Periodic Reporting for period 2 - BIG4 (BIG4 - Biosystematics, Informatics and Genetics of the big 4 insect groups: training tomorrow's researchers and entrepreneurs)
Reporting period: 2017-01-01 to 2018-12-31
All BIG4 activities are at the crossroads of several Workpackages: WP1, Big data sets assembly and compatibility for biosystematics, begun data collection. WP1 trained ESRs in extraction of huge DNA data from the suboptimal museum insect specimens, with first samples of Lepidoptera. Some ESRs produced big genomic or morphological data for a taxon-based and bulk sample-based project, which meant learning programming and de novo genome assembly for large-scale phylogenetic data. Some ESRs got insight into complex morphologies of their study insect groups and prepared them for integration in the phylogeny. WP2, Statistical phylogenetic analysis, brought statistical phylogenetics into the efficient study of big insect groups. Statistical phylogenetics underlies almost every project in BIG4, and WP2 developed a much needed training package in RevBayes software. Several ESRs ran their phylogenetic analyses for various insect groups, some already published as peer reviewed papers. A few ESRs worked on a large collaborative dated phylogenetic analysis of the entire insect Order Coleoptera. WP3 Genomics exposed ESRs to the possibilities of genomics and next-generation sequencing techniques in biosystematics projects. ERA7 developed a cloud-based data sharing infrastructure. Some ESRs implemented Next Generation Sequencing and got phylogenetically informative markers across various target taxa, either traditionally preserved museum-based specimens or properly preserved modern DNA-tissues. WP4, Citizen-science and informatics for biodiversity, created ‘DINA-Specify’ and ‘The Naturalist’ online training packages. The SME-based ESR implemented machine learning for automated high precision identification of several insect groups. An app for citizen scientists to track distributions and abundance of Swedish ladybugs was developed and successfully implemented receiving high media attention in Sweden. WP5, Semantic publishing, outreach and dissemination, led by PENSOFT modernized the workflow for publishing huge biodiversity data about four biggest insect groups. The core development of semantic publishing is an Open Biodiversity Knowledge Management System that is already changing data publishing in the field.