EJT editorial standard for the semantic enhancement of specimen data in taxonomy literature

This paper describes a set of guidelines for the citation of zoological and botanical specimens in the European Journal of Taxonomy. The guidelines stipulate controlled vocabularies and precise formats for presenting the specimens examined within a taxonomic publication, which allow for the rich data associated with the primary research material to be harvested, distributed and interlinked online via international biodiversity data aggregators. Herein we explain how the EJT editorial standard was defined and how this initiative fits into the journal's project to semantically enhance its publications using the Plazi TaxPub DTD extension. By establishing a standardised format for the citation of taxonomic specimens, the journal intends to widen the distribution of and improve accessibility to the data it publishes. Authors who conform to these guidelines will benefit from higher visibility and new ways of visualising their work. In a wider context, we hope that other taxonomy journals will adopt this approach to their publications, adapting their working methods to enable domain-specific text mining to take place. If specimen data can be efficiently cited, harvested and linked to wider resources, we propose that there is also the potential to develop alternative metrics for assessing impact and productivity within the natural science

Specimens as research objects: reconciliation across distributed repositories to enable metadata propagation

Botanical specimens are shared as long-term consultable research objects in a global network of specimen repositories. Multiple specimens are generated from a shared field collection event; generated specimens are then managed individually in separate repositories and independently augmented with research and management metadata which could be propagated to their duplicate peers. Establishing a data-derived network for metadata propagation will enable the reconciliation of closely related specimens which are currently dispersed, unconnected and managed independently. Following a data mining exercise applied to an aggregated dataset of 19,827,998 specimen records from 292 separate specimen repositories, 36% or 7,102,710 specimens are assessed to participate in duplication relationships, allowing the propagation of metadata among the participants in these relationships, totalling: 93,044 type citations, 1,121,865 georeferences, 1,097,168 images and 2,191,179 scientific name determinations. The results enable the creation of networks to identify which repositories could work in collaboration. Some classes of annotation (particularly those regarding scientific name determinations) represent units of scientific work: appropriate management of this data would allow the accumulation of scholarly credit to individual researchers: potential further work in this area is discussed.Comment: 9 pages, 1 table, 3 figure

Automating the construction of higher order data representations from heterogeneous biodiversity datasets

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonDatasets created from large-scale specimen digitisation drive biodiversity research, but these are often heterogeneous: incomplete and fragmented. As aggregated data volumes increase, there have been calls to develop a “biodiversity knowledge graph” to better interconnect the data and support meta-analysis, particularly relating to the process of species description. This work maps data concepts and inter-relationships, and aims to develop automated approaches to detect the entities required to support these kinds of meta-analyses. An example is given using trends analysis on name publication events and their authors, which shows that despite implementation and widespread adoption of major changes to the process by which authors can publish new scientific names for plants, the data show no difference in the rates of publication. A novel data-mining process based on unsupervised learning is described, which detects specimen collectors and events preparatory to species description, allowing a larger set of data to be used in trends analysis. Record linkage techniques are applied to these two datasets to integrate data on authors and collectors to create a generalised agent entity, assessing specialisation and classifying working practices into separate categories. Recognising the role of agents (collectors, authors) in the processes (collection, publication) contributing to the recognition of new species, it is shown that features derived from data-mined aggregations can be used to build a classification model to predict which agent-initiated units of work are particularly valuable for species discovery. Finally, shared collector entities are used to integrate distributed specimen products of a single collection event across institutional boundaries, maximising impact of expert annotations. An inferred network of relationships between institutions based on specimen sharing relationships allows community analysis and the definition of optimal co-working relationships for efficient specimen digitisation and curation

(Socio-)ecological tools and insights for a changing climate

In one way or another, climate change is impacting all social, economic, and ecological systems on the planet. Scientists worldwide warn of catastrophic and irreversible damage to social and ecological systems in absence of rapid, far-reaching, and unprecedented shifts in energy and land use. Yet, many social systems continue to operate business-as-usual, and decision-making across multiple levels of social organization continues to neglect the use of scientific evidence to minimize long-term risk. Contemporary biodiversity losses are occurring on scales that surpass the major extinction events in geological records, threatening the loss of critical ecosystem services, such as pollination, that underpin myriad facets of human societies as well as ecosystem resilience. In my dissertation, I call into question conventional lethal sampling approaches for bumble bees, an economically and ecologically important pollinator group, and simultaneously advance non-lethal techniques. Additionally, with aims to advance climate action in Missouri, I investigate how state-level decision-makers and land-use experts are thinking about climate resilience in the context of rural Missouri. More specifically, in chapter one, I explore how the use of lethal sampling, a traditional entomological sampling approach, has changed over time with evidence of numerous declining bumble bee populations. Global declines of bumble bees are welldocumented and have spurred widespread conservation efforts. However, lethal sampling continues to serve as a common entomological practice despite conservation concern. In collaboration with a research team from the Galen lab, I review 411 bumble bee-related publications from 1970-2019 alongside records from over 230,000 pinned bumble bee pinned specimens to discern whether lethal sampling has decreased with heightened conservation awareness and availability of novel non-lethal sampling methods. Our literature review shows that lethal sampling of bumble bees has instead kept pace with publication output. Interestingly, the highest rates of lethal sampling are found in papers demonstrating conservation awareness and persist despite low scholarly impact in comparison to papers based on non-lethal alternatives. Facing numerous pressures, vulnerable bumble bee populations may be less resilient to traditional sampling norms than broadly assumed. We highlight non-lethal sampling alternatives and underscore the need for proactive, empirically informed sampling guidelines that reflect the conservation needs of bumble bee pollinators. In chapter two, I review advances in acoustic monitoring technologies for bumble bees and discuss potential applications. Acoustics show promise for use in bumble bee investigations, as bumble bees create a range of distinguishable sounds while flying, sonicating (buzzing on flowers to eject pollen) and interacting within the colony, making them amenable for acoustical surveys. Acoustics offer an alternative sampling approach that is affordable, scalable, and non-destructive, with potential to augment conservation and agricultural practices. Application of AMT to investigate bumble bees is still nascent in development, and improvements are needed across all stages of the AMT process, from sensor technologies and data transfer to audio classification and user interfaces. I review the sound-producing activities of bumble bees, highlighting extant research and underscoring opportunities for further investigation. I conclude by reiterating the importance of cross-disciplinary collaboration between ecologists and computer scientists to monitor and manage species of conservation concern. In chapter three, I advance acoustic applications in bumble bee research using a combination of field work and literature surveys. Leveraging technological advancements that allow for remote monitoring and automated processing of information, such as acoustics, has been identified as a key next step for pollinator research. I test whether the acoustics of bumble bee flight buzzes can be used to track morphological traits and phenological phases of foragers throughout the season. I used flight cage experiments and a literature survey to extend data on the relationship between the fundamental frequency of flight buzzes and body size across castes and species. I then use these data to test whether acoustics can track caste size dimorphisms across species and variation in intraspecific worker size. Next, I acoustically monitored wild bumble bee colonies in subalpine and alpine ecosystems in Colorado, United States, where I corroborated acoustic data with in-person observations to distinguish phenological phases (queens only vs. queens and workers) of the colonies. I demonstrate that remotely monitoring bumble bee colonies with acoustics can provide large datasets with cues for different morphological and phenological features of the colony and discuss potential applications. In chapter four, I investigate climate resilience in rural Missouri. Rural areas of the United States -- approximately 97 percent of the total land area -- often lag urban areas in the implementation of climate adaptation practices. Understanding how perspectives vary within and among actors in the rural land use decision-making ecosystem can help to identify catalysts and constraints for climate change adaptation planning and action. I conducted semi-structured interviews with 23 experts -- policymakers, state/federal agency professionals, non-profit organization leadership, and researchers -- at the nexus of rural land use, agriculture, natural resources, and conservation in Missouri to elucidate conceptualizations of climate resilience. I aligned interview questions with NOAA's Steps to Resilience to investigate participants' perceptions of the major vulnerabilities of rural communities and landscapes, threats to rural vitality, and potential concrete steps for making rural Missouri more resilient in the face of climate change. I then discuss examples of climate resilience in Missouri and conclude with suggestions for potential next steps towards climate resilience in the state.Includes bibliographical references

Simple identification tools in FishBase

Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further development. It explores the possibility of a holistic and integrated computeraided strategy

Population Genetics and Bumble Bee Conservation: Saving Species by Thinking Small

Pollinators have experienced a severe decline over the last few decades, and this includes bumble bee populations (g. Bombus). Bumble bees are important native pollinators, and here I investigate the health of local populations with molecular tools. The field of conservation genetics has created useful methodology for investigating the health and informing management strategies of threatened populations. This work investigates and describes the applications of population genetics, which uses span across the board. These applications are then brought back into the context of bumble bee conservation, and how they fit into the experimental plan I originally designed. I designed an experiment that utilized microsatellite loci to understand population dynamics of bumble bees (Bombus ssp.). Microsatellites are DNA segments that are highly variable within a population. Specimens where obtained via net collection throughout the summer of 2017. This thesis goes into the development of my experimental protocol and the future steps that would need to be taken to fully understand the local population dynamics of Bombus species. This project will go into the applications of research projects that identify areas in which genetic exchange is taking place, highlighting areas of importance for habitat protection and maintaining threatened populations. The aspects of genetic exchange between populations that essential for species survival over time are also discussed

DNA isolation from century-old specimens of Fucus virsoides for the valorization of the historical collections of the Herbarium Patavinum

In recent years, herbaria and historical collections have become important tools for dissemination, historical and scientific research, resources with numerous applications in various fields such as teaching, open communication among scholars, taxonomic stability and studies in different disciplines (botanical, ecological, anatomical and morphological, evolutionary, paleobotanical research). Particularly important is the discipline of herbariomics that allows, through the process of DNA extraction from herbarium specimens, followed by high-throughput DNA sequencing and bioinformatics analysis, to conduct investigations about several topics such as pollution, habitat change, invasive species and climate change. However, DNA damage caused by time and conservation methods in old herbarium samples, in addition to external DNA contamination, makes nucleic acid extraction and amplification difficult. Here we present the results of DNA extraction (CTAB method) and amplification (PCR) conducted on six samples of the endemic Adriatic alga Fucus virsoides J.Agardh, 1868, collected between 1908 and 1932 and now conserved in the Padua Botanical Garden Herbarium. Furthermore, since the amplification failed, the study focused on the analysis of the putative problems that led to this result. Although DNA amplification failed, the adopted protocol has allowed the extraction of a more than adequate amounts of DNA with a concentration between 113.75 and 565.20 ng/µL. Our results highlight the possibility of applying this extraction method to these specimens, so that it will be feasible in the near future to sequence their DNA. A future study comparing the DNA of ancient and fresh samples may verify the presence of deleterious mutations accumulated during the demographic decline that the species has suffered along the northern Adriatic coast in recent years, possibly due to climate change.In recent years, herbaria and historical collections have become important tools for dissemination, historical and scientific research, resources with numerous applications in various fields such as teaching, open communication among scholars, taxonomic stability and studies in different disciplines (botanical, ecological, anatomical and morphological, evolutionary, paleobotanical research). Particularly important is the discipline of herbariomics that allows, through the process of DNA extraction from herbarium specimens, followed by high-throughput DNA sequencing and bioinformatics analysis, to conduct investigations about several topics such as pollution, habitat change, invasive species and climate change. However, DNA damage caused by time and conservation methods in old herbarium samples, in addition to external DNA contamination, makes nucleic acid extraction and amplification difficult. Here we present the results of DNA extraction (CTAB method) and amplification (PCR) conducted on six samples of the endemic Adriatic alga Fucus virsoides J.Agardh, 1868, collected between 1908 and 1932 and now conserved in the Padua Botanical Garden Herbarium. Furthermore, since the amplification failed, the study focused on the analysis of the putative problems that led to this result. Although DNA amplification failed, the adopted protocol has allowed the extraction of a more than adequate amounts of DNA with a concentration between 113.75 and 565.20 ng/µL. Our results highlight the possibility of applying this extraction method to these specimens, so that it will be feasible in the near future to sequence their DNA. A future study comparing the DNA of ancient and fresh samples may verify the presence of deleterious mutations accumulated during the demographic decline that the species has suffered along the northern Adriatic coast in recent years, possibly due to climate change

Skate Tapeworms Revisited: A Modern Approach

Members of the rhinebothriidean family Echeneibothriidae de Beauchamp, 1905, parasitize skates exclusively and represent one of the most diverse elements of their cestode fauna. Although skates represent one of the most speciose orders of elasmobranchs, their superficial morphological homogeneity has led to a convoluted taxonomic history, hindering studies of their parasites. Recent advances in the taxonomy and systematics of skates allow for more informed assessments of the diversity, distributions, and patterns of host associations of skate cestodes. Most of the 35 species of echeneibothriids known prior to this study occur in skates distributed in the northern hemisphere, despite the fact that the number of skate species is comparable in both hemispheres. Examination of the spiral intestine of 24 species of skates, 17 from the southern hemisphere, resulted in the recognition of 42 species of echeneibothriids, 32 of these new to science. The amount of novelty recovered prompted the development of a template for the description of new species in the family that conform to the standards now commonly practiced in the description of cestodes from elasmobranchs. An account of the cestode fauna found in each of the skate species examined is provided. Species of echeneibothriids were morphologically circumscribed using a combination of characters of their scoleces. Global diversity of echeneibothriids is estimated to be 376 species. Descriptions for two new species of Echeneibothrium are also provided. Molecular characterization of all species for which suitable material was available is given. Data from two molecular markers, the D1–D3 regions of 28S rDNA and ITS-1, were obtained and used to infer a phylogeny for the family Echeneibothriidae. The monophyly of the family is confirmed but the two most speciose echeneibothriid genera, Echeneibothrium and Pseudanthobothrium, are not monophyletic as currently circumscribed. Of the 14 skate species examined, 12 hosted more than one species of echeneibothriid. In most cases, congeners parasitizing the same skate species were found to not be each other’s closest relatives. Cophylogenetic analyses using different methods yielded conflicting results, suggesting that the host association patterns we observe in cestodes of skates may be the result of aspects other than cophylogeny alone