Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research

Ecological forecasts of insect range dynamics: a broad range of taxa includes winners and losers under future climate

Species distribution models are the primary tools to project future species' distributions, but this complex task is influenced by data limitations and evolving best practices. The majority of the 53 studies we examined utilized correlative models and did not follow current best practices for validating retrospective or future environmental data layers. Despite this, a summary of results is largely unsurprising: shifts toward cooler regions, but otherwise mixed dynamics emphasizing winners and losers. Harmful insects were more likely to show positive outcomes compared with beneficial species. Our restricted ability to consider mechanisms complicates interpretation of any single study. To improve this area of modeling, more classic field and lab studies to uncover basic ecology and physiology are crucial.

Forest habitats and plant communities strongly predicts Megachilidae bee biodiversity

Megachilidae is one of the United States' most diverse bee families, with 667 described species in 19 genera. Unlike other bee families, which are primarily ground nesters, most megachilid bees require biotic cavities for nesting (i.e., wood, pithy stems, etc.). For this group, the availability of woody-plant species may be as important as nectar/pollen resources in maintaining populations. We studied Megachilidae biodiversity in the continental United States. We confirmed that the highest species richness of Megachilidae was in the southwestern United States. We examined the relationship between species richness and climate, land cover, tree species richness, and flowering plant diversity. When examining environmental predictors across the conterminous United States, we found that forested habitats, but not tree diversity, strongly predicted Megachilidae richness. Additionally, Megachilidae richness was highest in areas with high temperature and low precipitation, however this was not linearly correlated and strongly positively correlated with flowering plant diversity. Our research suggests that the availability of nesting substrate (forested habitats), and not only flowering plants, is particularly important for these cavity-nesting species. Since trees and forested areas are particularly susceptible to climate change, including effects of drought, fire, and infestations, nesting substrates could become a potential limiting resource for Megachilidae populations.

Insect collecting bias in Arizona with a preliminary checklist of the beetles from the Sand Tank Mountains

Background

The State of Arizona in the south-western United States supports a high diversity of insects. Digitised occurrence records, especially from preserved specimens in natural history collections, are an important and growing resource to understand biodiversity and biogeography. Underlying bias in how insects are collected and what that means for interpreting patterns of insect diversity is largely untested. To explore the effects of insect collecting bias in Arizona, the State was regionalised into specific areas. First, the entire State was divided into broad biogeographic areas by ecoregion. Second, the 81 tallest mountain ranges were mapped on to the State. The distribution of digitised records across these areas were then examined.A case study of surveying the beetles (Insecta, Coleoptera) of the Sand Tank Mountains is presented. The Sand Tanks are a low-elevation range in the Lower Colorado River Basin subregion of the Sonoran Desert from which a single beetle record was published before this study.

New information

The number of occurrence records and collecting events are very unevenly distributed throughout Arizona and do not strongly correlate with the geographic size of areas. Species richness is estimated for regions in Arizona using rarefaction and extrapolation. Digitised records from the disproportionately highly collected areas in Arizona represent at best 70% the total insect diversity within them. We report a total of 141 species of Coleoptera from the Sand Tank Mountains, based on 914 digitised voucher specimens. These specimens add important new records for taxa that were previously unavailable in digitised data and highlight important biogeographic ranges.Possible underlying mechanisms causing bias are discussed and recommendations are made for future targeted collecting of under-sampled regions. Insect species diversity is apparently at best 70% documented for the State of Arizona with many thousands of species not yet recorded. The Chiricahua Mountains are the most densely sampled region of Arizona and likely contain at least 2,000 species not yet vouchered in online data. Preliminary estimates for species richness of Arizona are at least 21,000 and likely much higher. Limitations to analyses are discussed which highlight the strong need for more insect occurrence data.

Is the world wormier than it used to be? We'll never know without natural history collections

Many disease ecologists and conservation biologists believe that the world is wormier than it used to be-that is, that parasites are increasing in abundance through time. This argument is intuitively appealing. Ecologists typically see parasitic infections, through their association with disease, as a negative endpoint, and are accustomed to attributing negative outcomes to human interference in the environment, so it slots neatly into our worldview that habitat destruction, biodiversity loss and climate change should have the collateral consequence of causing outbreaks of parasites. But surprisingly, the hypothesis that parasites are increasing in abundance through time remains entirely untested for the vast majority of wildlife parasite species. Historical data on parasites are nearly impossible to find, which leaves no baseline against which to compare contemporary parasite burdens. If we want to know whether the world is wormier than it used to be, there is only one major research avenue that will lead to an answer: parasitological examination of specimens preserved in natural history collections. Recent advances demonstrate that, for many specimen types, it is possible to extract reliable data on parasite presence and abundance. There are millions of suitable specimens that exist in collections around the world. When paired with contemporaneous environmental data, these parasitological data could even point to potential drivers of change in parasite abundance, including climate, pollution or host density change. We explain how to use preserved specimens to address pressing questions in parasite ecology, give a few key examples of how collections-based parasite ecology can resolve these questions, identify some pitfalls and workarounds, and suggest promising areas for research. Natural history specimens are 'parasite time capsules' that give ecologists the opportunity to test whether infectious disease is on the rise and to identify what forces might be driving these changes over time. This approach will facilitate major advances in a new sub-discipline: the historical ecology of parasitism.

Towards a Roadmap for Advancing the Catalogue of the World’s Natural History Collections

Natural history collections are the foundations upon which all knowledge of natural history is constructed. Biological specimens are the best documentation of variation within each species, increasingly serve as curated sources for reference DNA, and are frequently our only evidence for historical species distribution. Collections represent an enormous multigenerational investment in research infrastructure for the biological sciences, but despite this importance most of the holdings of these institutions remain invisible on the Internet, inaccessible to taxonomists from other countries and hidden from computational biodiversity research.

Although comprehensive digitisation of the complete holdings of each natural history collection is the long-term goal, this is an expensive and labor-intensive task and will not be completed in the near future for all collections. However, many benefits could quickly be achieved by publishing high-quality metadata on each collection to increase its visibility, provide the foundations for further digitisation and enable researchers to discover and communicate with collections of interest.

This paper summarises the results from a consultation activity carried out in 2020 as part of the SYNTHESYS+ (Synthesys of Systematic Resources), “Developing implementation roadmaps for priority infrastructure areas as part of cooperative RI for biodiversity” project. This consultation was primed through an ideas paper, and introductory webinars and conducted as a facilitated two-week online multilingual discussion around 26 topics grouped under four broad headings (Users, Content, Technology and Governance). The results of these discussions are summarised here, along with the wider context of existing and planned initiatives.

scAnt-an open-source platform for the creation of 3D models of arthropods (and other small objects)

We present scAnt, an open-source platform for the creation of digital 3D models of arthropods and small objects. scAnt consists of a scanner and a Graphical User Interface, and enables the automated generation of Extended Depth Of Field images from multiple perspectives. These images are then masked with a novel automatic routine which combines random forest-based edge-detection, adaptive thresholding and connected component labelling. The masked images can then be processed further with a photogrammetry software package of choice, including open-source options such as Meshroom, to create high-quality, textured 3D models. We demonstrate how these 3D models can be rigged to enable realistic digital specimen posing, and introduce a novel simple yet effective method to include semi-realistic representations of approximately planar and transparent structures such as wings. As a result of the exclusive reliance on generic hardware components, rapid prototyping and open-source software, scAnt costs only a fraction of available comparable systems. The resulting accessibility of scAnt will (i) drive the development of novel and powerful methods for machine learning-driven behavioural studies, leveraging synthetic data; (ii) increase accuracy in comparative morphometric studies as well as extend the available parameter space with area and volume measurements; (iii) inspire novel forms of outreach; and (iv) aid in the digitisation efforts currently underway in several major natural history collections.

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.

Decline of Amateur Lepidoptera Collectors Threatens the Future of Specimen-Based Research

Amateur butterfly and moth collectors in the United States have procured more Lepidoptera specimens than professional scientists. The advent of large government-supported database efforts has made a quantitative examination of the impact of amateur collecting of these insects possible. We reviewed trends in Lepidoptera collecting since 1800, using more than 1 million United States lepidopteran specimens that have been collected into public databases. Our findings show a steep rise in the collection of specimens after World War II, followed by a short plateau and sharp decline in the late 1990s. In contrast, the rate of observations submitted to database groups dramatically increased around 2005. Declining acquisition of Lepidoptera specimens may compromise critically important testing of contemporary and future ecological, conservation, and evolutionary hypotheses on a grand scale, particularly given documented declines in insect populations. We suggest that increasing collaboration between professional and community-based scientists could alleviate the decline in amateur-collected specimens.

Importance of building a digital species index (spindex) for entomology collections: A case study, results and recommendations

The Entomology Collection at the Academy of Natural Sciences of Drexel University (ANSP) contains approximately four million insect specimens including some of the oldest in the Western Hemisphere. Like most large entomology collections, no complete inventory of the species represented in the collection was available and even a physical search for a species could not ensure that all available specimens would be recovered for study. Between 2010 and 2014, we created a species-level index (called here spindex) of all species and their specimen counts at ANSP, along with each species’ location in the collection. Additional data captured during the project included the higher level classification of each species and type of specimen preparation. The spindex is searchable online: http://symbiont.ansp.org/entomology/. The spindex project documented 96,126 species in the ANSP Entomology Collection, representing about 10% of the described insect fauna. Additionally, over 900 putative primary types were discovered outside the Primary Type Collection. The completion of this project has improved access to the collection by enabling scientists and other users worldwide to search these collection holdings remotely and has facilitated staff in curation, research, collection management and funding proposals. A spindex is an important tool that is overlooked for planning and carrying out specimen level digitisation. This project is a case study for building a species-level index. A detailed protocol is provided, along with recommendations for other collections, including cost estimates and strategies for tracking progress and avoiding common obstacles.

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.

Small herbaria contribute unique biogeographic records to county, locality, and temporal scales

PREMISE

With digitization and data sharing initiatives underway over the last 15 years, an important need has been prioritizing specimens to digitize. Because duplicate specimens are shared among herbaria in exchange and gift programs, we investigated the extent to which unique biogeographic data are held in small herbaria vs. these data being redundant with those held by larger institutions. We evaluated the unique specimen contributions that small herbaria make to biogeographic understanding at county, locality, and temporal scales.

METHODS

We sampled herbarium specimens of 40 plant taxa from each of eight states of the United States of America in four broad status categories: extremely rare, very rare, common native, and introduced. We gathered geographic information from specimens held by large (≥100,000 specimens) and small (<100,000 specimens) herbaria. We built generalized linear mixed models to assess which features of the collections may best predict unique contributions of herbaria and used an Akaike information criterion-based information-theoretic approach for our model selection to choose the best model for each scale.

RESULTS

Small herbaria contributed unique specimens at all scales in proportion with their contribution of specimens to our data set. The best models for all scales were the full models that included the factors of species status and herbarium size when accounting for state as a random variable.

CONCLUSIONS

We demonstrated that small herbaria contribute unique information for research. It is clear that unique contributions cannot be predicted based on herbarium size alone. We must prioritize digitization and data sharing from herbaria of all sizes.

Digitisation of private collections

Results are presented of a study investigating solutions and procedures to incorporate private natural history collections into the international collections data infrastructure. Results are based on pilot projects carried out in three European countries aimed at approaches on how to best motivate and equip citizen collectors for digitisation:

1) In Estonia, the approach was to outline tools for registering, digitising and publishing private collection data in the biodiversity data management system PlutoF.

2) In Finland, the functionality of FinBIF, a portal offering a popular Notebook Service for citizens to store observations has been expanded to include collection specimens related to a field gathering event.

3) In the Netherlands private collection owners were approached directly and asked to start digitising their collection using dedicated software, either by themselves or with the help of volunteers who were recruited specifically for this task.

In addition to management tools, pilots also looked at motivation, persons undertaking the work, scope, planning, specific knowledge or skills required and the platform for online publication. Future ownership, legality of specimens residing in private collections and the use of unique identifiers are underexposed aspects effecting digitisation. Besides streamlining the overall process of digitising private collections and dealing with local, national or international challenges, developing a communication strategy is crucial in order to effectively distribute information and keep private collection owners aware of ongoing developments.

Besides collection owners other stakeholders were identified and for each of them a roadmap is outlined aimed at further streamlining the data from private collections into the international infrastructure.

In conclusion recommendations are presented based on challenges encountered during this task that are considered important to really make significant progress towards the overall accessibility of data stored in privately held natural history collections.

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.

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.