging as these specimens are digitized, mobilized, and interlinked online. This virtual biodiversity resource is attracting new users who are accelerating traditional applications of herbaria and generating basic and applied scientific innovations, including e-monographs and floras produced by diverse, interdisciplinary, and inclusive teams; robust machine-learning algorithms for species identification and phenotyping; collection and synthesis of ecological trait data at large spatiotemporal and phylogenetic scales; and exhibitions and installations that convey the beauty of plants and the value of herbaria in addressing broader societal issues.

A set of principles and practical suggestions for equitable fieldwork in biology

Field biology is an area of research that involves working directly with living organisms in situ through a practice known as “fieldwork.” Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of the core team members. However, existing power imbalances stemming from geopolitical history, discrimination, and professional position, among other factors, perpetuate inequities when conducting these research endeavors. After reflecting on our own research programs, we propose four general principles to guide equitable, inclusive, ethical, and safe practices in field biology: be collaborative, be respectful, be legal, and be safe. Although many biologists already structure their field programs around these principles or similar values, executing equitable research practices can prove challenging and requires careful consideration, especially by those in positions with relatively greater privilege. Based on experiences and input from a diverse group of global collaborators, we provide suggestions for action-oriented approaches to make field biology more equitable, with particular attention to how those with greater privilege can contribute. While we acknowledge that not all suggestions will be applicable to every institution or program, we hope that they will generate discussions and provide a baseline for training in proactive, equitable fieldwork practices.

Can Artificial Intelligence Help in the Study of Vegetative Growth Patterns from Herbarium Collections? An Evaluation of the Tropical Flora of the French Guiana Forest

A better knowledge of tree vegetative growth phenology and its relationship to environmental variables is crucial to understanding forest growth dynamics and how climate change may affect it. Less studied than reproductive structures, vegetative growth phenology focuses primarily on the analysis of growing shoots, from buds to leaf fall. In temperate regions, low winter temperatures impose a cessation of vegetative growth shoots and lead to a well-known annual growth cycle pattern for most species. The humid tropics, on the other hand, have less seasonality and contain many more tree species, leading to a diversity of patterns that is still poorly known and understood. The work in this study aims to advance knowledge in this area, focusing specifically on herbarium scans, as herbariums offer the promise of tracking phenology over long periods of time. However, such a study requires a large number of shoots to be able to draw statistically relevant conclusions. We propose to investigate the extent to which the use of deep learning can help detect and type-classify these relatively rare vegetative structures in herbarium collections. Our results demonstrate the relevance of using herbarium data in vegetative phenology research as well as the potential of deep learning approaches for growing shoot detection.

Unlocking the Entomological Collection of the Natural History Museum of Maputo, Mozambique

Background

The collections of the Natural History Museum of Maputo have a crucial role in the safeguarding of Mozambique's biodiversity, representing an important repository of data and materials regarding the natural heritage of the country. In this paper, a dataset is described, based on the Museum’s Entomological Collection recording 409 species belonging to seven orders and 48 families. Each specimen’s available data, such as geographical coordinates and taxonomic information, have been digitised to build the dataset. The specimens included in the dataset were obtained between 1914–2018 by collectors and researchers from the Natural History Museum of Maputo (once known as “Museu Alváro de Castro”) in all the country’s provinces, with the exception of Cabo Delgado Province.

New information

This paper adds data to the Biodiversity Network of Mozambique and the Global Biodiversity Information Facility, within the objectives of the SECOSUD II Project and the Biodiversity Information for Development Programme. The aforementioned insect dataset is available on the GBIF Engine data portal (https://doi.org/10.15468/j8ikhb). Data were also shared on the Mozambican national portal of biodiversity data BioNoMo (https://bionomo.openscidata.org), developed by SECOSUD II Project.

Data integration enables global biodiversity synthesis

The accessibility of global biodiversity information has surged in the past two decades, notably through widespread funding initiatives for museum specimen digitization and emergence of large-scale public participation in community science. Effective use of these data requires the integration of disconnected datasets, but the scientific impacts of consolidated biodiversity data networks have not yet been quantified. To determine whether data integration enables novel research, we carried out a quantitative text analysis and bibliographic synthesis of >4,000 studies published from 2003 to 2019 that use data mediated by the world's largest biodiversity data network, the Global Biodiversity Information Facility (GBIF). Data available through GBIF increased 12-fold since 2007, a trend matched by global data use with roughly two publications using GBIF-mediated data per day in 2019. Data-use patterns were diverse by authorship, geographic extent, taxonomic group, and dataset type. Despite facilitating global authorship, legacies of colonial science remain. Studies involving species distribution modeling were most prevalent (31% of literature surveyed) but recently shifted in focus from theory to application. Topic prevalence was stable across the 17-y period for some research areas (e.g., macroecology), yet other topics proportionately declined (e.g., taxonomy) or increased (e.g., species interactions, disease). Although centered on biological subfields, GBIF-enabled research extends surprisingly across all major scientific disciplines. Biodiversity data mobilization through global data aggregation has enabled basic and applied research use at temporal, spatial, and taxonomic scales otherwise not possible, launching biodiversity sciences into a new era.

Hares and rabbits (Leporidae) in collection of the Šariš Museum, Bardejov (Slovakia)

The Natural History Department of the Šariš Museum, Bardejov, Slovakia, was established in 1956 by PhMr. Tibor Weisz. The mammal collection consists of more than 5 000 specimens of 67 mammal species of the Slovakian fauna. The museum mostly represents the fauna of north-eastern Slovakia, i.e. the transition area between the Eastern and Western Carpathians and adjacent to the northernmost part of the Pannonian Basin. In the paper, data are presented on hare and rabbit specimens deposited in the collection of the Šariš Museum in Bardejov (SMB), Slovakia. In total, data were evaluated on 27 specimens of the brown hare (Lepus europaeus) from twelve sites of Slovakia (n = 19), one site of Czech Silesia (n = 1), and from unknow localities (n = 7). Individuals were acquired in 1958–1971, but mainly in 1965–1966 (n = 19, 70.4 %). Among them, one specimen had signs of „albinism“ and was collected from Zlaté village. The collection also includes a skull of a brown hare with anomalous dentition. Similarly, two skulls of the mountain hare (Lepus timidus) obtained from the Danish preparator N. H. Gustaffson were evaluated. Three rabit specimens were also found in the collection, including two skulls of the wild rabbit (Oryctolagus cuniculus) and a skin-mount and skull of a domestic rabbit (Oryctolagus cuniculus forma domestica). The collection contains 20 adult specimens (15 males and 5 females) with body size values recorded in the protocol cards. Mammalogical collections in the Šariš Museum in Bardejov represent an outstanding scientific time capsule. All stored specimens in this particular and other similar collections, including those in local museums, will largely be needed and used as datasets by ecologists and conservationists in the future. It is necesary to preserve the collections, to computerise and digitise their inventories and the wealth of information they represent. At present, most of these data are not accessible electronically or online. Therefore, such collections, including that in Bardejov, must be sustained for a long term, which will require increased funding for their physical and scientific preservation.

Building Natural History Collections for the Twenty-First Century and Beyond

Natural history collections (NHCs) are important resources for a diverse array of scientific fields. Recent digitization initiatives have broadened the user base of NHCs, and new technological innovations are using materials generated from collections to address novel scientific questions. Simultaneously, NHCs are increasingly imperiled by reductions in funding and resources. Ensuring that NHCs continue to serve as a valuable resource for future generations will require the scientific community to increase their contribution to and acknowledgement of collections. We provide recommendations and guidelines for scientists to support NHCs, focusing particularly on new users that may be unfamiliar with collections. We hope that this perspective will motivate debate on the future of NHCs and the role of the scientific community in maintaining and improving biological collections.

Patterns in research and data sharing for the study of form and function in caviomorph rodents

The combination of morphometrics, phylogenetic comparative methods, and open data sets has renewed interest in relating morphology to adaptation and ecological opportunities. Focusing on the Caviomorpha, a well-studied mammalian group, we evaluated patterns in research and data sharing in studies relating form and function. Caviomorpha encompasses a radiation of rodents that is diverse both taxonomically and ecologically. We reviewed 41 publications investigating ecomorphology in this group. We recorded the type of data used in each study and whether these data were made available, and we re-digitized all provided data. We tracked two major lines of information: collections material examined and trait data for morphological and ecological traits. Collectively, the studies considered 63% of extant caviomorph species; all extant families and genera were represented. We found that species-level trait data rarely were provided. Specimen-level data were even less common. Morphological and ecological data were too heterogeneous and sparse to aggregate into a single data set, so we created relational tables with the data. Additionally, we concatenated all specimen lists into a single data set and standardized all relevant data for phylogenetic hypotheses and gene sequence accessions to facilitate future morphometric and phylogenetic comparative research. This work highlights the importance and ongoing use of scientific collections, and it allows for the integration of specimen information with species trait data. Recientemente ha resurgido el interés por estudiar la relación entre morfología, ecología, y adaptación. Esto se debe al desarrollo de nuevas herramientas morfométricas y filogenéticas, y al acceso a grandes bases de datos para estudios comparados. Revisamos 41 publicaciones sobre ecomorfología de roedores caviomorfos, un grupo diverso y bien estudiado, para evaluar los patrones de investigación y la transparencia para la liberación de datos. Registramos los tipos de datos que se utilizaron para cada estudio y si los datos están disponibles. Cuando estos datos se compartieron, los redigitalizamos. Nos enfocamos en los ejemplares consultados, y en datos que describen rasgos ecológicos y morfológicos para las especies estudiadas. Los estudios que revisamos abarcan el 63% de las especies de caviomorfos que actualmente existen. Encontramos que raramente fueron compartidos los datos que se tomaron para especies, y menos aún para ejemplares. Los datos morfológicos y ecológicos eran demasiado heterogéneos e exiguos para consolidar en un solo banco de datos; debido a esta circunstancia, creamos tablas relacionales con los datos. Además, enlazamos todas las listas individuales de especímenes para crear un solo banco de datos y estandarizamos todos los datos pertinentes a hipótesis filogenéticas, así como los números de acceso de secuencias genéticas, para así facilitar eventuales estudios comparados de morfometría y filogenia. Este trabajo resalta la importancia de las colecciones científicas y documenta su uso, además permitiendo la futura integración de datos derivados de ejemplares con datos sobre rasgos ecomorfológicos a nivel de especie.

Low-cost observations and experiments return a high value in plant phenology research

Plant ecologists in the Anthropocene are tasked with documenting, interpreting, and predicting how plants respond to environmental change. Phenology, the timing of seasonal biological events including leaf-out, flowering, fruiting, and leaf senescence, is among the most visible and oft-recorded facets of plant ecology. Climate-driven shifts in plant phenology can alter reproductive success, interspecific competition, and trophic interactions. Low-cost phenology research, including observational records and experimental manipulations, is fundamental to our understanding of both the mechanisms and effects of phenological change in plant populations, species, and communities. Traditions of local-scale botanical phenology observations and data leveraged from written records and natural history collections provide the historical context for recent observations of changing phenologies. New technology facilitates expanding the spatial, taxonomic, and human interest in this research by combining contemporary field observations by researchers and open access community science (e.g., USA National Phenology Network) and available climate data. Established experimental techniques, such as twig cutting and common garden experiments, are low-cost methods for studying the mechanisms and drivers of plant phenology, enabling researchers to observe phenological responses under novel environmental conditions. We discuss the strengths, limitations, potential hidden costs (i.e., volunteer and student labor), and promise of each of these methods for addressing emerging questions in plant phenology research. Applied thoughtfully, economically, and creatively, many low-cost approaches offer novel opportunities to fill gaps in our geographic, taxonomic, and mechanistic understanding of plant phenology worldwide.

Digitization and the Future of Natural History Collections

Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization—the conversion of specimen data into accessible digital content—has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0)—whereby specimens are digitized within NHCs—to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds on the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data links, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical issues of global change.

The Changing Uses of Herbarium Data in an Era of Global Change: An Overview Using Automated Content Analysis

Widespread specimen digitization has greatly enhanced the use of herbarium data in scientific research. Publications using herbarium data have increased exponentially over the last century. Here, we review changing uses of herbaria through time with a computational text analysis of 13,702 articles from 1923 to 2017 that quantitatively complements traditional review approaches. Although maintaining its core contribution to taxonomic knowledge, herbarium use has diversified from a few dominant research topics a century ago (e.g., taxonomic notes, botanical history, local observations), with many topics only recently emerging (e.g., biodiversity informatics, global change biology, DNA analyses). Specimens are now appreciated as temporally and spatially extensive sources of genotypic, phenotypic, and biogeographic data. Specimens are increasingly used in ways that influence our ability to steward future biodiversity. As we enter the Anthropocene, herbaria have likewise entered a new era with enhanced scientific, educational, and societal relevance.

Species characteristics affect local extinctions

PREMISE OF THE STUDY

Human activities threaten thousands of species with extinction. However, it remains difficult to predict extinction risk for many vulnerable species. Species traits, species characteristics such as rarity or habitat use, and phylogenetic patterns are associated with responses to anthropogenic environmental change and may help predict likelihood of extinction.

METHODS

We used historical botanical data from Kalamazoo County, Michigan, USA, to examine whether species traits (growth form, life history, nitrogen-fixation, photosynthetic pathway), species characteristics (community association, species origin, range edge, habitat specialization, rarity), or phylogenetic relatedness explain local species loss at the county level.

KEY RESULTS

Across Kalamazoo County, prairie species, species at the edge of their native range, regionally rare species, and habitat specialists were most likely to become locally extinct. Prairie species experienced the highest local extinction rates of any habitat type, and among prairie species, regionally rare and specialist species were most vulnerable to loss. We found no evidence for a phylogenetic pattern in plant extinctions.

CONCLUSIONS

Our study illustrates the value of historical datasets for understanding and potentially predicting biodiversity loss. Not surprisingly, rare, specialist species occupying threatened habitats are most at risk of local extinction. As a result, identifying mechanisms to conserve or restore rare or declining species and preventing further habitat destruction may be the most effective strategies for reducing future extinction.

A Novel Automated Mass Digitisation Workflow for Natural History Microscope Slides

The Natural History Museum, London (NHM) has embarked on an ambitious programme to digitise its collections. One aim of the programme has been to improve the workflows and infrastructure needed to support high-throughput digitisation and create comprehensive digital inventories of large scientific collections. This paper presents the workflow developed to digitise the entire Phthiraptera (parasitic lice) microscope slide collection (70,663 slides). Here we describe a novel process of semi-automated mass digitisation using both temporary and permanent barcode labels applied before and during slide imaging. By using a series of barcodes encoding information associated with each slide (i.e. unique identifier, location in the collection and taxonomic name), we can run a series of automated processes, including file renaming, image processing and bulk import into the NHM's collection management system. We provide data on the comparative efficiency of these processes, illustrating how simple activities, like automated file renaming, reduces image post-processing time, minimises human error and can be applied across multiple collection types.

Using herbaria to study global environmental change

During the last centuries, humans have transformed global ecosystems. With their temporal dimension, herbaria provide the otherwise scarce long-term data crucial for tracking ecological and evolutionary changes over this period of intense global change. The sheer size of herbaria, together with their increasing digitization and the possibility of sequencing DNA from the preserved plant material, makes them invaluable resources for understanding ecological and evolutionary species' responses to global environmental change. Following the chronology of global change, we highlight how herbaria can inform about long-term effects on plants of at least four of the main drivers of global change: pollution, habitat change, climate change and invasive species. We summarize how herbarium specimens so far have been used in global change research, discuss future opportunities and challenges posed by the nature of these data, and advocate for an intensified use of these 'windows into the past' for global change research and beyond.

Biological collections for understanding biodiversity in the Anthropocene

Global change has become a central focus of modern biology. Yet, our knowledge of how anthropogenic drivers affect biodiversity and natural resources is limited by a lack of biological data spanning the Anthropocene. We propose that the hundreds of millions of plant, fungal and animal specimens deposited in natural history museums have the potential to transform the field of global change biology. We suggest that museum specimens are underused, particularly in ecological studies, given their capacity to reveal patterns that are not observable from other data sources. Increasingly, museum specimens are becoming mobilized online, providing unparalleled access to physiological, ecological and evolutionary data spanning decades and sometimes centuries. Here, we describe the diversity of collections data archived in museums and provide an overview of the diverse uses and applications of these data as discussed in the accompanying collection of papers within this theme issue. As these unparalleled resources are under threat owing to budget cuts and other institutional pressures, we aim to shed light on the unique discoveries that are possible in museums and, thus, the singular value of natural history collections in a period of rapid change.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.

The history and impact of digitization and digital data mobilization on biodiversity research

The first two decades of the twenty-first century have seen a rapid rise in the mobilization of digital biodiversity data. This has thrust natural history museums into the forefront of biodiversity research, underscoring their central role in the modern scientific enterprise. The advent of mobilization initiatives such as the United States National Science Foundation's Advancing Digitization of Biodiversity Collections (ADBC), Australia's Atlas of Living Australia (ALA), Mexico's National Commission for the Knowledge and Use of Biodiversity (CONABIO), Brazil's Centro de Referência em Informação (CRIA) and China's National Specimen Information Infrastructure (NSII) has led to a rapid rise in data aggregators and an exponential increase in digital data for scientific research and arguably provide the best evidence of where species live. The international Global Biodiversity Information Facility (GBIF) now serves about 131 million museum specimen records, and Integrated Digitized Biocollections (iDigBio) in the USA has amassed more than 115 million. These resources expose collections to a wider audience of researchers, provide the best biodiversity data in the modern era outside of nature itself and ensure the primacy of specimen-based research. Here, we provide a brief history of worldwide data mobilization, their impact on biodiversity research, challenges for ensuring data quality, their contribution to scientific publications and evidence of the rising profiles of natural history collections.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.