More than just records: analysing natural history collections for biodiversity planning

Digitization of natural history collections: A guideline and nationwide capacity building workshop in Malaysia

Natural history museum collections are the most important sources of information on the present and past biodiversity of our planet. Most of the information is primarily stored in analogue form, and digitization of the collections can provide further open access to the images and specimen data to address the many global challenges. However, many museums do not digitize their collections because of constraints on budgets, human resources, and technologies. To encourage the digitization process, we present a guideline that offers low-cost and technical knowledge solutions yet balances the quality of the work and outcomes. The guideline describes three phases of digitization, namely preproduction, production, and postproduction. The preproduction phase includes human resource planning and selecting the highest priority collections for digitization. In the preproduction phase, a worksheet is provided for the digitizer to document the metadata, as well as a list of equipment needed to set up a digitizer station to image the specimens and associated labels. In the production phase, we place special emphasis on the light and color calibrations, as well as the guidelines for ISO/shutter speed/aperture to ensure a satisfactory quality of the digitized output. Once the specimen and labels have been imaged in the production phase, we demonstrate an end-to-end pipeline that uses optical character recognition (OCR) to transfer the physical text on the labels into a digital form and document it in a worksheet cell. A nationwide capacity workshop is then conducted to impart the guideline, and pre- and postcourse surveys were conducted to assess the confidence and skills acquired by the participants. This paper also discusses the challenges and future work that need to be taken forward for proper digital biodiversity data management.

A workflow for expanding DNA barcode reference libraries through 'museum harvesting' of natural history collections

Natural history collections are the physical repositories of our knowledge on species, the entities of biodiversity. Making this knowledge accessible to society - through, for example, digitisation or the construction of a validated, global DNA barcode library - is of crucial importance. To this end, we developed and streamlined a workflow for 'museum harvesting' of authoritatively identified Diptera specimens from the Smithsonian Institution's National Museum of Natural History. Our detailed workflow includes both on-site and off-site processing through specimen selection, labelling, imaging, tissue sampling, databasing and DNA barcoding. This approach was tested by harvesting and DNA barcoding 941 voucher specimens, representing 32 families, 819 genera and 695 identified species collected from 100 countries. We recovered 867 sequences (> 0 base pairs) with a sequencing success of 88.8% (727 of 819 sequenced genera gained a barcode > 300 base pairs). While Sanger-based methods were more effective for recently-collected specimens, the methods employing next-generation sequencing recovered barcodes for specimens over a century old. The utility of the newly-generated reference barcodes is demonstrated by the subsequent taxonomic assignment of nearly 5000 specimen records in the Barcode of Life Data Systems.

Analysis of intrinsic evolutionary factors leading to microendemic distributions in New Caledonian leaf beetles

Microendemicity, or the condition of some species having local ranges, is a relatively common pattern in nature. However, the factors that lead to this pattern are still largely unknown. Most studies addressing this issue tend to focus on extrinsic factors associated with microendemic distributions, such as environmental conditions, hypothesising a posteriori about underlying potential speciation mechanisms, linked or not to these conditions. Here, we use a multi-faceted approach mostly focusing on intrinsic factors instead, namely diversification dynamics and speciation modes in two endemic sibling genera of leaf beetles with microendemic distributions, Taophila and Tricholapita, in a microendemicity hotspot, New Caledonia. Results suggest that the diversification rate in this lineage slowed down through most of the Neogene and consistently with a protracted speciation model possibly combined with several ecological and environmental factors potentially adding rate-slowing effects through time. In turn, species accumulated following successive allopatric speciation cycles, possibly powered by marked geological and climatic changes in the region in the last 25 million years, with daughter species ranges uncorrelated with the time of speciation. In this case, microendemicity seems to reflect a mature state for the system, rather than a temporary condition for recent species, as suggested for many microendemic organisms.

Natural history collections recapitulate 200 years of faunal change

Changing species assemblages represent major challenges to ecosystems around the world. Retracing these changes is limited by our knowledge of past biodiversity. Natural history collections represent archives of biodiversity and are therefore an unparalleled source to study biodiversity changes. In the present study, we tested the value of natural history collections for reconstructing changes in the abundance and presence of species over time. In total, we scrutinized 17 080 quality-checked records for 242 epibenthic invertebrate species from the North and Baltic Seas collected throughout the last 200 years. Our approaches identified eight previously reported species introductions, 10 range expansions, six of which are new to science, as well as the long-term decline of 51 marine invertebrate species. The cross-validation of our results with published accounts of endangered species and neozoa of the area confirmed the results for two of the approaches for 49 to 55% of the identified species, and contradicted our results for 9 to 10%. The results based on relative record trends were less validated. We conclude that, with the proper approaches, natural history collections are an unmatched resource for recovering early species introductions and declines.

Dataset of host records for introduced parasitoid wasp species (Hymenoptera) in New Zealand

Background

The introduction of species to new regions is occurring at an increasing rate. These introductions typically consist of species that are deliberately introduced for the purposes of biological control of pests or of species that are accidentally introduced through human-mediated transport networks.

Understanding the potential and actual impacts of these introduced species requires comprehensive information on their geographic distributions and biological associations.

However, apart from a few well-known case studies, such information is lacking for many introduced species which severely hinders further assessment of risks and impact.

New information

A dataset is provided on host associations, geographic distributions and dates of collection for both deliberately and accidentally-introduced parasitoid wasp species (Hymenoptera) in New Zealand. Information was obtained by digitising specimens from the New Zealand Arthropod Collection. Dates of records range from 1921 to 2017.

The dataset includes 1265 specimen records, representing 127 parasitoid species from 12 families, with host records for 177 host species from 61 families and eight insect orders.

These data provide baseline information to help evaluate the risk from introduced parasitoids to non-target and native species.

Mapping Africa's Biodiversity: More of the Same Is Just Not Good Enough

Species distribution data are fundamental to the understanding of biodiversity patterns and processes. Yet, such data are strongly affected by sampling biases, mostly related to site accessibility. The understanding of these biases is therefore crucial in systematics, biogeography, and conservation. Here we present a novel approach for quantifying sampling effort and its impact on biodiversity knowledge, focusing on Africa. In contrast to previous studies assessing sampling completeness (percentage of species recorded in relation to predicted), we investigate whether the lack of knowledge of a site attracts scientists to visit these areas and collect samples of species. We then estimate the time required to sample 90% of the continent under a Weibull distributed biodiversity sampling rate and the number of sampling events required to record $ \ge $50% of the species. Using linear and spatial regression models, we show that previous sampling has been strongly influencing the resampling of areas, attracting repeated visits. This bias has existed for over two centuries, has increased in recent decades, and is most pronounced among mammals. It may take between 172 and 274 years, depending on the group, to achieve at least one sampling event per grid cell in the entire continent. Just one visit will, however, not be enough: in order to record $ \ge $50% of the current diversity, it will require at least 12 sampling events for amphibians, 13 for mammals, and 27 for birds. Our results demonstrate the importance of sampling areas that lack primary biodiversity data and the urgency with which this needs to be done. Current practice is insufficient to adequately classify and map African biodiversity; it can lead to incorrect conclusions being drawn from biogeographic analyses and can result in misleading and self-reinforcing conservation priorities. [Amphibians; birds; mammals; sampling bias; sampling gaps; Wallacean shortfall.].

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.

Using insect natural history collections to study global change impacts: challenges and opportunities

Over the past two decades, natural history collections (NHCs) have played an increasingly prominent role in global change research, but they have still greater potential, especially for the most diverse group of animals on Earth: insects. Here, we review the role of NHCs in advancing our understanding of the ecological and evolutionary responses of insects to recent global changes. Insect NHCs have helped document changes in insects' geographical distributions, phenology, phenotypic and genotypic traits over time periods up to a century. Recent work demonstrates the enormous potential of NHCs data for examining insect responses at multiple temporal, spatial and phylogenetic scales. Moving forward, insect NHCs offer unique opportunities to examine the morphological, chemical and genomic information in each specimen, thus advancing our understanding of the processes underlying species' ecological and evolutionary responses to rapid, widespread global changes.This article is part of the theme issue 'Biological collections for understanding biodiversity in the anthropocene'.

Variation in the diversity and richness of parasitoid wasps based on sampling effort

Parasitoid wasps are a mega-diverse, ecologically dominant, but poorly studied component of global biodiversity. In order to maximise the efficiency and reduce the cost of their collection, the application of optimal sampling techniques is necessary. Two sites in Auckland, New Zealand were sampled intensively to determine the relationship between sampling effort and observed species richness of parasitoid wasps from the family Ichneumonidae. Twenty traps were deployed at each site at three different times over the austral summer period, resulting in a total sampling effort of 840 Malaise-trap-days. Rarefaction techniques and non-parametric estimators were used to predict species richness and to evaluate the variation and completeness of sampling. Despite an intensive Malaise-trapping regime over the summer period, no asymptote of species richness was reached. At best, sampling captured two-thirds of parasitoid wasp species present. The estimated total number of species present depended on the month of sampling and the statistical estimator used. Consequently, the use of fewer traps would have caught only a small proportion of all species (one trap 7–21%; two traps 13–32%), and many traps contributed little to the overall number of individuals caught. However, variation in the catch of individual Malaise traps was not explained by seasonal turnover of species, vegetation or environmental conditions surrounding the trap, or distance of traps to one another. Overall the results demonstrate that even with an intense sampling effort the community is incompletely sampled. The use of only a few traps and/or for very short periods severely limits the estimates of richness because (i) fewer individuals are caught leading to a greater number of singletons; and (ii) the considerable variation of individual traps means some traps will contribute few or no individuals. Understanding how sampling effort affects the richness and diversity of parasitoid wasps is a useful foundation for future studies.

The Three Rs of Animal Research: What they Mean for the Institutional Animal Care and Use Committee and Why

The Institutional Animal Care and Use Committee (IACUC) is entrusted with assessing the ethics of proposed projects prior to approval of animal research. The role of the IACUC is detailed in legislation and binding rules, which are in turn inspired by the Three Rs: the principles of Replacement, Reduction, and Refinement. However, these principles are poorly defined. Although this provides the IACUC leeway in assessing a proposed project, it also affords little guidance. Our goal is to provide procedural and philosophical clarity to the IACUC without mandating a particular outcome. To do this, we analyze the underlying logic of the Three Rs and conclude that the Three Rs accord animals moral standing, though not necessarily "rights" in the philosophical sense. We suggest that the Rs are hierarchical, such that Replacement, which can totally eliminate harm, should be considered prior to Reduction, which decreases the number of animals harmed, with Refinement being considered last. We also identify the need for a hitherto implicit fourth R: Reject, which allows the IACUC to refuse permission for a project which does not promise sufficient benefit to offset the pain and distress likely to be caused by the proposed research.

Poles Apart: Comparing Trends of Alien Hymenoptera in New Zealand with Europe (DAISIE)

Developing generalisations of invasive species is an important part of invasion biology. However, trends and generalisations from one part of the world may not necessarily hold elsewhere. We present the first inventory and analysis of all Hymenoptera alien to New Zealand, and compare patterns from New Zealand with those previously published from Europe (DAISIE). Between the two regions there was broad correlation between families with the highest number of alien species (Braconidae, Encyrtidae, Pteromalidae, Eulophidae, Formicidae, Aphelinidae). However, major differences also existed. The number of species alien to New Zealand is higher than for Europe (334 vs 286), and major differences include: i) the much lower proportion of intentionally released species in New Zealand (21% vs 63% in Europe); and ii) the greater proportion of unintentionally introduced parasitoids in New Zealand (71.2% vs 22.6%). The disharmonic ‘island’ nature of New Zealand is shown, as a high proportion of families (36%) have no native representatives, and alien species also represent >10% of the native fauna for many other families. A much larger proportion of alien species are found in urban areas in New Zealand (60%) compared to Europe (~30%), and higher numbers of alien species were present earlier in New Zealand (especially <1950). Differences in the origins of alien species were also apparent. Unlike Europe, the New Zealand data reveals a change in the origins of alien species over time, with an increasing dominance of alien species from Australasia (a regional neighbour) during the past 25 years. We recommend that further effort be made towards the formation, and analysis, of regional inventories of alien species. This will allow a wider range of taxa and regions to be examined for generalisations, and help assess and prioritise the risk posed by certain taxa towards the economy or environment.

Tracking changes in natural history collections utilization: A case study at the Museum of Southwestern Biology at the University of New Mexico

Natural history collections (NHCs) are used in many fields of study, but general knowledge regarding their uses is poor. Because of this, funding and support for NHCs frequently fluctuate. One way in which collections professionals can illustrate a collection’s contribution to a variety of fields is based on the collection’s history of use. Tracking NHC utilization through time can increase NHC value to others outside of the collection, allow for the analysis of changes in specimen-based research trends, and assist in effective collection management. This case study focuses on NHC usage records held by the Museum of Southwestern Biology (MSB), a currently growing university collection used in many research fields, and presents methods for quantifying collections utilization through time. Through an exploration of these data, this paper illustrates MSB’s growth and changes in research produced over time and offers explanations for the changes observed. Last, this study provides suggestions for how collections professionals can most greatly benefit from considering NHC records as a data source. Understanding NHC usage from “the collection’s perspective” provides a new way for NHC professionals to understand NHCs’ value in the context of the research it supports and demonstrates the importance of this key infrastructure to a broader audience.

Insights from natural history collections: analysing the New Zealand macroalgal flora using herbarium data

Herbaria and natural history collections (NHC) are critical to the practice of taxonomy and have potential to serve as sources of data for biodiversity and conservation. They are the repositories of vital reference specimens, enabling species to be studied and their distribution in space and time to be documented and analysed, as well as enabling the development of hypotheses about species relationships. The herbarium of the Museum of New Zealand Te Papa Tongarewa (WELT) contains scientifically and historically significant marine macroalgal collections, including type specimens, primarily of New Zealand species, as well as valuable exsiccatae from New Zealand and Australia. The herbarium was initiated in 1865 with the establishment of the Colonial Museum and is the only herbarium in New Zealand where there has been consistent expert taxonomic attention to the macroalgae over the past 50 years. We examined 19,422 records of marine macroalgae from around New Zealand collected over the past 164 years housed in WELT, assessing the records in terms of their spatial and temporal coverage as well as their uniqueness and abundance. The data provided an opportunity to review the state of knowledge of the New Zealand macroalgal flora reflected in the collections at WELT, to examine how knowledge of the macroalgal flora has been built over time in terms of the number of collections and the number of species recognised, and identify where there are gaps in the current collections as far as numbers of specimens per taxon, as well as with respect to geographical and seasonal coverage.