Rosa Rubicondior: Refuting Creationism - How Butterfly Genomes Confirm Darwin's Conclusion

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1,000 butterfly and moth genomes to investigate evolution, climate change resilience, and tackle food security issues

Geneticists at the Wellcome Sanger Institute have just completed the sequencing of 1,000 European butterflies and moths. Their results are already feeding into research papers, such as that by Asia E. Hoile, Peter W. H. Holland & Peter O. Mulhair, in BMC Genomics. The Wellcome Sanger team have published their results in Trends in Ecology & Evolution

In 1858, Charles Darwin and Alfred Russel Wallace proposed the theory of evolution by natural selection, or as they described it, the origin of species by the preservation of favoured races. Darwin then elaborated on that central idea and concluded that the ‘tree of life’ would branch in ways consistent with diversification from common origins.

Creationists, on the other hand, claim all species were created by magic in their present form just a few thousand years ago, with no evolution and no common ancestry.

Darwin's Tree of Life sketch

Neither Darwin nor Wallace knew anything about DNA or genomes, or that mutations in DNA would become ‘favoured’ in particular environmental niches, driving diversification. They developed their ideas purely from the observable morphological and behavioural similarities and differences among species.

So, if the creationists are right, what should we see in these 1,000 genome sequences?

We should see no similarities between related species and no branching family tree when comparing taxa above the species level, because, on the creationist view, there was no diversification and no common origin.

But if Darwin was right, what should we expect to see?

We would expect nested hierarchies, with homologous genes diverging progressively the further apart species sit on the family tree. We would expect to see mutations that confer advantages in particular niches, and the emergence of new genes through duplication and repurposing.

And that is precisely what we see. The genomes reveal descent with modification and a family tree that clearly reflects shared origins – the result of evolutionary processes acting over deep time. Crucially, we find no evidence whatsoever of special creation without ancestry. In other words, the genomes of these 1,000 European butterflies and moths are exactly what we would expect if Darwin and Wallace were right and the biblical creation story were wrong.

And, to add insult to injury for creationists who hold it as an article of faith that genetic information can't be created without the assistance of their putative magic designer, very many of the evolutionary changes were the result of gene duplication and repurposing and, in at least one instance of horizontal gene transfer from a bacterium.

Background^ The Evolution of European Butterflies and Moths.
Origins of the Lepidoptera

Butterflies and moths (order Lepidoptera) originated in the late Carboniferous to early Permian but diversified substantially during the Mesozoic. Molecular evidence places their last common ancestor at roughly 300–250 million years ago. The appearance of flowering plants (angiosperms) during the Cretaceous—around 100 million years ago**—triggered one of the most dramatic adaptive radiations in insect history.

Arrival and Diversification in Europe

The modern European fauna emerges from several geological and climatic processes:

Tertiary (Palaeogene and Neogene) Radiation

After the end-Cretaceous extinction, Europe hosted a warm, forested environment that encouraged diversification. Several major Lepidopteran lineages established themselves, especially:

Pieridae (whites, sulphurs)
Lycaenidae (blues, coppers)
Nymphalidae (fritillaries, admirals)
Geometridae and Noctuidae (moths)

These groups radiated alongside Europe’s rapidly changing angiosperm flora.
Climatic Oscillations and Glacial Cycles

The Pleistocene glaciations (2.6 million – 11,700 years ago) were decisive. Europe repeatedly cycled between:

Ice coverage, eliminating Lepidoptera from northern and central regions
Southern refugia, especially in Iberia, Italy, the Balkans, and Anatolia

From these refugia, butterflies and moths recolonised Europe repeatedly, creating:

Genetic structuring (east–west and north–south lineages)
Distinct subspecies
Evidence of bottlenecks and rapid expansions
Many European species still bear clear signatures of these refugial histories.
Hybridisation and Secondary Contact

When glacial boundaries retreated, previously isolated populations met again. This produced:

Hybrid zones (e.g., Papilio machaon, Pararge aegeria)
Introgression events detectable genome-wide
Cases where hybridisation appears to have fuelled adaptive variation

Genomics consistently confirms these patterns.

Co-evolution with Host Plants

Larval host-plant specialisation is a central driver of diversification, especially among:

Lycaenids (often highly specialised)
Pierids (adapted to Brassicaceae chemistry)
Nymphalids (multiple transitions among plant families)

Genomic data show repeated gene duplications and enzymatic innovations for handling plant chemical defences, particularly in detoxification pathways (e.g., P450s, GSTs, UGTs).

Post-Glacial Expansion and Modern Distributions
After the last glacial maximum (~20,000 years ago):

Warm-adapted species expanded northward.
Cold-adapted species either contracted uphill or became trapped on “sky islands” (e.g., Erebia).
Climate-driven range shifts shaped the modern mosaic of endemic and widespread species.

Some genera, such as Erebia, have undergone rapid alpine diversification, while others, like Vanessa and Pieris, are globally dispersed and expand readily.

Human Influence and Recent Evolution

Over the last few thousand years:

Agriculture altered host-plant availability
Deforestation and reforestation shifted habitats
Climate warming has driven northward and altitudinal expansions
Some species show rapid, contemporary evolution in voltinism, diapause, and phenology

The new Sanger dataset will help document these changes at a genomic level.

What Genomics Has Revealed So Far

Prior genomic studies already show:

Strong phylogenetic signal across families and genera
Nested hierarchies exactly matching Darwinian predictions
Patterns of shared ancestry consistent with deep-time evolution
Gene families associated with diversification, such as:

Detoxification enzymes
Odour and taste receptors
Wing-patterning genes (e.g., WntA, optix, cortex)

The new 1,000-genome project expands this dramatically and will clarify:

Europe’s glacial-refugial history
The timing of radiations
Adaptive responses to climate and food plants
Patterns of gene duplication and loss
The genomic basis of mimicry, colouration, and ecological specialisation
Summary

European butterflies and moths are the outcome ofhundreds of millions of years of evolution, shaped by:

The rise of angiosperms
Climatic upheavals and glacial cycles
Plant–insect co-evolution
Hybridisation and range shifts
Recent human impacts

Their genomes not only preserve deep evolutionary history but also provide a powerful dataset for testing evolutionary theory itself — precisely the context this blog post is addressing.

The work of the Wellcome Sanger Institute scientists is summarised in this news article.

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 addressing agricultural pests.
A major milestone has been reached, with experts across Europe, including those at the Wellcome Sanger Institute in Cambridge, UK, sequencing 1,000 species of butterflies and moths. This includes almost all UK butterflies, opening the door to help understand and protect UK 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 (26 November) 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.

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 species^1.1. 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 and existing species, so they can be accurately monitored, and investigate the factors that might have led to new species or population decline. 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 65 per cent decrease in flying insects in the UK since 2021^2.1, understanding more about the evolution of resilient species could help inform and protect other species.

For example, there is a project in Czechia that is using reference genomes from Project Psyche as part of its biodiversity monitoring programme, showing the real-world impact of having reference genomes for these species.

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 unchanged^3.1.

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 the UK, butterfly reference genomes have been used to discover more about why the Black-veined White butterfly (Aporia crataegi) disappeared from Britain in the 1920s. 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^4.1.

The availability of high-quality reference genomes, provided by collaborative initiatives such as Project Psyche, makes modern genomics research possible beyond a handful of select species. In particular, examining genomic footprints of decline in eradicated or extinct species would just not be feasible without the availability of such reference genomes.

Dr Saad Arif, who led the research mentioned above on the Black-veined White butterfly at Oxford Brookes University.

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 Charlotte Wright, co-lead of Project Psyche at the Wellcome Sanger Institute.

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 is 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.

Dr Joana Meier, co-lead of Project Psyche at the Wellcome Sanger Institute.

It was only a few years ago that the first, draft butterfly and moth genomes were sequenced. The genomes now being produced for Project Psyche are of extraordinarily high quality and show how engaged researchers and new technologies are transforming our understanding of the natural world. Darwin would be pleased that his “endless forms” are receiving the attention they deserve.

Professor Mark Blaxter, co-lead of Project Psyche at the Wellcome Sanger Institute.

Publication:
Wright, Charlotte J.; Wahlberg, Niklas; Vila, Roger; et al
Project Psyche: reference genomes for all Lepidoptera in Europe
Trends in Ecology & Evolution (2025) DOI: 10.1016/j.tree.2025.10.007

Highlights
Lepidoptera are key to ecosystem functioning as herbivores, pollinators, and prey, and are important indicators of ecosystem health. They also include many species of economic and agricultural importance. Given the increasingly alarming decline of insects, understanding key challenges such as population fragmentation and factors explaining ecological resilience are urgently needed.

Building on other large-scale biodiversity sequencing initiatives under the Earth Biogenome Project umbrella, Project Psyche aims to generate unprecedented genomic resources for Lepidoptera.

The Project Psyche community encompasses diverse researchers, amateur lepidopterists, conservation practitioners, and industry experts united by a common vision of the importance of lepidopteran genomes.

With 1000 high-quality genomes already generated in a standardised manner, Project Psyche is fuelling diverse research areas, including comparative genomics, phylogenomics, conservation, molecular evolution, and population genomics.

Sequencing all 11 000 species will set a sound foundation for genomics and greatly foster monitoring of all Lepidoptera in Europe, empowering effective biodiversity management and policy, locally and globally.

Abstract
Project Psyche is a transnational initiative to generate and study chromosome-level reference genomes of all ~11 000 species of Lepidoptera (butterflies and moths) found in Europe. Here, we describe the decentralised network of collection and sequencing hubs that has enabled rapid progress, the standardised protocols for sampling and sequencing, and the collaborative framework for data analysis. With over 1000 species already sequenced, Lepidoptera are at the forefront of biodiversity genomics with the most reference genomes of any eukaryotic order. The completed pan-European catalogue of openly accessible lepidopteran genomes will transform our understanding of evolution and ecology, inform conservation, and foster advances in management of pests and invasive species. We highlight research areas that will benefit from this large-scale genome dataset.

Lepidoptera as a window into ecology and evolution
With ~160 000 described species [1], Lepidoptera encompass ~10% of all known eukaryotic species. This megadiversity is the product of more than 230 million years of evolution [2., 3., 4.], with numerous species central to many pivotal ecological functions, including herbivory and pollination. Lepidoptera include flagship species for conservation and the protection of entire ecosystems [5]. Some species are devastating agricultural, forestry, and textile pests [6,]. Their spectacular phenotypic diversity, intimate interactions with host plants and social insects, and cultural importance have fascinated researchers, hobbyists, and the public alike for centuries, making them ideal for citizen science and connecting society with nature and entomology. This long-term interest in butterflies and moths has made them one of the best-studied taxonomic orders. Consequently, we possess a detailed knowledge of their taxonomy, life history, distribution, demography, and ecology. The lepidopteran research community has been proactive in adopting genomics to understand the evolution and ecology of specific species, including the genetics of wing patterns [8], the impacts of climate change [9], and the biology of migration [10]. Coupled with citizen recordings and extensive long-term monitoring programs, genomes allow us to gain unique insights into the drivers of ever faster insect declines and ecosystem changes [11]. Moreover, many natural history collections, which encompass millions of Lepidoptera specimens, are now being catalogued [12], offering opportunities for integrating insights from museum collections with genomic studies.

Reference genomes are the foundation for all genomic studies. They unite microevolutionary (see Glossary) studies using short-read resequencing, RNA, or epigenetics data that are mapped to the reference genome, while providing connections to macroevolutionary studies via phylogenomics and comparative genomics. Generating chromosomally resolved, high-quality genomes from the outset, rather than producing a larger number of cheaper, low-quality genomes, provides broad, future-proof utility. Due to ongoing technological advances and decreasing sequencing costs, generating thousands of chromosome-level genomes is now feasible. Indeed, the Earth Biogenome Project (EBP) aims to generate reference genomes for all eukaryotic life on Earth [13]. This moonshot goal will be reached through the collaborative efforts of many biodiversity genomics initiatives. Here, we present Project Psyche, an ambitious trans-national project to generate chromosome-level reference genomes for all ~11 000 species of Lepidoptera occurring in Europe. The project was named after the Greek goddess of the soul, Psyche, depicted with butterfly wings, and after the ancient Greek word for butterfly itself. Project Psyche strives to make all reference genomes and analytic datasets openly available and easily accessible to all. Through a decentralised workflow for genome generation and analysis, together with early-career researcher training, Project Psyche promotes equity in biodiversity genomics.

Lepidopteran genomes are typically small (~500 Mb) and their holocentric chromosomes [14] lack large, often difficult-to-assemble localised centromeric regions [15]. These features facilitate a standardised, large-scale approach to genome assembly and analysis, enabling cross-species comparisons with minimised methodological biases. Project Psyche also benefits from the progress made by other large-scale biodiversity sequencing projects such as the Darwin Tree of Life (DToL) project [16] and the European Reference Genome Atlas (ERGA) [17], which have developed standardised, high-throughput methods for sequencing biodiversity.

Generating chromosome-level reference genomes across an entire, highly diverse order represents a paradigm change for biology. Reference genomes for all species of Lepidoptera in Europe will enable a deeper understanding of biodiversity through the exploration of general principles in evolution and ecology and allow pressing societal challenges to be addressed. Here, we highlight how Psyche genomes will deepen our understanding of the drivers of species and ecological diversification, genome and cobiont evolution, and the evolutionary basis of adaptation. We also discuss the potential of genomics for conservation and new solutions to societal problems. Accelerating research in these areas is timely given the pressing threats of global change and biodiversity loss.

Wright, Charlotte J.; Wahlberg, Niklas; Vila, Roger; et al
Project Psyche: reference genomes for all Lepidoptera in Europe
Trends in Ecology & Evolution (2025) DOI: 10.1016/j.tree.2025.10.007

Copyright: © 2025 The authors.
Published by Elsevier Ltd. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

The sequencing of 1,000 European butterflies and moths provides yet another large, independent dataset that makes sense only in the light of evolution. The patterns uncovered—nested hierarchies, shared genetic architecture, lineage-specific mutations, gene duplications and repurposing, and a branching family tree that maps cleanly onto ecological and geographical history—are precisely what Darwin and Wallace predicted more than 160 years ago on the basis of morphology alone. Genomics has simply filled in the detail, confirming their central insight with a precision they could never have imagined.

Nothing in these results suggests discrete acts of special creation or fixed, unrelated “kinds”. Instead, every genome reveals descent with modification operating over deep time. The signals of common ancestry are so pervasive and so internally consistent that they provide one of the most comprehensive validations of the theory of evolution available in modern biology.

Crucially, this research is not merely compatible with evolutionary theory—it depends on it. Comparative genomics, phylogenetic reconstruction, molecular clocks, gene-family evolution, population structure, and the interpretation of adaptive change all assume the framework Darwin and Wallace established. Without the theory of evolution, the data would be an unintelligible jumble. With it, the relationships between these 1,000 species become entirely coherent, predictable and scientifically productive.

Far from biologists “abandoning” evolution, as creationists like to imagine, the field has never been more deeply rooted in it. The more data we gather—from butterflies and moths to mammals, plants and microbes—the clearer the picture becomes. Evolution remains the unifying foundation of modern biology, and these genomes provide yet another demonstration that the natural world fits Darwin’s and Wallace’s explanation perfectly, while offering no support whatsoever for the creationist alternative.

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