Periodic Reporting for period 2 - iBioGen (Twinning for European excellence in Island Biodiversity Genomics)
Période du rapport: 2019-12-01 au 2022-02-28
Islands harbour some of Earth’s most precious ecosystems, with faunas and floras of unique evolutionary history, which are at the same time vulnerable to environmental change, invasive alien species and over-exploitation. Current advances in genomics are transforming our understanding of biological diversity and leading to new discoveries that can limit biodiversity decline and therefore benefit current and future human societies. Biodiversity genomics is a new and fast-growing discipline that uses DNA data for the study of species diversity and the processes that generate and maintain this diversity. iBioGen aimed to significantly enhance the scientific and innovation performance of a Widening country (Cyprus) in the field of biodiversity genomics, by establishing a European network of excellence on the use of genomics for understanding and protecting island biodiversity. As an island country, Cyprus is ideally placed to promote scientific excellence in island biodiversity genomics, but the local research institutions have been lagging behind due to networking deficiencies. Networking gaps have been also delaying the necessary methodological unification and theoretical synthesis in biodiversity genomics. By linking the University of Cyprus (UCY) with three internationally-leading partners in biodiversity genomics (The Natural History Museum – NHM, Consejo Superior de Investigaciones Científicas – CSIC and Centre National de la Recherche Scientifique – CNRS), this project aimed to stimulate research excellence and international visibility of UCY, while improving the networking efficiency and innovation in this growing field. Additionally, the iBioGen project sought to integrate biodiversity genomics with monitoring and conservation initiatives and promote public awareness of the uniqueness and importance of island biota.
The scientific strategy of iBioGen included a comprehensive set of coordination, training, networking and dissemination actions. The work performed during the project duration and the main outputs are summarised below:
- Five annual meetings of the iBioGen consortium, which set the framework for an efficient coordination among partners.
- Three training visits of UCY PhD students and postdocs at NHM on transcriptomics, metagenomics and statistical analyses for ecology and evolution.
- Two international workshops on metabarcoding data analysis. A web resource for self-training in ‘Bioinformatic methods for Biodiversity Metabarcoding’ has been created and it is freely available.
- Five staff exchanges among the partners, with the aim to enhance methodological unification, protocol standardisation, knowledge transfer and collaborative research.
- An international symposium on “Next Generation Biodiversity Monitoring”, which generated an opinion paper that put forward a framework for an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis.
- An international symposium on “Synthesizing island biodiversity theory for community-wide genetic data” within the context of the International Conference “Island Biology 2019” in La Réunion, which generated a review manuscript on ecological, population genetic, and macroevolutionary models that can be extended to incorporate community-scale genetic variation.
- An international working group entitled “Toward harmonisation for the generation of metabarcoding data: Soil Biodiversity and Terrestrial Arthropod modules”, which generated a manuscript and a video presenting the harmonised protocols.
- An international working group entitled “Collective and harmonised HTS approaches to inventory arthropod on islands: laying the foundations of an Island Genomic Observatories network”, which generated a manuscript that sets the framework for an island Genomics Observatories network.
- An international working group on ecological-evolutionary synthesis, which generated the iBioGen R package: a suite of tools for studying ecological, evolutionary, and multi-scale processes within island communities.
- A systematic review of the COI metabarcoding literature which includes a set of recommendations to improve bioinformatic harmonisation.
- Three research manuscripts using data from the soil arthropod communities of the Cyprus forests and applying a range of analytical approaches, which are expected to promote Cyprus as a model system for biodiversity research.
- A piece of software that identifies putative NUMTs and other erroneous sequences in metabarcoding data.
- A TED-Ed lesson teaching the idea, methodology and applications of DNA metabarcoding to younger generations.
- A professional video demonstrating how the UCY researchers work in the field and in the lab to discover hidden biodiversity using DNA and highlighting the uniqueness of Cyprus’ biodiversity.
- Four educational programs and a permanent exhibit were designed and implemented in the Environmental Education Centres in Cyprus, which teach different aspects of the iBioGen project that were considered relevant and suitable for primary and secondary school kids.
- Further dissemination and outreach through the project brochure, the iBioGen website and social media pages and press releases.
- Two seminars and eight meetings with local stakeholders were held in Cyprus, which set the basis for exploitation of results beyond the end of the project.
- Five annual meetings of the iBioGen consortium, which set the framework for an efficient coordination among partners.
- Three training visits of UCY PhD students and postdocs at NHM on transcriptomics, metagenomics and statistical analyses for ecology and evolution.
- Two international workshops on metabarcoding data analysis. A web resource for self-training in ‘Bioinformatic methods for Biodiversity Metabarcoding’ has been created and it is freely available.
- Five staff exchanges among the partners, with the aim to enhance methodological unification, protocol standardisation, knowledge transfer and collaborative research.
- An international symposium on “Next Generation Biodiversity Monitoring”, which generated an opinion paper that put forward a framework for an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis.
- An international symposium on “Synthesizing island biodiversity theory for community-wide genetic data” within the context of the International Conference “Island Biology 2019” in La Réunion, which generated a review manuscript on ecological, population genetic, and macroevolutionary models that can be extended to incorporate community-scale genetic variation.
- An international working group entitled “Toward harmonisation for the generation of metabarcoding data: Soil Biodiversity and Terrestrial Arthropod modules”, which generated a manuscript and a video presenting the harmonised protocols.
- An international working group entitled “Collective and harmonised HTS approaches to inventory arthropod on islands: laying the foundations of an Island Genomic Observatories network”, which generated a manuscript that sets the framework for an island Genomics Observatories network.
- An international working group on ecological-evolutionary synthesis, which generated the iBioGen R package: a suite of tools for studying ecological, evolutionary, and multi-scale processes within island communities.
- A systematic review of the COI metabarcoding literature which includes a set of recommendations to improve bioinformatic harmonisation.
- Three research manuscripts using data from the soil arthropod communities of the Cyprus forests and applying a range of analytical approaches, which are expected to promote Cyprus as a model system for biodiversity research.
- A piece of software that identifies putative NUMTs and other erroneous sequences in metabarcoding data.
- A TED-Ed lesson teaching the idea, methodology and applications of DNA metabarcoding to younger generations.
- A professional video demonstrating how the UCY researchers work in the field and in the lab to discover hidden biodiversity using DNA and highlighting the uniqueness of Cyprus’ biodiversity.
- Four educational programs and a permanent exhibit were designed and implemented in the Environmental Education Centres in Cyprus, which teach different aspects of the iBioGen project that were considered relevant and suitable for primary and secondary school kids.
- Further dissemination and outreach through the project brochure, the iBioGen website and social media pages and press releases.
- Two seminars and eight meetings with local stakeholders were held in Cyprus, which set the basis for exploitation of results beyond the end of the project.
iBioGen developed and implemented a sustainable framework for scientific excellence at UCY in the field of island biodiversity genomics. Thanks to the iBioGen project, the UCY team is now capable of applying independently and successfully state-of-the-art biodiversity genomic approaches and implement them in newly funded research projects on the biodiversity of Cyprus. The success rate in research funding applications and the scientific output of UCY has been significantly increased, while the iBioGen activities have boosted the international visibility and networking capacity of UCY in the field of biodiversity genomics. The iBioGen networking activities also had a positive impact on the scientific capacity of the advanced partners, through stimulating knowledge transfer among research teams of complementary expertise and fostering interdisciplinarity.
Furthermore, the iBioGen activities generated an important impact on the field of biodiversity genomics by promoting protocol harmonization for genomic data generation at a global scale and laying the foundations of a Genomic Observatories network on islands. Another major impact relates to the development of a methodological framework for biodiversity analysis of community-scale genomic data. The iBioGen project made important steps towards an empirical and conceptual unification in island biodiversity research by developing models which incorporate one or more axes of biodiversity data, while integrating population genetic variation at the scale of the whole community. Finally, the iBioGen activities had an important impact on biodiversity stakeholders and the general public (with a special focus on younger generations), towards understanding, valuing and protecting the “hidden” biological diversity that is revealed through genomic approaches.
Furthermore, the iBioGen activities generated an important impact on the field of biodiversity genomics by promoting protocol harmonization for genomic data generation at a global scale and laying the foundations of a Genomic Observatories network on islands. Another major impact relates to the development of a methodological framework for biodiversity analysis of community-scale genomic data. The iBioGen project made important steps towards an empirical and conceptual unification in island biodiversity research by developing models which incorporate one or more axes of biodiversity data, while integrating population genetic variation at the scale of the whole community. Finally, the iBioGen activities had an important impact on biodiversity stakeholders and the general public (with a special focus on younger generations), towards understanding, valuing and protecting the “hidden” biological diversity that is revealed through genomic approaches.