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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.

Executive Board Council of Countries Committees Our Partners Pilot Project Former Contributors top OUR COMMUNITY ERGA is an bottom-up initiative based on people, consisting of hundreds of scientists across the entire European continent and beyond. Research institutions, infrastructure facilities as well as partner genome projects will play an important role within ERGA. Finally, ERGA will have a focus on societal needs particularly related to Biodiversity conservation. For that purpose, ERGA will work engaging governmental and non-governmental entities and will closely involve citizens in different actions. Executive Board Executive Board executive-board@erga-biodiversity.eu Robert Waterhouse Chair Ann Mc Cartney Vice Chair Olga Vinnere Pettersson Vice Chair Rosa Fernández Scientific Officer Elena Bužan Partnership Officer Chiara Bortoluzzi Dissemination Officer Lada Lukić Bilela Social Integration Officer Camila Mazzoni Funding Opportunities Officer Jaakko Pohjoismäki Genomic Outreach Officer List of Former Executive Board Members > Council of Country Representatives Contact the national representatives for more information on the ERGA community in your country! Andorra Andorra@erga-biodiversity.eu Manel Niell List of Former Council Members > Council of Countries Committees SSP - Sampling & Sample Processing samples@erga-biodiversity.eu More > DAC - Data Analysis Committee analysis@erga-biodiversity.eu More > Media & Communications media@erga-biodiversity.eu More > Social Justice Committee socialjustice@erga-biodiversity.eu More > SAC - Sequencing and Assembly Committee assembly@erga-biodiversity.eu More > ITIC - IT & Infrastructure Committee itinfra@erga-biodiversity.eu More > CS - Citizen Science citizenscience@erga-biodiversity.eu More > Annotation Committee annotation@erga-biodiversity.eu More > ELSI - Ethical, Legal, and Social Issues elsi@erga-biodiversity.eu More > TKT - Training and Knowledge Transfer training@erga-biodiversity.eu More > Committees Our Partners Our Partners ERGA is the pan-European partner of the Earth Biogenome Project (EBP) Affiliated Initiatives Associated Partners Pilot Project Pilot Project Committee Coordinators pilot@erga-biodiversity.eu Giulio Formenti Alice Mouton Ann Mc Cartney Learn more about the Pilot Project Former Contributors SSP - Sampling & Sample Processing Committee Filter by Type Astrid Böhne (Former Committee Chair) Former Contributors

analysis@erga-biodiversity.eu < Back DAC - Data Analysis Committee analysis@erga-biodiversity.eu The Data Analysis Committee (DAC) aims at fostering collaboration and knowledge sharing in genomic data analysis among ERGA members, and enhancing the development of applications in genomics. DAC has the goal to develop and implement standard protocols for downstream data analysis, providing high standard frameworks and pipelines to tackle research questions with different groups of organisms. Additionally, together with the Training and Transfer of Knowledge committee (TKT), DAC is responsible for providing training opportunities to the ERGA and general scientific communities through the organization of workshops and conferences. Finally, DAC aspires to improve translational communication with stakeholders and citizen scientists by actively engaging with the Citizen Science committee (CS committee) activities, to influence species management and protect earth’s biodiversity (V.1.0 02.05.2023) Chair Tereza Manousaki Coordinator João Pimenta Leader of the Population Genomics Subcommittee Mari Jose Ruiz Leader of the Phylogenomics Subcommittee Pascalia Kapli Iker Irisarri Leader of the Comparative Genomics Subcommittee Toni Gabaldón Leader of the Functional Genomics Subcommittee Steven Van Belleghem Steering Committee José Melo-Ferreira Elena Buzan (CS committee representative) Alice Mouton (TKT committee representative) Joan Pons Committee Resources 💡ERGA Knowledge Hub ERGA BioGenome Analysis and Applications seminars DAC Playlist: Genomic erosion and biodiversity conservation Events Introducing Genomic Connections - a brand new podcast! Press Releases Conservation genomics of the sand-dune shrub Armeria pungens at the latitudinal edges of its distribution Press Releases ERGA News #28 - April 2025 ERGA Newsletter

Committees SSP - Sampling & Sample Processing samples@erga-biodiversity.eu More > DAC - Data Analysis Committee analysis@erga-biodiversity.eu More > Media & Communications media@erga-biodiversity.eu More > Social Justice Committee socialjustice@erga-biodiversity.eu More > SAC - Sequencing and Assembly Committee assembly@erga-biodiversity.eu More > ITIC - IT & Infrastructure Committee itinfra@erga-biodiversity.eu More > CS - Citizen Science citizenscience@erga-biodiversity.eu More > Annotation Committee annotation@erga-biodiversity.eu More > ELSI - Ethical, Legal, and Social Issues elsi@erga-biodiversity.eu More > TKT - Training and Knowledge Transfer training@erga-biodiversity.eu More >