Utsugi Jinbo

Current progress in DNA barcoding and future implications for entomology

DNA barcoding is a technique for identifying organisms based on a short, standardized fragment of genomic DNA. The standardized sequence region is called a DNA barcode because it is like a barcode tag for each taxon. Since the proposition of this concept and the launch of a large project named the Barcode of Life, this simple technique has attracted attention from taxonomists, ecologists, conservation biologists, agriculturists, plant‐quarantine officers and others, and the number of studies using the DNA barcode has rapidly increased. The extreme diversity of insects and their economical, epidemiological and agricultural importance have made this group a major target of DNA barcoding. However, there is some controversy about the utility of DNA barcoding. In this review, we present an overview of DNA barcoding and its application to entomology. We also introduce current advances and future implications of this promising technique.

Evolution of host utilization patterns in the seed beetle genus Mimosestes Bridwell (Coleoptera: Chrysomelidae: Bruchinae).

The evolutionary history of diet breadth expansion and intergeneric host shifts in the seed beetle genus Mimosestes were reconstructed to investigate the process of host range expansion in phytophagous insects. The evolutionary correlation between diet breadth and variation in oviposition behavior of Mimosestes was also examined to estimate the process of generalist evolution within the genus. Ancestral state reconstruction based on a molecular phylogeny inferred from three mitochondrial markers (16S rRNA, 12S rRNA, and COI) and one nuclear marker (EF-1alpha) revealed that host utilization patterns were shaped by repeated colonizations to novel or pre-adapted host plants. Neither plant genus and species group level host conservatism nor an evolutionary tendency toward specialization was found in the genus, contrary to the expectations of plant-insect co-evolutionary theory. In addition, statistical analyses revealed that diet breadth was significantly correlated with oviposition behavior, suggesting that behavioral factors such as the oviposition preferences of female seed beetles affect the expansion of diet breadth in generalists.

Towards a Data Hub for Biodiversity with LOD

Because of a huge variety of biological studies focused on different targets, i.e., from molecules to ecosystem, data produced and used in each field is also managed independently so that it is difficult to know the relationship among them. We aim to build a data hub with LOD to connect data in different biological fields to enhance search and use of data across the fields. We build a prototype data hub on taxonomic information on species, which is a key to retrieve data and link to databases in different fields. We also demonstrate how the data hub can be used with an application to assist search on other database.

Presenting and preserving the change in taxonomic knowledge for linked data

Taxonomic knowledge provides a scientific name to each organismal group and is thus indispensable information for understanding biodiversity. However, the various perspectives of classifying organisms and changes in taxonomic knowledge have led to inconsistent classification information among different databases and repositories. To have a precise understanding of taxonomy, one needs to integrate relevant data across taxonomic databases. This is difficult to establish due to the ambiguity in taxon interpretation. Most researchers in earlier stages employed the Linked Open Data (LOD) technique to establish links in taxonomy transition. However, they overlooked the temporal representation of taxa and underlying knowledge of the change in taxonomy, so it is difficult for learners to gain perspective on how some identifiers of taxa are linked. To this end, this research is aimed at developing a model for presenting and preserving the change in taxonomic knowledge in the Resource Description Framework (RDF). Specifically, the proposed model takes advantage of linking Internet resources representing taxa, presenting historical information of taxa, and preserving the background knowledge of the change in taxonomic knowledge in order to enable a better understanding of organisms. We implement a prototype to demonstrate the feasibility and the performance of our approach. The results show that the proposed model is able to handle various practical cases of changes in taxonomic works and provides open and accurate access to linked data for biodiversity.

Larval host records of butterflies in Japan

Using Japanese literature, we created a consolidated list of host records of butterflies in Japan. The list used the host records described in eight major illustrated reference books, two checklists, and 14 other pieces of literature. The presence of larvae on plants, the observation of larvae eating plants or insects in the field were considered as host records. We collected all species recorded in Japan. Scientific, family, and Japanese names of butterflies were consolidated using the BINRAN database (http://binran.lepimages.jp/). Scientific and Japanese names of host plants were based on the YList database (http://ylist.info/). If scientific names of host plants were not found in YList, we used scientific names based on The Plant List (http://www.theplantlist.org/). Family names of host plants were based on the Catalogue of Life database (http://www.catalogueoflife.org/). Scientific, family, and Japanese names of host insects were based on the MOKUROKU database (http://konchudb.agr.agr.kyushu-u.ac.jp/mokuroku/) for Hymenoptera and the catalogue of the Paraneoptera of Japan published by the Entomological Society of Japan for Hemiptera. We also provided the references of each host record and the original names described in the referred literature. Two datasets, HostDB and ReferenceDB, were created to include 3600 records of butterfly larval hosts in Japan, along with scientific and Japanese names of each species and a literature list. These datasets will be useful for basic and applied biological studies of butterflies. Data files are stored in the Ecological Research Data Archives (http://db.cger.nies.go.jp/JaLTER/ER_DataPapers/) and available from http://hostbj.lepumus.net/. These datasets are published under the Creative Commons License Attribution-ShareAlike 4.0 (CC BY-SA, https://creativecommons.org/licenses/by-sa/4.0/).

Descriptions of two new species of Vietomartyria Hashimoto & Mey (Lepidoptera, Micropterigidae) from South China, with reference to autapomorphies of the genus

Two new species of micropterigids, Vietomartyria nankunshana Hirowatari & Hashimoto sp. nov. and V. nanlingana Hirowatari & Jinbo sp. nov., are described from Nankunshan and Nanling (Guangdong, China), respectively. The genus Vietomartyria Hashimoto & Mey, 2000, which was originally established as a monotypic genus, is redefined based on the following autapomorphies shared by the three species: (i) the long basal stalk of each flagellomere; (ii) the many (>100) minute serrate projections near the gonopore of aedeagus; and (iii) the gonopore situated dorsally near the apex.

Presenting and Preserving the Change in Taxonomic Knowledge for Linked Data (Extended Abstract).

Linked Open Data (LOD) technology enables web of data and exchangeable knowledge graphs through the Internet. However, the change in knowledge is happened everywhere and every time, and it becomes a challenging issue of linking data precisely because the misinterpretation and misunderstanding of some terms and concepts may be dissimilar under different context of time and different community knowledge. To solve this issue, we introduce an approach to the preservation of knowledge graph, and we select the biodiversity domain to be our case studies because knowledge of this domain is commonly changed and all changes are clearly documented. Our work produces an ontology, transformation rules, and an application to demonstrate that it is feasible to present and preserve knowledge graphs and provides open and accurate access to linked data. It covers changes in names and their relationships from different time and communities as can be seen in the cases of taxonomic knowledge.

Development of a Threatened Species Portal in the Asia-Pacific Region

Biodiversity, ecological, climatological, and environmental data, as well as valid models (e.g., Ecological Niche Modeling) are required to develop indicators that are more effective in assessing the drivers and states of biodiversity (GEO BON 2010). In particular, biodiversity data provide indispensible information for conservation plans. However, a critical problem is that most existing data are inaccessible or unavailable because they are either scattered among many databases or are unpublished (Meier and Dikow 2004; Guralnick et al. 2007). The promotion of open access to biodiversity data and making these data reusable for conservation strategies is one of the main goals of GEO BON.

Data Discovery Mechanisms for Biodiversity Resources in the Asia-Pacific Region

As the importance of biodiversity has been recognized, researchers, governmental officers, and people attracted by biodiversity have collected enormous amounts of biodiversity data for many uses (e.g., research studies, to inform the conservation of a specific area, management decision-making, leisure). These data are also valuable for formulating biodiversity indicators, assessing predictive distribution areas using models, and documenting the current status of endangered species (see Chap. XX). However, data sets of biodiversity are widely dispersed, and most are unavailable to people who are not directly involved in specific projects for which such data were collected because of the lack of a global data-sharing framework. One of the motivations for construction of the Group on Earth Observations Biodiversity Observation Network (GEO BON) architecture is to change this situation by creating a global network of data-collecting activities supported by a data-sharing framework accompanied by an information system (Scholes et al. 2008).