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We are happy to announce that the Earth BioGenome Project ( EBP ) has formally recognised the European Reference Genome Atlas (ERGA) as its first regional node representing the European continent. This marks a significant milestone in the long-standing collaboration between the two initiatives and strengthens the biodiversity genomics community in Europe and beyond. The first EBP Regional Node Since the early establishment of ERGA in 2020, we have been connected to the EBP as part of the Network of Affiliated Projects . More recently, the EBP has defined a procedure for the establishment of Regional Nodes  - initiatives responsible for “coordinating EBP-related activities across broad geographical areas, including continents and political unions”. In the last years, ERGA has grown into a community of over 1000 members, taking a leading role as a hub for connecting hundreds of people and institutions, producing reference genomes for European biodiversity, and promoting valuable knowledge dissemination and exchange. The broad scope and inclusive nature of our community meant ERGA was well positioned to become the very first regional node of the Earth BioGenome Project. We are delighted to take on this role and excited about the opportunity of contributing to the EBP at a new level. ERGA as of May, 2025 - a growing community committed to the development of biodiversity genomics in Europe. *Genome assemblies linked to the ERGA umbrella bioproject at the European Nucleotide Archive produced by ERGA Affiliate Initiatives such as the Darwin Tree of Life, the Catalan BioGenome Project, the ATLASea Marine Genomes Project, the Biodiversity Genomics Project, and others. “The EBP is excited to designate ERGA as its first Regional Node, which encompasses biodiversity genomics research across the European continent. ERGA’s outstanding organization and state-of-the-art infrastructure will significantly contribute to the EBP’s goal of sequencing all 1.8 million named eukaryotic species in 10 years, providing solutions for species conservation and mitigating the effects of climate change on economically important plant and animal species.” Harris Lewin, EBP's Executive Council Chair. “As the EBP regional node, ERGA plays an important role in connecting and coordinating efforts in the region, from large-scale projects to individual researchers all contributing to assembling the atlas of reference genomes for biodiversity in Europe.” Robert Waterhouse , ERGA chair. “The official recognition of the European Reference Genome Atlas (ERGA) as the European node of the Earth BioGenome Project marks the culmination of years of dedication by a passionate and engaged community. From the initial brainstorming sessions during the pandemic—with over 100 participants—to the progress made through Biodiversity Genomics Europe and other initiatives, ERGA has grown into a well-known, inclusive community. Together with the growing number of projects under its umbrella, ERGA is now playing a pivotal role in democratising access to high-quality genomics for biodiversity research across Europe.” Camila Mazzoni , ERGA founding chair. Alignment of goals  The recognition of ERGA as an EBP Regional Node reinforces our community’s commitment to build and foster a global EBP network, aligning our goals and contributing to sequence the genomes of all living eukaryotic species on Earth. Following the requirements for EBP regional nodes, ERGA is committed to:  Coordinate activities with the EBP and EBP-affiliated projects as described in our governance document   Adhere to and promote recommendations and guidelines issued by EBP Committees, Councils, or the Secretariat. Click here  for a view of a model of the organisational structure of the EBP as a global network of interconnected communities. Click here  to learn more about the ERGA community and structure. Other Relevant Links EBP Regional Node Application The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

This month's ERGA BioGenome Analysis & Applications Seminar will feature three short talks on the topic of genomic erosion and biodiversity conservation. Learn more below about the featured talks and speakers: Hernán E. Morales, Samuel Speak, and Xuejing Wang. 🕚 Tuesday, April 29th 2025 - 11:00 AM CEST 📅 Add the seminar to your calendar Watch the recorded seminar: Genomic erosion and biodiversity conservation The seminar will be divided in three parts (around 15 minutes each): Using genomes through time to study diversity loss - Hernán E. Morales The biodiversity crisis is driving the loss of critical genomic diversity essential for species survival and adaptation. Even after population recovery, genetic diversity may continue to decline—a phenomenon known as "genetic drift debt." To investigate this, we compare whole genomes from pre-decline (100+ year-old museum specimens) and post-decline (modern) populations of endangered bird species with varied decline trajectories. We assess how population declines affect deleterious, functional, and neutral variation, and use simulations to evaluate how demographic history and conservation actions influence extinction risk and recovery. Our aim is to uncover the evolutionary dynamics of genomic erosion. Scoring deleterious alleles in endangered species – Samuel Speak Captive breeding programmes can act as insurance populations against extinction and to preserve genetic diversity of endangered species. However, due to their small size, the survival of these populations is threatened by inbreeding depression resulting from high genetic load. We developed the LoadLift pipeline which utilises Combined Annotation-Dependent Depletion (CADD) scores from model species to estimate the genetic load within ultraconserved elements (UCEs) of individuals. Six pink pigeons (Nesoenas mayeri) were analysed with LoadLift and in silico crossings, to identify optimal mate pairings expected to show the least inbreeding depression. LoadLift was further used to assess the genetic load of the whooping crane (Grus americana), to compare the methods of LoadLift and SNPeff, showing good correspondence in their classifications of deleterious mutations. LoadLift aims to maximise the potential of ex situ populations for species conservation and restoration by enabling captive-breeding managers to reduce inbreeding depression and maintain long-term viable populations. Genomic erosion through the lens of comparative genomics – Xuejing Wang The loss of genetic diversity and the species’ response can vary widely depending on their evolutionary histories, life-history traits and demographic trajectories. Comparative genomics offers a powerful framework to explore the dynamics of genomic erosion across species. We compared the genomes of three Mauritius birds with additional 36 birds spanning the avian phylogeny, to investigate the genomic consequences of their demographic collapses. We found that historical population sizes influenced current genetic health, with higher heterozygosity linked to greater heterozygous load and the ratio of effective to census population size predicted a species' conservation status. We also found significant differences in genetic load and genome structure between taxonomic groups, showing the value of multispecies comparisons. Speakers Hernán Morales studied Biology at UNAM, Mexico, and completed an MSc at the University of Groningen, Netherlands. He earned his PhD from Monash University, Australia, and joined the Globe Institute at the University of Copenhagen in 2019. In 2023, he established the Evolutionary and Conservation Genomics Group that utilizes (paleo)genomics, quantitative genomics, and evolutionary modelling methods to explore the mechanisms behind the generation, preservation, and loss of biodiversity. Samuel Speak is a Postdoctoral Research Scientist in the Haerty Group at the Earlham Institute, working to identify loci associated with aquaculture relevant traits related to environmental stress within Tilapia species. Prior to this position, he was a NERC ARIES DTP PhD student at the University of East Anglia, the Natural History Museum London and Chester Zoo working on the conservation genomics of endangered bird species in zoos. During which he focused on quantifying the genetic load of individuals in captive breeding programs using CADD scores within the ultraconserved elements of the genomes. Applying this to threatened species including the pink pigeon ( Nesoenas mayeri ) and the whooping crane ( Grus americana ). Xuejing Wang is a postdoc working in Evolutionary and Conservation Genomics Group in Globe Institute, University of Copenhagen. She currently works on the conservation genomics of Mauritius kestrel and other endangered birds, focusing on demographic history, temporal genetic dynamics and genetic load. During her PhD in University of Bern, she worked on the population genomics and evolution of an insular mammal, the Orkney vole.

At this month's ERGA Plenary meeting , taking place on Monday, April 28 at 15:00 CEST , Dr. Thomas Mathers will present his work on a Tree of Life pilot project focused on improving reference genome assemblies for challenging species, along with new insights from complete bird microchromosome assemblies. More details can be found below. Watch the recorded talk: Abstract Chromosomally complete reference genomes for challenging species: overcoming sequencing dropout in bird microchromosomes Large genome assembly projects aim to generate chromosomally complete reference genomes across the tree of life. Typically, these projects rely on PacBio HiFi long-read sequencing and HiC to deliver reference genomes at scale. This approach results in high-quality genome assemblies that meet or exceed gold standard metrics for most lineages. However, some species are recalcitrant to assembly and challenges remain to generate high-quality genome assemblies for all taxa. Within vertebrates, birds present a substantial assembly challenge due to the presence of tiny, hard to assemble, microchromosomes. These chromosomes have distinct genetic and epigenetic features and are highly fragmented in PacBio HiFi de novo  assemblies, to the extent that in many cases the full complement of chromosomes cannot be identified. In this talk, I present results from a Tree of Life pilot project to improve the reference genomes of 20 bird species using Oxford Nanopore long-read sequencing. We find that using PacBio HiFi reads for de novo  assembly results in up to 70% missing gene content on the 10 smallest bird chromosomes due to sequence coverage dropout. I will discuss the possible causes for this sequence dropout and highlight new insights from complete microchromosome assemblies. Speaker's Bio Thomas Mathers Tom is a former BBSRC Future Leader (Discovery) Fellow at the John Innes Centre where he studied the evolutionary genomics of crop pest host range and is currently a Senior Computer Biologist at the Welcome Sanger Institute working on the Tree of Life Project. At Sanger, Tom carries out genome curation, develops tools to support curation efforts and leads projects making use of Tree of Life genomes to improve genome assembly methods and gain insights into basic biology through genome analysis. Recent projects include assembly and comparative analysis of bird microchromosomes, identification and evolution of supernumerary B chromosomes and sex chromosome turnover in flies. 🔔 To receive the Zoom link and join this and our upcoming plenary meetings, register as an ERGA member . ▶️ You can watch all previous ERGA Plenary talks here . If you would like to suggest a speaker or topic for a future plenary session, please contact us at training@erga-biodiversity.eu . We welcome your input!

In June 2024, a dedicated team of seven researchers from various European institutions led by Rosalía Piñeiro, interim associate professor at the University of A Coruña (Spain), launched a conservation genomics project to evaluate genetic erosion of the coastal shrub Armeria pungens  at the margins of its distribution. To this end, cutting-edge genomic indicators of a central population will be compared with the northern and southern margins of the species range. This project aligns with the mission of ERGA by generating state-of-the-art genomic resources of an Iberian coastal plant species threatened by housing, tourism, and agriculture thanks to the consolidation of an interdisciplinary network across Spain, Portugal and France.  Cíes Islands, northernmost population of A. pungens in NW Spain (photo credit: R. Piñeiro) Sines, Central population of A. pungens in Portugal. Photo by I. Marques. The genus Armeria  has a main centre of diversity located in the Iberian Peninsula, where 54 species occur. Notably, the central Portuguese and southwestern Spanish Atlantic coasts exhibit the highest diversity of coastal Armeria,  with 9 coastal species that show endemic or fragmented distributions.  The ongoing case study focuses on the sand-dune shrub A. pungens , an obligate outcrosser that exhibits a continuous range along the central and southwestern Iberian coasts. It is also present in two disjunct areas on continental islands: the Cíes islands, an offshore archipelago in Galicia, NW Spain, and the Mediterranean islands of Corsica and Sardinia. The immediate release of a high-quality reference genome of A. pungens   under the second round of the BGE-ERGA call  opens new possibilities for implementing advanced population genetics approaches. These approaches allow evaluating the conservation status of Armeria  populations on the valuable southern Iberian coastal ecosystems using genome-wide data and cutting-edge conservation genetics statistics. We will generate three genomic datasets with ddRAD:  i.  A “northern dataset”, collected in Cíes islands population, ca. 400 km. away from the closest continental population;  ii. A “southern dataset”, in Trafalgar population, as part of the Gulf of Cadiz, and   iii. A “central dataset” from Sines, in central Portugal.  Trafalgar, southernmost population of A. pungens in SW Spain. Photo by R. Piñeiro. The genomic data generated will be analysed using two novel methods that use a high-quality genome to investigate if putative bottlenecks in marginal populations have resulted in the accumulation of deleterious genetic variants and in the reduction of the effective population sizes that might compromise their long-term adaptability :  Estimation of effective population size, Ne Ne is important in conservation genetics as it is related to the loss of genetic diversity by drift by random mating of individuals. In 2022 Ne was for the first time introduced in the Convention of Biological Diversity (goal A and target 4) as an indicator of genetic erosion. However, obtaining reliable estimates of contemporary Ne from genomic data is challenging in the absence of high-quality reference genomes, as both closely and loosely linked genetic polymorphisms are needed.  Here, we will implement novel methods to provide reliable estimates of Ne in the marginal (“northern and southern datasets”) and central populations (“central dataset”). 2. Estimation of deleterious mutations The negative effect of deleterious mutations at the margins of species has been highlighted by theoretical models, but empirical evidence is scarce and restricted to model organisms ( Groß et al . 2018; Liu et al. , 2022) . Here we will compare the percentage of deleterious alleles in marginal and central populations by identifying likely deleterious mutations based on their detrimental effect on the protein, e.g. introducing stop codons. The genetic load will be calculated as the proportion of homozygous sites with deleterious mutations.  This study contributes to societal issues by supporting the preservation of dune ecosystems through genomic resources for monitoring native species. Sand dunes are biodiversity hotspots vital for nutrient cycling and soil stability that host specialized species. The rapid economic growth since the 1970s has exacerbated the pressure on these ecosystems. Nevertheless, there is hope for conservation efforts, as a significant portion of the Atlantic Iberian coastline remains in a relatively natural state. In order to build links with the local communities we count on the support of the Atlantic Islands National Park, the Habitat Naturalist Group -a non-profit organization founded in 1979 that is a leading conservation association in Galicia-, and the biomarathon of Spanish Flora project. About the Authors The research team is composed of seven ERGA members tailored to specific aspects of the project. Rosalía Piñeiro (University of A Coruña, UDC) contributes with expertise in plant genomics and Armeria  evolution. Manuel Pimentel, Elvira Sahuquillo (UDC) and Isabel Marques (University of Lisbon) will lead the fieldwork in Portugal and Spain. Ana González Tizón (UDC, head of UDCiencia), coordinates scientific outreach activities. Finally, Myriam Heuertz (INRA) and Marta Vila (UDC) will estimate contemporary Ne.

Text by Salvador Carranza Malpolon monspessulanus , the Western Montpellier snake - Photos by Daniel Fernández. A Milestone for ERGA in Reptile Genomics In 2024, a collaborative team of researchers members of the  European Reference Genome Atlas ( ERGA )  initiative successfully sequenced the genome of Malpolon monspessulanus , the Western Montpellier snake, under the Biodiversity Genomics Europe Project ( BGE ). This project, conducted across multiple institutions—including the Institute of Evolutionary Biology (IBE), the National Center for Genomic Analysis (CNAG), and Centre de Recerca i Educació Ambiental de Calafell  (CREAC)—represents a significant advancement in reptile genomics, providing valuable data for evolutionary and conservation research. Malpolon monspessulanus  is widely distributed across Western Europe and North Africa, yet its genomic information has remained largely unexplored. By generating a high-quality reference genome , this project contributes to ERGA’s broader objective of building a comprehensive genomic resource for European biodiversity, facilitating future research on reptilian genetics, adaptation, conservation, and venom evolution. 🔗 Read the Genome Report: https://preprints.arphahub.com/article/155085/ Distribution of the Western Montpellier snake as compiled by the IUCN Red List of Threatened Species. Version 2025-1. Photo by Daniel Fernández. Deciphering Venom Evolution in Colubrid Snakes A key aspect of this research is its contribution to understanding venom evolution in snakes of the family Colubridae. Unlike vipers and elapids, which have front-fanged venom delivery systems, M. monspessulanus  is opisthoglyphous (rear-fanged), possessing venom-producing glands that have long intrigued evolutionary biologists. However, the genetic basis of venom production in colubrids remains poorly characterized. By sequencing and annotating its genome, we will be able to identify key genes involved in venom synthesis and evolution, shedding light on the development of venom systems across snake lineages. This research has important implications for evolutionary biology, toxinology, and potential biomedical applications. Understanding venom composition at the genomic level could provide insights into novel bioactive compounds with potential therapeutic uses. An adult female Western Montpellier snake. Video by Jaume Martín. From Fieldwork to Genomic Insights The project involved field expeditions to collect high-quality tissue samples, followed by state-of-the-art sequencing and genome assembly using long-read technologies. The genome annotation will reveal genetic markers linked to venom composition, environmental adaptation, and evolutionary history. Beyond its evolutionary significance, this research highlights important conservation challenges faced by M. monspessulanus . A major threat to populations is entrapment in man-made wells, where snakes frequently fall and are unable to escape, leading to increased mortality. As part of the project, researchers conducted field visits to these wells to rescue trapped individuals, providing an opportunity to sample populations while contributing to conservation efforts. These findings will help assess human-induced risks to reptile populations and guide potential mitigation strategies. To the rescue: researchers visit wells to rescue trapped reptiles and collect information about the populations. Photos by Jaume Martín and Salvador Carranza. The newly generated genome will serve as a foundation for comparative studies on reptilian venom evolution, enhancing our understanding of how venom genes have diversified across different snake species. Acknowledgments and Future Directions This research was made possible through the Biodiversity Genomics Europe Project and the ERGA initiative, with key contributions from IBE, CNAG, and CREAC. The genome of Malpolon monspessulanus  is part of a larger effort to sequence the genomes of highly venomous, mildly venomous, and non-venomous snakes across the phylogenetic tree of snakes, aiming to uncover the genetic mechanisms driving the evolution of venom systems. Special thanks go to the Genomics Unit at IBE for producing the Hi-C library and to the sequencing teams and bioinformatics experts at CNAG for their meticulous work in ensuring the accuracy of the genome assembly. As ERGA continues to expand its genomic resources, this initiative will provide essential data to enhance our understanding of venom evolution, reptile biodiversity, and conservation genetics, bridging the gap between fundamental research and applied scientific advancements.

At this month's ERGA Plenary meeting , taking place on Monday, March 17 at 15:00 CET , Ancuța Fedorca will introduce the new COST Action Genetic Nature Observation and Action (GENOA). More details can be found below. Abstract Genetic Nature Observation & Action - GENOA CA23121 Genetic diversity is fundamental for adaptation and essential to species survival, hence for nature’s contributions to people. Furthermore, genetic knowledge supports the effective use of resources to ensure the holistic protection of biodiversity. While genetic diversity data and indicators are available, they are often not integrated into species management and monitoring schemes in Europe due to a lack of capacity. Furthermore, current national policies and practices have not yet ‘adapted’ to the new Global Biodiversity Framework. In order to better understand genetic diversity in species and their populations and actively use it to monitor and safeguard biodiversity, there is an urgent need to refine, assess, inform and facilitate the implementation of genetic diversity data and indicators across European countries. This implementation of genetic diversity data should be achieved by including practitioners, companies, policymakers and the wider public. The needs of all these stakeholders should be investigated and taken into account in order for collaborations to be inclusive and effective, as such, building knowledge, capacity and trust among partners. Hence, GENOA will co-create and improve the procedures, methods and data on genetic diversity (indicators) and co-develop tailored dissemination packages to reach out to and exchange with targeted stakeholders to enable a better understanding of genetic diversity information. In addition, the monitoring, reporting and application of genetic data will improve, which will contribute to the conservation of biodiversity at all levels. 🔗 https://www.cost.eu/actions/CA23121/ Speaker's Bio Ancuța Fedorca Ancuța Fedorca is a leading expert in conservation genetics and the sustainable use of biological diversity. She has played a key role in numerous international and national research projects, driving advancements in environmental research and integrating genetic diversity into conservation policy. As an internationally recognized scientist, she has contributed to high-impact scientific publications, furthering global understanding of genetic diversity and its role in conservation. Currently, Ancuța leads COST Action GENOA (CA23121), a dynamic network of scientists, practitioners, and decision-makers working together to enhance genetic diversity assessment. In this initiative we are spearheading efforts to refine methodologies, improve genetic diversity indicators, and develop targeted dissemination strategies to bridge the gap between research and policy. 🔔 To receive the Zoom link and join this and our upcoming plenary meetings, register as an ERGA member .

Researchers discuss the significance of this new genome and the need for collaborations beyond academia to protect the future of one of Europe’s most iconic mountain dwellers. The first high-quality reference genome sequence for the iconic chamois ( Rupicapra rupicapra ) was produced as part of the Biodiversity Genomics Europe Project and is now openly available . We spoke  with Profs. Elena Bužan and Boštjan Pokorny, Slovenian researchers whose work supports the science-based management of the chamois and other native species. They share insights on the Alpine chamois, its significance to local communities, the many applications of a new reference genome, and the importance of collaborating with stakeholders beyond academia to ensure the effective conservation of this and other species. Watch the video for highlights of this conversation and read the full interview below: Prof. Elena Bužan is a molecular ecologist at the University of Primorska. She applies evolutionary genetics to biogeography and conservation biology, with main focus on the impact of habitat fragmentation and degradation on genetic population structure of small mammals and ungulates such as the chamois. Prof. Boštjan Pokorny is dean of the Faculty of Environmental Protection, Velenje, Slovenia, chair of the scientific council of the Hunter’s Association of Slovenia and a senior researcher at the Slovenian Forestry Institute. Could you introduce the northern chamois and briefly describe the main conservation challenges faced by this species? Elena Bužan: The northern chamois is one of the two chamois species found in Europe (the second one is southern chamois) and it is the most abundant ungulate species in Europe and the near East. According to recent taxonomic studies, the northern chamois is divided into seven subspecies, some of which are quite threatened due to factors such as population isolation, poaching, overhunting, human disturbance in the environment, habitat degradation and loss and also climate change happening now in mountainous regions. Despite all these issues, the Alpine chamois  - the subspecies for which we just sequenced the reference genome - is categorized as “least concern” in the IUCN’s Red List of Threatened species, so is not considered to be of a very high conservation concern. Boštjan Pokorny: The Alpine chamois is an iconic inhabitant of Alpine areas in Europe, including Slovenia, and this is one of the reasons why we nominated this subspecies to have its genome sequenced. In Slovenia, the whole management and conservation program for the species is based on sustainable management made by hunters. As Elena said, even though the northern chamois is still considered as “least concern” by the IUCN, in the Alpine area this subspecies have recently experienced several threads that lead to decline of local subpopulations - particularly in high mountain areas. There are several reasons behind this decline; very important are climatic changes that have affected and will continue to affect the Alpine chamois. Scientists observed very clearly that there has been a switch in the patterns of vegetation growth in the alpine high mountain areas. Due to the rise in temperatures, the vegetation period - the growing season for vegetation - is now starting earlier, while the reproduction period (mating season) for the chamois remains the same or is even delayed towards the end of the year. This leads to a difficult situation for chamois and other wildlife: before, the main breeding season was in sync with the peak of vegetation availability (and quality), but now this timing has been disrupted. Indeed, we can see a discrepancy between the moment when the best food resources are available and the moment when the animals are having their offspring. This is of course very negative for the species and the effect is really dramatic in some areas. Scientists in Europe have observed this effect very clearly both considering the decrease of the animal’s body mass - which is essential for having higher reproductive potential - as well as the lower number and winter survival of offspring. In summary, even if the (sub)species is abundant and classified as “least concern” it still experiences several threats to its conservation. Another issue are the interspecific interactions - meaning interactions with other species. The red deer is an example: this species is going up into the mountain regions coming in very close vicinity to chamois. These new interactions have direct and indirect effects on the chamois since the two species now compete for the same food and other resources. I believe the main conservation threads to the northern chamois are climatic change and the introduction of competition with other ungulates (red deer) coming into the Alps, but also the direct effect of people (mainly due to disturbance) should not be neglected. How will the newly sequenced alpine chamois reference genome help address these conservation challenges? Elena: First of all, I would like to say that the whole scientific community working on chamois genetics will greatly benefit from the reference genome. Having this kind of standard resource and harmonization in downstream analyses will improve our ability to compare data across different labs - something that has been very challenging until now when using various  molecular techniques and approaches. With the reference genome, we now have the possibility to move forward, for example, with whole-genome sequencing for various populations, which allows for better data comparisons among scientists conducting genomic studies across the chamois’ distribution range. An annotated reference genome will provide numerous opportunities, including studying adaptation to future climate change, estimating effective population sizes, and possible hybridisation events. Having these tools is crucial for developing a comprehensive and holistic approach to genetic studies of the species across Europe. It is important to understand what is happening in populations across different regions, including the Pyrinenian and Apennine Peninsula, the Alps, the Balkan region, the Caucasus, and the Carpathians. Now is the right time to unite scientists working on chamois genetics to conduct truly comprehensive studies that will improve future research, management, and even conservation efforts.  This is particularly relevant because some chamois subspecies are protected under the Habitats Directive , meaning they require specific conservation measures. A well-developed reference genome will help ensure that management and conservation strategies are based on the best possible scientific data. Boštjan:  Exactly, genetic analysis provides crucial information, such as estimating population abundance. In high-altitude areas, it is possible to count individuals, but this becomes much more challenging in forested regions where chamois are also present. In such cases, modern techniques like genetic analysis become essential, creating a win-win situation for both conservation and management. Another application of the reference genome relates to potential reintroduction of the species. In the Southeastern Balkans, for example, there is potential for the reintroduction of the species in some mountain areas where it once existed but is no longer present. From this perspective, the new reference genome and comprehensive population data will be crucial for selecting the right populations for translocation. It may even be necessary to mix individuals from different populations to achieve the best possible outcome from the genetic viewpoint. While this is not currently a priority in our region, it is definitely essential for Southeastern Europe. As far as I know, this is also one of the expected outcomes of a case study within the BGE Project. Different subspecies of Northern chamois are found across Europe - the new reference genome will allow researchers to conduct comprehensive studies that will improve future research, management, and conservation efforts for the species across its wide distribution. Photos by Swen_Stroop, matkovci, Skouatroulio, Gianluca68 from Getty Images Genomic projects are often highly collaborative and involve a lot of people. Is this also the case in this work with the chamois? Elena:  Yes, it’s very important to realize that as scientists working with genomics we are always missing the perspective from the field. Even if collaborating with ecologists, it’s not enough, we always need more data from people who are in the field in direct contact with the species. For this reason it was really important for us to establish collaborations with hunters and local communities - they give us feedback about what is really happening in the field which enables us to react and investigate the changes using scientific methods.  We do have quite a lot of experience working in this collaborative way. There are many ongoing projects in my research group that started because of questions or concerns that local hunters had and so they decided to approach us. Boštjan:   In the case of the Alpine chamois, we were asked both by the Slovenian Hunters Association  as well as the Triglav National Park  to develop scientific based backgrounds for developing monitoring and management programmes for the species. And a very important part of this research to improve species management includes using genomic data to answer several key questions, such as abundance estimates, evaluating species resilience to factors like parasites etc. It is really important that the end-users - doesn't matter if they are conservationists or members from the hunter’s association - really recognize the potential of science and that we help by providing some directions on how to improve the species management.  Elena:   Especially because these stakeholders are increasingly open to using genetic information. It’s also a great moment for collaboration, as the cost of generating genetic data - once considered too expensive - has significantly decreased. It's encouraging to see that even end-users can now afford to finance genetic analyses, which will help raise awareness of how valuable genetic data can be. This information is essential for estimating genetic diversity, improving population management, assessing adaptive potential, and determining effective population size. In many cases, we still lack a clear understanding of population sizes and genetic health, both of which are crucial for long-term adaptation and conservation efforts. Can you tell us a bit more about the situation in Slovenia? How was the start of this productive collaboration between academic scientists and other sectors interested in chamois conservation? Elena : I can say that this collaboration is very connected to the first interest from the Triglav National Park, which is our largest national park. About ten years ago, we started collaborating with them, and at that time, we had already published the first genetic study, which was based on microsatellites. Over time, this collaboration expanded, including cooperation with hunters as well. Boštjan : Basically, as Elena mentioned, the first study was published based on the interest of the Triglav National Park, and afterwards people working in wildlife management - in this specific case, chamois management - recognized the potential of genetics. The scientific community in Slovenia, working on wildlife, is very closely connected with the Hunters Association. For example, the Hunters Association of Slovenia established a Scientific council more than a decade ago - this is a unique situation in Europe. This council consists of nearly all experts working on wildlife monitoring, management, and research, including Elena and myself. Importantly, there are several members, like Elena, who are not hunters, which helps build trust and facilitate communication. In most European countries, researchers will simply ask hunters for samples, but they don’t always respect their knowledge, expertise, or the realities of their work.  Without mutual trust between both communities (hunters and scientists), collaboration is impossible. We would like to introduce this approach across Europe, and many countries are already adopting it because the scientific community recognizes the value of such collaboration. But if we focus solely on the chamois, it holds both an iconic and symbolic value for hunters. This species is highly recognized and valuable. It is even featured in the logo of the Hunters Association, not only in Slovenia but in several other regions. Historically, reaching the high-altitude areas where chamois live was challenging, making both hunting and managing the species difficult. Additionally, chamois do not have negative impacts on other sectors of society, such as landowners, particularly in mountain regions. From this perspective, it is truly a symbolic species, and hunters deeply appreciate and value it. When hunters notice issues in the field, such as a declining population trend of chamois, it raises serious concerns. For example, if the wild boar population were to decrease, hunters likely wouldn’t react strongly or would nowadays even do all the best to control the population. However, for chamois, a population decline is alarming. In response, population managers turn to scientists, relying on our expertise to improve management strategies. This short clip produced by the Triglav National Park and Julian Prealps Natural Park highlights the beautiful natural landscapes protected by the park and the many species found in the area. Can you expand a bit on the role of the hunting association and other non-academic actors in the research for chamois conservation? Do they help you collect the samples or other data? Boštjan : While sample and data collection represents one aspect of citizen science, we believe it is crucial not to limit our understanding of citizen science to just that role. Of course, the easiest approach is to ask for help with data collection, observations, and similar contributions. However, in many citizen science studies, we fail to use the full potential of citizen scientists, particularly their personal knowledge. When it comes to field observations, understanding general ecology, or interpreting animal behavior, citizen scientists - especially those with direct experience - can sometimes have knowledge comparable to that of scientists working in offices or laboratories. This makes their involvement not just beneficial but essential. The real challenge and opportunity lie in engaging citizen scientists not just as data collectors but as active contributors who help shape research questions and guide studies in the right direction. For example, in chamois research, the knowledge held by hunting associations across the Alpine region is invaluable. Their expertise can help define key research problems, focus on the most relevant questions, and even aid in interpreting study outcomes.   While citizen scientists may not always grasp the complex genetic results generated in a laboratory, they can certainly understand their practical implications. There is also an important distinction between different types of citizen scientists. The general public, for example, may contribute observations and data through apps, but they may lack the deep expertise needed to interpret broader ecological patterns. In contrast, groups such as hunters and fishermen are unique in that they not only engage with nature but also possess in-depth knowledge and experience. This is why including citizen scientists, especially those with specialized expertise, is so crucial for projects like this. Elena:   I would say that local and traditional knowledge, which can be held by specific groups such as hunters, fishermen, beekeepers, and others, is invaluable. Additionally, the knowledge possessed by local communities is especially important, particularly in alpine areas where long-standing traditions and histories exist. These communities can provide a lot of information about species - knowledge that we could never acquire solely through laboratory work or a few years of field observations. Their understanding is built on decades of observations, passed down from generation to generation, as they live as an integral part of these natural habitats. Learn more: ERGA-BGE Reference Genome of the Northern chamois (Rupicapra rupicapra): Europe’s most abundant mountain ungulate | bioRxiv   Northern Chamois IUCN Red List assessment  Ongoing BGE Case Study: Genetic adaptation of Northern chamois ecotypes to climate change and habitat loss Interview and editing by Luísa Marins

In June 2024, a team of researchers from the Department of Biology of the University of Padova undertook a project to sequence the genome of the striped Venus clam Chamelea gallina , with the support of  Biodiversity Genomics Europe - European Reference Genome Atlas (BGE-ERGA). This project stems from the ongoing PLASTICVONG case study, which combines cutting-edge genomics, analytical chemistry, risk assessment, and the evaluation of possible impact of micro- and nano-plastics on clam physiology.  Specimens of C. gallina  were collected from the Central Adriatic Sea. Then, genomic DNA and total RNA from hemolymph, gills, digestive gland, mantle, and gonads were individually purified and quantified. Long-read PacBio sequencing has already provided a draft genome assembly, which will be further scaffolded with Hi-C DNA sequencing to achieve a chromosome-level genome. RNA sequencing will be used to refine gene annotations and will open the way to transcriptomic studies. Legend: Striped Venus clams on sand and for sale in a Barcelona market. Assessing the impact of micro- and nano-plastics on clam physiology is crucial for ensuring food safety. Photos:  Holger Krisp, CC BY 4.0 via Wikimedia Commons  and via Getty Images. Linking the genetic blueprint of C. gallina  with the functional clam responses to micro- and nano-plastics, this work will provide a knowledge basis for improving the management of this marine resource and seafood quality.  The initiative is made possible by PLASTICVONG (code IZS AM 07/22 RC, coordinator Dr. Federica Di Giacinto), funded under the “programma di Ricerca Corrente 2022” of the Italian Ministry of Health, and the BGE project. We extend our gratitude to Dr. Holger Krisp for permitting us to use his art-photos of C. gallina . About the Authors Paola Venier is an associate professor in Microbiology with experience in genetic toxicology and functional genomics. She is part of the Human Genetics and Functional Genomics group of the Department of Biology, University of Padova (Italy), PLASTICVONG partner, and the ERGA member coordinating the generation of the high-quality clam genome. Umberto Rosani is a researcher in Genetics interested in the evolution of animal genomes, with a particular focus on defense molecules. He works at the Department of Biology of the University of Padova (Italy) and holds a courtesy position at Stony Brook University (US). Bortoletto Enrico is a postdoctoral researcher at the Department of Biology, University of Padova, Italy. As an ERGA member, he is contributing to the assembly of the C. gallina  reference genome.

Triplefin blenny in the Adriatic Sea ©Sandra Bracun This BGE case study, led by the Svardal Lab at the University of Antwerp, builds upon two recently sequenced chromosome-level reference genomes from the ERGA pilot project. The project involves multiple European research institutions, including the Marine Biology Station Piran, the University of Graz, and the Natural History Museum Rijeka. It focuses on the widespread Triplefin Blenny ( Tripterygion tripteronotum ) and the vulnerable brackish-to-freshwater Adriatic Dwarf Goby ( Knipowitschia panizzae ). While high-quality genomes for both species have been sequenced, RNA sequencing is the next crucial step to complete the genomic work and support conservation efforts. Triplefin blenny - Photos by Sandra Bracun. The Triplefin Blenny ( Tripterygion tripteronotum ) is an ideal model for speciation studies due to its isolation by Adriatic Sea currents and its role in research on vision-related behavior for predator avoidance. In contrast, the Adriatic Dwarf Goby ( Knipowitschia panizza e) and its relatives face significant conservation challenges due to taxonomic uncertainties, habitat loss, and climate change. Whole-genome re-sequencing, leveraging high-resolution genomic resources, will clarify taxonomy and population distribution, providing essential data for conservation.  Sampling the Adriatic Dwarf Goby in the estuaries of Koper, Slovenia. ©Maximilian Wagner As we gather more information, understanding the genomic basis of adaptation is essential for comparing and elucidating biodiversity patterns. By sequencing the transcriptomes of both species, we will not only complete the genomic dataset but also provide unprecedented insights into the genomic pathways that drive and sustain biodiversity in these species. This project also highlights the ERGA community’s expertise in high-quality genome production. We extend our gratitude to those involved, including Dr. Marcelo Kovacic, Dr. Domen Trkov, Dr. Maximilian Wagner, and Henrique Leitão. About the Authors At the Svardal lab  we investigate the development and changes in Earth's natural diversity through genome sequencing and mathematical modeling. By studying genomic variations, we gain essential insights into evolutionary history, population connections, demographic patterns, and adaptations.

https://tridubire.github.io In 2023 a high-quality reference genome for the clover Trifolium dubium  was generated as part of the ERGA Pilot Project . This was significant not only for its scientific value but also for its cultural importance, as T. dubium , or the lesser trefoil, is broadly accepted as being the shamrock - a well-loved national symbol of Ireland. At University College Dublin (UCD) we have been using this genome to investigate the evolutionary history of this culturally important species and to place it in the broader evolutionary context of the Trifolium  genus. Trifolium  includes a number of agriculturally significant species, namely white clover ( T. repens ) and red clover ( T. pratense ), which are commonly used as forage crops due to their high-protein content and nitrogen-fixing capabilities, both reducing the need for synthetic fertilisers and improving soil health. T. dubium is noted for its production of condensed tannins, that reduce bloat in dairy cattle, and its frost tolerance, potentially offering benefits over white and red clover during the Irish winter. Understanding the genetics underlying these beneficial traits in T. dubium  has applications in informing breeding programs to improve other clover cultivars. T. dubium, with its distinctive yellow flower and trifoliate leaves, mythologised to have been used by St. Patrick to explain the Holy Trinity. Photos by Katie Herron. This study has now expanded to include a population genomics study of T. dubium , as part of BGE’s “Enhancing Biodiversity Genomics Applications” program. We plan on using pooled sequencing (pool-seq) to assess the genetic variation within and between populations of T. dubium across Ireland, sampling from both mainland Ireland as well as outlying islands. We aim to explore the species’ adaptive potential, gene flow and demographic history. By providing a genetic baseline for T. dubium  in Ireland, the project will support the tracking of changes in genetic diversity over time, the identification of potential threats from environmental changes, and ultimately guide conservation strategies to preserve this culturally significant species. A key component of our project is our outreach and educational efforts through which we hope to elevate the profile of biodiversity genomics in Ireland. By involving schools, we aim to engage students in real scientific research, promoting STEM education and fostering a deeper appreciation for biodiversity at local level. Field sampling of T. dubium across Ireland. Photos by Katie Herron and Graham Hughes. This project will not only provide valuable data for the scientific community but also contribute to the broader goals of BGE-ERGA by underscoring the importance of high-quality reference genomes in supporting the conservation of European biodiversity. Additionally, this study can serve as a model for other widespread species in Ireland, demonstrating the utility of the application of genomic methods in conservation and agriculture. This project has received funding from the European Union under the European Union’s Horizon Europe research and innovation programme, co-funded by the Swiss Government and the British Government. About the Authors Katie Herron is a PhD student at UCD, focusing on the genomics of Trifolium dubium  and is a member of ERGA. Ann Mc Cartney is an Assistant Researcher in the Genomics Institute at University of California, Santa Cruz and an Adjunct Assistant Professor at UCD. She is also vice-chair of ERGA and is a member of the Executive Board of the EBP. Graham Hughes is an assistant professor at UCD, and the director of the UCD Centre for Bioinformatics. He also sits on the ERGA Council of Representatives as representative for Ireland.