Biology subjects

Ruggieri, A. A.

Publications and source records attributed to Ruggieri, A. A..

4 recordsLinked to original sources

bioRxiv2025

Polygenic basis of incipient reproductive isolation in hybridizing populations is revealed by pangenomic and epigenetic divergence

Incipient reproductive isolation in the presence of gene flow has traditionally been attributed to a small number of major-effect loci under strong selection, representing only a minor fraction of the genome. Using the Heliconius erato adaptive radiation--a butterfly species with populations at varying levels of genetic differentiation--we employed a pan-genome approach to investigate genome-wide mutational divergence, epigenetic changes, and structural variation contributing to divergence. In contrast to earlier studies that identified only a few highly divergent loci, our high-resolution analysis reveals widespread divergence across the genome, suggesting polygenic barriers to gene flow. Epigenetic divergence assessed using ATAC-seq, highlights population-specific differences in chromatin accessibility, which may reflect SNPs distribution or precede genetic differentiation by reshaping regulatory landscapes. We also identified new structural variants, including polymorphic indels in open chromatin, that further associate with genomic divergence. Together, these findings show that the genomic landscape of H. erato is shaped by a dynamic interplay of mutational changes, epigenetic modifications, and structural variation. We emphasize the role of developmental, behavioral, and ecological adaptations and provide a broader perspective on the functional genetic basis of genome-wide divergence in Heliconius. This emerging polygenic framework offers a more detailed understanding of how reproductive barriers evolve under ongoing gene flow.

evolutionary biology↗

bioRxiv2025

Gut microbiota as a modulator of circadian neural development in the honey bee model.

Disruption in gut microbiota during the early postnatal period can disrupt normal neural development and result in long-term behavioral alterations1. Similar to other neural systems, the circadian clock mechanism continues to mature after birth2, yet how microbial disturbances in the early period influence the onset of circadian rhythms and the development of central clock mechanisms remains poorly understood. Here we studied whether early-life gut dysbiosis affects the ontogeny of behavioral circadian rhythms and the maturation of clock neurons using the honey bee (Apis mellifera), a model organism that shares features of postnatal development of behavioral circadian rhythm and clock system3-5 with humans6. Our findings demonstrate that antibiotic-treated and gnotobiotic-reared bees display reduced rhythmicity compared to controls. These treatments also impair the development of the circadian pacemaker, marked by fewer Pigment-Dispersing Factor (PDF)-expressing neurons. Additionally, antibiotic exposure increased the expression of the Insulin-like Growth Factor Binding Protein Acid Labile Subunit (IGFALS) in early ages, which stabilizes the IGF-1/27, a hormone important for neurodevelopmental processes42. Together, these results identify gut microbiota as a modulator of circadian development. Our work provides an understanding of how early-life microbial disruptions influence the development of circadian rhythms, providing information that may extend to other animals, including humans.

neuroscience↗

bioRxiv2022

Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies

Heliconius butterflies, a speciose genus of Mullerian mimics, represent a classic example of an adaptive radiation that includes a range of derived dietary, life history, physiological and neural traits. However, key lineages within the genus, and across the broader Heliconiini tribe, lack genomic resources, limiting our understanding of how adaptive and neutral processes shaped genome evolution during their radiation. We have generated highly contiguous genome assemblies for nine new Heliconiini, 29 additional reference-assembled genomes, and improve 10 existing assemblies. Altogether, we provide a major new dataset of annotated genomes for a total of 63 species, including 58 species within the Heliconiini tribe. We use this extensive dataset to generate a robust and dated heliconiine phylogeny, describe major patterns of introgression, explore the evolution of genome architecture, and the genomic basis of key innovations in this enigmatic group, including an assessment of the evolution of putative regulatory regions at the Heliconius stem. Our work illustrates how the increased resolution provided by such dense genomic sampling improves our power to generate and test gene-phenotype hypotheses, and precisely characterize how genomes evolve.

evolutionary biology↗

bioRxiv2022

A butterfly pan-genome reveals a large amount of structural variation underlies the evolution of chromatin accessibility

Despite insertions and deletions being the most common structural variants (SVs) found across genomes, not much is known about how much these SVs vary within populations and between closely related species, nor their significance in evolution. To address these questions, we characterized the evolution of indel SVs using genome assemblies of three closely related Heliconius butterfly species. Over the relatively short evolutionary timescales investigated, up to 18.0% of the genome was composed of indels between two haplotypes of an individual H. charithonia butterfly and up to 62.7% included lineage-specific SVs between the genomes of the most distant species (11 Mya). Lineage-specific sequences were mostly characterized as transposable elements (TEs) inserted at random throughout the genome and their overall distribution was similarly affected by linked selection as single nucleotide substitutions. Using chromatin accessibility profiles (i.e., ATAC-seq) of head tissue in caterpillars to identify sequences with potential cis-regulatory function, we found that out of the 31,066 identified differences in chromatin accessibility between species, 30.4% were within lineage-specific SVs and 9.4% were characterized as TE insertions. These TE insertions were localized closer to gene transcription start sites than expected at random and were enriched for several transcription factor binding site candidates with known function in neuron development in Drosophila. We also identified 24 TE insertions with head-specific chromatin accessibility. Our results show high rates of structural genome evolution that were previously overlooked in comparative genomic studies and suggest a high potential for structural variation to serve as raw material for adaptive evolution.

genomics↗