Biology subjects

Freitas, A. V.

Publications and source records attributed to Freitas, A. V..

6 recordsLinked to original sources

bioRxiv2026

Metabolic stress reveals widespread accumulation of cap-unmethylated RNAs

RNA polymerase II transcripts are capped with N7-methylguanosine (mG), a conserved modification essential for mRNA function. Although traditionally viewed as constitutive, we developed a mass spectrometry-based method to demonstrate that in both yeast and mammalian cells, a substantial population of mRNAs lack cap methylation in response to SAM-limiting conditions and oxidative stress, which may be frequently encountered across organisms. Through developing two transcriptome-wide approaches, we found that methylation is enriched on specific transcripts and uncovered an unexpected connection between histone H3K36me3 and cap methylation, with both marks preferentially associated with stress-responsive MAPK signaling pathways. Strikingly, cap-unmethylated mRNAs exhibit features of canonical mRNAs--they are polyadenylated, exported to the cytosol, and translated. Enforced cap methylation reduces cell growth under SAM limitation, suggesting that unmethylated mRNAs confer an adaptive advantage during stress. These findings establish mRNA cap methylation as a dynamic, regulated modification and a previously underappreciated layer of gene expression control.

cell biology↗

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↗

bioRxiv2024

Genomics of Neotropical biodiversity indicators: two butterfly radiations with rampant chromosomal rearrangements and hybridisation

A major question in evolutionary biology is what drives the diversification of lineages. Rapid, recent radiations are ideal systems for addressing how new species arise because they still show key morphological and ecological adaptations associated with speciation. While most studied recent radiations have evolved in an insular environment, less research has been carried out on continental radiations with complex species interactions. Melinaea and Mechanitis butterflies (Nymphalidae: Ithomiini) have rapidly radiated in the Neotropics. They are classical models for Amazonian biogeography and colour pattern mimicry and have been proposed as biodiversity indicators. We generated reference genomes for five species of each genus, and whole-genome resequencing data of most species and subspecies covering a wide geographic range to assess phylogeographic relationships, patterns of hybridisation and chromosomal rearrangements. Our data help resolve the classification of these taxonomically challenging butterflies and reveal very high diversification rates. We find rampant evidence of historical hybridisation and putative hybrid species in both radiations, which may have facilitated their rapid diversification. Moreover, dozens of chromosomal fusions and fissions were identified between congeneric species, and even some within species. We conclude that interactions between geography, hybridisation and chromosomal rearrangements have contributed to these two rapid radiations in the highly diverse Neotropical region. We suggest that rapid radiations may be spurred by repeated periods of geographic isolation during Pleistocene climate oscillations, combined with lineage-specific rapid accumulation of incompatibilities during allopatric phases, followed by secondary contact with some gene exchange. Significance StatementUnderstanding factors contributing to rapid speciation is a key aim of evolutionary biology. Here we focus on two rapid radiations of Neotropical butterflies. Our genomic data with broad taxonomic and geographic coverage reveal rampant hybridisation and chromosomal rearrangements, each likely contributing to the high diversification rates. Our study highlights the use of genomic data to resolve taxonomically challenging species groups and elucidate drivers of diversification in rapid radiations. We show that for biodiversity hotspots with recent radiations, barcoding is insufficient to characterise species richness due to gene flow and recent speciation. The taxonomic implications of both introgression and karyotype diversity for species delimitation are important to consider during monitoring and management of biodiversity in these vulnerable habitats.

evolutionary biology↗

bioRxiv2023

Codon optimality modulates protein output by tuning translation initiation

The impact of synonymous codon choice on protein output has important implications for understanding endogenous gene expression and design of synthetic mRNAs. Synonymous codons are decoded at different speeds, but simple models predict that this should not drive protein output. Instead, translation initiation should be the rate limiting step for production of protein per mRNA, with little impact of codon choice. Previously, we used a neural network model to design a series of synonymous fluorescent reporters and showed that their protein output in yeast spanned a seven-fold range corresponding to their predicted translation elongation speed. Here, we show that this effect is not due primarily to the established impact of slow elongation on mRNA stability, but rather, that slow elongation further decreases the number of proteins made per mRNA. We combine simulations and careful experiments on fluorescent reporters to show that translation is limited on non-optimally encoded transcripts. Using a genome-wide CRISPRi screen, we find that impairing translation initiation attenuates the impact of slow elongation, showing a dynamic balance between rate limiting steps of protein production. Our results show that codon choice can directly limit protein production across the full range of endogenous variability in codon usage.

molecular biology↗

bioRxiv2020

The latitudinal diversity gradient in brush-footed butterflies (Nymphalidae): conserved ancestral tropical niche but different continental histories.

The latitudinal diversity gradient (LDG) is arguably one of the most striking patterns in nature. The global increase in species richness toward the tropics across continents and taxonomic groups stimulated the formulation of many hypotheses to explain the underlying mechanisms of this pattern. We evaluated several of these hypotheses to explain spatial diversity patterns in the butterfly family, Nymphalidae, by assessing the contributions of speciation, extinction, and dispersal to the LDG, and also the extent to which these processes differ among regions at the same latitude. We generated a new, time-calibrated phylogeny of Nymphalidae based on 10 gene fragments and containing ca. 2,800 species ([~]45% of extant diversity). Neither speciation nor extinction rate variations consistently explain the LDG among regions because temporal diversification dynamics differ greatly across longitude. For example, we found that Neotropical nymphalid diversity results from low extinction rates, not high speciation rates, and that biotic interchanges with other regions were rare. Southeast Asia was also characterized by a low speciation rate but, unlike the Neotropics, was the main source of dispersal events through time. Our results suggest that global climate change throughout the Cenozoic, particularly during the Eocene-Oligocene transition, combined with the conserved ancestral tropical niches, played a major role in generating the modern LDG of butterflies.

ecology↗

bioRxiv2018

The Trials and Tribulations of Priors and Posteriors in Bayesian Timing of Divergence Analyses: the Age of Butterflies Revisited

The need for robust estimates of times of divergence is essential for downstream analyses, yet assessing this robustness is still rare. We generated a time-calibrated genus-level phylogeny of butterflies (Papilionoidea), including 994 taxa, up to 10 gene fragments and an unprecedented set of 12 fossils and 10 host-plant node calibration points. We compared marginal priors and posterior distributions to assess the relative importance of the former on the latter. This approach revealed a strong influence of the set of priors on the root age but for most calibrated nodes posterior distributions shifted from the marginal prior, indicating significant information in the molecular dataset. We also tested the effects of changing assumptions for fossil calibration priors and the tree prior. Using a very conservative approach we estimated an origin of butterflies at 107.6 Ma, approximately equivalent to the Early Cretaceous-Late Cretaceous boundary, with a credibility interval ranging from 89.5 Ma (mid Late Cretaceous) to 129.5 Ma (mid Early Cretaceous). This estimate was robust to alternative analyses changing core assumptions. With 994 genera, this tree provides a comprehensive source of secondary calibrations for studies on butterflies.

evolutionary biology↗