The project focused on two populations of aquatic warbler: Biebrza Valley marshes and Western Pomerania. Photos by Justyna Kubacka and Knyva.

Genomic diversity was similar across all the studied populations. However, this amount of genomic variation is shown by endemic island passerines with small populations. Recent inbreeding – identified with long runs of homozygosity (ROHs) was elevated in West Pomerania, indicating enhanced genetic drift in the last 20-100 years before sampling.
Relatedness – Aquatic warblers from West Pomerania were more interrelated than the Biebrza birds, pointing to lack of immigration and low population size in the former.

With the dense genomic data, the team was also able to do detective work and track back historical changes in effective population size. This parameter shows how strong the work of genetic drift is, which depends mostly on population size. The results were consistent with the decline in numbers and showed a recent genetic bottleneck around the industrial era in the mid-1800s, when wetland destruction accelerated. This result was especially clear for the Biebrza samples. For West Pomerania, the effective population size was much lower over the examined period than in Biebrza. A picture of a founding event, followed by expansion in the mid-1800s and then a steep drop was revealed. Therefore, genomic diversity of West Pomerania could have been depleted at least twice. 

Historical changes in effective population size revealed a clear genetic bottleneck in Biebrza around the industrial revolution, when wetland degradation accelerated. In West Pomerania, effective population size has been lower and genomic diversity appears to have gone through a bottleneck twice.

Finally, the team checked whether the two populations bear signs of genetic divergence. Results indicated only very week genetic differentiation and no clear evidence for two separate genetic populations. Apparently, either insufficient time has passed for genetic change to accumulate between West Pomerania and Biebrza, or some weak connectivity had been maintained. Nevertheless, it was too little to stop genomic erosion in West Pomerania.

While the analysis relied on historical samples, it brings an important insight for present day conservation efforts. A large-scale translocation project is being carried out to restore the nearly lost West Pomerania population. The results of the ERGA-BGE project indicate that genetic drift and inbreeding could have contributed to its swift decline. To restore this population through translocation while avoiding the genomic history repeating itself, it is crucial to improve the breeding habitat and extend its area. It is also fundamental to enlarge or create stepping-stone habitats between West Pomerania and the nearest large and stable populations, to restore gene exchange.

The work could not have been performed without the collectors, Prof. Andrzej Dyrcz, Dr Benedikt Giessing, Dr Jarosław Krogulec and Grzegorz Kiljan. For a quarter of century, the samples were curated by Prof. Michael Wink at the Heidelberg University and by Dr Martin Päckert at the Senckenberg Natural History Collections in Dresden, Germany. The project 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. The bioinformatic analysis was conducted with the support of the Interdisciplinary Centre for Mathematical and Computational Modelling at the University of Warsaw, Poland (ICM UW).

About the Author

Dr Justyna Kubacka is an evolutionary ecologist and ornithologist and is constantly gaining skills in population genomics. She works at the Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw. She belongs to the aquatic warbler genome team of the ERGA Pilot reference genome project. In her free time, she loves doing cross-country skiing and gardening.

Cíes Islands, northernmost population of A. pungens in NW Spain. Photo by: R. Piñeiro

Sines, Central population of A. pungens in Portugal. Photo by: I. Marques

We will generate three genomic datasets with ddRAD: 

1. A “northern dataset”, collected in Cíes islands population, ca. 400 km. away from the closest continental population; 
2. A “southern dataset”, in Trafalgar population, as part of the Gulf of Cadiz, and3.
3. A “central dataset” from Sines, in central Portugal.

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: 

1. 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.

Header image: Trafalgar, southernmost population of A. pungens in SW Spain. Photo by: R. Piñeiro

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 by: Holger Krisp, CC BY 4.0 via Wikimedia Commons and via Getty Images.

A striped Venus clam (Chamelea gallina). Photo by: Paola Venier

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.

Header image: Striped Venus clams on sand. Photo by: Holger Krisp, CC BY 4.0 via Wikimedia Commons and via Getty Images.

Sampling the Adriatic Dwarf Goby in the estuaries of Koper (Slovenia) and The Adriatic Dwarf Goby collected in a net. Photos by: Maximilian Wagner

Triplefin blenny (Tripterygion tripteronotum) in the Adriatic Sea. Photo by: Sandra Bracun

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.

Header image: Triplefin blenny (Tripterygion tripteronotum) in the Adriatic Sea. Photo by: Sandra Bracun

TRIDUBIRE is Ireland’s first population genomics study of the lesser trefoil, Trifolium dubium – known to many as the shamroc. Project website: https://tridubire.github.io/

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.

Header image: T. dubium, with its distinctive yellow flower and trifoliate leaves, mythologised to have been used by St. Patrick to explain the Holy Trinity. Photo by: Katie Herron

A well conserved population of the red coral, Corallium rubrum in the Medes Islands marine reserve. Photo by: Joaquim Garrabou

Header image: Close-up photo of the Mediterranean red coral. Photo by: Joaquim Garrabou

Graphical Abstract: The history of the first introductions and our main goals. Artwork by: Filippo Nicolini

The introduced Formica paralugubris colonies have a huge impact on local arthropods biodiversity and biomass. Photo by: Iacopo Nerozzi

We collaborate with a broad range of stakeholders and our goal is to increase the awareness of the public about the role of  biodiversity genomics in conservation actions, especially towards less charismatic invertebrate species.

We aim to promote the creation of more consistent legislation across various regions, thereby facilitating the protection of these species. In this context, F. paralugubris may serve as a valuable model for disseminating the possible pros and cons of human-mediated introductions of alien species. In fact, although F. paralugubris and red wood ants are classified as “Near Threatened” by the IUCN Red List, regulations governing their protection vary significantly across European countries.

This project is funded by the Horizon Europe program, by the European Union – NextGenerationEU, under the National Recovery and Resilience Plan (NRRP), Project title “National Biodiversity Future Center -NBFC” (project code CN_00000033), with additional support from the Canziani Bequest and “Ricerca Fondamentale Orientata” funds from the University of Bologna. We also thank BGE-ERGA for providing a collaborative platform that made this research possible.

Header image: A social interaction between workers of the same huge and widespread colony. These photos were shot on one of the sampled nests by: Iacopo Nerozzi

A fertile first-generation hybrid between mountain hare and brown hare, confirmed by genotyping. Such hybrids seem to come with a cost to the mountain hare while potentially benefitting the local adaptation of brown hares. The background fence belongs to private property and is not related to keeping animals captive. Game camera photo, UEF hare research group. Photo by: BGE/ERGA

Chromosomal-level reference genome assemblies enable detailed analysis of species hybridisation, as these preliminary results of the presented study demonstrate. Upper panel: Example of mountain hare chromosomal segments in the genome of a brown hare individual from the Oulu region in Finland. The chromosomes appear in reverse alphabetical order from top to bottom. The Y-chromosome has been excluded as it lacks recombination. The red regions are homozygous, and the yellow regions are heterozygous with mountain hare genomic sequence. Lower panel: A closeup of the red section of chromosome 18, showing example gene loci in this region. Read more about the two genomes here. Photo by: Zsófia Fekete.

Understanding the dynamics of the unique genetic interaction between the two hare species not only teaches us about the evolutionary processes of local adaptation in species range expansion but also provides valuable insight for informed conservation efforts for the mountain hare. This project is funded by the Horizon Europe program, with additional previous support from the Research Council of Finland (the xHARES consortium, grant no. 329264), and Portuguese FCT, Fundação para a Ciência e a Tecnologia (doi: 10.54499/PTDC/BIA-EVL/1307/2020), to the Portuguese collaborators. We also thank BGE-ERGA for providing a collaborative platform that made this research possible.

Header image: The brown hare (Lepus europaeus) and the mountain hare (Lepus timidus) had their genomes sequenced as part of the ERGA Pilot Project. Photo by: BGE/ERGA.

Oysters sampled from oyster farm. Photo by: BGE/ERGA

Oyster infested by molluscs and Polydora worms. Photo by: BGE/ERGA

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.

Header image: Polydora worm from the oyster sampled in the Adriatic Sea. Photo by: BGE/ERGA.

Photo by: Bojan Paprica

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.

Photo by: 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!

Header image: 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.