SPP 1991:  Taxon-Omics: New approaches for discovering and naming biodiversity

• Subject Area: Biology
• Term: since 2017
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 313688472

Taxonomy is the science most directly relevant for documenting and understanding changes in biodiversity, whether from species loss or from species introduction. Over the past 10 years, taxonomy has undergone a major shift because of its move towards DNA-based data. This has opened new avenues for collaboration and the ability to answer questions that could not be tackled before. At the same time, we live amid a global wave of biodiversity loss. Modern taxonomic approaches are therefore needed to discover, name, and quantify organismal diversity, which is the basis for documenting, understanding, and confronting changes in biodiversity. The naming of the discovered organisms, using standardized conventions, is the basis for linking new information to existing knowledge, and the resulting classification permits effective communication as well as extrapolation of findings. This priority research program will focus on three areas: (i) discovery and delimitation of species or other evolving units of interest, (ii) accelerating the naming process and generating updatable identification tools, classifications, or monographs, and (iii) Efficient or novel use of natural history collections through automated image analysis, genetic or genomic data from historic specimens or living collections, or new ways of comparing and quantifying traits. This Priority Programme will bring together teams working on the systematics/taxonomy of animals, fungi, plants, or eukaryotic microorganisms, using similar technical and conceptual approaches. Annual meetings will include international speakers who will interact with early-career systematists in small discussion sections, focused on the sharing of both concepts and methods.Approaches to be applied or developed will include automatic specimen identification with computer-vision or barcoding approaches; new tools to utilize internal morphological characters, such as micro-computed tomography (micro-CT); and bioinformatics for species delimitation from high-throughput sequencing (HTS). Phylogenetics is quickly migrating towards HTS data, and some sequencing methods also provide allelic information suitable for coalescent-based phylogenetic analyses at the species level. Exchange of students and collaboration among labs, especially as regards the application of new methods, will strengthen hypothesis-based research in systematics because collaborating PIs will challenge each other intellectually. The proposed program is interdisciplinary in combining taxonomy (a branch of biology), computer science, bioinformatics, and didactics (of biology). This is a unique time for such a priority program because Germany has top-rated natural history collections as well as systematists on the faculties of many of its universities, guaranteeing that this Priority Program will have a disproportionate impact on the academic training of the next generation of taxonomists and comparative biologists.

• DFG Programme: Priority Programmes
• International Connection: Argentina, Australia, Austria, Bolivia, Brazil, Canada, China, Costa Rica, Czech Republic, Ecuador, Georgia, Indonesia, Ireland, Italy, Norway, Portugal, Russia, Sweden, United Kingdom, USA

Projects

• A MuseOMICS approach to scrutinise DNA barcode failure: testing the causes for taxonomic incongruence patterns in phytophagous Hymenoptera and Orthoptera through hybridization capture using RAD probes. (Applicants Hawlitschek, Ph.D., Oliver ;  Schmidt, Stefan )
• An approach for managing specimen-sample-taxon-trait data from the 27 projects of the DFG priority program 1991 ‘Taxon-Omics’ (Applicant Vences, Miguel )
• Analyzing historical plant-pollinator interactions by conducting pollen metabarcoding on museum specimens of German bumblebee species (Applicants Gemeinholzer, Birgit ;  Keller, Alexander ;  Ohl, Michael ;  Steffan-Dewenter, Ingolf )
• Applying integrative multispecies coalescent models to tackle the long-standing problem of species delimitation in allopatrically distributed populations (Applicant Meyer, Axel )
• Biological soil crusts as unique microecosystem represent a suitable model system to address taxonomy and cryptic diversity of microalgal key players (Applicant Glaser, Karin )
• Comparative and experimental wing pattern genomics in Lepidoptera (Applicants Espeland, Marianne ;  Hundsdoerfer, Anna K. )
• Concepts, tools and support for managing, archiving, mobilizing and integrating taxonomic data (Applicants Kostadinov, Ivaylo ;  Vences, Miguel )
• Continuing the deep molecular characterization of eukaryotic microorganisms´ diversity and community composition in forest soils and the canopy region using a metatranscriptomics approach (micDiv II) (Applicants Bonkowski, Michael ;  Schlegel, Martin )
• Coordination Funds (Applicant Begerow, Dominik )
• Coordination Funds (Applicant Begerow, Dominik )
• Deep mobilization of natural history collections of microscopic organisms using high throughput image analyses and interlinking with molecular data (MobiDiC - MOBIlization of a DIatom Collection) (Applicants Beszteri, Bánk ;  Nattkemper, Ph.D., Tim )
• Deep molecular characterization of eukaryotic microorganisms´ diversity and community composition in forest soils and the canopy region across biomes using a multiple barcoding approach - micDiv (Applicants Bonkowski, Michael ;  Schlegel, Martin )
• Developing, calibrating and applying a genomic toolbox for species delimitation in Palearctic and tropical amphibians (Applicants Hofreiter, Michael ;  Vences, Miguel )
• Elevational replacement, higher tropical mountain passes and isolated sky islands: untangling neutral and adaptive processes driving radiation of Andean Apocynaceae (Applicants Liede-Schumann, Sigrid ;  Nürk, Nicolai M. )
• Establishing a standardized and universally applicable set of nuclear-encoded markers for genome-wide multi-locus species delimitation of metazoans (Applicants Ahrens, Dirk ;  Mayer, Christoph ;  Misof, Ph.D., Bernhard ;  Niehuis, Oliver ;  Podsiadlowski, Lars )
• Exploring genomic methods for delimiting species in radiations of terrestrial snails (Applicant Hausdorf, Bernhard )
• Exploring the hidden diversity of widespread predatory amoebae of the order Vampyrellida (Rhizaria) (Applicant Hess, Sebastian )
• FrogCap for the Taxonomic Gap: Harnessing Hybrid Enrichment for Next-Generation Taxonomy (Applicant Hofreiter, Michael )
• From field to museum: Harnessing the power of third generation sequencing to establish a simple and cost-effective multiplex approach for spider taxonomy (Applicant Kennedy, Susan )
• Genomics of Hybridization and Species Delimitation in Cichlid Fishes (Applicant Meyer, Axel )
• Hybrid zones among Palearctic amphibian lineages as a model to understand temporal patterns of species formation and refine methods of species delimitation (Applicant Vences, Miguel )
• Innovative integration of high-throughput DNA barcoding, transcriptome-based constrained phylogenetics, hyperspectral imaging, and morphology to assess and characterize a poorly known fauna (Applicant Pauls, Steffen U. )
• Integrated approaches to address taxonomic problems in the Prasiolaceae (Trebouxiophyceae, Chlorophyta) (Applicant Heesch, Svenja )
• Jungle Genomics - overcoming the Linnean shortfall with Nanopore sequencing in biodiversity hotspots (Applicant Schaefer, Hanno )
• Lecanomics: New ways of species detection and recognition in a ubiquitous group of lichens (Applicant Printzen, Christian )
• Making efficient use of herbarium specimens – Hybrids in Veronica as case example (Applicant Albach, Dirk )
• Mapping sequences to protist morphospecies (Applicant Nitsche, Frank )
• Marine heterotrophic alveolates: a genomic and morphometric single cell approach. (Applicant John, Uwe )
• Microgastropod Taxon-Omics: Towards a probabilistic and automated species-discovery system (Applicant Wilke, Thomas )
• Molecular evidence for sectional classification of shrub willows (Salix L. subg. Chamaetia/Vetrix) based on RAD sequencing data (Applicant Wagner, Natascha D. )
• Molecular taxonomy of aquatic hyphomycetes by safeguarding of historical collections (Applicant Baschien, Christiane )
• New approaches for high throughput species discovery and delimitation within unicellular eukaryotes exemplified by choanoflagellates (Applicant Nitsche, Frank )
• New approaches for species delimitation from genome data with examples to two widespread fireflies (Lamprohiza splendidula and Photinus pyralis) (Applicants Catalan, Ph.D., Ana ;  Höhna, Sebastian )
• Ophiuroid phylogenomics: Illuminating “dark” abyssal biodiversity (Applicant Martinez Arbizu, Pedro M. )
• Phylogenomic analyses from archival DNA (Applicant Hofreiter, Michael )
• Phylogenomics of the genus Hypoxylon based on 50 new high quality genomes and with special emphasis on the H. rubiginosum complex (Applicants Cox, Russell J. ;  Kalinowski, Jörn ;  Stadler, Marc )
• Proteomic fingerprinting for species identification – discriminatory power and optimal analyses procedures for integrated molecular and morphological datasets in zooplankton biodiversity assessments (Applicant Renz-Gehnke, Jasmin )
• Re-evaluating taxonomy and distribution patterns of the Xanthophyceae (Stramenopiles) (Applicant Rybalka, Nataliya )
• Resolving intricate taxonomies by using type material, Hyb-Seq and geometric morphometrics. – A proof-of-concept from the nasty Xanthium L. (Applicant Tomasello, Salvatore )
• Setting-up a methodological pipeline for species delimitation and species network reconstruction in polyploid complexes (Applicants Oberprieler, Christoph ;  Vogt, Robert )
• Species Delimitation in East African Cichlid Fish Adaptive Radiations (Applicant Meyer, Axel )
• Species delimitation in the apomictic polyploid Ranunculus auricomus complex using an integrative TaxonOMICs approach (Applicant Hörandl, Elvira )
• Sponge TaxonOMICs V2 (Applicants Erpenbeck, Dirk ;  Vargas Ramírez, Sergio ;  Wörheide, Gert )
• TaxonOMICS of Australian Chenopods: a multifaceted study to resolve one of Australia’s most challenging plant families (Applicant Kadereit, Gudrun )
• The CARRARA pipeline: Using machine-learning techniques for automated species delimitation in intensively hybridising plant genera based on herbarium specimens (Applicants Hellwig, Frank ;  Oberprieler, Christoph ;  Vogt, Robert )
• The genomic basis of host specificity as tool for species recognition and delimitations in Ustilaginales - a parasite group with high gene flow (Applicants Begerow, Dominik ;  Kemler, Martin )
• Types and genomes - Solving a conflict in frequently hybridizing taxa of Veronica (Applicant Albach, Dirk )
• Using herbarium specimens to study evolutionary change related to climate warming - novel uses of natural history collections through specimen and label images (Applicant Renner, Susanne Sabine )

• Spokesperson: Professor Dr. Dominik Begerow