My postdoctoral study is designed to develop protocols and procedures to obtain genomic DNA data from degraded old museum specimens using HTS (e.g., exome-capture and/ or mtDNA genome sequencing) using SE Asian frogs as focal taxa. Specimens housed in natural history museums are essential raw materials for studies of cryptic speciation that is very common in the tropics. These studies require molecular genetic tools that, to date, could only be applied to freshly collected tissue samples. Because HTS is based on short-fragment sequencing technology, it is more effective at obtaining sequence data from historical specimens than Sanger sequencing, particularly for very old samples collected more than 100 years ago. HTS methods will be tested to assess the phylogenetic and taxonomic position of the Asian ranid frogs with gastromyzophorous tadpoles, a group that has defied taxonomic clarification for decades. This proposed study is well aligned to the Work Programme of Horizon 2020 Marie Sklodowska-Curie Actions. The results of this study will be a valuable baseline to assess the feasibility of and to improve exome-capture techniques aimed at retrieving historical DNA from type specimens for future studies. This study will be the first to investigate the evolution of gastromyzophory in Asian ranid frogs. It will also emphasize the need to apply modern techniques in tropical countries with high biodiversity as a critical step in quantifying its diversity and developing conservation actions for cryptic species. Apart from that, this study is an exceptional step towards advancing my career and establish myself as an independent researcher in the field of phylogenetics systematics. Furthermore, I will be able to actively contribute to disseminate my science to broader audience and play an important role as a catalyst for a long term collaborations between the institutions in Germany, USA, and Indonesia in phylogenomic, systematics, and biogeographic studies.

European natural history collections are a critical infrastructure for meeting the most important challenge humans face over the next 30 years – mapping a sustainable future for ourselves and the natural systems on which we depend – and for answering fundamental scientific questions about ecological, evolutionary, and geological processes. Since 2004 SYNTHESYS has been an essential instrument supporting this community, underpinning new ways to access and exploit collections, harmonising policy and providing significant new insights for thousands of researchers, while fostering the development of new approaches to face urgent societal challenges. SYNTHESYS+ is a fourth iteration of this programme, and represents a step change in evolution of this community. For the first time SYNTHESYS+ brings together the European branches of the global natural science organisations (GBIF, TDWG, GGBN and CETAF) with an unprecedented number of collections, to integrate, innovate and internationalise our efforts within the global scientific collections community. Major new developments addressed by SYNTHESYS+ include the delivery of a new virtual access programme, providing digitisation on demand services to a significantly expanded user community; the construction of a European Loans and Visits System (ELViS) providing, for the first time, a unified gateway to accessing digital, physical and molecular collections; and a new data processing platform (the Specimen Data Refinery), applying cutting edge artificial intelligence to dramatically speed up the digital mobilisation of natural history collections. The activities of SYNTHESYS+ form a critical dependency for DiSSCo - the Distributed System of Scientific Collections, which is the European collection communities ESFRI initiative. DiSSCo will undertake the maintenance and sustainability of SYNTHESYS+ products at the end of the programme.

DIVERSify is a consortium of scientists, farmers, advisors, breeders and SMEs to co-construct a new approach and tools to investigate the mechanisms underpinning the benefits associated with cropping plant teams, and the crop traits and agronomic practices promoting these benefits. Focussing on arable and grassland systems, the six objectives are to: 1) identify current best practice for plant teams through participatory engagement with agricultural practitioners and scientific literature; 2) determine the mechanisms promoting positive plant-plant and plant-environment interactions using ecological principles to define experimentally the underpinning processes; 3) devise improved plant teams and identify potential breeding targets with a trait-based approach and novel tool to select crop types and deployment strategies that promote performance; 4) collaborate with stakeholders in European pedo-climatic regions and beyond to validate and demonstrate plant teams and devise practical crop management prescriptions; 5) construct a plant teams decision aid for practitioners by collating trait and agronomy data in a framework that can be interrogated for information on crop selection and management in different regions; and 6) work with stakeholders and RUR-6 for participatory knowledge exchange between different actors, EU policy and wider society through an appropriate and targeted array of communication media and activities. The co-innovation approach will allow tacit and scientific knowledge to be applied to real-world challenges in plant team cropping for developing practical solutions, in the form of teams with improved productivity, pest and disease control and environmental benefits. Knowledge exchange on crop traits, management and the decision aid will have impact on farmers, advisors, breeders, science and policy, improving awareness and overcoming barriers to uptake of plant teams for yield stability, diversification, sustainability and resilience.

Many multicellular organisms have a division between germline and soma. It has been long-standing dogma that all these cells have the same genome as they develop from a single cell. However, programmed DNA elimination can remove DNA during germline–soma differentiation and thereby lead to dramatic differences in genome organization between tissues. The evolution and function of programmed DNA elimination remains mysterious due to technological limitations and lack of an evolutionary framework. However, a role of this phenomenon in minimizing germline–soma genetic conflict has been suggested. This conflict arises when developmental gene expression is beneficial for the germline but deleterious for the soma. The aim of this proposal is to test whether programmed DNA elimination allows germline-specific expression of developmental genes to minimize germline–soma conflict. Using the germline-restricted chromosome (GRC) of the zebra finch as a unique study system, I have recently pioneered high-throughput genomics to overcome previous limitations. Combining my novel approach with transcriptomics, proteomics, cytogenetics, and developmental and functional genomics will provide unprecedented insights into the evolution and function of germline–soma genome differences. First, I will establish the so far first GRC study system by generating a zebra finch GRC reference assembly. Second, I will test how the GRC is inherited and maintained in zebra finch populations. Third, I will elucidate the long-term evolutionary history of GRCs across songbirds to reveal genes that are most conserved and thus candidates for GRC function. Fourth, I will trace GRC expression and elimination across zebra finch development, and functionally validate candidate genes. Altogether, I will establish an evolutionary framework which will significantly advance our understanding of programmed DNA elimination during germline–soma differentiation, a phenomenon likely widespread across the Tree of Life.

The Biodiversity Genomics Europe (BGE) ProjectThe Biodiversity Genomics Europe (BGE) Project has the overriding aim of accelerating the application of genomic science to enhance understanding of biodiversity, monitor biodiversity change, and guide interventions to address its decline. BGE coordinates and upscales DNA barcoding and reference genome generation in the context of European biodiversity. The Project develops synergies by aligning efforts and resources of the DNA barcoding and genome sequencing communities across the continent. The BGE objectives with derived ambitions: CAPACITY: To establish functioning biodiversity genomics networks at the European level to connect and grow community capacity to use genomic tools to help tackle the biodiversity crisis With the ambition to (a) Future-proof our networks on biodiversity genomics research, (b) lower access thresholds to biodiversity genomics research, and (c) promote co-creation and citizen engagement. PRODUCTION - To establish and implement large-scale biodiversity genomic data-generating pipelines for Europe to accelerate the production and accessibility of genomic data for biodiversity characterisation, conservation and biomonitoring With the ambition to (a) establish distributed and inclusive capacity, (b) build economies of scale and (c) connect previously disjoined resources to deliver relevant knowledge. APPLICATION - To apply genomic tools to enhance understanding of pan-European biodiversity and biodiversity declines to improve the efficacy of management interventions and biomonitoring programmes. With the ambition to (a) improve the use of biodiversity genomics data in science policy and (b) establish European-wide large scale biodiversity genomics research mechanisms. The BGE Consortium is comprised of 33 partners across 20 countries and brings together, for the first time at this scale, the two communities for barcoding and reference genome to implement its aspirational programme.