Biology subjects

Kronforst, M. R.

Publications and source records attributed to Kronforst, M. R..

11 recordsLinked to original sources

bioRxiv2026

Evolution of compound eye cell types shapes visual behaviors across Heliconius butterflies

The evolution of visual systems is tightly linked to the diversification of visually guided behaviors. Using Heliconius butterflies, renowned for their rapid diversification of wing color patterns and corresponding visual mate preferences, we investigate the evolution of compound eye cell types across a complete speciation continuum. By integrating population genomics, chromatin conformation capture, and single-nucleus multi-omics, we uncover multi-modal mechanisms driving visual system evolution. Within a population polymorphic for mate preference, we identify senseless-2 as a glia-expressing candidate visual preference gene. Across species, we reveal that photoreceptors, particularly the color-sensing R7s, are the fastest-evolving cell types. Furthermore, we molecularly characterize novel R2/5 and R7 photoreceptor subtypes, showing that cellular subfunctionalization arises through the co-option of existing gene regulatory networks. Together, this comparative single-cell analysis of compound eyes bridges microevolutionary transcriptomic divergence with macroevolutionary cellular innovations.

evolutionary biology↗

bioRxiv2025

Parallel Selection for Longevity in Mammals and Birds

Most studies of aging biology to date have involved the manipulation of short-lived model organisms, while the existing anti-aging mechanisms in naturally occurring long-lived vertebrates have generally remained undiscovered or understudied. The technological advances of the recent "omics revolution" have enabled comparative genomics studies, which have started to unravel genetic signatures of longevity in vertebrates. Building on prior studies and incorporating a novel approach to detecting convergent positive selection, we conducted the first genome-wide survey of positive and purifying selection among hundreds of long-lived mammals and birds, two major vertebrate taxa with notable parallels in their evolutionary history. We discovered an extensive network of shared pathways under purifying selection in both mammals that are exceptionally long-lived for their body size (ELL) and large-bodied long-lived (LLL) birds. In our positive selection survey, we identified 16 genes, involved in eight distinct hallmarks of aging, with concordant signals of positive selection in LLL mammals and LLL birds at neighboring amino acid residues. These included two genes directly involved in cholesterol metabolism, as well as genes whose products clear oxidized metabolites and regulate peroxisomal autophagy. These striking parallels between long-lived mammals and birds, both in broad pathways under purifying selection, as well as in instances of genes under parallel positive selection in LLL mammals and LLL birds, together imply an ancient shared genetic toolkit for longevity, deeply conserved and repeatedly modified to produce longevity in diverse lineages. SignificanceWhile aging is nearly universal in vertebrates, lifespan can vary by several orders of magnitude. Further, extraordinarily long-lived species are dispersed throughout the mammalian and avian phylogenies, indicating repeated evolutionary origins of long life. In the first genome-wide survey of positive and purifying selection in long-lived mammals and birds, we found a striking level of parallelism in the signatures of selection in long-lived species in both clades. These included an extensive network of shared pathways under purifying selection, as well as several novel genes under parallel positive selection. Our results identify multiple novel candidate pathways and genes for further study, and provide evidence for the convergent evolution of extended lifespan.

evolutionary biology↗

bioRxiv2025

Phylogeny, systematics and evolution of mimicry patterns in Neotropical limenitidine butterflies

The Neotropical butterfly genus Adelpha Hubner exhibits remarkable species diversity and striking convergence in wing colour patterns potentially explained by mimicry, making it an exceptional model for exploring trait evolution and its relationship with speciation. To date, unresolved phylogenetic relationships hinder a comprehensive understanding of the evolutionary biology of the genus. Using a novel multi-marker dataset combining one mitochondrial and 15 nuclear gene fragments, we generate the most comprehensive phylogeny of the genus Adelpha to revisit its systematics and investigate the evolution of mimicry colour patterns. Our data set encompasses 83 of the 87 known extant species and six Limenitis species that were recently excluded from Adelpha (134 of c. 160 subspecies in total), collectively displaying 14 distinct mimicry patterns. We provide conclusive evidence that corroborates previous work on the polyphyly of Adelpha as historically conceived, and describe the genus Adelphina Paez & Willmott n. gen. to stabilize the nomenclature, both genera representing Neotropical limenitidines. The comprehensive phylogeny provided in this study lays a solid foundation for future research into the processes driving diversification within these species interacting through mimicry. Ancestral character state reconstruction reveals gradual evolution of mimicry pattern. The more common mimicry pattern IPHICLUS (forewing with orange subapical spot and white band) is inferred as ancestral, but repeated convergent evolution is also recovered. Evolutionary convergence is also observed for the second most abundant mimicry pattern, COCALA (orange-white banded). Increased rates of mimicry pattern evolution are also found toward the equator. These results underscore the complexity of mimicry evolution in the Neotropical limenitidines i.e., Adelpha and Adelphina, emphasizing the need to explore its interplay with other biotic and abiotic factors.

evolutionary biology↗

bioRxiv2025

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. AUTHOR SUMMARYUnderstanding how a largely shared genome can encode the potential to develop multiple morphs while simultaneously restricting this potential to one sex has long been of interest to evolutionary and developmental biologists. This phenomenon, called sex-limited polymorphism, is widespread, occurring in organisms like crustaceans, insects, fish, birds, and mammals. Recent empirical work has begun to identify the genes controlling the switch between phenotypes, but the differences between developmental programs leading to those phenotypes remain unclear. Here we use a classic example of sex-limited polymorphism - female mimicry in swallowtail butterflies - to compare how closely related species have evolved to use the same gene, doublesex, in the development of multiple female morphs. Using a combination of functional experiments, we show that despite the shared use of doublesex, the developmental genetics underlying sex-limited polymorphism have evolved to function quite differently between two species that last shared a common ancestor approximately 15 million years ago.

evolutionary biology↗

bioRxiv2024

Supergene evolution via gain of auto-regulation

Development requires the coordinated action of many genes across space and time, yet numerous species have evolved the ability to develop multiple discrete, alternate phenotypes1-5. Such polymorphisms are often controlled by supergenes, sets of tightly-linked loci that function together to control development of a polymorphic phenotype6-10. Although theories of supergene evolution are well-established, the mutations that cause functional differences between supergene alleles have been difficult to identify. The doublesex gene is a master regulator of insect sexual differentiation but has been co-opted to function as a supergene in multiple Papilio swallowtail butterflies, where divergent dsx alleles control development of discrete non-mimetic or mimetic female wing shapes and color patterns11-15. Here we demonstrate that the Papilio alphenor supergene evolved via recruitment of six new cis-regulatory elements (CREs) that control allele-specific dsx expression. Most dsx CREs, including four of the six new CREs, are bound by the DSX transcription factor itself. Our findings provide experimental support to classic supergene theory and suggest that autoregulation may provide a simple route to supergene origination and to the co-option of pleiotropic genes into new developmental roles.

evolutionary biology↗

bioRxiv2023

Synchrotron-source micro-x-ray computed tomography for examining butterfly eyes

1. Comparative anatomy is an important tool for investigating evolutionary relationships amongst species, but the lack of scalable imaging tools and stains for rapidly mapping the microscale anatomies of related species poses a major impediment to using comparative anatomy approaches for identifying evolutionary adaptations. 2. We describe a method using synchrotron source micro-x-ray computed tomography (syn-{micro}XCT) combined with machine learning algorithms for high-throughput imaging of Lepidoptera (i.e., butterfly and moth) eyes. Our pipeline allows for imaging at rates of [~] 15 min/mm3 at 600 nm3 resolution. Image contrast is generated using standard electron microscopy labeling approaches (e.g., osmium tetroxide) that unbiasedly labels all cellular membranes in a species independent manner thus removing any barrier to imaging any species of interest. 3. To demonstrate the power of the method, we analyzed the 3D morphologies of butterfly crystalline cones, a part of the visual system associated with acuity and sensitivity and found significant variation within six butterfly individuals. Despite this variation, a classic measure of optimization, the ratio of interommatidial angle to resolving power of ommatidia, largely agrees with early work on eye geometry across species. 4. We show that this method can successfully be used to determine compound eye organization and crystalline cone morphology. Our novel pipeline provides for fast, scalable visualization and analysis of eye anatomies that can be applied to any arthropod species, enabling new questions about evolutionary adaptations of compound eyes and beyond.

ecology↗

bioRxiv2022

Divergent expression of aristaless1 and aristaless2 is associated with embryonic appendage and pupal wing development in butterflies

Aristaless is a major regulator of developmental processes. It is well known for its role during appendage specification and extension across animals. Butterflies and moths have two copies of aristaless, aristaless1 (al1) and aristaless2 (al2), as a result of a gene duplication event. Previous work in Heliconius has shown that both copies appear to have novel functions related to wing color patterning. Here we expand our knowledge on the expression profiles associated with both ancestral and novel functions of Al1 across embryogenesis and wing pigmentation. Furthermore, we characterize Al2 expression, providing a comparative framework for understanding the role of gene duplicates in novel and ancestral roles. Our work shows that both Al1 and Al2 expression are associated with developing sensory appendages (leg, mouth, spines, and eyes) in embryos. Interestingly, Al1 appears to show higher expression earlier in embryogenesis while the highest levels of Al2 expression are shifted to later stages of embryonic development. Furthermore, Al1 localization appears extranuclear while Al2 co-localizes tightly with nuclei earlier, and then also expands outside the nucleus later in development. We observed similar cellular expression patterns for Al1 and Al2 in pupal wings when examining their roles in pigmentation. We also describe, for the first time, how Al1 localization appear to correlates with zones of Anterior/Posterior elongation of the body during embryonic growth, showcasing a possible new function related to Aristaless previously described role in appendage extension. Overall, these data suggest similar developmental roles associated with the extension/formation of specific appendages for both duplicates. However, we describe that such functions might be regulated by spatially and temporally complex patterns of expression for al1 and al2. This work expands our knowledge of Aristaless function and expression following gene duplication and the implications of the duplication on butterfly development. Finally, and more fundamentally, our study helps clarify principles behind sub-functionalization and gene expression evolution associated with developmental functions following gene duplication events.

developmental biology↗

bioRxiv2022

Genetic and peripheral visual system changes underlie evolving butterfly mate preference

Many studies have linked genetic variation to behavior, but less is known about how that variation alters the neural circuits that drive behavior. We investigated the genetic and neurobiological basis of courtship preference variation in Heliconius butterflies, which use vision to identify appropriate mates based on wing color patterns. We found that Heliconius cydno preference variation was strongly associated with genetic variation and differential expression of senseless-2, a gene predominantly expressed in the eye. Further measurements of photoreceptor sensitivities revealed differences in inter-photoreceptor inhibition of ultraviolet-sensitive cells corresponding to courtship preference variation. Our results reveal a genetic basis for preference/cue co-evolution, suggest a link between sens-2 and visual system variation, and support the idea that changing peripheral neural computations can significantly alter essential behaviors. SummaryGenetic and expression variation of senseless-2 and inter-photoreceptor inhibition predict visual mate preference in a clade of diverse butterflies.

evolutionary biology↗

bioRxiv2022

Sex-limited diversification of the eye in Heliconius butterflies

Butterflies have evolved an immense diversity in eye organization to support a range of vision-based behaviors including courtship, oviposition, and foraging. This diversity has been surveyed extensively across the butterfly phylogeny, and here we take a complementary approach to characterize the eye within a group of closely related Heliconius butterflies. Using a combination of immunostaining for different opsins and eyeshine for determining the distribution of light-filtering screening pigments, we identified several sexually dimorphic features of eye organization where male eyes varied and female eyes did not. Ultraviolet (UV) sensitive photoreceptors varied in which of two UV opsins were expressed, including co-expression of both within single photoreceptors, and these differences were consistent with a role in courtship and conspecific identification. Additional differences across species and sex included the distribution of three ommatidial types defined by the expression pattern of UV and blue opsins, the distribution of a red screening pigment, and which ommatidial types expressed the red screening pigment. We hypothesize that female eyes are optimized for a dimorphic behavior such as oviposition, while male eyes adapt to other selective pressures such as the local light environment.

neuroscience↗

bioRxiv2020

Divergence, gene flow and the origin of leapfrog geographic distributions: The history of color pattern variation in Phyllobates poison-dart frogs

The geographic distribution of phenotypic variation among closely related populations is a valuable source of information about the evolutionary processes that generate and maintain biodiversity. Leapfrog distributions, in which phenotypically similar populations are disjunctly distributed and separated by one or more phenotypically distinct populations, represent geographic replicates for the existence of a phenotype, and are therefore especially informative. These geographic patterns have mostly been studied from phylogenetic perspectives to understand how common ancestry and divergent evolution drive their formation. Other processes, such as gene flow between populations, have not received as much attention. Here we investigate the roles of divergence and gene flow between populations in the origin and maintenance of a leapfrog distribution in Phyllobates poison frogs. We found evidence for high levels of gene flow between neighboring populations but not over long distances, indicating that gene flow between populations exhibiting the central phenotype may have a homogenizing effect that maintains their similarity, and that introgression between "leapfroging" taxa has not played a prominent role as a driver of phenotypic diversity in Phyllobates. Although phylogenetic analyses suggest that the leapfrog distribution was formed through independent evolution of the peripheral (i.e. leapfrogging) populations, the elevated levels of gene flow between geographically close populations poise alternative scenarios, such as the history of phenotypic change becoming decoupled from genome-averaged patterns of divergence, which we cannot rule out. These results highlight the importance of incorporating gene flow between populations into the study of geographic variation in phenotypes, both as a driver of phenotypic diversity and as a confounding factor of phylogeographic inferences.

evolutionary biology↗

bioRxiv2017

The Molecular Genetic Basis of Herbivory between Butterflies and their Host-Plants

Interactions between herbivorous insects and their host-plants are a central component of terrestrial food webs and a critical topic in agriculture, where a substantial fraction of potential crop yield is lost annually to pests. Important insights into plant-insect interactions have come from research on specific plant defenses and insect detoxification mechanisms. Yet, much remains unknown about the molecular mechanisms that mediate plant-insect interactions. Here we use multiple genome-wide approaches to map the molecular basis of herbivory from both plant and insect perspectives, focusing on butterflies and their larval host-plants. Parallel genome-wide association studies in the Cabbage White butterfly, Pieris rapae, and its host-plant, Arabidopsis thaliana, pinpointed a small number of butterfly and plant genes that influenced herbivory. These genes, along with much of the genome, were regulated in a dynamic way over the time course of the feeding interaction. Comparative analyses, including diverse butterfly/plant systems, showed a variety of genome-wide responses to herbivory, yet a core set of highly conserved genes in butterflies as well as their host-plants. These results greatly expand our understanding of the genomic causes and evolutionary consequences of ecological interactions across two of Natures most diverse taxa, butterflies and flowering plants.

genomics↗