Biology subjects

Kawahara, A. Y.

Publications and source records attributed to Kawahara, A. Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Genomics and CT imaging reveal diversity in silk genes and gland morphology of webspinners

Webspinners (Insecta: Embioptera) are an unusual insect order that are known for their subsocial behavior and prolific silk-production. Due to their unique foreleg silk glands, and spider-like ability to produce silk throughout their entire life cycle, webspinners are hypothesized to have evolved silk independently from other arthropod lineages. To date, there are no reference-quality genomes available for the order, preventing the study of their silk gene origination and diversification. Here, we assembled PacBio HiFi reference genomes and characterized the silk genes present in two webspinner species, Aposthonia ceylonica and Oligotoma nigra. The genomes reveal multiple full-length copies of the primary Embioptera silk gene, e-fibroin, that have undergone both ancestral and recent gene duplications within the group. For both species, all e-fibroin paralogs show the presence of complex repeat units consisting of multiple exons and introns that are remarkably homogenized across each gene. We also used CT-scanning of the internal silk glands to provide details concerning the localization of silk production in foreleg tarsi, and interspecific morphology. Article summaryThis study introduces the first high-quality genomes for webspinners, enabling new research on silk for evolutionary biologists and materials scientists alike. The authors sequenced two embiopteran species, Aposthonia ceylonica and Oligotoma nigra, to compare silk genes and gland structure using micro-computed tomography, an imaging method that shows internal anatomy in detail. They found multiple copies of the primary silk gene in both species that likely arose from multiple duplication events at different evolutionary times. These silk genes exhibit unusual gene structure with hierarchically organized repeat units that are highly homogenized within a gene. The findings show that silk genes have a complex evolutionary history in webspinners and provide a foundation for studying silk diversity within the order, and in the broader context of insect silk.

evolutionary biology↗

bioRxiv2026

Conservation of declining Florida ecosystems is critical for an at-risk butterfly

Assessing the availability of protected habitats for at-risk species is needed to determine how the spatial distribution of land cover and land use shapes conservation outcomes. The Loammi skipper (Atrytonopsis loammi) is a nonmigratory, prairie-associated butterfly that has experienced a significant reduction in its formerly widespread southeastern United States distribution over the past several decades. Observations in recent years have been limited to a small number of isolated Florida populations, and it is unclear how much suitable habitat remains and what proportion of that habitat is protected. Here we used publicly available community science data and collected specimens to identify the predominant land cover types occupied by A. loammi. We then quantified the extent to which each of these land cover types overlap with protected areas to estimate the proportion of the butterflys current distribution that occurs on managed conservation lands. Our findings show that A. loammi relies heavily on protected lands, with over half of the total area of the most strongly associated habitats located within protected areas. Given the continued expansion of human-modified landscapes in Florida and the reliance of A. loammi on protected lands, the long-term persistence of A. loammi will likely depend on the conservation and effective management of its remaining suitable habitat. Implications for insect conservationOur results highlight the critical role of protected areas in sustaining at-risk insect populations, particularly for species with limited dispersal and shrinking ranges. More broadly, they suggest that conserving and restoring protected habitats while maintaining connectivity are essential strategies for effective insect conservation in rapidly developing regions.

ecology↗

bioRxiv2026

Convergent evolutionary selection unravels the genetic basis of audition in moths

Hearing in Lepidoptera mediates a range of ecologically important behaviours, including mate communication, predator avoidance, and acoustic signalling. In moths, the evolution of predator-prey interactions with bats has further shaped hearing through a sensory arms race, with repeated co-option of auditory organs to detect and evade echolocating predators. Despite significant prior characterization of the neurophysiology and behaviour of hearing in moths, the genetic basis of hearing is poorly understood in most insects. In this study, we identify a core set of putative auditory genes in Lepidoptera using a combination of homology-based searches from Drosophila and evolutionary rate analyses. We find 56 genes present across all species and investigate whether gene copy number varies among non-hearing and hearing lineages and among 3 different ear types. We discovered seven genes associated with ear type and one with ear presence, but did not find significant losses in gene copy number in non-hearing species. We identified three genes (btv, Dnai2, and nompB) with strong evidence of selection in hearing clades and five genes with weaker evidence of selection. We discuss the potential roles of btv, nompB, and Dnai2 in ciliary transport and the aging of hair cells, as well as the possibility of actively amplified hearing. Our study serves as a primer and resource for further gene mining and functional testing of auditory genes in moths and other insects.

evolutionary biology↗

bioRxiv2026

Endangered Species Act listing is linked with greater research effort for U.S. butterflies

Conservation strategies for at-risk species can be aided significantly by research on topics such as ecology, life history, and threats, yet research effort is lacking for many species facing elevated extinction risk. Here we investigated whether listing under the U.S. Endangered Species Act (ESA) was associated with research effort for U.S. butterflies, and whether that effort was higher before or after ESA listing. We found that ESA-listed species had significantly more peer-reviewed publications than non-listed species after accounting for species range and taxonomic family. Further, we showed that more papers were published per year after ESA listing than before. These findings confirm that ESA-listed species benefit from greater research attention that can support data-informed conservation efforts. However, the relative scarcity of studies prior to ESA listing, as well as the lack of research for many unlisted, at-risk taxa, underscores the need for proactive, strategic research effort to inform conservation action.

zoology↗

bioRxiv2026

Superposition eyes of diurnal and nocturnal hawkmoths are imperfect spheres and lack acute zones.

Superposition compound eyes improve sensitivity by pooling light from multiple facets and are widespread among nocturnal insects, including moths and beetles. Optical theory predicts that superposition eyes must be nearly spherical to form coherent images and therefore lack highly pronounced acute zones with high spatial resolution. To examine this, we imaged eyes of six hawkmoths (Sphingidae) spanning diurnal and nocturnal activity with high-resolution microcomputed tomography. Our automated pipeline created detailed eye maps quantifying morphological parameters. We measured local eye curvature (radial distance), interommatidial angle ({Delta}{varphi}), facet size and crystalline cone skewness (tilt of cone axes relative to the local surface normal). All species show more curvature in the dorso-ventral plane with flattening in the antero-posterior plane. However, their eyes still retain near-spherical curvature globally, with diurnal species showing greater distortion. For facet parameters, spatial acuity is generally highest (lowest {Delta}{varphi}) near the eye center and decreases gradually toward the periphery. However, overall variation in spatial acuity is low and these eyes lack distinct acute zones. Facet size gradually changes from center to periphery, increasing in some species and decreasing in the others. Cone skewness is present in all six species (0{degrees}-10{degrees}), but in two diurnal species of hummingbird hawkmoths it increases markedly in the posterior region (15{degrees}-30{degrees}) possibly compensating for regional eye flatness. This paper provides foundational data of ommatidial and eye shape measurements and advances our assumptions about how superposition eyes function.

animal behavior and cognition↗

bioRxiv2025

Environmental Variation Promotes Convergent Evolution and Rapid Diversification of Wing Shape and Color in Skipper Butterflies

Predation is a key driver of speciation and phenotypic diversification, yet how antipredator traits evolve and persist over evolutionary time remains poorly understood. We generated target sequence capture and whole-genome sequencing data for the skipper butterfly subfamily Eudaminae (Hesperiidae) to test whether antipredator defenses, in interaction with environmental variation, promote diversification. We focus on two antipredation wing traits: hindwing tails, which deflect predator attacks, and blue-green coloration, which may enhance motion dazzle and be used as warning coloration. Applying phylogenomics, morphometrics, and comparative methods, we model trait evolution in relation to diel activity and geographic distribution and find that hindwing tails repeatedly evolved at least seven times and blue-green coloration at least fifteen times. Both traits are associated with elevated speciation rates, but evolutionary transitions toward tailless wings and non-iridescent coloration occurred more frequently than trait gains, indicating high evolutionary lability of these antipredator defenses. Trait loss, particularly pronounced in tropical diurnal species, may reflect trade-offs in flight performance, shifts in predation guilds, or the evolution of alternative defensive traits. Our findings highlight rampant convergent evolution of wing traits that are under strong predator-mediated selection. By identifying how antipredator defenses and environmental contexts influence phenotypic and species diversification, this study provides new insights into the ecological and evolutionary processes underlying insect diversity.

evolutionary biology↗

bioRxiv2025

Gene family evolution reveals dietary adaptations in butterflies and moths

Butterflies and moths (Lepidoptera) are a hyperdiverse lineage of nearly 160,000 described species and their evolutionary success is postulated to be tightly correlated with the radiation of their primary host -- angiosperms. Previous studies found that a significant number of emergent gene families are specific to Lepidoptera, with many genes linked to odorant receptors and peptidases, suggesting that such genetic innovations may be linked to their diversification. Here, we use genomic resources to identify lineage-specific gene families in four nested lepidopteran clades (e.g. Lepidoptera, Glossata, Ditrysia, and Apoditrysia). Among nearly a hundred gene families specific to each group, a handful of gene families have specific and interpretable functions. We found that many digestion-related gene families emerged early in the evolution of Lepidoptera, followed by genes associated with detoxification and immunity. This result aligns with the evolutionary transition in ancient Lepidoptera diets to terrestrial plants, highlighting the emergence of detoxification mechanisms in the megadiverse Ditrysia as a critical adaptation driven by the proliferation of plant chemical defenses. We also found gene families originating from horizontal gene transfer (HGT) events, likely introduced from bacteria and fungi to the common ancestors of Lepidoptera and Ditrysia, respectively. These HGT-derived genes likely played a pivotal role in supporting the dietary transition from algae, diatoms, and aquatic plant debris to fungi and primitive terrestrial plants, ultimately enabling the adaptation to the most dominant angiosperm species.

evolutionary biology↗

bioRxiv2025

Climate and regional plant richness drive diet specialization in butterfly caterpillars

Studies of coevolution, ecosystem processes, and latitudinal diversity gradients are improved by understanding variation in resource specialization. Insect herbivory is one of the most ubiquitous terrestrial ecological associations that drives the evolution of plants and insects. However, a broad understanding of how and why herbivore diet specificity varies worldwide is lacking. Here, we use global datasets of butterfly and plant distributions to investigate patterns and drivers of butterfly larval diet breadth. Hostplant richness and phylogenetic diversity showed non-monotonic latitudinal patterns that narrowed near the equator and temperate latitudes and broadened at mid-tropical latitudes and the poles. Diet breadth showed a negative relationship with plant family richness, but we also uncovered an interaction between precipitation seasonality and temperature. Our study builds on 60 years of study of butterfly-hostplant evolution to provide valuable insights into how these processes continue to shape plant and herbivore dynamics in response to global environmental changes.

ecology↗

bioRxiv2024

Sex-specific chemosensory gene expression in the whitelined sphinx moth (Lepidoptera: Hyles lineata) suggests a role for odorant-binding proteins in host plant choice

The whitelined sphinx moth, Hyles lineata, is a generalist during both the larval and adult stages with a broad geographic range extending across North and Central America. Within the genus Hyles there have been multiple transitions to a narrower host plant range, making Hyles an ideal group to study the evolution and mechanisms of host plant selection. We characterize sex- and appendage-specific chemosensory gene expression in H. lineata, the oldest extant member of the genus. We also describe female-specific gene expression in appendages used to sense plant surfaces as a means of identifying candidate genes involved in host plant choice. Sensilla on these appendages house sensory neurons and support cells that express chemosensory genes, receptors, and small proteins that bind, shuttle, and transport small molecules to allow detection of odorants and other small molecules. We considered genes detected more frequently in the female leg and ovipositor samples to be candidate oviposition-relevant genes. Most chemosensory genes of interest were detected in both sexes, while several odorant receptors were only detected in females. We identified 18 putative chemosensory genes that were specific to female legs, ovipositors, or both body parts. However, most of these genes did not reach statistical criteria to be considered differentially expressed. Instead, a set of OBPs show statistically significant female-biased expression in legs and ovipositors. These genes may serve as candidates for future study of the evolution and mechanisms of oviposition behavior in this species and its relatives. SummaryThe sphinx moth genus Hyles contains both generalist and specialized feeders, making it an ideal system to study the evolution of host plant breadth. The whitelined sphinx moth (Hyles lineata) is a generalist feeder at both adult and larval stages and is the oldest lineage of the genus. In this analysis of sex-specific gene expression, Godfrey and colleagues identify several odorant binding proteins as being more frequently detected in female appendages used to assess host plants. These genes could play a role in host plant selection and can be targets for future mechanistic studies on this species.

evolutionary biology↗

bioRxiv2024

Macroevolutionary Constraint and Selection on Anti-Bat Moth Tails

Elaborate traits evolve via intense selective pressure, overpowering ecological constraints. Hindwing tails that thwart bat attack have repeatedly originated in moon moths (Saturniidae), with longer tails having greater anti-predator effect. Here, we take a macroevolutionary approach to evaluate the evolutionary balance between predation pressure and possible limiting environmental factors on tail elongation. To trace the evolution of tail length across time and space, we inferred a time-calibrated phylogeny of the entirely tailed moth group (Actias + Argema) and performed ancestral state reconstruction and biogeographical analyses. We generated metrics of predation via estimates of bat abundance from nearly 200 custom-built species distribution models and environmental metrics via estimates of bioclimatic variables associated with individual moth observations. To access community science data, we developed a novel method for measuring wing lengths from un-scaled photos. Integrating these data into phylogenetically-informed mixed models, we find a positive association between bat predation pressure and moth tail length and body size, and a negative association between environmental factors and these morphological traits. Regions with more insectivorous bats and more consistent temperatures tend to host longer-tailed moths. Our study provides insight into tradeoffs between biotic selective pressures and abiotic constraints that shape elaborate traits across the tree-of-life.

evolutionary biology↗

bioRxiv2023

Phylogenomics recovers multiple origins of portable case-making in caddisflies (Insecta: Trichoptera), the world's most common underwater architects

Caddisflies (Trichoptera) are among the most diverse groups of freshwater animals with more than 16,000 described species. They play an outsized role in freshwater ecology and environmental engineering in streams, rivers, and lakes. Because of this, they are frequently used as indicator organisms in biomonitoring programs. Despite their importance, key questions concerning the evolutionary history of caddisflies, such as the timing and origin of larval case-making, have been unanswered due to the lack of a well-resolved phylogenetic tree. To shed light on these questions in Trichoptera, we estimated a phylogenetic tree using a combination of transcriptomes and targeted enrichment data for 206 species, representing 48 of 52 extant families and 174 genera. We calibrated and dated the tree with a set of 33 carefully selected fossils. The first caddisflies originated in the Permian and the major suborders began to diversify in the Triassic. Ancestral state reconstruction and diversification analysis revealed that portable case-making evolved in three separate lineages and shifts in diversification occurred in concert with key evolutionary innovations other than case-making.

evolutionary biology↗

bioRxiv2023

A high-quality genome assembly of the ghost moth Druceiella hillmani provides new evidence of genome size augmentation in Hepialidae

Ghost moths are an unusual family of primitive moths (Lepidoptera: Hepialidae) known for their large body size and crepuscular adult activity. These moths represent an ancient lineage, frequently have soil dwelling larvae, and are adapted to high elevations, deserts, and other extreme environments. Despite being rather speciose with more than 700 species, there is a dearth of genomic resources for the family. Here, we present the first high quality, publicly available hepialid genome, generated from an Andean species of ghost moth, Druceiella hillmani. Our genome assembly has a length of 2,586 Mbp with contig N50 of 28.1 Mb and N50 of 29, and BUSCO completeness of 97.1%, making it one of the largest genomes in the order Lepidoptera. Our assembly is a vital resource for future research on ghost moth genomics.

evolutionary biology↗

bioRxiv2023

New genome reveals molecular signatures of adaptation to nocturnality in moth-like butterflies (Hedylidae)

Nearly all animals have a preferred period of daily activity (diel-niche), which is strongly influenced by the light environment. Sensory systems, particularly vision, are adapted to light, and evolutionary transitions to novel light environments, especially light limited ones, can impose strong constraints on eye evolution, color, and motion vision. The adaptive changes in sensory abilities of animals during these transitions, both at the genetic and neural levels, are largely unexplored. Butterflies and moths, with their diverse diel-niche shifts, are an ideal group for investigating the gene evolution linked to these transitions. While most butterflies are day-flying, hedylid butterflies are unique in being primarily nocturnal, and they represent an important evolutionary shift from diurnality to nocturnality in this clade. Here, we sequence the first high-quality Hedylidae genome and functionally annotate genes to understand genomic changes associated with shifts in diel niche. Comparing Hedylidae visual genes against day- and night-flying Lepidoptera species revealed that visual genes are highly conserved, with no major losses. However, hedylid butterfly opsins were more similar to nocturnal moths than their diurnal congeners. Tests on the evolutionary rates (dN/dS) confirmed that color vision opsins were under strong selection, similar to nocturnal moths. We propose that a convergent event of sequence evolution took place when these butterflies became nocturnal, approximately 98 million years ago.

evolutionary biology↗

bioRxiv2023

Substantial urbanization-driven declines of larval and adult moths in a subtropical environment

Recent work has shown the decline of insect abundance, diversity, and biomass, with potential implications for ecosystem services. These declines are especially pronounced in regions with high human activity, and urbanization is emerging as a significant contributing factor. However, the scale of these declines and the traits that determine variation in species-specific responses remain less well understood, especially in subtropical and tropical regions, where insect diversity is high and urban footprints are rapidly expanding. Here, we surveyed moths across an entire year in protected forested sites across an urbanization gradient to test how caterpillar and adult life stages of subtropical moths (Lepidoptera) are impacted by urbanization. Specifically, we assess how urban development affects the total abundance of caterpillars and adult moths, and quantify how richness and phylogenetic diversity of macro-moths are impacted by urban development. Additionally, we determine the effects of urban warming on species-specific adult macro-moth abundance while accounting for urban development and explore how life-history traits condition species responses to urban stressors. At the community level, we find that urban development decreases caterpillar biomass and adult moth abundance. We also find sharp declines of adults in response to urban development across the moth phylogeny, leading to a decrease in species richness and phylogenetic diversity in more urban sites. Finally, our study found that smaller macro-moths are less impacted by urban development than larger macro- moths in subtropical environments, perhaps highlighting the tradeoffs of metabolic costs of urban heat island effects favoring smaller moths over the relative benefits of dispersal for larger moths. In summary, our research underscores the far-reaching consequences of urbanization on moths and provides compelling evidence that urban forests alone may not be sufficient to safeguard biodiversity in cities.

ecology↗

bioRxiv2023

Phylogeny and divergence time estimation of Io moths and relatives (Lepidoptera: Saturniidae: Automeris)

The saturniid moth genus Automeris includes 145 described species. Their geographic distribution ranges from the eastern half of North America to as far south as Peru. Automeris moths are cryptically colored, with forewings that resemble dead leaves, and conspicuously colored, elaborate eyespots hidden on their hindwings. Despite their charismatic nature, the evolutionary history and relationships within Automeris and between closely related genera, remain poorly understood. In this study, we present the most comprehensive phylogeny of Automeris to date, including 80 of the 145 described species. We also incorporate two morphologically similar hemileucine genera, Pseudautomeris and Leucanella, as well as a morphologically distinct genus, Molippa. We obtained DNA data from both dry-pinned and ethanol-stored museum specimens and conducted Anchored Hybrid Enrichment (AHE) sequencing to reconstruct a high-quality dataset for phylogenetic analysis. The resulting phylogeny supports Automeris as a paraphyletic genus, with Leucanella and Pseudautomeris nested within, with the most recent common ancestor dating back to 21 mya. This study lays the foundation for future research on various aspects of Automeris biology, including anti-predator defense mechanisms, ecological adaptations, geographical distribution patterns, and potential drivers of speciation.

evolutionary biology↗

bioRxiv2023

The developmental gene disco regulates diel-niche evolution in adult moths

AbstractAnimals shift activity periods to reduce predation, minimize competition, or exploit new resources, and this can drive sensory system evolution. But adaptive mechanisms underlying niche- shifts are poorly understood, and model organisms are often too distantly related to reveal the genetic drivers. To address this, we examined expression patterns between two closely related silk moths that have undergone temporal niche divergence. We found 200-700 differentially expressed genes, including day upregulation in eye development and visual processing genes, and night upregulation of antennal and olfactory brain development genes. Further, clusters of circadian, sensory, and brain development genes co-expressed with diel-activity. In both species, eight genes showed expression significantly correlated to diel activity, and are involved in vision, olfaction, brain development, neural plasticity, energy utilization, and cellular maintenance. We repeatedly recovered disco, a zinc- finger transcription factor involved in antennal development, circadian activity, and optic lobe brain development in flies. While disco mutants have circadian arrhythmia, most studies attribute this to improper clock neuron development, not adult circadian maintenance. Comparing predicted 3D protein structure across moth and fly genetic models revealed disco likely retained developmental function with a conserved zinc finger domain, but gained functional zinc finger domains absent in D. melanogaster. These regions have several mutations between nocturnal and diurnal species that co- occur with higher levels of predicted phosphorylation sites. With robust circadian expression, functional nocturnal and diurnal mutations, and structural and sequence conservation, we hypothesize that disco may be a master regulator contributing to diel-activity diversification in adult moths. SignificanceInsect diel-activity patterns are diverse, yet the underlying evolutionary processes are poorly understood. Light environment powerfully entrains circadian rhythms and drives diel-niche and sensory evolution. To investigate its impact, we compared gene expression in closely related day- and night-active wild silk moths, with otherwise similar ecologies. Expression patterns that varied with diel activity included genes linked to eye development, neural plasticity and cellular maintenance. Notably, disco, which encodes a zinc-finger transcription factor involved in pupal Drosophila optic lobe and antennal development, shows robust adult circadian mRNA cycling in moth heads, is highly conserved in moths, and has additional zinc-finger domains with specific nocturnal and diurnal mutations. We hypothesize that disco may contribute to diversification of adult diel-activity patterns in moths.

evolutionary biology↗

bioRxiv2023

CRISPR-based diagnostics detects invasive insect pests

Rapid identification of organisms is essential across many biological and medical disciplines, from understanding basic ecosystem processes and how organisms respond to environmental change, to disease diagnosis and detection of invasive pests. CRISPR-based diagnostics offers a novel and rapid alternative to other identification methods and can revolutionize our ability to detect organisms with high accuracy. Here we describe a CRISPR-based diagnostic developed with the universal cytochrome-oxidase 1 gene (CO1). The CO1 gene is the most sequenced gene among Animalia, and therefore our approach can be adopted to detect nearly any animal. We tested the approach on three difficult-to-identify moth species (Keiferia lycopersicella, Phthorimaea absoluta, and Scrobipalpa atriplicella) that are major invasive pests globally. We designed an assay that combines recombinase polymerase amplification (RPA) with CRISPR for signal generation. Our approach has a much higher sensitivity than other real time-PCR assays and achieved 100% accuracy for identification of all three species, with a detection limit of up to 120 fM for P. absoluta and 400 fM for the other two species. Our approach does not require a lab setting, reduces the risk of cross-contamination, and can be completed in less than one hour. This work serves as a proof of concept that has the potential to revolutionize animal detection and monitoring.

genetics↗

bioRxiv2022

Uncovering hidden genetic diversity: allelic resolution of insect and spider silk genes

Arthropod silk is vital to the evolutionary success of hundreds of thousands of species. The primary proteins in silks are often encoded by long, repetitive gene sequences. Until recently, sequencing and assembling these complex gene sequences has proven intractable given their repetitive structure. Here, using high-quality long-read sequencing, we show that there is extensive variation--both in terms of length and repeat motif order--between alleles of silk genes within individual arthropods. Further, this variation exists across two deep, independent origins of silk which diverged more than 500 million years ago--(1) the insect clade containing caddisflies and butterflies and (2) spiders. This remarkable convergence in previously overlooked patterns of allelic variation across multiple origins of silk suggests mechanisms for the generation and maintenance of structural protein-coding genes. Future genomic efforts to connect genotypes to phenotypes should account for such allelic variation.

genomics↗