Conference Agenda

Environmental DNA (eDNA) analysis has blossomed into an indispensable tool for monitoring and researching various ecosystems over the past few decades. Conservationists and researchers are constantly seeking innovative tools to better understand and protect our planet's biodiversity. Advancing in technology and methodology enabled eDNA analysis to broaden its scope of applications, thus gaining popularity, finding a vital role in conservation efforts. For example, by analysing DNA traces left behind by various species, the presence of endangered or elusive animals could be assessed, aiding in conservation planning and management. Early advancements in DNA-based taxon identification were also significantly boosted by next-generation sequencing technologies. The rapid evolution of eDNA analysis in the 2020s highlighted, though, the necessity for optimizing protocols to adapt to different conditions. The swift pace of advancements, however, brought forth challenges in maintaining methodological standards, which are essential for facilitating cross-study data mining. Conservation management and planning can greatly benefit from eDNA-driven ecological insights, particularly in enhancing strategies for connectivity, spatial prioritization, and habitat restoration. The available technologies and methods offer a non-invasive, efficient, and often more comprehensive means of assessing biodiversity and ecological health, which is crucial for informed conservation decision-making.

Species extinctions increase at a global scale, rapid inventorying of our planet’s biodiversity is becoming essential. It is a pressing need to investigate insect biodiversity and accelerate species discovery and description, especially for species belonging to megadiverse and understudied groups, also known as “dark taxa”. Phoridae (Diptera) are a great example of a "dark taxon". The use of an integrative methodology based on multiple data sources is probably the best approach to face up to the task of describing “dark” taxa. Here, we use the Large-scale Integrative Taxonomy (LIT) approach to sort 10,000 Megaselia Rondani (Phoridae) into 277 preliminary species hypotheses based on next-generation sequencing barcode clusters obtained with a 3% threshold. Each cluster was passed through predictors for incongruence indices between barcode clusters and morphology, and a subset of specimens were subsequently morphologically examined for each cluster. This study led to the description of twelve new species and a 12% increase in species for Germany. We provided species estimates and our results suggest that a 15% further increase in species richness may occour at the sampling sites. As this estimate was mostly based on samples from southern Germany, the species count will likely increase with expanded geographic sampling.

Threats to biodiversity have escalated in recent years, and therefore science and innovation are urgently needed to address these challenges. Molecular tools can aid critical conservation efforts. For example, understanding how species with temperature-dependent sex determination, such as sea turtles, will be impacted by global warming is vital for their survival. To understand the risks of extreme population feminization, we used whole genome methylation analyses to identify biomarkers for monitoring primary sex ratios in loggerhead turtles nesting in Cabo Verde. Despite the major advance this sexing method represents, research should not occur in isolation. Instead, robust collaboration between scientists and the civil society is essential. The Turtle Project integrates R&D with NGOs' needs and community engagement to develop evidence-based strategies for sea turtle protection. In this talk, I will highlight the links between our research, conservation, and community outreach.

Understanding, mitigating, and reversing biodiversity loss requires a broad range of tools and approaches. There is increasing recognition of the importance of genetic diversity as a vital component of biodiversity and on the utility of genetic tools, such as DNA barcoding and eDNA, to assess and monitor species and communities. Yet, lack of access to genomic tools to generate the data required to guide and improve conservation efforts can prohibit their utility. ORG.one is a project designed to support equitable, faster, and more localised sequencing of endangered species.

Existing projects to sequence endangered species have made good progress; however, they can be limited by complex workflows and the requirement to send samples to centralised, often overseas, locations for sequencing. ORG.one enables biologists to rapidly study those species close to the sample’s origin, using the latest sequencing approaches to develop high quality de novo draft genome assemblies. In this talk, I will discuss how these genomes are forming the foundations for developing biodiversity monitoring efforts, identifying conservation challenges (e.g. hybridisation) and solutions (e.g. disease resistance alleles), and upskilling a community of conservation geneticists. With its partners, ORG.one is focusing on delivering and demonstrating the impactful benefits of genomics for conservation.

Epigenetic variation refers to reversible chemical changes involved in the regulation phenotypes without, modifying the nucleotide sequence of the DNA. Ecological epigenetics is a rapidly growing research field and epigenetics has been identified as a new tool also in conservation biology. One key research direction is using epigenetic changes as biomarkers of past or current exposure to environmental stressors and a marker of individual physiological stress. Interestingly, especially early life stressors may have long-lasting effects through epigenetic changes, even through generations, that could contribute to explain (slow) population responses to environmental changes. Along with a broader overview, I provide case examples of epigenetic changes to environmental changes, such as chemical pollution and radiation, using wild bird populations as the study systems. I also describe how early-life stress may have long-lasting consequences on the stress-axis via epigenetic changes. Our work demonstrates how various environmental stressors change DNA methylation in many key pathways. I also discuss future of using epigenetics as biomarker. All in all, epigenetics provides a fruitful new research area in conservation research.

Biodiversity conservation calls for a comprehensive approach that spans multiple biological levels. Delineating conservation units and predicting population resilience is essential for effective conservation management. Yet the genetic tools required cannot always detect signals of short-term ecological dynamics. Epigenetic modifications carry valuable information to gain insights from the individual to the population and species levels. Here, we provide a toolbox for monitoring epigenetics signals that can be directly applied in various conservation contexts. The primary focus of our toolbox is on DNA methylation, for which conservation tools are already available. For instance, the identification of biomarkers associated with age or infection can facilitate the determination of an individual’s health status. On the other hand, whole genome epigenetic information can identify epigenetic signatures of rapid selection linked to environmental stress and therefore facilitate the quantification of the adaptive potential of populations. Lastly, we introduce the upcoming use of methods, beyond sequence level information, as conservation tools, such as epi-eDNA (epigenetic-environmental-DNA) and benefits associated with understanding gene regulation. Overall, our proposed holistic approach refines conservation strategies, ensuring species adaptive potential and persistence. Epigenetic insights offer a transformative pathway to protect endangered species effectively, by considering their molecular dynamics within changing environments.