Comparative genomics of the mimicry switch in Papilio dardanus

A shared gene but distinct dynamics regulate mimicry polymorphisms in closely related species

Sex-limited polymorphisms, such as mating strategies in male birds and mimicry in female butterflies, are widespread across the tree of life and are frequently adaptive. Considerable work has been done exploring the ecological pressures and evolutionary forces that generate and maintain genetic variation resulting in alternative sex-limited morphs, yet little is known about their molecular and developmental genetic basis. A powerful system to investigate this is Papilio butterflies: within the subgenus Menelaides, multiple closely related species have female-limited mimicry polymorphism, with females developing either derived mimetic or ancestral non-mimetic wing color patterns. While mimetic color patterns are different between species, each polymorphism is controlled by allelic variation of doublesex (dsx). Across several species, we found that the mimetic and non-mimetic females develop male-like color patterns when we knockdown dsx expression, establishing that dsx controls both sexual dimorphism and polymorphism. We also found that mimetic dsx alleles have unique spatiotemporal expression patterns between two species, Papilio lowii and Papilio alphenor. To uncover the downstream genes involved in the color pattern switch between both species, we used RNA-seq in P. lowii and compared the results to previous work in P. alphenor. While some canonical wing patterning genes are differentially expressed in females of both species, the temporal patterns of differential expression are notably different. Our results indicate that, despite the putative ancestral co-option and shared use of dsx among closely related species, the mimicry switch functions through distinct underlying mechanisms.

Genomic evolution and patterns of horizontal gene transfer in Papilio

The Papilio genus, known for its ecological and phenotypic diversity, is a valuable model for evolutionary studies. This study conducted a comparative genomic analysis of 11 Papilio species, revealing species-specific gene family expansions, including the UDP-glucosyltransferase 2 gene associated with insect detoxification, particularly expanding in Papilio polyxenes. Our analysis also revealed 199 horizontal gene transfer (HGT) acquired genes from 76 microbial species, with Pseudomonadota and Bacillota as common HGT donors across these genomes. Furthermore, we examined the evolutionary patterns of nine ABC transporter subfamilies, uncovering potential links between gene family evolution and environmental adaptation. This study provides new insights into evolutionary relationships and genomic adaptations within the Papilio genus, contributing to broader butterfly evolutionary research.

Penetrance interactions of colour pattern loci in the African Monarch and their implications for the evolution of dominance

Scoring the penetrance of heterozygotes in complex phenotypes, like colour pattern, is difficult and complicates the analysis of systems in which dominance is incomplete or evolving. The African Monarch (Danaus chrysippus) represents an example where colour pattern heterozygotes, formed in the contact zone between the different subspecies, show such intermediate dominance. Colour pattern in this aposematic butterfly is controlled by three loci A, B and C. The B and C loci are closely linked in a B/C supergene and significant interaction of B and C phenotypes is therefore expected via linkage alone. The A locus, however, is not linked to B/C and is found on a different chromosome. To study interactions between these loci we generated colour pattern heterozygotes by crossing males and females bearing different A and B/C genotypes, collected from different parts of Africa. We derived a novel scoring system for the expressivity of the heterozygotes and, as predicted, we found significant interactions between the genotypes of the closely linked B and C loci. Surprisingly, however, we also found highly significant interactions between C and the unlinked A locus, modifications that generally increased the resemblance of heterozygotes to homozygous ancestors. In contrast, we found no difference in the penetrance of any of the corresponding heterozygotes from crosses conducted either in allopatry or sympatry, in reciprocal crosses of males and females, or in the presence or absence of endosymbiont mediated male-killing or its associated neoW mediated sex-linkage of colour pattern. Together, this data supports the idea that the different colour morphs of the African Monarch meet transiently in the East African contact zone and that genetic modifiers act to mask inappropriate expression of colour patterns in the incorrect environments.

Colour polymorphism associated with a gene duplication in male wood tiger moths

Colour is often used as an aposematic warning signal, with predator learning expected to lead to a single colour pattern within a population. However, there are many puzzling cases where aposematic signals are also polymorphic. The wood tiger moth, Arctia plantaginis, displays bright hindwing colours associated with unpalatability, and males have discrete colour morphs which vary in frequency between localities. In Finland, both white and yellow morphs can be found, and these colour morphs also differ in behavioural and life-history traits. Here, we show that male colour is linked to an extra copy of a yellow family gene that is only present in the white morphs. This white-specific duplication, which we name valkea, is highly upregulated during wing development. CRISPR targeting valkea resulted in editing of both valkea and its paralog, yellow-e, and led to the production of yellow wings. We also characterise the pigments responsible for yellow, white, and black colouration, showing that yellow is partly produced by pheomelanins, while black is dopamine-derived eumelanin. Our results add to a growing number of studies on the genetic architecture of complex and seemingly paradoxical polymorphisms, and the role of gene duplications and structural variation in adaptive evolution.

Genomic architecture and functional unit of mimicry supergene in female limited Batesian mimic Papilio butterflies

It has long been suggested that dimorphic female-limited Batesian mimicry of two closely related Papilio butterflies, Papilio memnon and Papilio polytes, is controlled by supergenes. Whole-genome sequencing, genome-wide association studies and functional analyses have recently identified mimicry supergenes, including the doublesex (dsx) gene. Although supergenes of both the species are composed of highly divergent regions between mimetic and non-mimetic alleles and are located at the same chromosomal locus, they show critical differences in genomic architecture, particularly with or without an inversion: P. polytes has an inversion, but P. memnon does not. This review introduces and compares the detailed genomic structure of mimicry supergenes in two Papilio species, including gene composition, repetitive sequence composition, breakpoint/boundary site structure, chromosomal inversion and linkage disequilibrium. Expression patterns and functional analyses of the respective genes within or flanking the supergene suggest that dsx and other genes are involved in mimetic traits. In addition, structural comparison of the corresponding region for the mimicry supergene among further Papilio species suggests three scenarios for the evolution of the mimicry supergene between the two Papilio species. The structural features revealed in the Papilio mimicry supergene provide insight into the formation, maintenance and evolution of supergenes. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.

Association mapping of colour variation in a butterfly provides evidence that a supergene locks together a cluster of adaptive loci

Supergenes are genetic architectures associated with discrete and concerted variation in multiple traits. It has long been suggested that supergenes control these complex polymorphisms by suppressing recombination between sets of coadapted genes. However, because recombination suppression hinders the dissociation of the individual effects of genes within supergenes, there is still little evidence that supergenes evolve by tightening linkage between coadapted genes. Here, combining a landmark-free phenotyping algorithm with multivariate genome-wide association studies, we dissected the genetic basis of wing pattern variation in the butterfly Heliconius numata. We show that the supergene controlling the striking wing pattern polymorphism displayed by this species contains several independent loci associated with different features of wing patterns. The three chromosomal inversions of this supergene suppress recombination between these loci, supporting the hypothesis that they may have evolved because they captured beneficial combinations of alleles. Some of these loci are, however, associated with colour variations only in a subset of morphs where the phenotype is controlled by derived inversion forms, indicating that they were recruited after the formation of the inversions. Our study shows that supergenes and clusters of adaptive loci in general may form via the evolution of chromosomal rearrangements suppressing recombination between co-adapted loci but also via the subsequent recruitment of linked adaptive mutations. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.

Convergent flight morphology among Müllerian mimic mutualists

Müllerian mimicry involves a signal mutualism between prey species, shaped by visually hunting predators, and recent work has emphasized the importance of color pattern. Predators respond to more than color pattern, however, and other traits are much less studied. This article examines the hypothesis of convergent evolution in flight-related morphology among eight mimicry complexes composed of 51 butterfly species (Nymphalidae, Danainae, Ithomiini) from a single community in Ecuador. Phylogenetic comparative analyses of 14 variables indicated strong morphological differences between mimicry complexes belonging to three clusters of morphological space ("large yellow transparent," "tiger," and "transparent"), not the eight predicted based on color pattern alone. Analyses found convergence within mimicry complexes, convergence between mimicry complexes within morphospace clusters, and divergence between mimicry complexes from different morphospace clusters. These three clusters differed in size, and body and wing shape, predicting that flight biomechanics also converge (i.e., locomotor mimicry). Potential constraints on evolution of morphological mimicry related to predator discrimination, and evolutionary rates, likely e xplain why flight-related morphology differences were limited to three clusters of morphological space. Finally, the added complexity that flight-related morphology brings to signals between predator and prey indicates that evolutionary switches in color pattern are not all equally likely, potentially limiting the evolution of color patterns if they do not match morphology.

Evolution of sexual development and sexual dimorphism in insects

Most animal species consist of two distinct sexes. At the morphological, physiological, and behavioral levels the differences between males and females are numerous and dramatic, yet at the genomic level they are often slight or absent. This disconnect is overcome because simple genetic differences or environmental signals are able to direct the sex-specific expression of a shared genome. A canonical picture of how this process works in insects emerged from decades of work on Drosophila. But recent years have seen an explosion of molecular-genetic and developmental work on a broad range of insects. Drawing these studies together, we describe the evolution of sexual dimorphism from a comparative perspective and argue that insect sex determination and differentiation systems are composites of rapidly evolving and highly conserved elements.

The evolution and genetics of sexually dimorphic 'dual' mimicry in the butterfly Elymnias hypermnestra

Sexual dimorphism is a major component of morphological variation across the tree of life, but the mechanisms underlying phenotypic differences between sexes of a single species are poorly understood. We examined the population genomics and biogeography of the common palmfly Elymnias hypermnestra, a dual mimic in which female wing colour patterns are either dark brown (melanic) or bright orange, mimicking toxic Euploea and Danaus species, respectively. As males always have a melanic wing colour pattern, this makes E. hypermnestra a fascinating model organism in which populations vary in sexual dimorphism. Population structure analysis revealed that there were three genetically distinct E. hypermnestra populations, which we further validated by creating a phylogenomic species tree and inferring historical barriers to gene flow. This species tree demonstrated that multiple lineages with orange females do not form a monophyletic group, and the same is true of clades with melanic females. We identified two single nucleotide polymorphisms (SNPs) near the colour patterning gene WntA that were significantly associated with the female colour pattern polymorphism, suggesting that this gene affects sexual dimorphism. Given WntA's role in colour patterning across Nymphalidae, E. hypermnestra females demonstrate the repeatability of the evolution of sexual dimorphism.

Tissue-specific developmental regulation and isoform usage underlie the role of doublesex in sex differentiation and mimicry in Papilio swallowtails

Adaptive phenotypes often arise by rewiring existing developmental networks. Co-option of transcription factors in novel contexts has facilitated the evolution of ecologically important adaptations. doublesex (dsx) governs fundamental sex differentiation during embryonic stages and has been co-opted to regulate diverse secondary sexual dimorphisms during pupal development of holometabolous insects. In Papilio polytes, dsx regulates female-limited mimetic polymorphism, resulting in mimetic and non-mimetic forms. To understand how a critical gene such as dsx regulates novel wing patterns while maintaining its basic function in sex differentiation, we traced its expression through metamorphosis in P. polytes using developmental transcriptome data. We found three key dsx expression peaks: (i) eggs in pre- and post-ovisposition stages; (ii) developing wing discs and body in final larval instar; and (iii) 3-day pupae. We identified potential dsx targets using co-expression and differential expression analysis, and found distinct, non-overlapping sets of genes-containing putative dsx-binding sites-in developing wings versus abdominal tissue and in mimetic versus non-mimetic individuals. This suggests that dsx regulates distinct downstream targets in different tissues and wing colour morphs and has perhaps acquired new, previously unknown targets, for regulating mimetic polymorphism. Additionally, we observed that the three female isoforms of dsx were differentially expressed across stages (from eggs to adults) and tissues and differed in their protein structure. This may promote differential protein-protein interactions for each isoform and facilitate sub-functionalization of dsx activity across its isoforms. Our findings suggest that dsx employs tissue-specific downstream effectors and partitions its functions across multiple isoforms to regulate primary and secondary sexual dimorphism through insect development.

Mimicry diversification in Papilio dardanus via a genomic inversion in the regulatory region of engrailed-invected

Polymorphic Batesian mimics exhibit multiple protective morphs that each mimic a different noxious model. Here, we study the genomic transitions leading to the evolution of different mimetic wing patterns in the polymorphic Mocker Swallowtail Papilio dardanus. We generated a draft genome (231 Mb over 30 chromosomes) and re-sequenced individuals of three morphs. Genome-wide single nucleotide polymorphism (SNP) analysis revealed elevated linkage disequilibrium and divergence between morphs in the regulatory region of engrailed, a developmental gene previously implicated in the mimicry switch. The diverged region exhibits a discrete chromosomal inversion (of 40 kb) relative to the ancestral orientation that is associated with the cenea morph, but not with the bottom-recessive hippocoonides morph or with non-mimetic allopatric populations. The functional role of this inversion in the expression of the novel phenotype is currently unknown, but by preventing recombination, it allows the stable inheritance of divergent alleles enabling geographic spread and local coexistence of multiple adaptive morphs.

Contrasting genomic and phenotypic outcomes of hybridization between pairs of mimetic butterfly taxa across a suture zone

Hybrid zones, whereby divergent lineages come into contact and eventually hybridize, can provide insights on the mechanisms involved in population differentiation and reproductive isolation, and ultimately speciation. Suture zones offer the opportunity to compare these processes across multiple species. In this paper we use reduced-complexity genomic data to compare the genetic and phenotypic structure and hybridization patterns of two mimetic butterfly species, Ithomia salapia and Oleria onega (Nymphalidae: Ithomiini), each consisting of a pair of lineages differentiated for their wing colour pattern and that come into contact in the Andean foothills of Peru. Despite similarities in their life history, we highlight major differences, both at the genomic and phenotypic level, between the two species. These differences include the presence of hybrids, variations in wing phenotype, and genomic patterns of introgression and differentiation. In I. salapia, the two lineages appear to hybridize only rarely, whereas in O. onega the hybrids are not only more common, but also genetically and phenotypically more variable. We also detected loci statistically associated with wing colour pattern variation, but in both species these loci were not over-represented among the candidate barrier loci, suggesting that traits other than wing colour pattern may be important for reproductive isolation. Our results contrast with the genomic patterns observed between hybridizing lineages in the mimetic Heliconius butterflies, and call for a broader investigation into the genomics of speciation in Ithomiini - the largest radiation of mimetic butterflies.

Butterfly Mimicry Polymorphisms Highlight Phylogenetic Limits of Gene Reuse in the Evolution of Diverse Adaptations

Some genes have repeatedly been found to control diverse adaptations in a wide variety of organisms. Such gene reuse reveals not only the diversity of phenotypes these unique genes control but also the composition of developmental gene networks and the genetic routes available to and taken by organisms during adaptation. However, the causes of gene reuse remain unclear. A small number of large-effect Mendelian loci control a huge diversity of mimetic butterfly wing color patterns, but reasons for their reuse are difficult to identify because the genetic basis of mimicry has primarily been studied in two systems with correlated factors: female-limited Batesian mimicry in Papilio swallowtails (Papilionidae) and non-sex-limited Müllerian mimicry in Heliconius longwings (Nymphalidae). Here, we break the correlation between phylogenetic relationship and sex-limited mimicry by identifying loci controlling female-limited mimicry polymorphism Hypolimnas misippus (Nymphalidae) and non-sex-limited mimicry polymorphism in Papilio clytia (Papilionidae). The Papilio clytia polymorphism is controlled by the genome region containing the gene cortex, the classic P supergene in Heliconius numata, and loci controlling color pattern variation across Lepidoptera. In contrast, female-limited mimicry polymorphism in Hypolimnas misippus is associated with a locus not previously implicated in color patterning. Thus, although many species repeatedly converged on cortex and its neighboring genes over 120 My of evolution of diverse color patterns, female-limited mimicry polymorphisms each evolved using a different gene. Our results support conclusions that gene reuse occurs mainly within ∼10 My and highlight the puzzling diversity of genes controlling seemingly complex female-limited mimicry polymorphisms.

Genomic evidence of human selection on Vavilovian mimicry

Vavilovian mimicry is an evolutionary process by which weeds evolve to resemble domesticated crop plants and is thought to be the result of unintentional selection by humans. Unravelling its molecular mechanisms will extend our knowledge of mimicry and contribute to our understanding of the origin and evolution of agricultural weeds, an important component of crop biology. To this end, we compared mimetic and non-mimetic populations of Echinochloa crus-galli from the Yangtze River basin phenotypically and by genome resequencing, and we show that this weed in rice paddies has evolved a small tiller angle, allowing it to phenocopy cultivated rice at the seedling stage. We demonstrate that mimetic lines evolved from the non-mimetic population as recently as 1,000 yr ago and were subject to a genetic bottleneck, and that genomic regions containing 87 putative plant architecture-related genes (including LAZY1, a key gene controlling plant tiller angle) were under selection during the mimicry process. Our data provide genome-level evidence for the action of human selection on Vavilovian mimicry.

A sheep in wolf's clothing: levels of deceit and detection in the evolution of cue-mimicry

In an evolutionary context, trusted signals or cues provide individuals with the opportunity to manipulate them to their advantage by deceiving others. The deceived can then respond to the deception by either ignoring the signals or cues or evolving means of deception-detection. If the latter happens, it can result in an arms race between deception and detection. Here, we formally analyse these possibilities in the context of cue-mimicry in prey-predator interactions. We demonstrate that two extrinsic parameters control whether and for how long an arms race continues: the benefits of deception, and the cost of ignoring signals and cues and having an indiscriminate response. As long as the cost of new forms of deception is less than its benefits and the cost of new forms of detection is less than the cost of an indiscriminate response, an arms race results in the perpetual evolution of better forms of detection and deception. When novel forms of deception or detection become too costly to evolve, the population settles on a polymorphic equilibrium involving multiple strategies of deception and honesty, and multiple strategies of detection and trust.

The mimetic wing pattern of Papilio polytes butterflies is regulated by a doublesex-orchestrated gene network

The swallowtail butterfly Papilio polytes is sexually dimorphic and exhibits female-limited Batesian mimicry. This species also has two female forms, a non-mimetic form with male-like wing patterns, and a mimetic form resembling an unpalatable model, Pachliopta aristolochiae. The mimicry locus H constitutes a dimorphic Mendelian 'supergene', including a transcription factor gene doublesex (dsx). However, how the mimetic-type dsx (dsx-H) orchestrates the downstream gene network and causes the mimetic traits remains unclear. Here we performed RNA-seq-based gene screening and found that Wnt1 and Wnt6 are up-regulated by dsx-H during the early pupal stage and are involved in the red/white pigmentation and patterning of mimetic female wings. In contrast, a homeobox gene abdominal-A is repressed by dsx-H and involved in the non-mimetic colouration pattern. These findings suggest that dual regulation by dsx-H, induction of mimetic gene networks and repression of non-mimetic gene networks, is essential for the switch from non-mimetic to mimetic pattern in mimetic female wings.

Parallel evolution of Batesian mimicry supergene in two Papilio butterflies, P. polytes and P. memnon

Batesian mimicry protects animals from predators when mimics resemble distasteful models. The female-limited Batesian mimicry in Papilio butterflies is controlled by a supergene locus switching mimetic and nonmimetic forms. In Papilio polytes, recent studies revealed that a highly diversified region (HDR) containing doublesex (dsx-HDR) constitutes the supergene with dimorphic alleles and is likely maintained by a chromosomal inversion. In the closely related Papilio memnon, which exhibits a similar mimicry polymorphism, we performed whole-genome sequence analyses in 11 butterflies, which revealed a nearly identical dsx-HDR containing three genes (dsx, Nach-like, and UXT) with dimorphic sequences strictly associated with the mimetic/nonmimetic phenotypes. In addition, expression of these genes, except that of Nach-like in female hind wings, showed differences correlated with phenotype. The dimorphic dsx-HDR in P. memnon is maintained without a chromosomal inversion, suggesting that a separate mechanism causes and maintains allelic divergence in these genes. More abundant accumulation of transposable elements and repetitive sequences in the dsx-HDR than in other genomic regions may contribute to the suppression of chromosomal recombination. Gene trees for Dsx, Nach-like, and UXT indicated that mimetic alleles evolved independently in the two Papilio species. These results suggest that the genomic region involving the above three genes has repeatedly diverged so that two allelic sequences of this region function as developmental switches for mimicry polymorphism in the two Papilio species. The supergene structures revealed here suggest that independent evolutionary processes with different genetic mechanisms have led to parallel evolution of similar female-limited polymorphisms underlying Batesian mimicry in Papilio butterflies.

Learning of salient prey traits explains Batesian mimicry evolution

Batesian mimicry evolution involves an initial major mutation that produces a rough resemblance to the model, followed by smaller improving changes. To examine the learning psychology of this process, we applied established ideas about mimicry in Papilio polyxenes asterius of the model Battus philenor. We performed experiments with wild birds as predators and butterfly wings as semiartificial prey. Wings of hybrids of P. p. asterius and Papilio machaon were used to approximate the first mutant, with melanism as the hypothesized first mimetic trait. Based on previous results about learning psychology and imperfect mimicry, we predicted that: melanism should have high salience (i.e., being noticeable and prominent), meaning that predators readily discriminate a melanistic mutant from appearances similar to P. machaon; the difference between the first mutant and the model should have intermediate salience to allow further improvement of mimicry; and the final difference in appearance between P. p. asterius and B. philenor should have very low salience, causing improvement to level off. Our results supported both the traditional hypothesis and all our predictions about relative salience. We conclude that there is good agreement between long-held ideas about how Batesian mimicry evolves and recent insights from learning psychology about the role of salience in mimicry evolution.

Tracing the origin and evolution of supergene mimicry in butterflies

Supergene mimicry is a striking phenomenon but we know little about the evolution of this trait in any species. Here, by studying genomes of butterflies from a recent radiation in which supergene mimicry has been isolated to the gene doublesex, we show that sexually dimorphic mimicry and female-limited polymorphism are evolutionarily related as a result of ancient balancing selection combined with independent origins of similar morphs in different lineages and secondary loss of polymorphism in other lineages. Evolutionary loss of polymorphism appears to have resulted from an interaction between natural selection and genetic drift. Furthermore, molecular evolution of the supergene is dominated not by adaptive protein evolution or balancing selection, but by extensive hitchhiking of linked variants on the mimetic dsx haplotype that occurred at the origin of mimicry. Our results suggest that chance events have played important and possibly opposing roles throughout the history of this classic example of adaptation.

Mimicry in butterflies: co-option and a bag of magnificent developmental genetic tricks

Butterfly wing patterns are key adaptations that are controlled by remarkable developmental and genetic mechanisms that facilitate rapid evolutionary change. With swift advancements in the fields of genomics and genetic manipulations, identifying the regulators of wing development and mimetic wing patterns has become feasible even in nonmodel organisms such as butterflies. Recent mapping and gene expression studies have identified single switch loci of major effects such as transcription factors and supergenes as the main drivers of adaptive evolution of mimetic and polymorphic butterfly wing patterns. We highlight several of these examples, with emphasis on doublesex, optix, WntA and other dynamic, yet essential, master regulators that control critical color variation and sex-specific traits. Co-option emerges as a predominant theme, where typically embryonic and other early-stage developmental genes and networks have been rewired to regulate polymorphic and sex-limited mimetic wing patterns in iconic butterfly adaptations. Drawing comparisons from our knowledge of wing development in Drosophila, we illustrate the functional space of genes that have been recruited to regulate butterfly wing patterns. We also propose a developmental pathway that potentially results in dorsoventral mismatch in butterfly wing patterns. Such dorsoventrally mismatched color patterns modulate signal components of butterfly wings that are used in intra- and inter-specific communication. Recent advances-fuelled by RNAi-mediated knockdowns and CRISPR/Cas9-based genomic edits-in the developmental genetics of butterfly wing patterns, and the underlying biological diversity and complexity of wing coloration, are pushing butterflies as an emerging model system in ecological genetics and evolutionary developmental biology. WIREs Dev Biol 2018, 7:e291. doi: 10.1002/wdev.291 This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Comparative Development and Evolution > Regulation of Organ Diversity Comparative Development and Evolution > Evolutionary Novelties.

Genetic architecture and balancing selection: the life and death of differentiated variants

Balancing selection describes any form of natural selection, which results in the persistence of multiple variants of a trait at intermediate frequencies within populations. By offering up a snapshot of multiple co-occurring functional variants and their interactions, systems under balancing selection can reveal the evolutionary mechanisms favouring the emergence and persistence of adaptive variation in natural populations. We here focus on the mechanisms by which several functional variants for a given trait can arise, a process typically requiring multiple epistatic mutations. We highlight how balancing selection can favour specific features in the genetic architecture and review the evolutionary and molecular mechanisms shaping this architecture. First, balancing selection affects the number of loci underlying differentiated traits and their respective effects. Control by one or few loci favours the persistence of differentiated functional variants by limiting intergenic recombination, or its impact, and may sometimes lead to the evolution of supergenes. Chromosomal rearrangements, particularly inversions, preventing adaptive combinations from being dissociated are increasingly being noted as features of such systems. Similarly, due to the frequency of heterozygotes maintained by balancing selection, dominance may be a key property of adaptive variants. High heterozygosity and limited recombination also influence associated genetic load, as linked recessive deleterious mutations may be sheltered. The capture of deleterious elements in a locus under balancing selection may reinforce polymorphism by further promoting heterozygotes. Finally, according to recent genomewide scans, balanced polymorphism might be more pervasive than generally thought. We stress the need for both functional and ecological studies to characterize the evolutionary mechanisms operating in these systems.

Independent evolution of sexual dimorphism and female-limited mimicry in swallowtail butterflies (Papilio dardanus and Papilio phorcas)

Several species of swallowtail butterflies (genus Papilio) are Batesian mimics that express multiple mimetic female forms, while the males are monomorphic and nonmimetic. The evolution of such sex-limited mimicry may involve sexual dimorphism arising first and mimicry subsequently. Such a stepwise scenario through a nonmimetic, sexually dimorphic stage has been proposed for two closely related sexually dimorphic species: Papilio phorcas, a nonmimetic species with two female forms, and Papilio dardanus, a female-limited polymorphic mimetic species. Their close relationship indicates that female-limited polymorphism could be a shared derived character of the two species. Here, we present a phylogenomic analysis of the dardanus group using 3964 nuclear loci and whole mitochondrial genomes, showing that they are not sister species and thus that the sexually dimorphic state has arisen independently in the two species. Nonhomology of the female polymorphism in both species is supported by population genetic analysis of engrailed, the presumed mimicry switch locus in P. dardanus. McDonald-Kreitman tests performed on SNPs in engrailed showed the signature of balancing selection in a polymorphic population of P. dardanus, but not in monomorphic populations, nor in the nonmimetic P. phorcas. Hence, the wing polymorphism does not balance polymorphisms in engrailed in P. phorcas. Equally, unlike in P. dardanus, none of the SNPs in P. phorcas engrailed were associated with either female morph. We conclude that sexual dimorphism due to female polymorphism evolved independently in both species from monomorphic, nonmimetic states. While sexual selection may drive male-female dimorphism in nonmimetic species, in mimetic Papilios, natural selection for protection from predators in females is an alternative route to sexual dimorphism.

Molecular evolution: breakthroughs and mysteries in Batesian mimicry

Recent studies appear to overthrow the hypothesis that, in butterfly species exhibiting Batesian mimicry, a multi-gene complex or 'supergene' controls the multiple differences between mimetic and non-mimetic individuals, suggesting instead that near-perfect mimicry can be produced by a set of changes within a single locus, together with changes in the genetic background.

Identification of doublesex alleles associated with the female-limited Batesian mimicry polymorphism in Papilio memnon

The female-limited Batesian mimicry polymorphism in Papilio butterflies is an intriguing system for investigating the mechanism of maintenance of genetic polymorphisms. In Papilio polytes, an autosomal region encompassing the sex-determinant gene doublesex controls female-limited mimicry polymorphism. In the closely related species P. memnon, which also exhibits female-limited Batesian mimicry polymorphism, we identified two allelic sequences of the doublesex gene that corresponded exactly with the mimetic and non-mimetic female phenotypes. Thus, the genetic basis of the mimicry polymorphism in P. memnon is similar to that in P. polytes. However, the mimetic and non-mimetic alleles of the two species were not identical, and the divergence of alleles occurred independently in P. memnon and P. polytes. Different mutation-selection processes may have resulted in the convergent patterns of mimicry polymorphism in these Papilio butterflies.

Genes controlling mimetic colour pattern variation in butterflies

Butterfly wing patterns are made up of arrays of coloured scales. There are two genera in which within-species variation in wing patterning is common and has been investigated at the molecular level, Heliconius and Papilio. Both of these species have mimetic relationships with other butterfly species that increase their protection from predators. Heliconius have a 'tool-kit' of five genetic loci that control colour pattern, three of which have been identified at the gene level, and which have been repeatedly used to modify colour pattern by different species in the genus. By contrast, the three Papilio species that have been investigated each have different genetic mechanisms controlling their polymorphic wing patterns.

Advances in finding Alba: the locus affecting life history and color polymorphism in a Colias butterfly

Although alternative life-history strategies exist within many populations, very little is known about their genetic basis and mechanistic insight into these traits could greatly advance the understanding of eco-evolutionary dynamics. Many species of butterfly within the genus Colias exhibit a sex-limited wing colour polymorphism, called Alba, which is correlated with an alternative life-history strategy. Here, we have taken the first steps in localizing the region carrying Alba in Colias croceus, a species with no genomic resources, by generating whole genome sequence of a single Alba mother and two sequencing pools, one for her Alba and another for her orange, offspring. These data were used in a bulk-segregant analysis wherein SNPs fulfilling the Mendelian inheritance expectations of Alba were identified. Then, using the conserved synteny in Lepidoptera, the Alba locus was assigned to chromosome 15 in Bombyx mori. We then identified candidate regions within the chromosome by investigating the distribution of Alba SNPs along the chromosome and the difference in nucleotide diversity in exons between the two pools. A region spanning ~ 5.7 Mbp at the 5' end of the chromosome was identified as likely to contain the Alba locus. These insights set the stage for more detailed genomic scans and mapping of the Alba phenotype, and demonstrate an efficient use of genomic resources in a novel species.

Behavioural mimicry in flight path of Batesian intraspecific polymorphic butterfly Papilio polytes

Batesian mimics that show similar coloration to unpalatable models gain a fitness advantage of reduced predation. Beyond physical similarity, mimics often exhibit behaviour similar to their models, further enhancing their protection against predation by mimicking not only the model's physical appearance but also activity. In butterflies, there is a strong correlation between palatability and flight velocity, but there is only weak correlation between palatability and flight path. Little is known about how Batesian mimics fly. Here, we explored the flight behaviour of four butterfly species/morphs: unpalatable model Pachliopta aristolochiae, mimetic and non-mimetic females of female-limited mimic Papilio polytes, and palatable control Papilio xuthus. We demonstrated that the directional change (DC) generated by wingbeats and the standard deviation of directional change (SDDC) of mimetic females and their models were smaller than those of non-mimetic females and palatable controls. Furthermore, we found no significant difference in flight velocity among all species/morphs. By showing that DC and SDDC of mimetic females resemble those of models, we provide the first evidence for the existence of behavioural mimicry in flight path by a Batesian mimic butterfly.

The functional basis of wing patterning in Heliconius butterflies: the molecules behind mimicry

Wing-pattern mimicry in butterflies has provided an important example of adaptation since Charles Darwin and Alfred Russell Wallace proposed evolution by natural selection >150 years ago. The neotropical butterfly genus Heliconius played a central role in the development of mimicry theory and has since been studied extensively in the context of ecology and population biology, behavior, and mimicry genetics. Heliconius species are notable for their diverse color patterns, and previous crossing experiments revealed that much of this variation is controlled by a small number of large-effect, Mendelian switch loci. Recent comparative analyses have shown that the same switch loci control wing-pattern diversity throughout the genus, and a number of these have now been positionally cloned. Using a combination of comparative genetic mapping, association tests, and gene expression analyses, variation in red wing patterning throughout Heliconius has been traced back to the action of the transcription factor optix. Similarly, the signaling ligand WntA has been shown to control variation in melanin patterning across Heliconius and other butterflies. Our understanding of the molecular basis of Heliconius mimicry is now providing important insights into a variety of additional evolutionary phenomena, including the origin of supergenes, the interplay between constraint and evolvability, the genetic basis of convergence, the potential for introgression to facilitate adaptation, the mechanisms of hybrid speciation in animals, and the process of ecological speciation.

The status of supergenes in the 21st century: recombination suppression in Batesian mimicry and sex chromosomes and other complex adaptations

I review theoretical models for the evolution of supergenes in the cases of Batesian mimicry in butterflies, distylous plants and sex chromosomes. For each of these systems, I outline the genetic evidence that led to the proposal that they involve multiple genes that interact during ‘complex adaptations’, and at which the mutations involved are not unconditionally advantageous, but show advantages that trade‐off against some disadvantages. I describe recent molecular genetic studies of these systems and questions they raise about the evolution of suppressed recombination. Nonrecombining regions of sex chromosomes have long been known, but it is not yet fully understood why recombination suppression repeatedly evolved in systems in distantly related taxa, but does not always evolve. Recent studies of distylous plants are tending to support the existence of recombination‐suppressed genome regions, which may include modest numbers of genes and resemble recently evolved sex‐linked regions. For Batesian mimicry, however, molecular genetic work in two butterfly species suggests a new supergene scenario, with a single gene mutating to produce initial adaptive phenotypes, perhaps followed by modifiers specifically refining and perfecting the new phenotype.

New genomes clarify mimicry evolution

For over 100 years, it has been known that polymorphic mimicry is often switched by simple mendelian factors, yet the physical nature of these loci had escaped characterization. Now, the genome sequences of two swallowtail butterfly (Papilio) species have enabled the precise identification of a locus underlying mimicry, adding to unprecedented recent discoveries in mimicry genetics.

Evolution of dominance mechanisms at a butterfly mimicry supergene

Genetic dominance in polymorphic loci may respond to selection; however, the evolution of dominance in complex traits remains a puzzle. We analyse dominance at a wing-patterning supergene controlling local mimicry polymorphism in the butterfly Heliconius numata. Supergene alleles are associated with chromosomal inversion polymorphism, defining ancestral versus derived alleles. Using controlled crosses and the new procedure, Colour Pattern Modelling, allowing whole-wing pattern comparisons, we estimate dominance coefficients between alleles. Here we show strict dominance in sympatry favouring mimicry and inconsistent dominance throughout the wing between alleles from distant populations. Furthermore, dominance among derived alleles is uncoordinated across wing-pattern elements, producing mosaic heterozygous patterns determined by a hierarchy in colour expression. By contrast, heterozygotes with an ancestral allele show complete, coordinated dominance of the derived allele, independently of colours. Therefore, distinct dominance mechanisms have evolved in association with supergene inversions, in response to strong selection on mimicry polymorphism.

The evolution of genetic dominance in polymorphic traits remains poorly understood. Here, the authors show that distinct dominance mechanisms have evolved in association with supergene inversions controlling wing pattern in Heliconius butterflies, in response to strong selection favouring mimicry.

The evolutionary genetics of highly divergent alleles of the mimicry locus in Papilio dardanus

BACKGROUND

The phylogenetic history of genes underlying phenotypic diversity can offer insight into the evolutionary origin of adaptive traits. This is especially true where single genes have large phenotypic effects, for example in determining polymorphic mimicry in butterflies. Here, we characterise the evolutionary history of two candidate genes for the mimicry switch in the polymorphic Batesian mimic Papilio dardanus coding for the transcription factors engrailed and invected.

RESULTS

We show that phased haplotypes associated with the dominant morphs f. poultoni and f. planemoides are phylogenetically highly divergent, in particular at non-synonymous sites. Some non-synonymous changes are shared between the divergent alleles suggesting either convergence or a shared ancestry. Gene trees for invected do not show this pattern. Despite their great divergence, all engrailed alleles of P. dardanus were monophyletic with respect to alleles of closely related species. Phylogenetic analyses therefore reveal no evidence for introgression from other species. A McDonald-Kreitman test conducted on a population sample from South Africa confirms a significant excess of intraspecific non-synonymous diversity in P. dardanus engrailed, suggesting long-term balanced polymorphism at this locus.

CONCLUSIONS

The divergence between engrailed haplotypes suggests an evolutionary history distorted by selection with multiple changes reflecting recurrent selective sweeps. The high level of intraspecific polymorphism observed is characteristic of balancing selection on this locus, as expected if the gene engrailed is under phenotypic selection for the maintenance of multiple mimetic morphs. Non-synonymous changes in key functional portions of a major transcription factor are likely to be deleterious but if maintained in a dominant allele at low frequency, heterozygosity would reduce the associated genetic load.