Our research tackles some fundamental evolutionary questions such as speciation, adaptation, and introgression. In particular, our work focuses on integrating experimental and computational approaches to study adaptive introgression in model and non-model organisms. Our research interests also include investigating anti-predator adaptation such as mimicry, aposematic coloration, and camouflage in insects.
an outgroup-free deep learning method for topology inference and introgression detection
Genetic admixture is a widespread phenomenon across diverse organisms. Conventional algorithms for inferring species relationship and detecting introgression often rely on outgroup data, which can be challenging to obtain and may introduce bias. Given the demonstrated efficacy and flexibility of neural networks in topology inference and introgression detection, we developed a deep learning-based method, ERICA-trio, to reconstruct evolutionary relationships among three taxa without requiring outgroup data. We trained and evaluated this network model using extensive simulated data that cover a broad range of evolutionary scenarios and parameter spaces. Our results demonstrate that ERICA-trio achieves accuracy and robustness comparable to the outgroup-dependent model. Leveraging the predicted topological proportions, we employed two strategies to identify genomic regions with potential introgression: one based on topological symmetry, and the other on the proportions of topology corresponding to gene flow. Both approaches were highly effective, particularly for detecting signatures of adaptive introgression. We further applied ERICA-trio to real genomic data from the Heliconius butterflies and successfully identified adaptive introgressed loci associated with mimicry wing patterns. In summary, our work extends the application of deep learning frameworks in evolutionary genomics, and presents a new tool for outgroup-free phylogenetic inference and introgression detection.
Link: https://doi.org/10.1093/bib/bbag453
Pangenome analyses reveal divergence and extensive introgression in two global corn pests
Introgression between closely related species can profoundly influence evolutionary trajectories, yet how genomic divergence interacts with introgression, especially in invasive hybridization, remains insufficiently understood. Structural variants (SVs), particularly chromosomal inversions, are key contributors to divergence and may modulate patterns of gene flow. The Asian corn borer (ACB) and European corn borer (ECB), two globally important agricultural pests, provide an excellent system to investigate these processes.We construct a graph-based pangenome from 23 high-quality genome assemblies to characterize genome-wide SVs and introgression between ACB and ECB. We identify over 216,000 SVs, most of which are associated with transposable elements and contribute to interspecific divergence. Population genomic analyses reveal widespread yet asymmetric introgression, predominantly from ACB into ECB populations in China. Introgressed regions are more prevalent in autosomes than in sex chromosomes and are enriched for genes involved in adaptive pathways. In contrast, large inversion regions on the Z chromosome exhibit strong genetic differentiation and reduced introgression, suggesting a role in maintaining species barriers. Notably, a highly divergent region containing the circadian clock gene period (per) shows signatures of selection. Functional validation using CRISPR/Cas9 demonstrates that per significantly influences diapause regulation, linking genomic divergence to adaptive phenotypic variation.
link: https://doi.org/10.1186/s13059-026-04216-6
link: https://doi.org/10.1186/s13059-026-04216-6
Molecular mechanism of female-specific wing degeneration in insects
Sexual dimorphism represents a striking dimension of morphological diversity both within and across taxa. Female-specific wing regression (FSWR) is common in insects, but the mechanisms underlying this regression remain largely unknown. We reveal that FSWR regulation involves sex-specific isoforms of DSX, a master regulator in the insect sex differentiation pathway, which oppositely regulate the expression of E93, the insect metamorphosis-controlling ‘adult factor’, during wing development. Mechanistically, DSXF represses, while DSXM activates, E93 expression through binding to DSX-binding motifs in FSWR lineages. This differential binding remodels chromatin accessibility and establishes a male-specific three-dimensional topology, facilitating the formation of an enhancer–promoter loop. Consequently, wing morphogenesis gene expression and wing blade cell type specification are promoted in males but suppressed in females. Taken together, our findings provide mechanistic insights into how the rewiring of two conserved signalling hubs into one axis can create regulatory degrees of freedom, thereby generating novel phenotypic variation able to fuel the exploitation of new ecological niches.
link: https://www.nature.com/articles/s41559-026-03107-0#Sec34
link: https://www.nature.com/articles/s41559-026-03107-0#Sec34
Comparative Genomics Illuminates the Adaptive Evolution of the Intertidal Spider
Spiders are renowned for their ecological versatility and silk-based innovations in materials science, yet marine environments remain virtually uncolonized by this predominantly terrestrial lineage. A striking exception is the obligate intertidal spider genus Desis, whose members have evolved extraordinary physiological and behavioural adaptations to persist in wave-swept, saline habitats that oscillate between land and sea. Here, we present a high-quality, chromosome-scale genome of the intertidal spider Desis jiaxiangi, together with a reference genome of the water spider Argyroneta aquatica, integrated with transcriptomic and proteomic data. This multi-omics framework reveals the genomic architecture underlying adaptation to life at the ocean's edge. Notably, we characterize a novel silk spidroin enriched with a unique GVGAKV motif, which may enhance silk hydrophobicity, and detect the duplication burst of hemocyanin genes likely supporting oxygen transport during submersion. Together, these findings reveal convergent molecular strategies for coping with extreme and fluctuating environments, and demonstrate how genomic innovation enables terrestrial lineages to invade marine-influenced ecosystems. Our study establishes Desis as powerful model for understanding adaptation at terrestrial–marine interface.
link: https://doi.org/10.1111/1755-0998.70147
An ancient genome duplication event drives the development and evolution of spinnerets in spiders
Key appendage innovations have driven the origin and expansion of arthropods, such as spinnerets enabling spiders to occupy three-dimensional space and diversify into more than 53,000 species. Here, we investigate the genetic basis of spinneret emergence in spiders by examining the complex history and functional importance of arachnid genome evolution. Using chromosome-scale genomes from newly sequenced spiders and the whip scorpion, we integrate evidence from macrosynteny and phylogenetic analyses to provide further strong support for a whole-genome duplication (WGD) event that occurred during early Arachnopulmonata evolution. Following this event, the abdominal-A gene pair not only exhibits functional divergence but also jointly facilitates the emergence of spinnerets. Furthermore, we integrated single-cell transcriptomic analyses and functional validation to confirm that the dachshund-1 gene also regulates spinneret development. The network of duplicated gene pairs may form a cornerstone in the origin and evolution of key morphological traits, revealing that the long-term effects of ancient WGDs on innovation and diversification also occurred in arthropods.
link: https://doi.org/10.1126/sciadv.adw2173
Mechanisms of Aristolochic Acid Resistance Insights
Aristolochic acids (AAs) are natural compounds found in Aristolochiaceae plants, to which humans are frequently exposed through environmental and medicinal sources. AAs are highly nephrotoxic and carcinogenic, mediated by oxidative stress and bioactivation-induced DNA damage and mutagenicity. Nevertheless, some Lepidoptera, including Pachliopta aristolochiae, feed exclusively on Aristolochiaceae and sequester AAs as a chemical defense. This is uncommon in nature and it is not yet fully understood how these insects avoid the lethal effects of AAs. To address this question, we investigate Pac. aristolochiae’s AA-resistance mechanisms by employing metabolic analyses, multiomics analyses, in situ imaging and more. Our findings indicate that AAs may be detoxified through biotransformation and a robust antioxidant system, involving candidate genes such as 15-oxo-prostaglandin 13-reductases (PGRs), cytochrome P450s, and catalases. Unexpectedly, DNA adducts, the covalent binding products from activated AA intermediates, are detected across most life stages of Pac. aristolochiae, revealing that Pac. aristolochiae can maintain genomic integrity despite a substantial burden (reaching over 1800 AA-DNA adducts per 108 nucleotides in adults, approximately 1 adduct per 55 000 nucleotides). Our study highlights insect AA tolerance as a means to discover human protective mechanisms, thereby suggesting new avenues for preventing AA-related diseases.
link: https://doi.org/10.1002/advs.202518072
link: https://doi.org/10.1002/advs.202518072
The pigment transporter Redboy confers programmed body colour transition in orchid mantises
Programmed phenotypic transition is prevalent throughout the tree of life, yet the concrete mechanisms that underpin this phenomenon are poorly understood. The orchid mantis (Hymenopus coronatus, Mantodea) is a model study system for programmed body colour transitions that displays a prominent black-red body colour in first-instar nymphs, then switches to a flowery white body colour in later-instar nymphs. Here we reveal that this body colour transition is achieved by the simultaneous excretion of decarboxylated-xanthommatin (red pigment) and the accumulation of uric acid (white pigment) in the epidermis during the first moult. This change in pigmentation is associated with a novel subtype of ABCG pigment transporter that we call ‘Redboy’ in Polyneoptera, which is upregulated by insect steroid hormone (ecdysone) during the first moult of orchid mantises. RNAi assay and pigment analyses show that Redboy functions together with the co-transporter White, exporting red pigments from and concurrently importing white pigments into the epidermal cells. Spectral reflectance analyses and predation experiments reveal that Redboy-conferred programmed body colour transition enhances predator avoidance during the first instar, and both prey attraction and predator avoidance in later instars. Our findings clarify how gene family evolution and hormone regulation coordinate programmed phenotypic transition and promote ecological adaptation in orchid mantises.
link: https://www.nature.com/articles/s41559-025-02737-0
The diversification of butterfly wing patterns: Progress and prospects
Butterfly wings display rich phenotypic diversity and are associated with complex biological functions, thus serving as an important evolutionary system to address the genetic basis and evolution of phenotypic diversification. We review recent butterfly studies that revealed complex functions underlying diversified wing patterns and describe the genetic and environmental factors involved in wing pattern determinations. These factors lead to inter-specific divergence, genetic polymorphism, and phenotypic plasticity, which in many cases are decided by several key genes. We also summarize the research advances on gene co-option as an important origin of functional complexity and evolutionary novelty. These findings reveal a pattern of evolutionary innovation within a constrained developmental framework during butterfly wing morphogenesis, but further research is required to gain a systematic and comprehensive understanding.
link: https://linkinghub.elsevier.com/retrieve/pii/S2214-5745(23)00134-7
link: https://linkinghub.elsevier.com/retrieve/pii/S2214-5745(23)00134-7
Potential and progress of studying mountain biodiversity by means of butterfly genetics and genomics
Mountains are rich in biodiversity, and butterflies are species-rich and have a good ecological and evolutionary research foundation. This review addresses the potential and progress of studying mountain biodiversity using butterflies as a model. We discuss the uniqueness of mountain ecosystems, factors influencing the distribution of mountain butterflies, representative genetic and evolutionary models in butterfly research, and evolutionary studies of mountain biodiversity involving butterfly genetics and genomics. Finally, we demonstrate the necessity of studying mountain butterflies and propose future perspectives. This review provides insights for studying the biodiversity of mountain butterflies as well as a summary of research methods for reference.
link: https://www.sciencedirect.com/science/article/pii/S1673852723001364
Inferring historical introgression with deep learning
Resolving phylogenetic relationships among taxa remains a challenge in the era of big data due to the presence of genetic admixture in a wide range of organisms. Rapidly developing sequencing technologies and statistical tests enable evolutionary relationships to be disentangled at a genome-wide level, yet many of these tests are computationally intensive and rely on phased genotypes, large sample sizes, restricted phylogenetic topologies, or hypothesis testing. To overcome these difficulties, we developed a deep learning-based approach, named ERICA, for inferring genome-wide evolutionary relationships and local introgressed regions from sequence data. ERICA accepts sequence alignments of both population genomic data and multiple genome assemblies, and efficiently identifies discordant genealogy patterns and exchanged regions across genomes when compared with other methods. We further tested ERICA using real population genomic data from Heliconius butterflies that have undergone adaptive radiation and frequent hybridization. Finally, we applied ERICA to characterize hybridization and introgression in wild and cultivated rice, revealing the important role of introgression in rice domestication and adaptation. Taken together, our findings demonstrate that ERICA provides an effective method for teasing apart evolutionary relationships using whole genome data, which can ultimately facilitate evolutionary studies on hybridization and introgression.
link: https://doi.org/10.1093/sysbio/syad033
