Exploiting information technology to uncover patterns in complex systems

USDA Accomplishments Report AD-421 (final report) Grant/Contract No: ILLU-875-380This project has involved the continuing development of a comprehensive database system, Mandala(http://www.inhs.illinois.edu/research/mandala/), for documenting information about specimens and taxonomic name history with its associated literature and illustrations.INHS Technical Report Prepared for USDA Accomplishments Report AD-421 (final report

Bringing Bugs into the System

While agriculture, a human-defined and delimited version of the natural world, is not generally touted for its biodiversity, the success or failure of an agroecosystem may hinge on how its biodiversity is managed. Researchers who study this world into which the greater biodiversity of the surrounding area ebbs and flows, attempt to control parts of the system such as the crop (e.g., cultivar, season-to-season rotation with other crops, susceptibility to pests and diseases, potential yield) and its management practices (e.g., planting date, plant density, tillage, pesticide and soil amendment regimes), but have little to no control over abiotic factors (e.g., weather, soils). These researchers will study specific components of agricultural systems with the goal of minimizing pests or diseases, increasing pollination services and yield, maximizing biological control opportunities, and optimizing cultural practices, including the choice or development of the crop cultivar itself. The data collected may be at various time (e.g., second-to-second meteorological measurements, daily or weekly trap catches, season-end yield assessments) and spatial (e.g. intra-plant to area-wide management) scales. The complex detail and rigorous methods are usually captured only in free text summary in scientific papers. Here, raw data are statistically analyzed but not published, significant differences in treatments highlighted, and conclusions drawn about the success or failure of various experimental regimes. Given the enormity of the research process, which often spans years to encompass multiple cropping seasons and investments in human expertise and numbers, it is little wonder that agricultural researchers often ignore the fact that their work could and should become a part of the greater biodiversity assessment of our planet. That an increasing number of journals require or request that authors provide access to raw data of their published studies is a positive step. However, journals and data repositories give little guidance for standardizing the data for discovery and reuse, and the issues of experimental design metadata, use of voucher specimens to anchor taxonomic observations, and measurements of facts at different time and spatial scales, further complicate the issue. I will explore these issues in the context of agricultural entomology research

Bringing Bugs into the System

While agriculture, a human-defined and delimited version of the natural world, is not generally touted for its biodiversity, the success or failure of an agroecosystem may hinge on how its biodiversity is managed. Researchers who study this world into which the greater biodiversity of the surrounding area ebbs and flows, attempt to control parts of the system such as the crop (e.g., cultivar, season-to-season rotation with other crops, susceptibility to pests and diseases, potential yield) and its management practices (e.g., planting date, plant density, tillage, pesticide and soil amendment regimes), but have little to no control over abiotic factors (e.g., weather, soils). These researchers will study specific components of agricultural systems with the goal of minimizing pests or diseases, increasing pollination services and yield, maximizing biological control opportunities, and optimizing cultural practices, including the choice or development of the crop cultivar itself. The data collected may be at various time (e.g., second-to-second meteorological measurements, daily or weekly trap catches, season-end yield assessments) and spatial (e.g. intra-plant to area-wide management) scales. The complex detail and rigorous methods are usually captured only in free text summary in scientific papers. Here, raw data are statistically analyzed but not published, significant differences in treatments highlighted, and conclusions drawn about the success or failure of various experimental regimes. Given the enormity of the research process, which often spans years to encompass multiple cropping seasons and investments in human expertise and numbers, it is little wonder that agricultural researchers often ignore the fact that their work could and should become a part of the greater biodiversity assessment of our planet. That an increasing number of journals require or request that authors provide access to raw data of their published studies is a positive step. However, journals and data repositories give little guidance for standardizing the data for discovery and reuse, and the issues of experimental design metadata, use of voucher specimens to anchor taxonomic observations, and measurements of facts at different time and spatial scales, further complicate the issue. I will explore these issues in the context of agricultural entomology research

The Sociological History of Transforming TDWG to Biodiversity Information Standards (TDWG)

Thirty-seven years—why celebrate this prime number anniversary of the founding of the Taxonomic Databases Working Group (TDWG) in 1985? Because we wanted to look at the history of TDWG through its people (and coincidentally, 37˚C is considered "normal" human temperature, so why not?). Records from 1985's inaugural meeting at the Conservatoire et Jardin botaniques in Geneva, Switzerland, 28–30 September show that it was attended by 12 representatives of the botanical community. Although the attendees were listed by salutation (i.e., Dr., Prof., Mr.) and by first initials along with surnames, the group was all male, composed mainly of European and American botanists with doctorates.How has TDWG morphed over these 37 years from a group of geeky botanists in the early days of museum computerization and six years before the World Wide Web was introduced to the public, to the organization known today as Biodiversity Information Standards (TDWG)? TDWG has always been an open and community-driven organization with decisions made by consensus. Anyone can become a member, individuals as well as institutions (including government agencies, non-governmental organizations, programs, and projects). Everything TDWG produces comes from the expertise, collaboration, and support of its members—people and organizations who create, manage, integrate, and analyze biodiversity information. Today's TDWG looks very different from the one in 1985, but the seeds of the organization were there, even then.While this presentation is about TDWG's history as an organization, its focus will be on the heart of TDWG: its people. We would like to show how the organization has evolved in terms of gender balance, inclusivity actions, and our engagement to promote and enhance diversity at all levels. But more importantly, where do we—as a community—want to go in the future

Agricultural Informatics Contributions to Biodiversity Science and Biodiversity Assessments

Agricultural biodiversity has long been ignored by the traditional biodiversity community and the aggregators of their data. The Arnaud et al. (2016) GBIF "Final Report of the Task Group on GBIF Data Fitness for Use in Agrobiodiversity," provided recommendations primarily regarding crops and their wild relatives, but did not address wider issues of crop pests (plant diseases and their vectors, arthropods) and management systems that affect the greater biodiversity of those crops. The Biodiversity Information Standards (TDWG) (2016) symposium, "Agricultural Biodiversity Standards & Semantics," highlighted the current status of agrobiodiversity data management and discussed major challenges in this field. This year’s symposium provides a progress report on addressing challenges such as crop management and experimental protocol standards and infraspecific taxonomic coverage. It dives deeper into trends in semantics and data mining for agriculture, and in application of standards to biodiversity assessments. This symposium provides specific examples where shared data management standards and practices across both basic and applied biodiversity research communities can lead to improved outcomes for both science and society. A discussion will follow the formal talks included in this symposium

Agricultural Informatics Contributions to Biodiversity Science and Biodiversity Assessments

Agricultural biodiversity has long been ignored by the traditional biodiversity community and the aggregators of their data. The Arnaud et al. (2016) GBIF "Final Report of the Task Group on GBIF Data Fitness for Use in Agrobiodiversity," provided recommendations primarily regarding crops and their wild relatives, but did not address wider issues of crop pests (plant diseases and their vectors, arthropods) and management systems that affect the greater biodiversity of those crops. The Biodiversity Information Standards (TDWG) (2016) symposium, "Agricultural Biodiversity Standards & Semantics," highlighted the current status of agrobiodiversity data management and discussed major challenges in this field. This year’s symposium provides a progress report on addressing challenges such as crop management and experimental protocol standards and infraspecific taxonomic coverage. It dives deeper into trends in semantics and data mining for agriculture, and in application of standards to biodiversity assessments. This symposium provides specific examples where shared data management standards and practices across both basic and applied biodiversity research communities can lead to improved outcomes for both science and society. A discussion will follow the formal talks included in this symposium

Honing the Visibility of TDWG: Communications expertise required

All organizations need clear and succinct mission and vision statements to communicate the purpose and overall goals of the group. These products provide the foundation for development of long(er) term strategic planning including communication plans. Logos offer us another way to highlight and brand what we do and why we do it. Periodically, for all organizations, these all need to be reviewed. The Biodiversity Information Standards (TDWG) Outreach and Communication Subcommittee took on this challenge and started a process to re-assess our current identity as presented in the existing original vision, mission, and logo. From the beginning, the subcommittee decided to follow a bottom-up method and invite all members to contribute to this process and refine its results. Community members had observed that the current logo, a simple lettering of the abbreviated old name and the organization's current name, needed to be revised to be more memorable and fit for use not only on the website, but for everything from slide decks to hex stickers for laptops. Similarly, some noted the mission and vision statements were combined and included other information like “how” TDWG works on its community-driven mission to make biodiversity data accessible. It was time to refresh TDWG’s brand with the additional challenge to keep reflecting the current values and long-standing traditions that characterize the community through a new more modern glass.Notable keys to our success in moving these goals forward started with leadership of the Outreach & Communications Committee Chair, from the Museum für Naturkunde Berlin, and the facilitation and expertise of a Communication (Comms) and Outreach specialist from DiSSCo (Distributed System of Scientific Collections). Having the skills and knowledge of the Comms person meant we benefited from a clear step-by-step process. All involved learned a lot about what to do, to expect, and whom to engage in the future for any similar reviews in other groups.In this talk, we'll take you on this journey and present the new products of the community-led process: TDWG’s Mission, Vision and the new logo. This is, however, just the starting point and there is more work to be done. The next step would be the development of a strategic plan based on this foundation as TDWG continues to work on inclusion, increased global participation, recognition of our expertise, and strategic leadership in the creation, maintenance, implementation, and adoption of our standards

<strong>An annotated catalogue of the New World Therevidae (Insecta: Diptera: Asiloidea)</strong>

Webb, Donald W., Gaimari, Stephen D., Hauser, Martin, Holston, Kevin C., Metz, Mark A., Irwin, Michael E., Kampmeier, Gail E., Algmin, Kristin (2013): An annotated catalogue of the New World Therevidae (Insecta: Diptera: Asiloidea). Zootaxa 3600 (1): 1-105, DOI: http://dx.doi.org/10.11646/zootaxa.3600.1.1, URL: http://dx.doi.org/10.11646/zootaxa.3600.1.

Episodic radiations in the fly tree of life

Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms, yet recent research has suggested that fly relationships have been obscured by multiple episodes of rapid diversification. We provide a phylogenomic estimate of fly relationships based on molecules and morphology from 149 of 157 families, including 30 kb from 14 nuclear loci and complete mitochondrial genomes combined with 371 morphological characters. Multiple analyses show support for traditional groups (Brachycera, Cyclorrhapha, and Schizophora) and corroborate contentious findings, such as the anomalous Deuterophlebiidae as the sister group to all remaining Diptera. Our findings reveal that the closest relatives of the Drosophilidae are highly modified parasites (including the wingless Braulidae) of bees and other insects. Furthermore, we use micro-RNAs to resolve a node with implications for the evolution of embryonic development in Diptera. We demonstrate that flies experienced three episodes of rapid radiation—lower Diptera (220 Ma), lower Brachycera (180 Ma), and Schizophora (65 Ma)—and a number of life history transitions to hematophagy, phytophagy, and parasitism in the history of fly evolution over 260 million y.This article is from Proceedings of the National Academy of Sciences 108 (2011): 5690–5695, doi:10.1073/pnas.1012675108.</p