Raquel Assis

Adaptive deletion of functional duplicate genes in Drosophila

This study shows gene deletion in Drosophila preferentially removes functionally unique, younger duplicates rather than degenerate ones, suggesting an adaptive role in genome streamlining.

Gene function predicts divergence across molecular levels

The paper develops a framework to compare evolutionary divergence across molecular levels and finds that divergence patterns vary by gene function and taxon.

Bacterial DNA invasion triggers transposable element proliferation and genome expansion

The paper identifies a link between bacterial horizontal gene transfer and transposable element proliferation in nut weevils, contributing to genome expansion and molecular innovation.

Taxonomic context and genomic architecture jointly shape expression divergence across animals

The paper quantifies expression divergence rates and patterns across Drosophila and mammals, showing higher divergence in Drosophila and specific effects of nested gene architecture.

Discriminating models of trait evolution

This paper introduces EvoDA, a supervised learning method for predicting evolutionary models of traits, showing improved performance over traditional methods in fungal phylogenies and gene expression evolution.

Ecological context structures duplication and mobilization of antibiotic and metal resistance genes in bacteria

The paper examines how ecological contexts influence the duplication and mobilization of antibiotic and metal resistance genes in bacteria across different environments.

Genomic insights into ancestry and infectious disease in 17th-century colonial Brazil

This study analyzes genomic and metagenomic data from 17th-century colonial Brazil remains to determine ancestry and potential causes of death, finding European genetic links and evidence of infectious diseases.

A tale of too many trees: a conundrum for phylogenetic regression

This paper investigates the consequences of gene tree-species tree mismatch in phylogenetic regression and finds high false positive rates when trees are mismatched.