Biology subjects

Pavinato, V. A. C.

Publications and source records attributed to Pavinato, V. A. C..

5 recordsLinked to original sources

bioRxiv2026

Estimating the evolutionary fitness of specific synonymous codon changes

Synonymous mutations do not alter proteins but undergo natural selection in many species. For Drosophila melanogaster, reports on selection strength vary from undetectable to surprisingly strong. Here we apply a new method to estimate the population selection coefficient (2 Ns) for all 134 ordered pairs of synonymous codon changes. The method uses ratios of site frequency spectra (SFS) for codon changes to neutral changes, and does not depend on divergence data, or codon frequencies, and is relatively insensitive to demographic history. Results indicate that natural selection on synonymous codons is weak, with |2 Ns|<2.07 for all pairs of codons and |2 Ns|<1 for 64% of codon changes. Despite being derived solely from polymorphism data, codon fitness estimates are strongly correlated with observed codon frequencies. A selection-mutation-drift model based on our 2 Ns estimates accurately predicts codon usage, while a model based on mutation alone fails. Codon fitnesses correlate strongly with a measure of codon frequency covariation among genes, and codons with large frequency differences between high- and low-expression genes have high fitness values. Finally, we detect clear signs that selection favors codon changes that stabilize mRNA secondary structure. By avoiding divergence data, which have multiple sources of additional variance, and focusing solely on allele frequencies, a clear picture emerges of selection on codon usage. The convergence of multiple independent lines of evidence (codon frequencies, expression-dependent usage, covariation patterns, and mRNA structure) validates this polymorphism-based approach and provides a coherent framework for understanding selection on synonymous site evolution. Significance statementSynonymous mutations do not change proteins yet affect gene expression in multiple ways. Here we provide the first fitness estimates for each type of synonymous codon change. Using only allele frequencies--without divergence data, codon counts, or assumptions about preferred codons--we estimate the fitness of all 134 single-step synonymous codon changes in Drosophila melanogaster. Results reveal weak but non-negligible selection, with codon fitness values accurately predicting codon usage patterns, including expression-dependent biases, codon covariation across genes, and mRNA secondary structure effects. This work offers the first comprehensive fitness estimates for individual synonymous mutations, providing a direct population-level view of how subtle genetic changes shape molecular evolution and establishing a general strategy for quantifying weak selection using polymorphism data alone.

evolutionary biology↗

bioRxiv2022

Expanding the stdpopsim species catalog, and lessons learned forrealistic genome simulations

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and to the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed framework stdpopsim seeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version of stdpopsim focused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release of stdpopsim (version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than three-fold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements to stdpopsim aim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone.

bioinformatics↗

bioRxiv2021

Joint inference of adaptive and demographic history from temporal population genomic data

Disentangling the effects of selection and drift is a long-standing problem in population genetics. Simulations show that pervasive selection may bias the inference of demography. Ideally, models for the inference of demography and selection should account for the interaction between these two forces. With simulation-based likelihood-free methods such as Approximate Bayesian Computation (ABC), demography and selection parameters can be jointly estimated. We propose to use the ABC-Random Forests framework to jointly infer demographic and selection parameters from temporal population genomic data (e.g. experimental evolution, monitored populations, ancient DNA). Our framework allowed the separation of demography (census size, N) from the genetic drift (effective population size, Ne) and the estimation of genome-wide parameters of selection. Selection parameters informed us about the adaptive potential of a population (the scaled mutation rate of beneficial mutations,{theta} b), the realized adaptation (the number of mutation under strong selection), and population fitness (genetic load). We applied this approach to a dataset of feral populations of honey bees (Apis mellifera) collected in California, and we estimated parameters consistent with the biology and the recent history of this species.

evolutionary biology↗

bioRxiv2020

There is more than chitin synthase in insect resistance to benzoylureas: Molecular markers associated with teflubenzuron resistance in Spodoptera frugiperda

Chitin synthesis inhibitors are successfully used in pest control and are an excellent option for use in integrated pest management programs due to their low non-target effects. Reports on field-evolved resistance of lepidopteran pests to chitin synthesis inhibitors and the selection of laboratory resistant strains to these products require a detailed investigation on the resistance mechanisms and on the identification of molecular markers to support the implementation of efficient monitoring and resistance management programs. Teflubenzuron is a chitin synthesis inhibitor highly effective in controlling lepidopteran pests, including nowadays the world widely distributed fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith, 1797) (Lepidoptera: Noctuidae). We report the selection of a laboratory strain of S. frugiperda resistant to teflubenzuron, and its use for the characterization of the inheritance of resistance, evaluation of cross-resistance to other chitin-synthesis inhibitors and the identification of a set of single nucleotide polymorphisms (SNPs) for use as candidate molecular markers for monitoring the evolution of resistance of S. frugiperda to teflubenzuron. The resistance of the selected strain of S. frugiperda to teflubenzuron was characterized as polygenic, autosomal, and incompletely recessive. The resistance ratio observed was nearly 1,365-fold. Teflubenzuron-resistant strain showed some cross-resistance to lufenuron and novaluron but not to chlorfluazuron. We also detected a set of 72 SNPs that could support monitoring of the resistance frequency to teflubenzuron in field populations. Our data contribute to the understanding of the resistance mechanisms and the inheritance of polygenic resistance of S. frugiperda to benzoylureas. We also contribute with candidate markers as tools for monitoring the emergence and spread of teflubenzuron resistance in S. frugiperda.

evolutionary biology↗

bioRxiv2019

Leveraging targeted sequencing for non-model species: a step-by-step guide to obtain a reduced SNP set and a pipeline to automate data processing in the Antarctic Midge, Belgica antarctica.

The sequencing of whole or partial (e.g. reduced representation) genomes are commonly employed in molecular ecology and conservation genetics studies. However, due to sequencing costs, a trade-off between the number of samples and genome coverage can hinder research for non-model organisms. Furthermore, the processing of raw sequences requires familiarity with coding and bioinformatic tools that are not always available. Here, we present a guide for isolating a set of short, SNP-containing genomic regions for use with targeted amplicon sequencing protocols. We also present a python pipeline--PypeAmplicon-- that facilitates processing of reads to individual genotypes. We demonstrate the applicability of our method by generating an informative set of amplicons for genotyping of the Antarctic midge, Belgica antarctica, an endemic dipteran species of the Antarctic Peninsula. Our pipeline analyzed raw sequences produced by a combination of high-multiplexed PCR and next-generation sequencing. A total of 38 out of 47 (81%) amplicons designed by our panel were recovered, allowing successful genotyping of 42 out of 55 (76%) targeted SNPs. The sequencing of [~]150 bp around the targeted SNPs also uncovered 80 new SNPs, which complemented our analyses. By comparing overall patterns of genetic diversity and population structure of amplicon data with the low-coverage, whole-genome re-sequencing (lcWGR) data used to isolate the informative amplicons, we were able to demonstrate that amplicon sequencing produces information and results similar to that of lcWGR. Our methods will benefit other research programs where rapid development of population genetic data is needed but yet prevented due to high expense and a lack of bioinformatic experience.

evolutionary biology↗