About the ‘ERGA iBOL Europe Connections’ series

The European Reference Genome Atlas (ERGA) and the European node of the International Barcode of Life (iBOL Europe), two international communities of scientists brought together under the Biodiversity Genomics Europe Project, are joining forces for “Connections,” a series of blog posts that explore the fascinating world of Biodiversity Genomics and the intersection of their communities. 

Blog 9 – How Biodiversity Genomics drives conservation impact

If you have been following our Connections series so far, you have learned that barcodes help us recognise which “book” of life we are holding, while reference genomes let us read every page. Today, we follow those pages out of the lab into the places where decisions are made. Biodiversity genomics has matured from proof-of-concept to a toolkit that can inform, for example, monitoring, species risk assessment, and management, and even market rules, by turning reads and assemblies into actions that matter for species, habitats, and the people depending on them.

The impact pathway usually begins with identification and baselines. DNA barcodes establish who is where. This matters when regulators need quick and reliable evidence to tighten protection for a declining bird population in a wetland. Or when managers must separate look-alike pest species in aquaculture, or when coastal engineers test whether a beach-nourishment scheme is compatible with an endemic fish. Reference genomes deepen the story. They reveal how a species works, what its population structure is, connectivity, and adaptive variation. All clues that tell us if a population can, for instance, cope with heatwaves, if a corridor is worth restoring, and which individuals should contribute to an ex-situ programme. In other words, barcodes inform us of their presence, and genomes explain how they function.

Consider fisheries and seafood safety. Genomics applied to widely fished pelagic species can clarify stock boundaries, helping fish stock management plans align with biology rather than old assumptions. At the same time, genomics in commercially harvested clams can support contamination assessment risks more precisely, so that consumer guidance and coastal policies rest on data rather than speculations. In both cases, genomics can improve sustainability and trust: what gets caught, what gets sold, what gets eaten, and what the sea can afford to give.

Public health is another frontier where decisions move at the speed of evidence. Genomics of mosquito complexes that transmit West Nile virus allows us to identify cryptic lineages and chemosensory genes tied to behaviour, turning a confusing species complex into a map for outbreak monitoring programmes. From these insights, SNP panels for routine surveillance, early detection of resistance to control measures, and area-specific interventions mandated by regional authorities can be designed.

On land, genomics can inform connectivity, reintroduction, and hybridisation policies. For example, in a rare Central European small mammal, its genomic structure showed how a modern drainage canal severed gene flow. The management recommendation is to restore corridors before populations slip past recovery. Alpine chamois and butterflies reveal country-level patterns of diversity and endemism. These data now feed directly into status reviews and legally binding conservation lists. In lowland wetlands, a long-distance migratory passerine with low diversity but ongoing gene flow gains a genetic monitoring plan that guides translocation choices and post-release tracking. Where climate change pushes related hare species into contact, genomic portraits of introgression help hunting and wildlife agencies adjust seasons and safeguards to protect vulnerable mountain lineages.

Plants illustrate the same arc from data to decision. Herbs harvested from the wild, dune shrubs that stabilise coasts, and aromatic species adapting to new climates all benefit from genome-enabled surveys that distinguish clonal spread from sexual reproduction, estimate contemporary effective size, and pinpoint variants tied to heat and frost. These findings shape seed-sourcing, habitat management, and Europe-wide genetic monitoring comparable across borders, museums, and herbaria.

What ties these stories together is not a single technology, but a way of working. Barcodes and genomes are generated in collaboration with end-users, including park services, fishery bodies, health authorities, farmers, and NGOs. Data are paired with training, screening tools, and communication adapted to local contexts. This results in a lasting impact that takes many forms, from field measurements to management plans, from genome browsers to policy briefs, and from classroom demonstrations to community-run surveys.

The book metaphor keeps us honest. Barcodes still tell us which titles we are holding, and reference genomes still let us read every page. But conservation impact starts when we file that book in the right library. We share it with the people who need it and use it to guide choices about land, water, and livelihoods. Biodiversity genomics is now doing exactly that, moving from pages to policies, with benefits that go far beyond the lab bench.

About the ‘ERGA iBOL Europe Connections’ series

The European Reference Genome Atlas (ERGA) and the European node of the International Barcode of Life (iBOL Europe), two international communities of scientists brought together under the Biodiversity Genomics Europe Project, are joining forces for “Connections,” a series of blog posts that explore the fascinating world of Biodiversity Genomics and the intersection of their communities. 

Blog 8 – Bioinformatics: reassembling the book of life

In our previous posts, we compared DNA to a book: barcodes help us identify which book we are holding, while reference genomes enable us to read every page. But here is the twist: by the time DNA leaves the wet lab, the book is broken as if we have run the pages through a “paper–shredder”. DNA extraction, library preparation, and DNA sequencing all turn the long DNA sequence into millions of pieces (Check the Connections blog #3 for an overview of these different steps of the genomic workflow). Bioinformatics is the art of turning that pile of shreds back into something we can read, search, and compare. It is the art that turns barcodes and reference genomes into usable knowledge.

Image 1: Informatics and advanced computing are necessary to analyse the huge amount of data generated for genomic research.

Bioinformatics is the product of molecular biology meeting computing. Bioinformatics facilitated the development of the first sequence alignments and substitution matrices, dynamic programming, the creation of searchable databases, and the first “find-it-fast” tools that supercharged homology searches. As sequencing scaled, assembly algorithms emerged, followed by hybrid approaches for long-read platforms. Alongside the algorithms came various file formats (FASTA/FASTQ/BAM/CRAM/GFF/GTF), workflow engines, and the hard-won lesson that reproducibility matters more than quick fixes.

For barcoding, the task is targeted: extract a standard marker (or “abstract”), check its quality, align it against a trusted database, and report the most accurate match with confidence. Think of well-indexed catalogues and fast look-ups, ideal for monitoring and quick assessments. For reference genomes, the task is editorial. Correct sequencing errors, assemble the million pieces into chromosomes, phase haplotypes, polish with multiple evidence tracks (long reads, linked reads, Hi-C, RNA-seq), and annotate genes and repeats.

That finished “book” enables population genomics, local adaptation, and conservation genomics studies.

Figure 2: Examples of some common bioinformatics tasks when working with genomic data from across the tree of life. Bioinformatics is the art that turns raw data into knowledge with useful applications for biodiversity.

Modern analyses involve dozens of steps, quality checks, trimming, deduplication, mapping, variant calling, assembly, scaffolding, annotation, all wrapped in containers and workflows to make sure a colleague can re-run them on Tuesday and get an answer on the same day. Good metadata is the structure that holds all the pages: sample, permit, locality, preservation, instrument, kit, and version numbers (Check this episode of the Genomic Connections Podcast to learn more about the importance of metadata). Without that structure, even the finest assembly becomes a vague curiosity.

 

A few field notes from the trenches

Everyone has a story of a 2 a.m. run that failed because a file was called final_FINAL_reallyFinal.fastq.gz. We have all been rescued by checksums, saved by containerised toolchains, and learned never to delete intermediate files before the multi-QC report is green. We name scripts after pets, we comment our code (eventually), and we celebrate the day a 500 GB BAM shrinks elegantly into a reproducible VCF.

Why does this matter to BGE? For iBOL Europe, robust bioinformatics means clean barcode libraries, sound assignments, and credible trend analyses. For ERGA, it means reference genomes that stand up to re-analysis and can power subsequent population, functional, and comparative genomics, the applications stakeholders care about (from conservation planning to bioeconomy uses).

Bioinformatics is not an afterthought: it is a research field itself! It is the bridge from sequencer output to decisions. Treat pipelines as publishable methods, treat metadata as data, and treat your future self as a collaborator who deserves clarity. In the next post, we will demonstrate how these computational foundations are applied in practical settings, including monitoring, policy, and management, without losing sight of the overall context (or the pages).

About the ‘ERGA iBOL Europe Connections’ series

The European Reference Genome Atlas (ERGA) and the European node of the International Barcode of Life (iBOL Europe), two international communities of scientists brought together under the Biodiversity Genomics Europe Project, are joining forces for “Connections,” a series of blog posts that explore the fascinating world of Biodiversity Genomics and the intersection of their communities. 

Blog 7 – Citizen science, allies, definitions, and common misconceptions

In our earlier “Connections” posts, we explored how DNA technologies, collaborative networks, and international policies shape biodiversity genomics. Today, we turn to another key element: the important role that non-professionals can have in science, or what is often called citizen science. We will unpack what this term means, clarify common misconceptions, and highlight why citizen scientists are vital to projects like Biodiversity Genomics Europe (BGE). It is a story about terminology and teamwork.

The term citizen science is surprisingly recent. One early recorded use dates back to 1989, when 225 volunteers collected rain samples for acid rain awareness for a U.S. project (Wikipedia). The term “citizen science” was formally added to the Oxford English Dictionary only in 2014,  defining it as a “scientific work undertaken by members of the general public, often in collaboration with or under the direction of professional scientists and scientific institutions.” A citizen scientist, likewise, is defined as a member of the public who engages in such work alongside professionals. Interestingly, “citizen” here simply means anyone; in other words, science by citizens of the world. Thus, a citizen scientist is anyone who is not a scientist but actively participates in real research.

Citizen scientists are:

Citizen scientists are not:

Biodiversity genomics relies on citizen scientists because the task is far larger than any research team can achieve alone. As species are vanishing at record speed, only a constant stream of data will give us the power to detect and address threats in time. Volunteers support this reach in different ways, such as hobby entomologists who photograph and submit insects for DNA barcoding, park rangers and hiking clubs who keep Malaise traps operating, or even coastal residents who filter seawater to capture the eDNA of invasive species. Their local knowledge reveals hidden habitats, while the DNA they collect flows directly into reference libraries and genome databases. The exchange is two-way. Participants gain new skills, a genuine sense of ownership, and a front‑row seat to cutting‑edge science. In return, they become ambassadors who share information about genomics, conservation, and responsible sampling within their communities.

Instead of being an optional extra, citizen science now powers the large‑scale, inclusive approach that modern biodiversity genomics demands. Science conducted with the public, for the lasting benefit of both people and the planet.

Stay tuned for our next post, where we will continue to explore the ever-expanding connections in the world of biodiversity genomics.

Within BGE, both ERGA and iBOL Europe carried out many activities involving citizen scientists, including, for instance, the Bioblitz in the Croatian Caves we talked about in our previous blog post.

You can learn more about BGE’s involvement with citizen scientists here.

About the ‘ERGA iBOL Europe Connections’ series

The European Reference Genome Atlas (ERGA) and the European node of the International Barcode of Life (iBOL Europe), two international communities of scientists brought together under the Biodiversity Genomics Europe Project, are joining forces for “Connections,” a series of blog posts that explore the fascinating world of Biodiversity Genomics and the intersection of their communities. 

Blog 6 – Biodiversity Hotspots & how to study them

What is a Biodiversity Hotspot?

Biodiversity hotspots are regions that are exceptionally rich in endemic species (those found nowhere else), into relatively small areas, but face important threats. Consequently, these Hotspots are global conservation priorities because they harbour a large portion of Earth’s biodiversity.

The European continent hosts such hotspots, and Biodiversity Genomics Europe, under a dedicated partnership agreement led by CSIC, the Spanish National Research Council, chose six priority countries to boost the generation of genomic resources for their most distinctive species:

What is a BioBlitz?

BioBlitzes, coordinated sampling efforts that unite taxonomists, genomicists, and volunteers, are beneficial in two ways. First, they act as a field classroom, immersing citizen scientists, from local residents to school students into science, strengthening community awareness. Second, DNA barcodes generated during an event provide information about which species are present, while reference-quality genomes built from those same species help us understand how they work, adapt, or decline. Data from barcodes and genomes are tightly coupled: barcodes provide real-time monitoring, while genomes reveal functional variation that informs management.

Legend: Click to learn more about barcoding and reference genomes.

BioBlitz in Croatia: Genomes in the dark – collecting in a hidden biodiversity hotspot

The Dinaric mountain range of Croatia is home to the world’s richest subterranean biomes and is the historical cradle of biospeleology (cave biology).

Cave species evolved in remarkably stable conditions, which makes them highly vulnerable to rising temperatures and other disturbances. Their subterranean habitats are isolated, and the organisms cannot survive on the surface, leaving them with no migration possibilities when the environment changes. This ecological trap makes genomic studies and the protection of their subterranean refuges increasingly urgent.

→ Did you know?  So far, 900+ cave species have been found in the Dinarides, with over 150 new ones reported in Croatia since 2002.

Photo credits: Martina Pavlek, Iva Cupic, Jana Bedek, TIn Rozman, Alen Kirin, Nikolina Kuharic.

Two cave-focused BioBlitzes took place in April and October 2024, one on the island of Mljet, the other in Velebit’s Cerovac caves. Participants learned how to locate invertebrates, recognize different species, and preserve specimens for barcoding and genome sequencing. More than forty cave species were secured. In addition, park staff and school groups were introduced to biodiversity genomics and learned more about how genomic resources can support biodiversity assessment, conservation, and restoration efforts by providing scientific evidence for informed management decisions. This outcome demonstrates how local partnerships and the use of genomic data can advance subterranean-biodiversity conservation.

About the ‘ERGA iBOL Europe Connections’ series

The European Reference Genome Atlas (ERGA) and the European node of the International Barcode of Life (iBOL Europe), two international communities of scientists brought together under the Biodiversity Genomics Europe Project, are joining forces for “Connections,” a series of blog posts that explore the fascinating world of Biodiversity Genomics and the intersection of their communities. 

Blog 5: DNA Rules & fair play

In our earlier posts, we celebrated the technical wizardry that empowers iBOL Europe’s DNA barcoding and ERGA’s reference-genome pipelines. Today, we zoom out from benchtop and bioinformatics queues to the rules for using those pipelines responsibly. The conversation here is based on two elements: the Nagoya Protocol on Access and Benefit Sharing (ABS) and the debate over Digital Sequence Information (DSI). Both are under the umbrella of the United Nations Convention on Biological Diversity (CBD), and both are poised to shape every barcoding run and every reference genome we produce.

The Nagoya Protocol, adopted in 2010 and enforced in 2014, translated the Convention’s promise of fair and equitable benefit‐sharing into operational obligations. Field teams who collect specimens must secure Prior Informed Consent and negotiate Mutually Agreed Terms before any genetic resource crosses a border. These administrative steps aim to curb scientific colonialism, foster respect for Indigenous knowledge systems, and channel royalties or capacity‐building back to the nation where the specimen was collected. iBOL Europe and ERGA already navigate this protocol daily, because each barcode voucher and each specimen used for the generation of a reference genome must carry a transparent legal pedigree.

The United Nations Convention on Biological Diversity. Source: https://www.cbd.int/convention/articles/default.shtml?a=cbd-01

The CBD entered into force in 1993, and the boom of sequence databases soon revealed a gap in the Convention. Indeed, the CBD focuses on physical samples, while genomic data travels instantly across digital platforms. The policy community coined the term Digital Sequence Information (DSI) to highlight this distinction – DSI refers to raw reads, assemblies, and barcodes. Since 2016, Parties to the Convention have sought a mechanism that extends benefit-sharing to these ‘files’ without impairing open science principles. Negotiators progressed at the Kunming–Montreal Conference of the Parties in 2022. This process led to the establishment of the Cali Fund for the Fair and Equitable Sharing of Benefits from the Use of Digital Sequence Information on Genetic Resources during COP16 in 2024/2025, aimed at collecting contributions from commercial users of DSI. COP16 laid the groundwork for implementing these mechanisms, and ongoing discussions will continue to fine-tune the system.

ABS permits are NOT “boring compliance forms” to rush through on the eve of submission. They are architectural blueprints for an equitable, reproducible, and future-proof research culture. The sooner biodiversity researchers integrate Nagoya thinking and prepare for DSI benefit-sharing, the smoother the path for publishing, sharing, and reusing our data sets will be. So, the next time you plan a field expedition or start assembling a genome, remember: ethics is not a speed bump; it’s the on-ramp to a legacy of science that everyone can share.