Latent gene network expression underlies partial re-evolution of a polyphenic trait in the worker caste of ants

The re-emergence of traits lost over evolutionary time has long fascinated biologists and sparked debate. Yet we still do not fully understand the developmental and evolutionary mechanisms that allow lost traits to reappear. This question is particularly relevant in species that exhibit polyphenism – the ability of the same genome to produce different forms in response to environmental signals.

Ants are a striking example of polyphenism in action. Within a single colony, the same genome can produce morphologically distinct queens, males and workers. One of the most remarkable polyphenic traits is the presence of ocelli, three simple light-sensing eyes on the top of the head. Queens and males consistently possess ocelli, but in workers they have been repeatedly lost and gained during evolution. Across different species, workers may have one, two or all three ocelli, suggesting that the trait has evolved independently multiple times.

This remarkable evolutionary flexibility led Vasquez-Correa et al. to propose that the developmental programme for forming ocelli remains dormant in workers, making it easier for the trait to reappear. To test this idea, the researchers reconstructed the evolutionary history of worker ocelli across the hyperdiverse ant subfamily Formicinae.

Their ancestral state reconstruction revealed a single evolutionary gain of worker ocelli, followed by multiple losses and independent reappearances. To understand how this repeated re-evolution occurred, the researchers examined ant head development, focusing on the eye-antennal disc. This tissue gives rise to the eyes, antennae, ocelli and head capsule.

Using hybridization chain reaction, a technique that visualizes gene activity in fixed tissues, they tracked the expression of genes involved in ocellus development throughout development. Remarkably, even in workers that lacked ocelli, key developmental genes were briefly active, suggesting that the underlying gene regulatory network remained intact. This retained developmental programme appears to have enabled the repeated evolution of ocelli in Formicinae workers and soldiers.

Polyphenism is widespread in nature, occurring at many levels of biological organization, from individual cells to complex societies. The findings of Vasquez-Correa et al. suggest that dormant developmental programmes may commonly persist after traits are lost, providing hidden evolutionary potential. If similar latent gene activity exists in other organisms, it could help explain how lost traits repeatedly re-evolve in new forms, offering fresh insights into the origins of evolutionary novelty.

Polyphenism is a form of developmental plasticity where alternative phenotypes develop from a single genome in response to environmental cues (Nijhout, 2003). It is a phylogenetically widespread feature of plants and animals that has evolved at different levels of biological organization (Hanna et al., 2024; West-Eberhard, 1989; West-Eberhard, 2003). For example, at the population level, the mouth form polyphenism in nematode worms produces alternative big tooth (omnivorous) or small tooth (bactivorous) mouth forms that develop in response to pheromones, crowding, salt concentration, temperature, and culturing substrate (Bento et al., 2010; Bose et al., 2012; Ragsdale et al., 2013; Werner et al., 2018). At the colony-level, caste polyphenism in eusocial insects produces morphologically differentiated queen and worker castes that develop in response to temperature and nutrition (Chandra et al., 2018; Evans and Wheeler, 2001; Korb, 2025; Rajakumar et al., 2024). And finally, at the cellular-level, polyphenism occurs within a multicellular individual, where a single genome gives rise to differentiated cell-types during development, such as between germline and somatic cells, in response to internal cues like morphogen gradients (Brunet and King, 2017; Davison and Michod, 2021; Devlin et al., 2023). Polyphenism has been proposed to promote, at the macroevolutionary scale, phenotypic diversification through the gain, loss, and re-evolution of alternative phenotypes (West-Eberhard, 2003). This is based on the idea that, once a polyphenic trait originates, one of the alternative morphs retains the capacity to produce the trait in the genome while the other is freer to evolve. This hypothesis has received support from a comparative study of mouth form polyphenism across 90 species of nematode worms showing a phylogenetic association between the gain and loss of alternative mouth form phenotypes and the phenotypic diversification of mouth parts (Susoy et al., 2015). Another supporting example is fat synthesis in parasitic wasps, which revealed an association between developmental plasticity and the loss and subsequent re-evolution of fat synthesis in one species (Peters et al., 2017; Visser et al., 2010; Visser et al., 2021). Yet, the underlying developmental and genetic processes facilitating the gain, loss, and re-evolution of polyphenic traits remain poorly understood. (Forni et al., 2026; Sommer, 2020; West-Eberhard, 2003).

Here, we address this question by focusing on caste polyphenism in the eusocial colonies of ants, which consists of a morphological division of labor between a winged reproductive queen caste and wingless non-reproductive worker caste in almost all 16,962 valid described ant species (AntWeb, 2026; Ward, 2014). The differential expression of polyphenic traits, such as wings, that develop in queens but not workers, are called ‘caste-specific’ traits (Miura, 2005). It has been shown that polyphenic traits, including caste polyphenism in ants, are produced during development by the differential expression of highly conserved gene regulatory networks (GRN) in response to environmental cues (Abouheif and Wray, 2002; Béhague et al., 2018; Casasa et al., 2021; Davidson et al., 2023; Lenuzzi et al., 2023; Rajakumar et al., 2024; Vizueta et al., 2025). However, how the expression of these GRNs influences the evolution of caste-specific traits in ants remains unknown.

Here we focus on the ocelli, which are three small single-lens eyes on the dorsal head of most flying insects. Ocelli complement the function of the compound eyes by mediating orientation using polarized light and in the synchronization of daily activity (Buschbeck and Bok, 2023; Krapp, 2009). We investigate the evolution of ocelli in a hyperdiverse subfamily of ants (Formicinae), where they are universally present in the winged reproductive caste (queens and males) as three large ocelli that aid in mating flights and dispersal (Moser et al., 2004; Narendra et al., 2016). In contrast, ocelli in the wingless worker caste are evolutionarily labile, showing dramatic variation across species in the presence/absence or number of ocelli in the worker caste (Johnson and Rutowski, 2022; Narendra et al., 2016; Narendra and Ribi, 2017; Schwarz et al., 2011; Figure 1A). In some species, adult workers completely lack ocelli, such as in Camponotus floridanus, while in others they are present and vary in number–there are species whose adult workers have all three ocelli or just one single ocellus, and these can be present in all or in only a subset of workers (Figure 1A). For example, workers in Cataglyphis bicolor have all three ocelli, which function in light sensing and navigation, acting as a celestial compass that provides crucial directional information (Fent and Wehner, 1985; Figure 1A). In contrast, all workers of Polyrachis bihamata have just a single medial ocellus (Hung, 1967; Figure 1A), and in workers of Dinomyrmex gigas, a single medial ocellus evolved only in a subset of individuals in the worker caste called ‘soldiers’ (or major workers) with large heads, but are absent in other individuals called ‘minor workers’ with small heads (AntWeb, 2026; Figure 1A). How this dramatic variation in ocelli in the worker caste of formicine ants has evolved remains poorly understood.

Figure 1

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This evolutionary lability of ocelli across the worker castes of formicine ants also provides an opportunity to understand how the GRN underlying development of ocelli influenced the evolution of this caste-specific trait. Ants are holometabolous insects, in which adult body parts develop from imaginal discs, semi-independent clusters of cells in the larvae (Held, 2002; Koch and Abouheif, 2019). In the fruit fly D. melanogaster, ocelli develop from the eye-antenna imaginal disc located at the ventral region of the head capsule. The eye-antenna imaginal disc also gives rise to the head capsule, eye, antenna, and maxillary palps (Held, 2002). D. melanogaster is the only insect where the GRN underlying ocelli development has been well characterized at the third larval stage (Blanco et al., 2009; Domínguez-Cejudo and Casares, 2015; Sabat et al., 2017; Figure 1B). The gene orthodenticle (otd; formerly known as ocelli-less) is a selector gene that is necessary for specifying the ocellar region in the developing head capsule. otd expression in the ocellar domain, together with other genes like hedgehog (hh), initiates the development of the ocellar region and the three ocelli (two lateral ocelli and one medial ocellus) in the eye-antennal disc. The activation of these genes regulates the expression of downstream genes, such as otd regulating the expression of defective proventriculus (dve; Blanco et al., 2009; Jean-Guillaume and Kumar, 2022; Yorimitsu et al., 2011), whereas hedgehog (hh) activates a portion of the retinal determination network, such as eyes absent (eya), twin of eyeless (toy), sine oculis (so), and atonal (ato). These retinal determination genes have been shown to be regulated by independent regulatory enhancers from the compound eye (Blanco et al., 2009; Blanco et al., 2010; Jean-Guillaume and Kumar, 2022; Figure 1B). Because the eye-antennae disc and the ocelli GRN have only been well characterized in D. melanogaster, it remains unknown whether they are conserved in ants.

To understand how the GRN underlying ocelli development may have influenced the evolution of this caste-specific trait, we first inferred the evolutionary history of ocelli in adult workers across the Formicinae using ancestral state reconstruction. We then characterized the eye-antennae disc in ants using three genes, eyeless (ey), distal-less (dll), and otd-1, which are known to mark the eyes (ey), the antenna (dll), and the head capsule and ocelli (otd-1). This characterization allowed us to investigate the expression of five key genes in the ocelli GRN, otd-1, hh, toy, eya, and so, during development of the winged and wingless castes across two formicine species.

Our developmental and evolutionary data provide evidence that the latent expression of genes in workers lacking ocelli as adults is part of a latently expressed ocelli GRN, which likely facilitated at least three independent evolutionary reversions of this trait in the worker caste of species within the Camponotini clade. The latent expression patterns of genes in the ocelli region of developing workers lacking ocelli as adults are the same as in males that will develop fully functional ocelli but are only interrupted late in larval development. Furthermore, the timing and pattern of these late interruptions coincide with the degree of development of rudimentary ocelli in minor worker and soldier pupae before they disappear in adults (Figure 7). This indicates that, although the expression of these genes is latent, they still retain the capacity to produce rudimentary ocelli in the pupal stage before they disappear in adults. And finally, although eya, toy, and so, are part of both the ocelli and compound eye GRNs in Drosophila, the ocelli GRN has its own distinct identity and the genes within this GRN have distinct regulatory elements and are selectively regulated (Jean-Guillaume and Kumar, 2022; Zimmerman et al., 2000). In ants, our data show that the selector gene for compound eye development in insects (eyeless / Pax-6) is expressed in the compound eyes and not ocelli, and the selector gene for ocelli (otd-1) is expressed in the ocelli and not compound eyes. We further show that the latent expression of toy, eye, and so are downregulated or absent in the ocellar region, but at the same time, are strongly. expressed in the regions of the compound eyes. Therefore, the mutually exclusive expression of the selector genes eyeless / Pax-6 in the compound eyes and otd-1 in ocelli suggests that, like in Drosophila, the compound eye and ocelli GRNs have distinct identities, ultimately leading to differential expression of downstream genes and production of different cell types; compound eyes are produced from multiple imaging-forming facets, while ocelli are produced from a single lens (Buschbeck and Bok, 2023; Jean-Guillaume and Kumar, 2022; Mishra et al., 2021). Altogether, our data show that the expression of these genes in workers lacking ocelli as adults is part of a latently expressed ocelli GRN.

Several hypotheses may explain how the ocelli GRN came to be latently expressed and maintained in developing workers that lack ocelli as adults. Perhaps the most simplistic hypothesis proposes that the presence of functional ocelli in adult queen and male castes maintains the ocelli GRN intact in the genome by keeping it under positive natural selection. This hypothesis assumes that this, as a side consequence, leads to expression of the ocelli GRN in the worker castes lacking ocelli. However, caste determination between queens and workers occurs through the action of a developmental threshold or switch, where a continuous environmental cue is translated into discrete phenotypic outcomes (Abouheif, 2021; MacMillan et al., 2025; Qiu et al., 2022; Rajakumar et al., 2024; Schultner et al., 2023). Once caste determination has occurred, the genome is expressed differentially during the developmental trajectories of queens and workers (Abouheif, 2021; Abouheif and Wray, 2002; Barkdull and Moreau, 2023; Béhague et al., 2018; Chandra et al., 2018; Khila and Abouheif, 2010; Qiu et al., 2022; Vizueta et al., 2025). These trajectories are decoupled, and consequently, can evolve largely independently (Abouheif, 2021; Powell et al., 2020; Vong et al., 2025). The dramatic variation in the number, size, and presence/absence of ocelli in worker castes across the Formicinae (see Figure 1) supports the largely independent evolution of ocelli in workers from those in queens, which always develop three ocelli. Furthermore, we observe similar patterns of variation in the wings and ovaries between queen and worker castes across ant species (Cronin et al., 2013; Khila and Abouheif, 2010; Monnin and Peeters, 2008; Rajakumar et al., 2018; Rajakumar et al., 2012). Therefore, while the presence of ocelli in males and queens maintains the ocelli GRN in the genome and creates a potential for expression of this GRN in developing workers lacking ocelli, this cannot solely explain how this latent expression became actualized (released and fixed) and what maintained it over millions of years.

One hypothesis for how this ocelli GRN became latently expressed and has been maintained in workers lacking ocelli is pleiotropy, which potentially results from the multiple roles that genes within the ocelli GRN play within the same imaginal disc (the eye-antennal disc). For instance, otd-1 and hh also determine the regional identity of the head capsule, while hh, toy, eya, and so also play key roles in compound eye development in specifying structures such as optic lobes, cone differentiation, and rhabdomeres development (Blanco et al., 2009; Domínguez-Cejudo and Casares, 2015; Jean-Guillaume and Kumar, 2022). Another example is the highly conserved developmental regulatory gene sonic hedgehog (shh), which plays a key role in limb development across animals. The vestigialization of hindlimbs in snakes and therefore the re-evolution of hindlimbs in extinct species across the phylogeny of the group is thought to be maintained during development through pleiotropic enhancers that drive shh expression. This means that the same enhancer (ZRS) that drives shh expression in the external genitalia also drives it (pleiotropically) in the developing limb region of snakes (Leal and Cohn, 2018). Future studies should attempt to explore whether expression of these conserved genes in multiple regions of the eye-antennal disc is driven by shared enhancers. Alternatively, we cannot rule out the hypothesis that the ocelli GRN has been co-opted to play a novel, yet currently unknown, function during worker larval development. Recent discoveries on the evolution of the wing GRN in ants provide support for this hypothesis. The wings, another nearly universal caste-specific trait in ants, develop in the reproductive male and queen caste, but are halted in the worker caste in response to environmental cues (Abouheif and Wray, 2002). The wing GRN is also found to be latently expressed in the wingless worker caste of ants and was thought to be functionless (Abouheif and Wray, 2002). However, it was recently discovered that the latent expression of this wing GRN in wingless worker caste acquired a novel function to generate big-headed soldiers in the hyperdiverse ant genus Pheidole (Rajakumar et al., 2018; Rajakumar et al., 2012).

Finally, our inference that this latent expression of the ocelli GRN in workers facilitated the partial reversion to a single medial ocellus is supported by: (1) the close phylogenetic relationship between species that lack ocelli in adult workers but retain a latent expression of the ocelli GRN (C. floridanus and P. rastellata), and those that underwent a partial phylogenetic reversion to a single medial ocellus (C. gibbinotus, D. gigas, and P. bihamata); (2) the presence of a developmental capacity or potential of the latent ocelli GRN expression to produce rudimentary ocelli in the pupal stage of C. floridanus workers that completely lack ocelli as adults; (3) the ability to experimentally induce only one, only two, or all three ocelli in similarly sized adult workers that normally lack them by applying high doses of Juvenile Hormone (JH) to worker-destined larvae in the ant Monomorium pharaonis (Li et al., 2024); and finally (4) in nature, the rare induction of a single medial ocellus by mermithid parasites in soldiers of Pheidole pallidula that typically lack ocelli in natural colonies (Laciny et al., 2019; Passera, 1976). The natural or experimental induction of worker individuals with only a single medial ocellus in different ant species also supports the inference that the single medial ocellus can be developmentally dissociated from the other two lateral ocelli. This suggests that reversion can facilitate the appearance of novel patterns of ocelli development in the workers if selected for.

In C. floridanus and P. rastellata, there is a latent ocelli GRN expression for all 3 ocelli, providing a springboard to facilitate the partial phylogenetic reversion to a single medial ocellus in C. gibbinotus, P. bihamata, and D. gigas. In the genus Polyrhachis, however, some species in the same subgenus as P. bihamata, such as P. bellicosa, have three ocelli. Because the phylogenetic relationships within this subgenus have yet to be resolved, the independent reversion of ocelli in the ancestor of this subgenus may have resulted either in a single ocellus as reflected in P. bihamata or in three ocelli as reflected in P. bellicosa, and two ocelli were subsequently lost giving rise to the single medial ocellus in P. bihamata (Hung, 1967). These possibilities further reinforce the different evolutionary pathways by which this latent potential may facilitate novelty after reversion.

Future functional, genomic, and comparative analyses of the ocelli GRN between larval stages, individuals within the worker caste, and species will ultimately reveal the architecture of the ocelli GRN and whether its underlying enhancers and promoters are modular or pleiotropic. This, in combination with manipulations of insect hormones, such as JH and ecdysone, would also elucidate whether variation in the size, presence/absence, number of ocelli is regulated by continuous or switch-like developmental mechanisms. And finally, determination of the organismal and ecological function of the ocelli will be important to understand the adaptive significance of the latent expression of the ocelli GRN at both the individual and colony-level.

More broadly, our findings suggest that the ancestral and latent GRN expression (also known as ancestral developmental potential) we observed may generally underlie polyphenic systems, including caste-specific traits in ants and other eusocial organisms. We therefore propose that ancestral developmental potentials facilitate the re-evolution of polyphenic traits (West-Eberhard, 2003), and when these potentials facilitate only the partial re-evolution of alternative phenotypes, novel phenotypic patterns appear. We hope our findings not only inspire future work testing these proposals in polyphenic organisms, but also in non-polyphenic ones, where the polyphenism occurs at the cellular level but not at the level of the whole organism. Here, the cellular polyphenism produces alternative cell-types from a single genome in response to internal cues, such as morphogen gradients within the organism. If alternative cell types retain homologs or serial homologs of specific traits (Jackman et al., 2025; Lynch, 2023), then this raises the possibility that ancestral and latent developmental potentials may generally facilitate re-evolution of alternative cell types in multicellular organisms.

All data reported in this paper are provided in Appendix 1—table 2. This paper does not report original code. Any additional information required to reanalyze the data reported in this paper is available from the corresponding author upon request.

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Author details

1. Angelly Vasquez-Correa

   1. Center for Evolutionary and Organismal Biology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
   2. McGill University, Department of Biology, Montreal, Canada

   Contribution

   Conceptualization, Data curation, Formal analysis, Validation, Investigation, Visualization, Methodology, Writing – original draft, Writing – review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-1478-8682

2. Johanna Arnet

   McGill University, Department of Biology, Montreal, Canada

   Contribution

   Data curation, Formal analysis

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0009-0000-2478-9446

3. Travis Chen

   1. Center for Evolutionary and Organismal Biology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
   2. McGill University, Department of Biology, Montreal, Canada

   Contribution

   Data curation, Formal analysis, Methodology

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0009-0003-6789-1928

4. Ehab Abouheif

   1. Center for Evolutionary and Organismal Biology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
   2. McGill University, Department of Biology, Montreal, Canada

   Contribution

   Conceptualization, Supervision, Funding acquisition, Validation, Investigation, Writing – original draft, Project administration, Writing – review and editing

   For correspondence

   abouheif@zju.edu.cn

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0001-7651-1737

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