1,000 BUTTERFLY AND MOTH GENOMES TO INVESTIGATE EVOLUTION, CLIMATE CHANGE RESILIENCE AND TACKLE FOOD SECURITY ISSUES

Unravelling the secrets hidden in the DNA of butterflies and moths could help aid nature conservation, transform our understanding of evolution, and uncover new ways of tackling agricultural pests.

 Image: Small Emperor moth (Saturnia pavonia), a widespread species in Europe, including Czechia, but its numbers are declining. Photo: Luke Lythgoe

A major milestone has been reached, with experts across Europe, including those at the Biology Centre CAS in České Budějovice, sequencing 1,000 species of butterflies and moths. This includes almost all Czech butterflies, opening the door to help understand and protect Czech biodiversity.

Project Psyche is an international initiative that aims to sequence all 11,665 species of butterflies and moths in Europe. This collaboration of researchers, taxonomists, policymakers, and citizen scientists published a new white paper in Trends in Ecology & Evolution. It details how the genomes of all butterflies and moths can help answer evolutionary questions and address challenges such as food security.

Image: In July 2025, Project Psyche, in cooperation with the COST Action 10kLepGenomes, organised a field conference in Mals, Bolzano, Italy. Photo: Irena Klečková

The Human Genome Project laid the foundation that revolutionised our knowledge of human health. 25 years on, and many species on Earth are yet to be understood in this way.

Butterflies and moths, collectively known as Lepidoptera, are major players in ecosystems all around the world and make up around 10 per cent of all known eukaryotic species¹. They are a hugely diverse group, key pollinators and an important part of the food chain, both as herbivores and prey. Although some species are major pests, impacting agriculture, forests, and textile crops.

Lepidoptera are also key biodiversity and climate change indicators as they react quickly to environmental changes or habitat degradation. This means that a decline in butterfly numbers can serve as an early warning for wider losses in wildlife. Many conservation projects count butterflies and moths as a way to monitor the health of an ecosystem and inform whether conservation efforts are working.

Integrating genomics into conservation can help identify new species, so they can be accurately monitored, and investigate the factors that might have led to new species or population decline². Genomes can also directly be used to estimate population size declines, connectivity between populations or levels of inbreeding. Given the ongoing decline in insect populations, with some data suggesting a 36 per cent decrease in grassland butterflies across Europe in just ten years, between 2011 and 2020³, understanding more about the evolution of resilient species could help inform and protect other species.

For example, there is a project in Czechia⁴ that is using reference genomes from Project Psyche as part of its conservation genomics programme in dry grasslands, showing the real-world impact of having reference genomes for these species. 

Image: Land-use changes have severely fragmented habitats in Czechia, with dry to semi-dry grasslands and steppes among the most threatened biotopes. These species-rich ecosystems urgently require conservation efforts. Photo: Daniel Linke

All 1,000 genomes produced so far are freely available. These are fuelling a range of research areas to understand more about how these insects evolved and diversified over the 230 million years of their existence. For example, a recent analysis of over 200 butterfly and moth genomes revealed that their chromosomes have remained largely unchanged⁵. 

Comparing the genomes of species that have disappeared, are declining, or are stable or growing can help us understand how environmental changes and human activities affect insect diversity and distribution.  

For example, in Czechia, butterfly reference genomes have been used to discover more about why the Gentian Blue butterfly (Phengaris alcon), an endangered and specially protected species in the country. This research compared museum butterfly specimens from extinct and existing populations to uncover possible genetic clues that could identify and manage at risk species in the future, especially those that are not well known or hard to track using traditional surveys. 

Image: Mating pair of Phengaris alcon, an endangered butterfly in Czechia. A conservation genomics initiative in the country aims to monitor the health of their populations (TAČR grant SS07010197). Photo: Zuzana Blažková

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Dr Pável Matos-Maraví, who leads the research mentioned above on conservation genomics of dry grassland butterflies at the Biology Centre CAS, said: “For Czechia, where many butterfly species are declining, access to high-quality genomes is transformative. It allows us to investigate why some populations persist while others vanish. Project Psyche is giving us the biological insights and genomic resources we urgently need to identify and protect threatened species in the country.”

Dr Charlotte Wright, co-lead of Project Psyche at the Wellcome Sanger Institute, said: “Working with members across the world to build Project Psyche and harness genomics is incredibly important. Due to the diversity of butterflies and moths, we work closely with local experts and taxonomists, as many species look identical until they are under a microscope. In some cases, we only know the species because of what plant it was feeding on as a caterpillar. Taxonomic expertise is fading. We hope that one of the lasting impacts of Project Psyche will be close engagement between taxonomists and genomics researchers to gain a deeper understanding of natural history. By working together, we will also build a genetically informed evolutionary tree that describes how all butterflies and moths in Europe are related to each other. This is the foundation to answering questions about the past and help to be more prepared for the future.” 

Dr Joana Meier, co-lead of Project Psyche at the Wellcome Sanger Institute, said: “Butterflies and moths are key players in our ecosystems, and an incredibly diverse group. The Project Psyche dataset already contains 1,000 species’ genomes, aiding current research and driving new understanding. Using these reference genomes, researchers can study genetic diversity, population structure, connectivity, and local adaptation across Europe. This knowledge is critical for effective biodiversity management and policy, locally and globally. For example, genomics can help with identifying at-risk species, developing smarter pest control, and finding new ways to help protect biodiversity.”

Notes: 

1. Hoile, A.E., Holland, P.W.H. & Mulhair, P.O. (2025) ‘Gene novelty and gene family expansion in the early evolution of Lepidoptera’. BMC Genomics. DOI: https://doi.org/10.1186/s12864-025-11338-x
2. Suchačková Bartoňová, A., Linke, D., Klečková, I., et al. (2023) ‘Incorporating genomics into insect conservation: Butterflies as a model group’. Insect Conservation and Diversity. DOI: https://doi.org/10.1111/icad.12643
3. Europe’s grassland butterflies in steep decline. Butterfly conservation charity. Available at: https://butterfly-conservation.org/news-and-blog/europes-grassland-butterflies-in-steep-decline
4. Historie, současnost a budoucnost motýlů (Lepidoptera) v druhově bohatém, avšak ohroženém biotopu v Česku. Project LUC25115, INTER-EXCELLENCE II, Ministerstvo školství, mládeže a tělovýchovy. https://old.starfos.tacr.cz/cs/project/LUC25115
5. Butterfly and moth genomes mostly unchanged despite 250 million years of evolution. Wellcome Sanger Institute News article available at https://www.sanger.ac.uk/news_item/butterfly-and-moth-genomes-mostly-unchanged-despite-250-million-years-of-evolution/ 

Publication: 

C. Wright, N. Wahlberg, R. Vila, et al. (2025) ‘Project Psyche: reference genomes for all Lepidoptera in Europe’. Trends in Ecology & Evolution. DOI:  https://doi.org/10.1016/j.tree.2025.10.007

Funding: 

This research was funded in part by Wellcome. A full acknowledgement list can be found in the publication.  

Selected websites:

Project Psyche is an international effort to sequence all 11,665 European butterflies and moths, providing an unprecedented, freely available, genomic resource. These are used to explore evolution and ecology, and inform conservation, agriculture, and biotechnology approaches. There are currently 184 members across 34 countries. The project – named after the Greek goddess of the soul, Psyche, who was depicted with butterfly wings – involves a wide network of researchers, local experts and stakeholders in conservation and industry across Europe and beyond. https://www.projectpsyche.org/ 

COST Action 10kLepGenomes: aims to take advantage of the massive amount of data being produced by genome initiatives, in order to understand pressing issues of biodiversity loss, pest control, and effects of climate change on local populations of organisms. The 10kLepGenomes COST Action organises workshops and training courses for Early Career Researchers, short term scientific missions, conferences, and more through five Working Groups. https://10klepgenomes.eu/

The Wellcome Sanger Institute

The Wellcome Sanger Institute is a world leader in genomics research. We apply and explore genomic technologies at scale to advance understanding of biology and improve health. Making discoveries not easily made elsewhere, our research delivers insights across health, disease, evolution and pathogen biology. We are open and collaborative; our data, results, tools, technologies and training are freely shared across the globe to advance science. https://www.sanger.ac.uk/