Search Results

In this project, researchers from the University of Bologna, in Italy (Federica Costantini, Barbara Mikac, and Eugenio Fossi) and the University of Dubrovnik in Croatia (Marijana Pećarević and Kruno Bonačić) join their forces to study alien species of the polychaete genus Polydora, invading farmed oysters in the Adriatic Sea, with the support of BGE funding. Aquaculture is one of the main vectors for the introduction and transport of alien species in the Mediterranean Sea. Recently, researchers from the University of Bologna discovered for the first time in the Mediterranean new alien shell-boring poychaete oyster pests, from the genus Polydora , in oyster farms in the northern Adriatic   Sea. Their introduction may have severe ecological and economic impacts. Movements of young and adult oysters among farms, performed regularly as a farming practice, might contribute to further translocation of these hitchhikers, which could also infest wild mollusks. Joint action of the neighboring Adriatic countries is needed to address the problem. The objectives of this project are to confirm the identity and define the distribution of shell-boring Polydora  species in oyster farms along the Adriatic coasts, clarify the provenance and way of their introduction in the Adriatic, and strengthen connections between scientists, aquaculture companies, monitoring, and legislation institutions as a base for the implementation of management measures for these   pests. Images of an Oyster farm in the Sacca di Goro lagoon, Italy, Northern Adriatic Sea and oysters being sampled from the farm. Italian and Croatian scientists sampled Polydora  from several oyster farms along the Adriatic coasts and analyzed them morphologically and genetically. Population genomics based on a genome sequencing approach (RAD-seq) is going to be used on the sampled populations. The sequencing of the reference genome for Polydora  is fundamental to map the sequenced reads for each sample and to SNP discovery to estimate diversity measures in pest species and to identify loci and alleles important for local adaptation . Analyzed data will indicate information on the routes of introduction of the species in the Adriatic Sea, on the connectivity patterns among populations, and the phylogenomic relationships between species within the genus. Oyster infested by molluscs and Polydora worms. A close-up look at the Polydora worm parasite from an oyster sampled in the Adriatic Sea. Through a series of actions (presentations at national and international conferences, meetings and round tables, and sending of reports) the scientific results obtained from this research will be communicated to aquaculture companies, governing and legislative institutions, public bodies working in environmental monitoring, and other public and private research institutions.

At this month's ERGA Plenary meeting (Monday, December 16 at 15:00 CET) we will hear from Amber Hartman Scholz about the outcomes of the UN Biodiversity Conference (COP16) that took place last October in Cali, Colombia and the consequences of the latest DSI decision for “real-world” scientists, database managers, and users of sequence data. The session will be moderated by Camila Mazzoni. Watch the talk: Abstract What happened at the UN Biodiversity Conference (COP 16) on Digital Sequence Information? Can I still use open public genetic sequence data? The Leibniz Institute DSMZ Science Policy and Internalization Department is actively engaged in the UN Convention on Biological Diversity as an academic stakeholder. At the UN Biodiversity Conference (COP16) in Cali, Colombia in October 2024 and, indeed, for the past several years, we have closely followed negotiations on digital sequence information (DSI) and access and benefit-sharing. While the COP15 decision on DSI in 2022 was encouraging because it moved towards a multilateral benefit-sharing (unlike the Nagoya Protocol), no details on how the mechanism would work were decided. The recent COP16 DSI decision operationalizes this new benefit-sharing mechanism and creates new financial obligations and requirements for databases. The talk will explain what the DSI decision means for “real-world” scientists, database managers, and users of sequence data. And, in parallel, show what science policy work entails and what is happening on the ground during UN negotiations. Speaker's Bio - Amber Hartman Scholz Dr. Amber Hartman Scholz is a microbiologist and Head of the Science Policy & Internationalization Department at the Leibniz Institute DSMZ in Braunschweig, Germany. She leads projects on international science policy especially on access and benefit sharing and digital sequence information. She led the DSMZ’s implementation to become a Registered Collection under the EU’s Nagoya Protocol regulation (511/2014) and co-founded both the DSI Scientific Network  and German Nagoya Protocol Hub . She held previous science policy posts in the US Federal and California state governments including at the White House Office of Science & Technology Policy. 🔔 To receive the Zoom link and join this and our upcoming plenary meetings, register as an ERGA member .

We are thrilled to announce the election of three new officers to the ERGA Executive Board ! Lada Lukić Bilela, Camila Mazzoni, and Jaakko Pohjoismäki have been appointed to three newly established officer roles. Their contributions will be instrumental in helping ERGA achieve its goals and bring its vision to life. Congratulations to our newly elected officers—we wish them great success! To learn more about each of the officers, check their introductory talks. This marks the third iteration of ERGA Executive Board elections, now a well-established process. The electoral procedure was followed closely by the voting ERGA Council, in accordance with the guidelines established by the ERGA governance Document .  The process also received crucial oversight from the Nominations Working Group and support from the Elections Supporting Team (Christian de Guttry, Diego de Panis and João Pimenta) and the JEDI Subcommittee . With these three new members, the ERGA Executive Board now comprises nine researchers with different roles. The new officer roles enhance the board’s reach and ability to support ERGA, enabling our community to grow and advance in new directions. Learn more about the newly created positions: Social Integration Officer This role ensures ERGA's ethical and socially responsible activities. The Integration Officer oversees Ethical, Legal, and Social Implications (ELSI), media relations, community engagement, and knowledge transfer, aligning these efforts with ERGA’s strategic goals. The focus is on managing the ethical and societal impact of ERGA’s work and promoting meaningful connections with the public and stakeholders. Funding Opportunities Officer The Funding Opportunities Officer is responsible for identifying and securing financial resources to support ERGA's initiatives. This role involves actively searching for grants and funding opportunities. It also guides teams through the application process, and enhancing ERGA’s visibility to attract resources. The officer plays a key role in increasing ERGA's financial sustainability. Genomic Outreach Officer This position focuses on promoting the use and value of reference genomes within ERGA and the broader community. The Genomic Outreach Officer identifies opportunities for applying reference genomes in various contexts, such as research, industry, and conservation. By promoting collaborations in genomic applications, ERGA expands its impact and visibility. Playlist - ERGA Executive Board - Introductory talks

In April 2024, a team of researchers from three countries launched a collaborative project under the BGE-ERGA umbrella entitled “Genetic adaptation of Northern chamois ( Rupicapra rupicapra ) ecotypes to climate change and habitat loss: A case study on the endangered subspecies of Balkan chamois ( R. r. balcanica )”. A team of experts from Bosnia and Herzegovina, Serbia and Slovenia led by Prof. Dr. Dragan Gačić is involved in this project, which is based at the University of Banja Luka - Faculty of Forestry. This case study will focus on the adaptive genetic variation observed in different ecotypes of the Northern chamoi s , with a special emphasis on the subspecies R. r. balcanica , the Balkan chamois,   which occupies central and southern Dinaric Mts. Recently, the species has been declining in Alpine and Dinaric areas and is sensitive to global increases in temperatures. The Balkan chamois occupies mountainous regions of the nine countries of the Balkan Peninsula, and in all these countries, populations are small and isolated. This subspecies is exposed to many threats, including: i) Shifts in temperature and precipitation patterns, ii) Habitat fragmentation and anthropogenic disturbances, iii) Hybridisation due to translocation of individuals of different subspecies.  The Balkan chamois in their natural habitat: climate change and habitat loss are some of the factors that threaten these high-mountain dwellers. Photo by Željko Sekulić. The primary goal of the project is to detect and understand hybridisation events/risks within selected populations, evaluate the resilience of populations in the face of environmental change, and comprehend the factors that influence their potential to persist and adapt. By utilising resequencing data, we can estimate the loss of genetic diversity and inbreeding resulting from population declines and fragmentation, which directly impact population fitness. In this study, we plan to incorporate samples/populations of Northern chamois from five different countries. Specifically, four countries (Bosnia and Herzegovina, Croatia, Serbia, and Montenegro) will contribute samples of the Balkan chamois. Additionally, Slovenia will provide samples of the Alpine chamois for comparative analysis. Furthermore, within Croatia, we intend to include a population located in the established artificial hybridisation zone of both chamois subspecies. Altogether, 120 samples will be included in the study. This project brings together researchers from Bosnia and Herzegovina, Serbia and Slovenia in a collaborative effort to understand the adaptive genetic variation of the endangered Balkan chamois and support its conservation. Photos by Bojan Paprica and Stefan Maglić. Stakeholders from Bosnia and Herzegovina and Serbia will be involved in interpretation and dissemination of results. The Hunting days meeting and workshops will be organised in collaboration with national parks and hunting organisations at international level, and separate training activities will be organized regarding hybridisation and the reintroduction action plan. Insights from this project will be essential for effective conservation, adjusting the management, and consequently, ensuring the long-term survival of Balkan chamois and other chamois subspecies. Stay tuned for more updates on our findings! Text by Dragan Gačić, University of Banja Luka - Faculty of Forestry.

At this month's ERGA Plenary meeting (Monday, November 18 at 15:00 CET) invited speaker Mirte Bosse will give a talk entitled "Captive Conservation Genomics - is that a thing?" Abstract Zoo populations can serve as an important resource for preserving threatened species. However, to ensure the sustainability of these populations, careful management is needed to maintain genetic diversity, minimize inbreeding, and prevent hybridization. Captive populations often face challenges due to small numbers of individuals, which can reduce genetic diversity and increase the risk of inbreeding. Additionally, these populations may diverge from their wild counterparts over time due to genetic drift, artificial selection, and adaptation to the captive environment. Modern genomic technologies can help assess the sustainability of captive populations and their potential for reintroduction by providing insights into genetic relationships, inbreeding, and harmful mutations. Genomic sequencing also allows for a deeper understanding of a species' evolutionary history, population structure, and local adaptations, which can be used to study how to optimize the genetic compatibility of reintroduced individuals with wild populations. This plenary discusses how expanding genomic tools using zoo animals can improve the management of endangered species beyond captivity. Speaker's Bio - Mirte Bosse Dr Mirte Bosse is affiliated with VU University in Amsterdam and Wageningen University. After her cum laude PhD graduation in Wageningen on the hybrid nature of pig genomes, she went 'from livestock to wildlife and now works in the field of conservation genomics. Here she uses the information stored in genome sequences to learn more about the history of endangered species. She develops genomics techniques to measure genetic health from genomes to get more insight into the dangers of inbreeding, now and in the future. Collaboration is key in conservation, therefore Mirte has long-term projects together with zoos to ensure the scientific findings are adopted in practice. She recently received a VIDI grant for her Asian Elephants project in which the genetic health of Asian elephants in European zoos and beyond is examined to explore reintroduction potential and find the perfect balance between in- and outbreeding. To receive the Zoom link and join this and our upcoming plenary meetings, register as an ERGA member .

Join the last ERGA BioGenome Analysis & Applications Seminar of the year! This time with a focus on functional genomics, featuring talks by Susana Coelho and Jaruwatana Sodai Lotharukpong. Don't miss it! 🕚 Wednesday, December 11th 2024 - 11:00 AM CET 📅 Add the seminar to your calendar Join us live on YouTube: Abstract Brown algae independently evolved sexual systems, complex multicellularity and (embryo) development, offering a unique perspective for exploring the general principles underlying the origin and evolution of these processes. Along with dozens of new reference genomes, the ongoing drive to generate transcriptomic data in brown algae have yielded new insights into shared developmental and evolutionary patterns across the tree of life, particularly the hourglass model. The hourglass model describes a recurring pattern in embryogenesis, where the evolutionarily divergent early and late embryonic stages are bridged by a conserved mid-embryonic period. In this talk, we present our recent findings of a transcriptomic hourglass in brown algae and discuss the bioinformatic challenges/solutions when working on non-model organisms. About the speakers Susana Coelho was born in Portugal and completed her PhD at the Marine Biological Association in the laboratory of Colin Brownlee (Plymouth, UK). She worked at the Centre National de la Recherche Scientifique (CNRS) in Roscoff (France) from 2006 where her lab focused in life cycle and reproduction of brown algae, and she had a key role in the establishment of the brown algae  Ectocarpus  as a model organism in evolutionary research. Between 2010 and 2020, she co-led the Algae Genetics Group in Roscoff, and was appointed Research Director at the CNRS in 2015. In 2020, she moved to Tubingen, Germany, where she is Director of the Algal Development and Evolution Department at the Max Planck Institute for Biology. Susana has led a number of large-scale research projects on the evolution and development of brown algae, including two ERC grants (SEXSEA and TETHYS), and she was awarded several prizes including the bronze medal of the CNRS (2015), the Trogoboff Prize of the French National Academy of Sciences (2017) and the Bettencourt Prize Coup d’Elan (2020).  Jaruwatana Sodai Lotharukpong is a PhD student at the Max Planck Institute for Biology in Tübingen. He was born in Japan, grew up in Thailand and completed his undergraduate and masters in London and Cambridge, respectively. Related publication Lotharukpong, J.S., Zheng, M., Luthringer, R. et al.  A transcriptomic hourglass in brown algae. Nature   635 , 129–135 (2024). https://doi.org/10.1038/s41586-024-08059-8

We are happy to invite you to the ERGA session during the Biodiversity Genomics Conference 2024! BG24 is an online, open conference and free to attend. ERGA will host a session on Monday, October 28th at 13:00 CET. Recorded talks: Session slide deck: https://zenodo.org/records/14008438 Check the programme below:

An ongoing project on ecological genomics of common thyme ( Thymus vulgaris ), ERGA-BGE was selected on April 2024 to support the assembly of a chromosome-level genome for T. vulgaris  under the call “Enhancing Biodiversity Genomics Applications for Ongoing Case Studies”. This study is led by researchers from Aarhus University in collaboration with researchers from the Center for Evolutionary and Functional Ecology (CNRS and Montpellier University), and builds upon decades of study of the ecological and evolutionary importance of common thyme chemotype diversity. Close-up view of a flowering thyme plant with the landscape in the background. Photo by Thomas Bataillon Thyme’s aromatic compounds not only have made it an important culinary and medicinal herb across human cultures, but these compounds also have multiple ecological roles, including defence against herbivore predation, resistance to abiotic stresses such as droughts and freezing and even influencing the species composition of surrounding plant communities. Something that is often not known is that there are multiple thyme scents. Thyme plants exhibit a huge diversity in the aromatic compounds they produce, giving rise to multiple chemotypes. For example, in Mediterranean common thyme it is possible to find up to 7 different chemotypes (scents). These different chemotypes can be broadly classified in two different ecotypes, the phenolic and non-phenolic, which provide adaptation to different habitats. Recent studies in Southern France have shown that the phenolic ecotype, which is better adapted to warm and dry conditions, has been expanding its habitat as a response to on-going climate change. The current project has produced a genetic dataset of exome sequencing capture of around 1000 thyme plants across different populations in Southern France. Within each population, a transect that captures a gradient of environmental conditions was sampled making sure that samples from both ecotypes were represented within each of the population. Moreover, for each sampling site along the transect, different environmental variables were measured. This design gives the optimal conditions to identify both the genetic variation responsible for ecotype formation and the genetic and environmental drivers of local adaptation. However, genomic analyses have already shown thyme has high genetic diversity, including structural variation involved in ecotype formation. The reference genome will allow better characterisation of thyme genomic landscape and identification of the relevant functional genetic variation and its genomic context . Ultimately, this will improve the management of thyme populations to ensure all of its chemotype diversity can be maintained, thus improving also the health of the Mediterranean ecosystems where thyme is a dominant plant, and help to better understand a so far successful adaptive response to climate change.   Bodil Ehlers with a thyme plant during field work and sampling, view of the landscape of the thyme ecosystem in Southern France. ( Photos by Thomas Bataillon) This work is part of the AromAdapt project funded by an Independent Research Fund Denmark grant awarded to Bodil Ehlers (Principal Investigator) from the Department of Ecoscience, Aarhus University, and Thomas Bataillon (co-PI) from the Bioinformatics Research Center, Aarhus University. The work is done in collaboration with John Thompson and Perrine Gauthier from the Center for Evolutionary and Functional Ecology at CNRS in Montpellier, Sylvain Santoni from the AGAP Institute (INRAE) and Marc Palmada-Flores from Universitat de Girona. This project is funded by the Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British government. About the Author Genís Garcia-Erill is a bioinformatician and evolutionary biologist. He is a postdoctoral researcher in Thomas Bataillon´s group in the Bioinformatics Research Center, Aarhus University, Denmark, and he is an ERGA member working in the assembly of the common thyme reference genome.