In a new publication, the European Reference Genome Atlas (ERGA) announces the success of its pilot project. This initiative assembled a large collaborative network of scientists and institutions across 33 countries to produce high-quality reference genomes of 98 European species—so far. The pilot project has provided valuable lessons and highlighted key challenges, positioning ERGA as a model for decentralized, inclusive and equitable biodiversity genomics initiatives around the world.

Among many of the project’s milestones are the first chromosome-level genome assemblies of species from Greece, one of Europe’s most biodiverse countries. Species such as the Cretan wall lizard (Podarcis cretensis) and Aristotle’s catfish (Silurus aristotelis) were sampled by local scientists in Greece to produce genomes that are now openly available for anyone across the world to access and study.

The findings are reported in an article published today in the journal npj Biodiversity.

These are but two examples of what can be achieved by uniting an international community of biodiversity scientists, fostering collaboration between and within countries. The ERGA pilot project emphasized equity and inclusion, with the goal that genomic research and resources are accessible to all, regardless of geographical origin. For many of the participating scientists and countries, the project offered the first opportunity to actively engage in the generation of state-of-the art reference genomic resources for their native biodiversity.

The ERGA pilot project was also successful in building momentum and bringing visibility to the growing importance of biodiversity genomics in Europe and beyond. Genomic data hold immense potential to inform conservation actions for endangered species and unlock discoveries in the fields of human health, bioeconomy, biosecurity and many other applications. For example, the greater argentine (Argentina silus) is among the species sequenced by the project—a commercially important fish species from the northern Atlantic.

This new reference genome will enable scientists to make more accurate assessments of the genetic status of the species’ populations, ultimately guiding management decisions to ensure that fishing practices are responsible and sustainable.

One of the species for which a high-quality reference genome is now also available for the first time is the white-tailed eagle (Haliaeetus albicilla). With this reference genome, it will be possible in future, for example, to investigate genetic disorders for which only the symptoms are currently known. This applies in particular to the so-called “pinching-off syndrome,” says bird of prey expert Dr. Oliver Krone from the Leibniz-IZW.

In this disease, the flight and control feathers of young white-tailed eagles are malformed and make flying impossible. The causes of this malformation of the feathers are genetic and are passed on recessively from both parent birds to the offspring. Furthermore, there are many possibilities to utilize the eagle genome for phylogenetic questions, Krone adds. For example, subpopulations could be differentiated from one another or isolated populations could be identified.

As the global scientific community strives to unlock the full potential of genomic data, the establishment of a Europe-wide collaborative network under the ERGA umbrella accelerates scientific progress and facilitates its translation into tangible benefits for biodiversity and society.

Additionally, the network helps scientists at all career stages to find and share opportunities for training, partnerships and funding. The ERGA pilot project was co-initiated in early 2021 by the then ERGA chair Dr. Camila Mazzoni from the Leibniz-IZW and the Berlin Center for Genomics in Biodiversity Research (BeGenDiv) who led calls with hundreds of genome scientists to set up and plan the collaborative project in an inclusive and decentralized way.

ERGA is the European node of the wider Earth BioGenome Project (EBP). In order to achieve its ambitious goal—to sequence all eukaryotic life on Earth—the EBP crucially needs worldwide participation and new, decentralized models of genome production.

The ERGA pilot project was able to show that a fully distributed, collaborative and coordinated genome production model is not only feasible but effective—even at a continental scale and without a central source of funding available. In fact, most of the project budget came from grassroots efforts by individual members and partnering institutions, with additional support from sequencing partners and commercial sequencing companies providing grants, discounts and in-kind contributions.

The ERGA pilot project helped to identify and address the many challenges of working at the international scale. These challenges include dealing with the legal and logistical hurdles of shipping biological samples across borders, resource disparities between countries and the search for balance between decentralization and the need for standardization to guarantee that only the highest possible reference genome assemblies which meet EBP metrics were produced by the project.

ERGA’s decentralized approach holds great promise for the future of biodiversity genomics. The pilot project’s success in building momentum and uniting researchers illustrates the power of this model.

By fostering international collaboration and focusing on inclusivity and equity, ERGA is setting new standards for biodiversity genomics. The lessons learned and the challenges identified and addressed in the pilot project will guide future efforts, promoting robust and standardized workflows and a comprehensive genomic database for species in Europe and beyond.

“The ERGA pilot demonstrated the importance of a well-connected scientific community that is willing to cooperate to achieve a major common goal. This success marks a significant milestone for ERGA, illustrating that such an initiative can be highly inclusive while still maintaining the high standards set by the Earth BioGenome Project (EBP) for reference genome production. This ERGA pilot project provides both an example and a roadmap for distributed efforts to build biogenomes across Europe and potentially beyond,” said Camila Mazzoni, former ERGA Chair and senior author of the article published—team leader “Evolutionary and conservation genomics” in the Leibniz-IZW Department of Evolutionary Genetics.

“The ERGA pilot project attempted to up-scale the generation of high-quality reference genomes across an entire continent. An endeavor of such magnitude was made possible only through its commitment to the principles of inclusion, equity and collaboration as well as the dedication of its diverse, transdisciplinary and cross-sectoral participants. I feel incredibly lucky to have worked alongside such an amazing group of colleagues to help kickstart the construction of a genomics encyclopedia of European species,” said Ann McCartney, Member of the ERGA Pilot Committee—Assistant Researcher at University of California Santa Cruz, and adjunct Assistant Professor at University College Dublin.

“When we took on the leadership of this project, we didn’t anticipate the extent of the work ahead. It was a challenging endeavor, but through perseverance and teamwork, we succeeded. We also had the invaluable support of sequencing centers, universities, and commercial companies who contributed to the ERGA pilot project, offering human resources for library creation, free sequencing and in-kind products. This experience was truly one of a kind,” said Alice Mouton, Member of the ERGA Pilot Committee—former FNRS postdoctoral researcher, and scientific collaborator at the University of Liège.

“ERGA was all a dream, until it wasn’t. Through this pilot project the prospect of uniting Europe under the flag of biodiversity genomics is now reality. We can be proud to have first established the process by which the genomes of many species will become available to the scientific community for conservation and beyond,” said Giulio Formenti, Member of the ERGA Pilot Committee—Research Assistant Professor at the Rockefeller University.

“The ERGA Pilot project is a significant milestone in the Earth BioGenome Project (EBP) and a major step forward for biodiversity genomics in Europe. As the first biodiversity genomics project coordinated at a continental scale, ERGA has demonstrated two fundamental principles on which the EBP was built—the first being that sequencing capacity will be geographically distributed, and the second being that any benefits derived from sequenced genomes would be shared equitably. ERGA is now poised to expand its goals to sequence thousands of genomes for conserving European biodiversity and the growth of a sustainable bioeconomy,” said Harris Lewin, Chair of the EBP Executive Council—Research Professor at ASU.

Adversity early in life can have permanent health consequences for people—even if their circumstances improve dramatically later on. Scientists use a cumulative adversity index, or CAI, which quantifies measures of hardship including poverty and stress, to understand health and longevity over the course of an individual’s life. This has been helpful in identifying specific measures governments, health care providers and families can take to improve people’s lives.

Wild animals may also experience adversity early in life, but the effect on their survival and longevity is unknown. While a similar tool could help scientists conserve animal populations by identifying the most influential stressors to mitigate, few populations have been studied over a long enough time to get the data needed to develop a CAI for that species.

UCLA biologists are changing that by creating the first cumulative adversity index for yellow-bellied marmots, based on 62 years of continuous data collection at the Rocky Mountain Biological Laboratory in Colorado. This is the second-longest study of individually marked mammals in the world.

The study, published in Ecology Letters, offers detailed steps for scientists with large datasets for other species to create their own CAI.

The index they developed identified some predictable but also surprising stressors with significant effects on marmot survival and longevity. For example, it was no surprise that a late start of the growing season reduced survival because marmots must gain weight during the summer for their seven- to eight-month hibernation. But the finding that summer drought had no effect was unexpected. Predation also played a smaller-than-anticipated role.

Not surprisingly, a mother’s death played a large role—but it still did even if it occurred after the pup was weaned. That may be because pups live with their mother for a full year after weaning.

To create the index, doctoral student Xochitl Ortiz-Ross selected data for female marmots born after 2001—when the researchers started quantifying physiological stress—that remained in one of the studied colonies until 2019, to guarantee an accurate record of their pedigree, age and lifetime experiences. Males typically disperse while females remain in the area where they are born, so biologists can observe females during their lifespan.

This population of marmots spans a 984-foot (300-meter) elevation change that divides the population into up-valley and down-valley groups, with different environmental and demographic conditions. The scientists trap individuals in the population biweekly from spring through late summer, when the marmots are active, collecting behavioral, morphological and physiological data.

Ortiz-Ross identified the following ecological, demographic and maternal measures of adversity, all of which can affect whether a pup survives its first year: late start of season; summer drought; predation pressure; large litters; male-biased litters; late weaning; poor maternal mass; high maternal stress; and maternal loss. She wanted to find out if these factors had any effect on the length of an individual’s lifespan after the first year.

These variables were fed into computer models that quantified standard, mild, moderate and acute adversity. All models yielded similar results. Moderate and acute cumulative adversity decreased the odds of pup survival by 30% and 40%, respectively.

Pup survival odds were significantly higher up-valley for all models, while maternal loss decreased survival odds in all models and by up to 64% in the moderate adversity model. Poor maternal mass decreased chances of survival by 77% only in the moderate adversity model, while late weaning decreased odds by 33% only in the standardized and raw models.

Surprisingly, drought increased odds of survival across all but the acute adversity model, with the greatest effect observed in the moderate adversity model.

The average adult lifespan was 3.8 years, but acute CAIs tripled the risk of adverse effects on life expectancy.

“We found that a CAI effectively captures short-term survival risk in yellow-bellied marmots, and even in the long term, increased adversity early in life lowered the adult lifespan,” Ortiz-Ross said. “Positive effects didn’t cancel out earlier adverse ones, suggesting that adversity does accumulate in marmots and can’t be fully recovered by positive experiences.”

The results supported the hypothesis that a CAI can be a useful tool to evaluate the long-term survival impact of multiple early life stressors in yellow-bellied marmots.

“What we’re facing in terms of biodiversity management is death by a thousand cuts. We typically study one factor at a time: humans, predators, climate and so forth,” said Daniel Blumstein, co-author and professor of ecology and evolutionary biology.

“But these impacts occur together and have a cumulative effect. We need a way to figure out which of these stressors—or which combination—has the biggest cumulative effect, and our research shows the CAI can do that for marmots.”

For example, conservation plans targeting this marmot population might target the down-valley group which, surprisingly, fared a little worse in reducing maternal mortality and improving the health of mothers. But they might not need to target reducing predation or countering the effects of summer drought; these did not turn out to be as important as expected.

The most endangered plant species in the Mariana Islands, the legume tree Serianthes nelsonii, faces persistent threats in its recovery. These have been identified as a short lifespan of habitat seedlings and rapid death of saplings transplanted from conservation nurseries.

The Plant Physiology Laboratory at the University of Guam addressed this conundrum by improving growth and survival of Serianthes seedlings through strategically placed mirrors beneath deeply shaded seedlings to increase available ambient light. The resulting paper has been published in the August issue of the journal Agronomy.

“We combined several known facts to develop the protocols,” said author Thomas Marler, retired University of Guam professor.

“First, the amount of sunlight that penetrates to the sub-canopy is minimal in Guam’s karst forest communities, and adding available light by installing lamps above Serianthes seedlings can increase longevity. Second, colored plastic mulch has been exploited for decades to reflect sunlight to improve crop production systems.”

The innovative protocol evolved from the widespread use of black plastic mulch in many crop production systems. The pioneers of the technology in the 1980s embraced the fact that growers were going to use plastic mulch anyway, so why not try various colors as a means of managing beneficial plant responses? Improved production systems were developed for numerous crops and included increased yield and reduced pest damage.

“Our first conception was to mimic these vegetable production protocols by exploiting commercially available plastic colored mulch products,” Marler said. “Then we realized that costs associated with a reflective product were less limiting for small-scale tree conservation approaches than for large-scale crop production settings.”

This led the team to instead employ mirrors—the most reflective product available.

The study revealed that the light reflected from the mirrors was more than 70% of incoming ambient light at midday in some cases. This boost in available light energy led to profound plant responses, as seedling survival increased more than 160% and growth in plant height increased more than 170% in one of the experiments.

Conservation practitioners often lack the information needed to improve management strategies designed for recovery of endangered tree species. But this newly developed protocol is ideal for the plant conservation toolbox because costs are minimal and improving plant performance is probable for every application. More importantly, there are no downsides as risks of harming the managed plants with the new procedure are negligible.