Museum Specimen Data Research Articles

A new genus of Cicadellini (Hemiptera: Cicadellidae) from the Oaxacan Cloud Forest, with taxonomic notes on allied red-striped genera

Cicadellinae is a relatively large subfamily of leafhoppers (Hemiptera: Cicadellidae) with a cosmopolitan distribution with most genera known to occur in the Neotropics. Mexico houses nearly 16% of the total genera and most are endemic, inhabiting threatened native forests. Here, a new unusual Mexican genus, Christopherus gen. nov., is described to accommodate a new species of Cicadellini, C. mictlantecuhtli sp. nov., collected in the endangered Cloud Forest of Sierra Juárez, Oaxaca State of Mexico, based on dry-pinned museum specimen data. The new taxa can be separated from other Neotropical Cicadellini genera easily using male genitalia features: (i) pygofer without processes, (ii) segment 10th without processes, (iii) paraphysis absent, and (iv) edeagus with single basal atrial process elongate and asymmetrical. The monotypic genus Gillonella with its type species, G. ampulla Nielson & Godoy, 1995, are redescribed. A detailed extensive morphological description and discussion to distinguish the new genus from allied red-striped Neotropical genera in Mexico, Central America, and South America are given. Distributional data for new taxa within Mexican forests is also provided.

New insight into drivers of mammalian litter size from individual‐level traits

The digitization and open availability of life history traits measured directly from individuals provide a key means of linking organismal function to environmental and ecological contexts at fine resolution. These linkages play a critical role in understanding trait‐mediated response to global change, with particular need to resolve them for taxa that are secretive and hard to monitor, like most mammals. In this study, we use digitized museum specimen and census data to document how climate and body size each shape a key life history trait – litter size – in 39 small mammals across North America. We employ mixed models to test associations between litter size, climate and body size, with a focus on joint estimation of inter‐ and intraspecific trends. Among species, no single climate predictor explained a large amount of litter size variation. Instead, interactions between temperature‐related (continentality, solar irradiation) and moisture‐related (annual precipitation, relative humidity) indices, along with body size, exert a stronger influence on litter size. We observed maximal litter sizes for species inhabiting seasonal or xeric regions under conditions of increased moisture availability, or conversely, mesic or aseasonal regions under conditions of reduced moisture availability. These patterns are consistent with primary productivity as a mechanistic driver of litter size. At the intraspecific level, litter size responds to continentality and temperature‐related indices experienced by populations, but is most strongly shaped by body size of individual females. We also find evidence of phylogenetic covariation in these intraspecific trends. Our study demonstrates how life history traits assembled from individual‐level biodiversity records improve precision and granularity of ecological studies, help to parse among‐ and within‐species trends, and foster improved understanding of tradeoffs between energetic supply and demand (e.g. reproduction) in wild mammals.

Ecological traits explain long-term phenological trends in solitary bees.

Across taxa, the timing of life-history events (phenology) is changing in response to warming temperatures. However, little is known about drivers of variation in phenological trends among species. We analysed 168 years of museum specimen and sighting data to evaluate the patterns of phenological change in 70 species of solitary bees that varied in three ecological traits: diet breadth (generalist or specialist), seasonality (spring, summer or fall) and nesting location (above-ground or below-ground). We estimated changes in onset, median, end and duration of each bee species' annual activity (flight duration) using quantile regression. To determine whether ecological traits could explain phenological trends, we compared average trends across species groups that differed in a single trait. We expected that specialist bees would be constrained by their host plants' phenology and would show weaker phenological change than generalist species. We expected phenological advances in spring and delays in summer and fall. Lastly, we expected stronger shifts in above-ground versus below-ground nesters. Across all species, solitary bees have advanced their phenology by 0.43 days/decade. Since 1970, this advancement has increased fourfold to 1.62 days/decade. Solitary bees have also lengthened their flight period by 0.44 days/decade. Seasonality and nesting location explained variation in trends among species. Spring- and summer-active bees tended to advance their phenology, whereas fall-active bees tended to delay. Above-ground nesting species experienced stronger advances than below-ground nesting bees in spring; however, the opposite was true in summer. Diet breadth was not associated with patterns of phenological change. Our study has two key implications. First, an increasing activity period of bees across the flight season means that bee communities will potentially provide pollination services for a longer period of time during the year. And, since phenological trends in solitary bees can be explained by some ecological traits, our study provides insight into mechanisms underpinning population viability of insect pollinators in a changing world.

Occupancy–detection models with museum specimen data: Promise and pitfalls

Abstract Historical museum records provide potentially useful data for identifying drivers of change in species occupancy. However, because museum records are typically obtained via many collection methods, methodological developments are needed to enable robust inferences. Occupancy–detection models, a relatively new and powerful suite of statistical methods, are a potentially promising avenue because they can account for changes in collection effort through space and time. We use simulated datasets to identify how and when patterns in data and/or modelling decisions can bias inference. We focus primarily on the consequences of contrasting methodological approaches for dealing with species' ranges and inferring species' non‐detections in both space and time. We find that not all datasets are suitable for occupancy–detection analysis but, under the right conditions (namely, datasets that are broken into more time periods for occupancy inference and that contain a high fraction of community‐wide collections, or collection events that focus on communities of organisms), models can accurately estimate trends. Finally, we present a case study on eastern North American odonates where we calculate long‐term trends of occupancy using our most robust workflow. These results indicate that occupancy–detection models are a suitable framework for some research cases and expand the suite of available tools for macroecological analysis available to researchers, especially where structured datasets are unavailable.

Unmasking complex migration syndromes and seasonal plumage colouration in the White‐naped Xenopsaris (Xenopsaris albinucha)

The White‐naped Xenopsaris Xenopsaris albinucha is an uncommon suboscine passerine with a disjunct distribution extending from Venezuela to the Southern Cone of South America. The ornithological literature concerning this species contains contradictory claims about potential migratory movements, although most authors consider it to be sedentary. In addition, observations of the species exhibiting a mix of male‐ and female‐like plumage during the non‐breeding season have raised the hypothesis that it may undergo seasonal colour changes – a trait often associated with migratory behaviour and seemingly uncommon in Neotropical birds. Here we use citizen science and museum specimen data to interrogate the hypotheses of migratory behaviour and seasonal phenotypic variation in the species. We found evidence for three disjunct breeding populations, of which one is resident, one is apparently partially migratory and one is fully migratory, with birds from the last two populations coming into contact during the non‐breeding season. We also found evidence for seasonal variation in the species' plumage colouration. Our results suggest that the White‐naped Xenopsaris has both resident and migratory populations and exhibits an eclipse plumage, and highlight the value of citizen science data to study seasonal variation in plumage colouration.

Climate drivers of adult insect activity are conditioned by life history traits.

Insect phenological lability is key for determining which species will adapt under environmental change. However, little is known about when adult insect activity terminates and overall activity duration. We used community-science and museum specimen data to investigate the effects of climate and urbanisation on timing of adult insect activity for 101species varying in life history traits. We found detritivores and species with aquatic larval stages extend activity periods most rapidly in response to increasing regional temperature. Conversely, species with subterranean larval stages have relatively constant durations regardless of regional temperature. Species extended their period of adult activity similarly in warmer conditions regardless of voltinism classification. Longer adult durations may represent a general response to warming, but voltinism data in subtropical environments are likely underreported. This effort provides a framework to address the drivers of adult insect phenology at continental scales and a basis for predicting species response to environmental change.

Toward Clarifying the Wyoming Ranges of the Vireo gilvus Complex

The Warbling Vireo (Vireo gilvus), generally recognized as one polytypic species, is widely distributed across North America, but differences in morphology, song, genetics, and ecology suggest the western and eastern populations may represent two species. Understanding their distributions enables tracking of range changes and other factors that might affect the conservation of populations. Therefore, I studied museum specimens, specimen data, and identifications provided by investigators recording songs to help clarify the ranges of the two taxa in Wyoming. Of 18 specimens in the U.S. National Museum collected from 1858 to 1930, I identify 15 as the western species V. swainsoni. These are spread over most of Wyoming, east to Crook and Albany counties. Only three represent the eastern species V. gilvus, two from Greybull, Big Horn Co., and one from Cheyenne. Whether the overlap represents sympatry of breeding populations in eastern Wyoming or overlap in migration remains to be determined.

Genomic and phenotypic divergence informs translocation strategies for an endangered freshwater fish.

Translocation, the movement of organisms for conservation purposes, can result in unintended introgression if genetic material flows between populations in new ways. The Bluemask Darter Etheostoma akatulo is a federally endangered species of freshwater fish inhabiting the Caney Fork River system and three of its tributaries (Collins River, Rocky River, and Cane Creek) in Tennessee. The current conservation strategy for Bluemask Darters involves translocating the progeny of broodstock from the Collins River (in the west) to the Calfkiller River (in the east) where the species had been extirpated. In this study, we use ddRAD sequence data from across the extant range to assess this translocation strategy in light of population structure, phylogeny, and demography. We also include museum specimen data to assess morphological variation among extant and extirpated populations. Our analyses reveal substantial genetic and phenotypic disparities between a western population in the Collins River and an eastern population encompassing the Rocky River, Cane Creek, and upper Caney Fork, the two of which shared common ancestry more than 100,000years ago. Furthermore, morphological analyses classify 12 of 13 Calfkiller River specimens with phenotypes consistent with the eastern population. These results suggest that current translocations perturb the evolutionary boundaries between two delimited populations. Instead, we suggest that repopulating the Calfkiller River using juveniles from the Rocky River could balance conflicting signatures of demography, diversity, and divergence. Beyond conservation, the microgeographic structure of Bluemask Darter populations adds another puzzle to the phylogeography of the hyperdiverse freshwater fishes in eastern North America.

Progress Out of a Pandemic: Global collections, data sharing, and changing standards of practice

The COVID-19 pandemic has disrupted all aspects of our lives, but has also spawned new opportunities. Months of multidisciplinary, global collaboration have explored the connections between natural history collections and COVID-19. Museums have unrivalled (and still largely untapped) potential to contribute data, methods, and expertise to prediction, mitigation, and prevention efforts related to zoonotic disease outbreaks (DiEuliis et al. 2016, Dunnum et al. 2017), and there is a clear need for ongoing collaboration across (at least) microbiology, disease ecology, and natural history collections. In addition, we note that the roadblocks to effective data access and integration related to microbes and their hosts are a microcosm of the larger data landscape; solving these issues in the context of COVID-19—from liberating data from publications to ensuring digital connections between voucher specimens and all derived viral genetic sequences—will improve biodiversity data access and use more broadly. Efforts since March 2020 have promoted collaboration across disciplines, international boundaries, and continents. At iDigBio, staff updated information about genetic/genomic resources available in US mammal collections; 24 records were added and information enhanced (Cortez and Soltis 2020). The Distributed System of Scientific Collections (DiSSCo) and the Consortium of European Taxonomic Facilities (CETAF) formed a worldwide COVID-19 Task Force (TaF). A US-led group formed the ViralMuse Task Force, working in concert with the TaF. Activities of the TaF centered on four areas: building a hub to coalesce knowledge from this group in a central location – including mining mammals-of-the-world literature, improving the metadata shared when publishing sequence data, encouraging virologists to voucher in museum collections, and gathering critical research questions around zoonotic disease from the scientific community. Through an online public event, this TaF shared work to date and critical next steps. Ongoing efforts include further refinement of metadata requirements for deposition of viral genetic data to include host specimen voucher identifiers, development of methods for better integration of bat and pathogen data from the literature and databases, analysis of community surveys, and development of webinars, symposia, and publications to report the work of the TaF. Members of the ViralMuse group worked to raise awareness of the critical value of and need for museum experts, collections data, and samples in any analyses of zoonotic events. ViralMuse members (Cook et al. 2020) stressed the need for collaborative action to: develop guidelines for keeping samples of both pathogens and hosts. develop and implement metadata requirements for physical specimens and samples. expand investment in infrastructure, both cyber and physical, to support archives of biological materials. increase communication and development of new channels of dialogue and collaboration among museum scientists, microbiologists, bioinformaticians, biomedical professionals, and disease ecologists. enhance financial support and realize strong leadership from federal agencies, international partners, and private foundations to develop proactive, multi-disciplinary approaches to future pandemics (see also da Silva et al. 2020). develop guidelines for keeping samples of both pathogens and hosts. develop and implement metadata requirements for physical specimens and samples. expand investment in infrastructure, both cyber and physical, to support archives of biological materials. increase communication and development of new channels of dialogue and collaboration among museum scientists, microbiologists, bioinformaticians, biomedical professionals, and disease ecologists. enhance financial support and realize strong leadership from federal agencies, international partners, and private foundations to develop proactive, multi-disciplinary approaches to future pandemics (see also da Silva et al. 2020). ViralMuse continues to advance these goals. To reach a broader audience, we published an article in The Conversation (Soltis et al. 2020). A new project, funded by the US National Science Foundation (NSF), is aimed at enhancing existing published museum specimen data relevant to one potential reservoir of SARS-CoV-2, horseshoe bats (Mast and Paul 2020). NSF has also provided support to foster continued collaboration, infrastructure development, and integration of communities of practice concerning zoonotic diseases (Soltis and Paul 2020). From a TDWG perspective, issues relating to data access, data standards, and data integration require attention. Methods to liberate data from publications need to be expanded, and proposed metadata requirements for viral genetic sequences need to be implemented by international databases and adopted by the community. A summit on collections management software could help align efforts to both store and share the necessary host-pathogen information in standards-compliant formats that support discovery, access, and citation/attribution. A new and effective communication strategy is needed to develop an integrated research community (comprising the biodiversity, collections, data science, disease ecology, microbiology, and One Health communities) and to support needed changes in standards of practice (emphasizing vouchering, data standards, and data integration).

Unity in Variety: Developing a collection description standard by consensus

Digitisation and publication of museum specimen data is happening worldwide, but far from complete. Museums can start by sharing what they know about their holdings at a higher level, long before each object has its own record. Information about what is held in collections worldwide is needed by many stakeholders including collections managers, funders, researchers, policy-makers, industry, and educators. To aggregate this information from collections, the data need to be standardised (Johnston and Robinson 2002). So, the Biodiversity Information Standards (TDWG) Collection Descriptions (CD) Task Group is developing a data standard for describing collections, which gives the ability to provide: automated metrics, using standardised collection descriptions and/or data derived from specimen datasets (e.g., counts of specimens) and a global registry of physical collections (i.e., digitised or non-digitised). automated metrics, using standardised collection descriptions and/or data derived from specimen datasets (e.g., counts of specimens) and a global registry of physical collections (i.e., digitised or non-digitised). Outputs will include a data model to underpin the new standard, and guidance and reference implementations for the practical use of the standard in institutional and collaborative data infrastructures. The Task Group employs a community-driven approach to standard development. With international participation, workshops at the Natural History Museum (London 2019) and the MOBILISE workshop (Warsaw 2020) allowed over 50 people to contribute this work. Our group organized online "barbecues" (BBQs) so that many more could contribute to standard definitions and address data model design challenges. Cloud-based tools (e.g., GitHub, Google Sheets) are used to organise and publish the group's work and make it easy to participate. A Wikibase instance is also used to test and demonstrate the model using real data. There are a range of global, regional, and national initiatives interested in the standard (see Task Group charter). Some, like GRSciColl (now at the Global Biodiversity Information Facility (GBIF)), Index Herbariorum (IH), and the iDigBio US Collections List are existing catalogues. Others, including the Consortium of European Taxonomic Facilities (CETAF) and the Distributed System of Scientific Collections (DiSSCo), include collection descriptions as a key part of their near-term development plans. As part of the EU-funded SYNTHESYS+ project, GBIF organized a virtual workshop: Advancing the Catalogue of the World's Natural History Collections to get international input for such a resource that would use this CD standard. Some major complexities present themselves in designing a standardised approach to represent collection descriptions data. It is not the first time that the natural science collections community has tried to address them (see the TDWG Natural Collections Description standard). Beyond natural sciences, the library community in particular gave thought to this (Heaney 2001, Johnston and Robinson 2002), noting significant difficulties. One hurdle is that collections may be broken down into different degrees of granularity according to different criteria, and may also overlap so that a single object can be represented in more than one collection description. Managing statistics such as numbers of objects is complex due to data gaps and variable degrees of certainty about collection contents. It also takes considerable effort from collections staff to generate structured data about their undigitised holdings. We need to support simple, high-level collection summaries as well as detailed quantitative data, and to be able to update as needed. We need a simple approach, but one that can also handle the complexities of data, scope, and social needs, for digitised and undigitised collections. The data standard itself is a defined set of classes and properties that can be used to represent groups of collection objects and their associated information. These incorporate common characteristics ('dimensions') by which we want to describe, group and break down our collections, metrics for quantifying those collections, and properties such as persistent identifiers for tracking collections and managing their digital counterparts. Existing terms from other standards (e.g. Darwin Core, ABCD) are re-used if possible. The data model (Fig. 1) underpinning the standard defines the relationships between those different classes, and ensures that the structure as well as the content are comparable across different datasets. It centres around the core concept of an 'object group', representing a set of physical objects that is defined by one or more dimensions (e.g., taxonomy and geographic origin), and linked to other entities such as the holding institution. To the object group, quantitative data about its contents are attached (e.g. counts of objects or taxa), along with more qualitative information describing the contents of the group as a whole. In this presentation, we will describe the draft standard and data model with examples of early adoption for real-world and example data. We will also discuss the vision of how the new standard may be adopted and its potential impact on collection discoverability across the collections community.

Virtual Systematics with Annotate: The Mexican archaeocyaths example

Digitization and online publishing of museum specimen data are happening worldwide. Studies based solely on online data become increasingly accessible. The current events, for example, reducing our transport-related carbon footprint or the COVID-19 pandemic, provide key opportunities to highlight the full value of digitized collections and their related tools, which allow us to continue our research from home or at least without travelling. Are existing data resources and tools adequate for engaging in a research project from beginning to end? To address this issue, we propose to use the Mexican archaeocyaths digitized collection from the Museum National d’Histoire Naturelle, Paris, France (MNHN) and the freeware Annotate in order to describe and identify all the archaeocyaths from the Mexican Cambrian reef. Archaeocyaths are aspiculate sponges that lived during the Cambrian Period. They were the first animals to build reefs. In the MNHN collection, they are found as thin-sections with several archaeocyaths per thin-section (Fig. 1). Multiple individuals are grouped under a single collection number and a single species name. The list of species in the thin-section is only captured on the paper label, and cannot currently be found online. To study an archaeocyaths' reef, the archaeocyaths have to be described and identified one by one, and the location of each specimen has to be accuratly captured. Is it possible to do this with Annotate? Can a palaeontologist use only digitized specimens and Annotate to study a complete fauna of a given time and space? Annotate is an image annotation tool for the natural sciences. It allows users to measure, count, and tag all the morphological structures of an organism. Photos may be imported from the Recolnat database or users may import their own photos. Users can measure lengths, surfaces, and angles, count occurrences and add points of interest. Users can also tag the different individuals to identify them. Morphological terms may be imported as a standardized list from Xper2 or Xper3. Xper3 is a web platform that manages descriptive data and provides interactive identification keys. The results of the measurements and annotations can be exported into CSV format (comma-separated values) or into a structured descriptive data (SDD) format. To identify an archaeocyath to genus level, we need to identify morphological structures and count the occurrence of some of them, and for an identification to the species level, we need to measure different additional parts. The standardized list of morphological terms has been imported from the archaeocyaths genera knowledge base and the list of measurements has been created directly in Annotate. Lengths (e.g., pore size, cup diameter), counts (e.g., number of septae, number of pores) and points of interest (e.g., tumuli, canals, septa) are easy to use. What are the key lessons learnt to remember at the end of this study? The digitized archaeocyaths from Mexico have been identified as easily with Annotate as if a microscope and thin sections were used. The CSV export provided quick access to statistics calculations. The main difference between a microscope and Annotate is the working time. Some functionalities of Annotate are not optimized, their uses are time consuming. For instance, the importation of photos is not really appropriate for archaeocyaths studies. Two sections (transversal and longitudinal) per specimen are necessary to see all the morphological structures. These two parts of the same rock are packed together with one collection number. While users can easily switch from one section to another with a microscope, they can not with Annotate. Annotate allows only one photo per collection number from Recolnat, but not images of the two sections and their metadata. The main difference between a microscope and Annotate is the working time. Some functionalities of Annotate are not optimized, their uses are time consuming. For instance, the importation of photos is not really appropriate for archaeocyaths studies. Two sections (transversal and longitudinal) per specimen are necessary to see all the morphological structures. These two parts of the same rock are packed together with one collection number. While users can easily switch from one section to another with a microscope, they can not with Annotate. Annotate allows only one photo per collection number from Recolnat, but not images of the two sections and their metadata. Although Annotate is not an intuitive tool to use it is still very powerful however, some training is required to fully take advantage of it, and there is no documentation available. This freeware has great potential as it can assist researchers in their work and proposes an alternative to the need to travel around the world to study a fossil.

Adding value to collections: improving the data associated with Crested Ibis Nipponia nippon specimens held in the Natural History Museum, Tring

In the bird collection of the Natural History Museum at Tring (NHMUK), and no doubt in many analogous collections elsewhere, older specimens are increasingly likely to have become divorced from some, or even all, of the data that once accompanied them. As the utility of such specimens for research depends in large part on their accompanying data, it is important, though time-consuming, to try to restore missing data to them. Stimulated by a genomic research project request to sample all Crested Ibis Nipponia nippon specimens in the NHMUK collection, this paper presents a case study of such an attempt. The results are used to highlight the importance that such investigation is factored into projects aiming to make museum specimen data available online.

Using museum specimens to estimate broad-scale species richness: Exploring the performance of individual-based and spatially explicit rarefaction.

Estimates of spatial patterns of broad-scale species richness are central to major questions in ecology, evolution and conservation. Yet, they are scarce due to incomplete information on species distributions. Often the only germane data derives from museum specimens collected during non-standardized sampling. Rarefaction, a promising approach to estimate broad-scale richness with these data, estimates the expected number of species represented in subsets of n specimens drawn from N specimens collected in a sampling unit. One version of rarefaction, known as individual-based rarefaction, assumes that the N specimens collected in a sampling unit constitute a random sample of individuals in that sampling unit. Another version, known as spatially explicit rarefaction, assumes that the N specimens collected in a sampling unit are spatially aggregated. We examined the working hypothesis that, when applied to museum specimen data, spatially explicit rarefaction is less biased than individual-based rarefaction because it reduces overestimation due to spatially aggregated sampling. We derived five predictions from this working hypothesis and tested them using computer simulation experiments based on a database of 129,782 plant specimens from Nicaragua, and sampling units of 5 x 5, 50 x 50, and 100 x 100 km. One experiment was a negative control, whereby we simulated collection of randomly chosen individuals from each sampling unit. In contrast, three other experiments included spatially aggregated sampling. In all experiments we applied individual-based and spatially explicit rarefaction to estimate richness, with n = 200 and n = 500 specimens. As expected, the experiment designed as a negative control did not support the working hypothesis. The other three experiments supported the working hypothesis in analyses of larger sampling units, but not in 5 x 5 km sampling units. The predictions we derived from the working hypothesis can be used to assess which rarefaction version is best in particular systems.

Abundance of an economically important nematode parasite increased in Puget Sound between 1930 and 2016: Evidence from museum specimens confirms historical data

Abstract Does disturbance increase or decrease parasite transmission among wildlife hosts? Ecologists cannot answer this controversial question, in part because few historical datasets rigorously document parasite abundance. Without such a baseline, it is difficult to determine whether contemporary ecosystems are experiencing elevated parasite burdens. Here, we investigate change over time in the abundance of a parasite that affects the economic value of a fish species. Clavinema mariae is a nematode parasite of benthic fishes that is common in English sole (Parophrys vetulus) of Puget Sound, WA. We obtained historical records of its abundance from the literature and from unpublished government agency data, and resampled the same locations using the same methods in 2017. We also used a new approach by estimating the C. mariae burden for museum specimens of English sole collected between 1930 and 2016. Both the historical data and museum specimen data suggested increases over time in C. mariae abundance, with robust agreement between the two approaches. In addition to documenting a previously unrecognised ~eightfold increase in the burden of an economically important parasite, our work demonstrates—for the first time—that parasitological examination of liquid‐preserved museum specimens can produce reliable data on long‐term trends in parasite abundance, at a much greater temporal resolution than is possible to obtain from historical records. Synthesis and applications. Defining a baseline state of infection is vital for natural resource management and policy, which must respond to the threat of disease; without such a baseline, managers attempting to maintain or recover the health of ecosystems under their stewardship are shooting in the dark. The method we present here—using museum specimens to reconstruct detailed chronologies of parasite abundance change—offers a solution. Our approach would allow managers to accurately characterise past disease states, informing the development of appropriate disease management targets. Given the broad representation and availability of liquid‐preserved specimens across ecosystems, geographic regions and host taxa, this solution may be feasible for the management of biological resources not only in marine ecosystems, but in freshwater and terrestrial ecosystems as well.

A Workflow for Adding Specimen Metadata to Images Captured in the Field

Museum collections and their use is bolstered by supplying robust and comprehensive metadata and supplementary assets, such as genetic samples, methodology metadata, and images. In speaking with and working alongside scientists interested in using museum specimen data for addressing ecological questions, it has often been brought up that understanding the context in which a specimen was collected can lend helpful insight. One such way of adding contextual information to our collections is the capture of in situ and habitat images in the field during collection. Managing and linking such images with specimen data poses a logistical challenge. Collections managers and field researchers at the Denver Botanic Gardens have created a workflow that allows for the recording of image metadata in the field and the eventual addition of Darwin Core occurrence metadata to in situ and habitat field image files. Designated field photographers, a role that can be filled by volunteers or paid field assistants, record information pertaining to each image they capture. Upon returning from the field, the data is uploaded to a MySQL database, alongside associated specimen and site data. The data is then queried in the form of a script and utilizing the ExifTool application, the information is then added to the XMP metadata of the image. Having this data embedded within the image not only aids in linking the corresponding field images with their specimen records, but also in the downstream management and access to images from the field. Here I present the current workflow we have developed and how its use has aided our effort to curate data rich specimens and images.

Phenomap - Challenges and Successes in Bringing Together Multiple Data Projects to Build New Visualizations of Phenotypic Information and Specimen Records

Connecting biodiversity data across databases is not as easy as one might think. Different databases use different identifiers and taxonomies and connecting these data often results in loss of information and precision. Here we present some of the challenges we faced with integrating multiple biodiversity data sets, including specimen data from the scientific collections, during a hackathon hosted by the Phenoscape project in December of 2017. The hackathon brought together a diverse group of participants, including biologists and software developers, to explore ways of using the computable phenotype data in the Phenoscape Knowledgebase (KB) (Edmunds et al. 2015). The KB contains ontology-annotated data that links evolutionary phenotypes from the comparative literature to model organism phenotypes enabling, e.g., the retrieval of candidate genes for evolutionary phenotypes and the generation of synthetic supermatrices of presence/absence characters. During this hackathon, our team explored how to link phenotype data in the KB to museum specimen data in iDigBio (Matsunaga et al. 2013) with the hope of creating visualizations including world maps showing species distributions with different character states and their phylogenetic relationships. We visualized lineage relationships by querying the Open Tree of Life (OT) (Hinchliff et al. 2015) website using data integrated by another group at the hackathon that linked KB and OT taxonomic identifiers. Phenoscape uses terms from anatomy, quality, and taxonomy ontologies to annotate characters and taxonomic information from the phylogenetic literature along with specimen information. When populating the KB, specimen identifiers such as occurrence identifiers, collector’s number, and catalog numbers were preserved if present in the literature. We found that these identifiers, although standard in the biodiversity domain, were mostly insufficient to uniquely identify the source specimen in iDigBio. As an alternative, we instead mapped all the occurrences of taxa using string matches of the genus and species from Vertebrate Taxonomy Ontology identifiers. Without specimen identifiers that are consistent across databases, we lost the ability to explore spatial and temporal variation of characters within genera and were only able to explore phenotypes and geographic distributions among genera. We look forward to discussing these issues with the collections community represented at this meeting by the Society for the Preservation of Natural History Collections (SPNHC). We developed an R Shiny application that integrates characters and taxa from Phenoscape with specimen records from iDigBio and phylogenies from OT, to visualize phenotypic characters and taxon distributions in three interactive panels. The app allows a user to visualize OT phylogenies and place presence/absence character data on the tree. Specifically, users can: select taxa or specific characters to visualize their geographic distributions, navigate a phylogeny browser which displays character and specimen data available for taxa under consideration, and view a heatmap of characters available for character and taxon combinations. Because of our challenges joining data, our distribution map leaves users with the impression that all individuals in a genus exhibit a character whereas the KB was populated with data describing individuals. We hope that with improved data standards and their use by more people, constructing applications like ours will become easier.

Establishment of the ARCTOS-GGBN Data Pipeline

Arctos (https://arctosdb.org), an online collection management information system, was developed in 1999 to manage museum specimen data and to make those data publicly available. The portal (arctos.database.museum) now serves data on over 3.5 million cataloged specimens from more than 130 collections throughout North America in an instance at the Texas Advanced Computing Center. Arctos also is a community of museum professionals that collaborates on museum best practices and works together to improve Arctos data richness and functionality for on-line museum data streaming. In 2017, three large Arctos genomics collections at the Museum of Southwestern Biology (MSB), Museum of Vertebrate Zoology, Berkeley (MVZ), and University of Alaska Museum of the North (UAM), received support from GGBN to create a pipeline for publishing data from Arctos to the GGBN portal. Modifications to Arctos included standardization of controlled vocabulary for tissues; changes to the data structure and code tables with regard to permit information, container history, part attributes, and sample quality; implementation of interfaces and protocols for parent-child relationships between tissues, tissue subsamples, and DNA extracts; and coordination with the DWC community to ensure that all GGBN data standards and formatting are included in the standard DWC export in order to finalize the pipeline to GGBN. The addition of these three primary Arctos biorepositories to the GGBN network will add over 750,000 tissue and DNA records representing over 11,000 species and 667 families. These voucher-based archives represent primarily vertebrate taxa, with growing collections of arthropods, endoparasites, and incipient collections of microbiome and environmental samples associated with online media and linked to GenBank and other external databases. The high-quality data in Arctos complement and significantly extend existing GGBN holdings, and the establishment of an Arctos-GGBN pipeline also will facilitate future collaboration between more Arctos collections and GGBN.

The use of avian museum specimen data in phenology studies: prospects and challenges

The use of avian museum specimen data in phenology studies: prospects and challenges

Museum specimen data reveal emergence of a plant disease may be linked to increases in the insect vector population.

The emergence rate of new plant diseases is increasing due to novel introductions, climate change, and changes in vector populations, posing risks to agricultural sustainability. Assessing and managing future disease risks depends on understanding the causes of contemporary and historical emergence events. Since the mid-1990s, potato growers in the western United States, Mexico, and Central America have experienced severe yield loss from Zebra Chip disease and have responded by increasing insecticide use to suppress populations of the insect vector, the potato psyllid, Bactericera cockerelli (Hemiptera: Triozidae). Despite the severe nature of Zebra Chip outbreaks, the causes of emergence remain unknown. We tested the hypotheses that (1) B. cockerelli occupancy has increased over the last century in California and (2) such increases are related to climate change, specifically warmer winters. We compiled a data set of 87,000 museum specimen occurrence records across the order Hemiptera collected between 1900 and 2014. We then analyzed changes in B.cockerelli distribution using a hierarchical occupancy model using changes in background species lists to correct for collecting effort. We found evidence that B.cockerelli occupancy has increased over the last century. However, these changes appear to be unrelated to climate changes, at least at the scale of our analysis. To the extent that species occupancy is related to abundance, our analysis provides the first quantitative support for the hypothesis that B.cockerelli population abundance has increased, but further work is needed to link B.cockerelli population dynamics to Zebra Chip epidemics. Finally, we demonstrate how this historical macro-ecological approach provides a general framework for comparative risk assessment of future pest and insect vector outbreaks.

Bats from Lebanon at the Natural History Museum, Vienna: a cautionary tale on the reliability of museum specimen data (Chiroptera)

Abstract Seven historical bat specimens of four species (Rhinolophus ferrumequinum, R. mehelyi, Taphozous nudiventris, Myotis myotis), attributed to originate from the territory of the present-day Lebanon, are deposited and documented in the modern database of the mammal collection of the Natural History Museum, Vienna, Austria (Naturhistorisches Museum Wien). Two of these species (R. mehelyi, T. nudiventris) have never been reported for Lebanon in the existing literature and recent surveys have also failed to find them in this country. Since these bats were collected in the period 1824–1885, the history of the all respective specimens was evaluated in detail. The revision brought rather unexpected results. Only one specimen (R. ferrumequinum) was found to come (most probably) from Lebanon, being collected by W. Hemprich and Ch. Ehrenberg in 1824. In the remaining six specimens, the origin could not be defined, thus rendering the statement that they were collected in Lebanon insecure. This case demonstrates that careful checks of modern interpretations of historical records are necessary when examining past distributions of organisms.