Rosa Rubicondior: Refuting Creationism - Evolving Butterfies Are Unkind To Creationists

Remapping the evolutionary tree of butterflies
A recent piece of research raises insurmountable problems for creationists trying to fit their definition of 'kind' into the real world of living organisms.

We often assume that closely related species look different from one another because visual cues are crucial for mate recognition. In many animals, especially birds, these differences help prevent interbreeding by acting as barriers to hybridisation. This makes particular sense in birds, where genetic architecture is unusually stable — chromosome numbers and gene mappings remain remarkably consistent — so, in theory, many closely related bird species could interbreed if not for the evolution of distinct plumage or mating displays. These are known as prezygotic barriers because they inhibit the formation of hybrid zygotes.

Given this, we might expect the same to apply to other vividly coloured groups like butterflies. But evolution doesn’t follow a single rulebook — it uses whatever tools are available. While visual cues are often important, other senses can also serve to maintain species boundaries. One of the most powerful is the sense of smell, particularly the use of pheromones.

Pheromones are widespread in the natural world, especially among insects. They’re used for everything from attracting mates to triggering mating behaviours. Some male moths, for instance, can detect a female’s pheromones from over a mile away and home in on her with astonishing precision — guided like a missile by the chemical trail.

Now, an international team of researchers has discovered that what was long thought to be a single species of glass-wing butterfly is actually a complex of six genetically distinct species. These butterflies all look nearly identical, thanks to strong selection pressure for Batesian and Müllerian mimicry — many are toxic, and they gain protection by resembling one another. Visual differences would reduce this shared advantage, so selection favours similarity, not distinction. But predators can't detect pheromones — so these butterflies have evolved subtle chemical differences instead, using scent as a hidden cue to prevent hybridisation.

Along with this chemical divergence, the researchers found significant genomic differences between the species, including striking variation in chromosome numbers — from just 13 to as many as 28. The team also discovered that the arrangement of the genes on the chromosomes is very volatile, so, different closely related species can have very different chromosomal arrangements, increasing the pressure for barriers to hybridization to evolve and allowing a species to rapidly radiate into new ecological niches.

So, the question for creationists is, how does this fit in with the definition of 'kinds' required for the Bible-literalist interpretation of taxonomy?

This fascinating study was conducted by a team including scientists from the Wellcome Sanger Institute, Universidad Regional Amazónica Ikiam in Ecuador, Universidade Estadual de Campinas in Brazil, the University of Cambridge, and others. Their findings are detailed in a paper published in Proceedings of the National Academy of Sciences, and summarised in a news release from the Wellcome Sanger Institute.

Background^ Glass-Wing Butterflies (Ithomiini). Family: Nymphalidae, subfamily: Danainae, tribe: Ithomiini:

Evolution and Taxonomy
Glass-wing butterflies belong to the tribe Ithomiini, within the subfamily Danainae (family Nymphalidae). This tribe comprises over 370 known species across roughly 50 genera. They are part of a broader group of brush-footed butterflies (Nymphalidae) and are most closely related to the milkweed butterflies (like the monarch).

The glassy transparency of their wings, caused by reduced scale density and specialised nanostructures, is a striking evolutionary adaptation. It likely evolved as part of their aposematic (warning) mimicry strategy, allowing subtle visibility while still resembling other toxic or unpalatable butterflies in their habitat. Many species are chemically defended, often by accumulating toxic alkaloids from host plants.

Ithomiines are also a textbook example of adaptive radiation in the Neotropics. Molecular phylogenetics suggests they began diversifying around 20–30 million years ago in South America, following the uplift of the Andes and the expansion of tropical forests.

Distribution
Glass-wing butterflies are endemic to the Neotropics, with their range extending from Mexico to southern Brazil and northern Argentina. The greatest diversity is found in the Amazon Basin and Andean foothills, where complex ecosystems and diverse microhabitats have driven their speciation.

They tend to inhabit humid, shaded forests, especially cloud forests and tropical lowlands, often flying slowly and staying close to the understorey. Their life cycles are closely tied to host plants in the Solanaceae (nightshade) family, from which they acquire both nutrition and chemical defences.

Mimicry Complexes
Glass-wing butterflies participate in Müllerian mimicry rings, where multiple toxic species evolve to share similar warning patterns, reinforcing predator learning. However, some also engage in Batesian mimicry, where non-toxic species mimic toxic ones. The tension between these mimicry systems and reproductive isolation pressures (like pheromones) plays a key role in their evolutionary dynamics.

The Creationist ‘Unkind’ Conundrum.

In creationist thinking, all six of these glass-wing butterflies—despite having very different genomes, chromosome counts ranging from 13 to 28, and being unable to interbreed—are lumped together as the same “kind”.

Meanwhile, humans and chimpanzees, whose genomes are about **98–99% identical** and who differ by only one chromosome pair, are declared to be entirely separate “kinds”.

The rule? There is no rule. “Kind” isn’t a biological category — it’s an elastic, made-up label, applied wherever it helps to defend a pre-determined conclusion.

Remapping the evolutionary tree of butterflies
A large international team has genetically mapped glasswing butterflies found across Central and South America, rewriting the evolutionary tree and highlighting six new species.
The team includes experts at the Wellcome Sanger Institute, Universidad Regional Amazónica Ikiam in Ecuador, Universidade Estadual de Campinas in Brazil, the University of Cambridge, and others.

The research, published today (28 July) in the Proceedings of the National Academy of Sciences (PNAS), starts to uncover new insights about these butterflies as well as factors involved in the rapid diversification of species and why some species are more capable of this. The findings help experts to understand more about how life has evolved until now and possibly suggest how it might change in the future.

For example, researchers found that in glasswing butterflies, even the most closely related species produce different pheromones, indicating that they can smell others of the same species. Given that all of these butterflies look the same to train birds that they are all toxic, this allows the butterflies to find a compatible mate.

By untangling the taxonomy of these butterflies, the team provides answers to questions that have remained unknown for at least 150 years. The researchers also present ten freely available reference genomes that can help to monitor and maintain insect populations in some of the most biodiverse areas of the world.

Butterflies are used in conservation as an indicator species, meaning they are used to track and monitor the levels of biodiversity and other insects in an area.

Glasswing (Ithomiine) butterflies are found across Central and South America and make up a substantial part of the butterfly species found there, making them good indicators of biodiversity in incredibly biodiverse areas, like the Amazon rainforest.

However, there are over 400 species of glasswing butterfly, and all species in an area look incredibly similar to discourage birds from eating them, with colouring that implies they are toxic.

Additionally, glasswing butterflies can undergo rapid radiation, where many new species arise from the same ancestor in a short period of time. As they are very closely related, it makes it difficult to visually identify and track the different species of butterflies.

To genetically untangle these butterflies, an international team including Sanger Institute scientists sequenced the genomes of almost all species of two particularly fast radiations of glasswing butterflies to remap their evolutionary trees. Of those species, 10 were sequenced to the gold standard of “reference quality” genomes that are freely available to the research community.

By genetically mapping these butterflies, the team highlighted that six subspecies were more genetically distinct than previously thought, leading to them being classified as new individual species. Also, understanding the species from a genomic perspective enables experts to highlight any visual differences that could be used to identify and track the different species, now that they are confirmed as genetically distinct.

The team also investigated if the genomes held clues as to why these butterflies had so many species, and what allowed them to develop so quickly. While most butterflies have 31 chromosomes, they found that in these glasswing butterflies, the number of chromosomes varies a lot, ranging between 13 and 28. While they have largely the same genes, these genes are packaged into chromosomes in different ways in each species, a process known as chromosomal rearrangement.

These chromosomal rearrangements have knock-on effects when it comes to mating. In order to reproduce, butterflies must produce eggs and sperm, but this relies on the butterfly’s chromosomes lining up. This means that if two butterflies with different chromosomal rearrangements mated, their offspring would be sterile because they would be unable to produce sperm or eggs. As a result, the butterflies have evolved a new mechanism using pheromones to detect potential mates with a chromosome arrangement that matches their own and therefore avoid producing sterile offspring.

The researchers suggest that the high level of chromosomal rearrangement in these butterflies is key to their ability to rapidly form new species, as once a population changes its chromosome number and thus forms its own species, it can more quickly adapt to different altitudes or host plants. Why they have such high levels of rearrangements remains a mystery and is something the scientists are working to uncover.

Understanding rapid radiation in insects could have implications for conservation research, understanding how species adapt to climate change, as well as possible implications for agriculture and pest control.

Glasswing butterflies are an incredibly adaptive group of insects that have been valuable in ecology research for around 150 years. However, until now, there was no genetic resource that allowed us to robustly identify different species, and it is difficult to monitor and track something that you can’t identify easily. With this new genetically informed evolutionary tree, and multiple new reference genomes, we hope that it will be possible to advance biodiversity and conservation research around the world, and help protect the butterflies and other insects that are crucial to many of Earth’s ecosystems.

Dr Eva van der Heijden, first author
Wellcome Sanger Institute and the University of Cambridge.

Having the reference genomes for the two groups of glasswing butterflies, Mechanitis and Melinaea, allowed us to take a closer look at how they have adapted to life in such close proximity to their relatives. These butterflies share the responsibility of warding off predators by displaying similar colour patterns, and by producing different pheromones they can successfully find mates and reproduce. Now that we have clarity on glasswing butterfly species, we can look for specific markings or differences between them, giving new ways to track them during fieldwork.

Dr Caroline Bacquet, co-senior author
Universidad Regional Amazónica Ikiam
Ecuador.

We are in the middle of an extinction crisis and understanding how new species evolve, and evolve quickly in some cases, is important for preserving species. Comparing butterflies that rapidly form new species to others that do not could benchmark how common this is in insects and highlight the factors involved. This, in turn, could identify any species that require closer conservation and possibly identify genes that are important in the adaptation process and might have uses in agriculture, medicine, or bioengineering. This research would not have been possible without global collaboration. We have one planet, and we must work together to understand and protect it.

Dr Joana Meier, co-senior author
Wellcome Sanger Institute

More information
This study was made possible by a large international collaboration. As well as those already mentioned, this work included researchers at Harvard University, USA, the Federal University of Pernambuco, Brazil, Technische Universität Braunschweig, Germany, the University of York, the University of Bristol, Université de Guyane, France, Universidad Nacional Mayor de San Marcos, Lima, Peru, Smithsonian Tropical Research Institute, Panama, University of Florida, USA, and Université des Antilles, Paris, France. A full list of contributors and affiliations can be found in the publication.

Publication:
E. van der Heijden, K. Näsvall, F. Seixas, et al. (2025)
Genomics of Neotropical biodiversity indicators: two butterfly radiations with rampant chromosomal rearrangements and hybridisation. PNAS 122(31) e2410939122 DOI: 10.1073/pnas.2410939122.

Significance
Understanding factors contributing to rapid speciation is a key aim of evolutionary biology. Here, we focus on two rapid radiations of Neotropical butterflies. Our genomic data with broad taxonomic and geographic coverage reveal widespread hybridization and rampant chromosomal rearrangements, each likely contributing to the high diversification rates. Our study highlights the use of genomic data to resolve taxonomically challenging species groups and elucidate drivers of diversification in rapid radiations. We show that for biodiversity hotspots with recent radiations, barcoding is insufficient to characterize species richness due to gene flow and recent speciation. The consideration of introgression and karyotype diversity underlying the dynamical species boundaries stimulates process-oriented taxonomic practice, which has important implications for monitoring and managing biodiversity in vulnerable habitats.

Abstract
A central question in evolutionary biology is what drives the diversification of lineages. Rapid, recent radiations are ideal systems for this question because they still show key morphological and ecological adaptations associated with speciation. While most research on recent radiations focuses on those occurring in insular environments, less attention has been given to continental radiations with complex species interactions. Here, we study the drivers of continental radiations of Melinaea and Mechanitis butterflies (Nymphalidae: Ithomiini), which have rapidly radiated in the continental Neotropics. They are classical models for Amazonian biogeography and color pattern mimicry and have been proposed as biodiversity indicators. We generated reference genomes for five species of each genus and whole-genome resequencing data of most species and subspecies covering a wide geographic range to assess phylogeographic relationships, hybridization patterns, and chromosomal rearrangements. Our data help resolve the classification of these taxonomically challenging butterflies and reveal very high diversification rates. We find rampant evidence of historical hybridization and putative hybrid species in both radiations, which may have facilitated their rapid diversification by enriching the genetic diversity. Moreover, we identified dozens of chromosomal fusions and fissions between congeneric species that have likely expedited reproductive isolation. We conclude that interactions between geography, hybridization and chromosomal rearrangements have contributed to these rapid radiations in the highly diverse Neotropical region. We hypothesize that rapid radiations may be spurred if repeated periods of geographic isolation are combined with lineage-specific rapid accumulation of incompatibilities, followed by secondary contact with some gene exchange.

Rapid radiations, where a lineage diversifies into many different species over a short time period, are ideal systems for studying how new species evolve (1, 2). They can be driven both by nonadaptive processes, such as the accumulation of differences during periods of allopatry leading to incompatibilities upon secondary contact, and by adaptive processes such as adaptation to different ecological niches or sexual selection for different traits and preferences (3, 4). Sympatric radiations require some degree of niche differentiation among the species for stable coexistence and sufficient reproductive isolation such that incipient lineages do not merge (2). While most lineages do not readily radiate even in the face of ecological opportunity, some are particularly prone to rapid radiations and do so repeatedly. We are only starting to understand the factors explaining these lineage-specific differences (5). Most knowledge stems from well-studied radiations that evolved in insular environments with little competition with other species and a relatively simple and geographically limited environment (e.g., Darwin’s finches on the Galapagos Islands, cichlid fishes in lakes or Hawaiian silverswords) (2, 6). However, many rapid radiations evolved on the more complex continents (7–9), and much less is known about drivers underlying their diversification. Reduced competition in insular environments allows niche specialization without being immediately outcompeted when a lineage is not yet well-adapted to its environment. However, competition can be strong in large continental areas such as the hyperdiverse Neotropics, potentially limiting (gradual) ecological speciation. The large and complex environments on continents may provide more opportunity for allopatric or parapatric divergence than small islands. The speed of accumulating incompatibilities in geographic separation may thus be particularly important in rapid radiations on continents.

Here, we study the drivers of diversification in two rapid continental radiations of the Neotropical butterfly tribe Ithomiini. Ithomiine butterflies (Nymphalidae: Danainae, ca. 400 species in 42 genera) are found across Central and South America (10, 11). They constitute a substantial part of the butterfly species assemblage and are regarded as good indicators of spatial patterns of biodiversity in the Neotropics, the most biodiverse area in the world (10, 12, 13). Sequestration of pyrrolizidine alkaloids from Asteraceae and Boraginaceae plants renders most Ithomiini unpalatable (14–18), and their color patterns advertise this unpalatability to predators. They form Müllerian mimicry rings, where locally co-occurring species converge in color patterns, thus sharing the cost of predator education (10, 19, 20). We focus on two ithomiine genera, Melinaea and Mechanitis, which have diversified fast, with most species younger than a million years (11, 21). The study of these radiations has been hampered by taxonomic challenges. Melinaea and Mechanitis are among the most taxonomically difficult of Ithomiini, as Fox noted (22): “these insects [are] so thoroughly confusing and so thoroughly confused by my predecessors.” The species do not differ in genital or other morphological characteristics and show substantial intraspecific wing pattern variation and mimicry between species. Barcoding does not reliably distinguish species either (23, 24). As prior studies have only used few or no genetic markers or did not have broad geographic coverage, the taxonomy is still partially unresolved, despite many taxonomic revisions (e.g., refs. 22 and 24–28).

While the exact causes of their rapid radiations are unknown, different contributing factors have been proposed. Ecological adaptation may be relevant as species show differences in microhabitats, host plants, mimicry rings, and altitude, but on the other hand, many species share habitats and host plants, and most species occur in the lowlands (25, 29–32). Ithomiine species also differ in male-specific androconial compounds (chemical compounds secreted from specialized wing scales where the fore- and hindwings overlap), which likely act as pheromones (33–35). As coexisting ithomiine species converge in color patterns, assortative mating likely relies strongly on chemical cues.

Allopatric accumulation of differences could also have played a role in the rapid diversification of Ithomiini, as this could have occurred in different rainforest refugia during climatic oscillations e.g., in the Pleistocene (26, 36), but see refs. 37 and 38) or on opposite sides of geographic barriers such as the Andes. Both climatic refugia and the Andes have been proposed as “speciation pumps” in the Neotropics (39), also for Ithomiini (40), where periods of allopatry followed by secondary contact create favorable circumstances for speciation.

Another factor that might contribute to the diversification of ithomiine butterflies is hybridization. Phylogenetic studies using a limited number of markers have revealed mito-nuclear discordances and paraphyletic taxa in Ithomiini (23, 38). This could be due to limited geographic or genetic resolution, incomplete lineage sorting (ILS) in the rapidly speciating lineages, or introgressive hybridization. While gene flow between sister lineages can homogenize gene pools, opposing speciation, recent studies have shown that sometimes introgressive hybridization from more distant relatives can facilitate rapid diversification by enriching the genetic diversity with novel, potentially adaptive variants or contributing to the origin of new hybrid species (41–45). Admixture has been shown to kickstart adaptive radiation (e.g., refs. 46 and 47), facilitate parallel adaptation (e.g., refs. 44 and 48), and novel adaptations (e.g., ref. 49), but the role in ithomiine diversification is hitherto unknown.

Ithomiine butterflies exhibit extensive chromosome number variation (50), which could also contribute to their rapid diversification. Offspring from parents with different karyotypes may suffer reduced fitness due to mismatch in pairing of homologous chromosomes that results in aneuploidy, meiotic failure, or hybrid sterility (51, 52). Furthermore, chromosomal rearrangements might facilitate divergence in the face of gene flow by reducing recombination, promoting the accumulation of incompatibilities (53) or linking together coadapted variants (54, 55). In Melinaea and Mechanitis butterflies, chromosome counts range from 13 to 30 (50). Chromosomal rearrangements likely contribute to reproductive isolation, as a cross between two closely related Melinaea species with different karyotypes resulted in nearly sterile hybrids (56). However, pervasive intraspecific variation in chromosome counts (50, 56) indicates that not all rearrangements reduce fitness and their role in speciation thus remains an open question.

Here, we generate 10 reference genomes and whole-genome resequencing data of almost all species and many subspecies across their geographic range to resolve taxonomic uncertainties and explore whether geography, introgressive hybridization, or chromosomal rearrangements may have played a role in the rapid diversification of Mechanitis and Melinaea butterflies.

E. van der Heijden, K. Näsvall, F. Seixas, et al. (2025)
Genomics of Neotropical biodiversity indicators: two butterfly radiations with rampant chromosomal rearrangements and hybridisation. PNAS 122(31) e2410939122 DOI: 10.1073/pnas.2410939122.

Copyright: © 2025 The authors.
Published by the National Academy of Sciences of the USA. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

For anyone familiar with evolutionary biology, this discovery makes perfect sense: a population once thought to be a single species has, over time, split into several, each reproductively isolated by subtle changes in chemical signalling. But for creationists—if they understood the subject—it’s an awkward fact that doesn’t fit neatly into their pre-packaged narrative.

First, the glass-wing butterflies illustrate speciation in action. Six distinct species have evolved from a common ancestor, not through some mysterious leap, but via small, testable, and measurable changes—in this case, differences in pheromones reinforced by genetic divergence. The very existence of these separate species within what creationists might call a “kind” shows that living populations are not fixed, immutable entities, but dynamic and changeable. Creationists often insist that “microevolution” can’t lead to “macroevolution”, but the line between them is entirely arbitrary. Here, the same processes they grudgingly accept — variation, selection, reproductive isolation — have produced entirely new, genetically distinct species with major chromosomal differences.

And this brings us to the unanswerable creationist problem: how do you decide what counts as a “kind”? Creationist taxonomies lump all six of these butterflies into the same “kind” despite their widely different genomes, chromosome counts, and inability to interbreed. Yet, in the same breath, they insist that humans and chimpanzees are separate “kinds” — even though our genomes are far more similar to one another than those of these butterflies. In other words, “kind” is not a scientific category at all, but a fluid, ad hoc label applied wherever it’s convenient for the argument.

Secondly, the butterflies’ evolutionary path shows how multiple selective pressures can shape species in ways that are *not* designed for some abstract “purpose”, but are compromises between competing demands. These species evolved to maintain identical warning colours for predator deterrence, while simultaneously developing invisible chemical cues to maintain reproductive boundaries. That’s exactly the sort of messy, contingent outcome evolution predicts—and exactly what an “intelligent designer” would have no reason to produce.

Finally, the genetic evidence is inescapable. These six species are not merely behaving differently; their genomes bear the signatures of long-term divergence, including major chromosome rearrangements. This is precisely the kind of molecular, structural, and behavioural integration that evolutionary theory explains, and creationism cannot. A creationist can deny fossils, but they can’t wish away DNA that tells a clear, step-by-step history of descent with modification.

In short, these glass-wing butterflies are living, flying examples of evolution’s creativity—unmistakable products of natural processes acting over time. They are also an unintentional but potent rebuttal to the idea that species were created as they are and have remained unchanged ever since.

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