D. A. Opulente

Functional and evolutionary integration of a fungal gene with a bacterial operon

The paper shows that the fungal gene ENB1, acquired from a bacterial operon, enables iron uptake in W/S clade yeasts and evolved through horizontal transfer and gene loss.

Diverse signatures of convergent evolution in cacti-associated yeasts

This study identifies convergent evolution in cacti-associated yeasts using genomic and phenotypic data, finding thermotolerance and horizontal gene transfer as key adaptive traits.

Saccharomycotina yeasts defy longstanding macroecological patterns

This study uses machine learning to model global yeast species distributions and finds they defy traditional macroecological patterns.

Machine learning illuminates how diet influences the evolution of yeast galactose metabolism

This study uses machine learning to analyze yeast genomes and growth data to uncover how diet influences the evolution of galactose metabolism.

Genomic and ecological factors shaping specialism and generalism across an entire subphylum

The paper analyzes genomic, metabolic, and ecological data from nearly all Saccharomycotina yeast species to show that intrinsic genetic factors, not trade-offs or extrinsic factors, drive variation in niche breadth.

Codon optimization, not gene content, predicts XYLose metabolism in budding yeasts

This study identifies codon optimization as the key predictor of xylose metabolism in budding yeasts, showing that gene content alone is insufficient.

Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

The paper studies genetic and phenotypic diversity across 1,800 Saccharomyces strains, revealing insights into macroevolutionary processes and gene flow effects on traits.

Substrate, temperature, and geographical patterns among nearly 2,000 natural yeast isolates

The paper analyzes nearly 2,000 natural yeast isolates to identify geographic, substrate, and temperature patterns among yeast taxa.

Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

This study constructs a genome-scale phylogeny of Ascomycota fungi, revealing contrasting modes of genome evolution across subphyla.

Eukaryotic acquisition of a bacterial operon

The paper reports the horizontal transfer of a bacterial operon into yeast, showing its adaptation to eukaryotic gene expression and iron acquisition in an insect gut environment.

Yeast de novo genes preferentially emerge from divergently transcribed, GC-rich intergenic regions

The paper identifies 703 de novo genes in 15 yeast species and finds they preferentially arise from GC-rich intergenic regions near divergent promoters and recombination hotspots.