C. T. Hittinger

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.

Aim18p and Aim46p are CHI-domain-containing mitochondrial hemoproteins in Saccharomyces cerevisiae.

The paper identifies Aim18p and Aim46p as mitochondrial hemoproteins in yeast with structural similarities to CHI proteins but distinct functional roles.

Functional divergence in a multi-gene family is a key evolutionary innovation for anaerobic growth in Saccharomyces cerevisiae

This study identifies TIR1 and TIR3 as essential for anaerobic growth in S. cerevisiae and shows their functional divergence from an ancient duplication event.

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.

An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function

The paper constructs an orthologous gene coevolution network from 332 budding yeast species to explore eukaryotic cellular and genomic structure and function, revealing insights into gene connectivity and environmental fitness.

A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny

The paper constructs a genome-scale fungal phylogeny using 1,644 species and multiple data matrices, finding robust relationships and identifying taxonomic discrepancies.

Signatures of optimal codon usage predict metabolic ecology in budding yeasts

This study shows that optimal codon usage in metabolic pathways correlates with ecological niches in budding yeasts, suggesting codon optimization can reveal metabolic ecology.

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.

Variation and selection on codon usage bias across an entire subphylum

This study examines codon usage bias across 327 budding yeast species, finding that while genetic drift drives global patterns, translational selection influences many genes and codons.

Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts

This study identifies two lineages in Hanseniaspora yeasts, showing the FEL lineage lost more cell cycle and DNA repair genes than the SEL lineage, likely due to accelerated evolution and increased mutational load.

Pathogenic Budding Yeasts Isolated outside of Clinical Settings

The paper isolates pathogenic budding yeasts from non-clinical environments, finding associations with fruits, soil, and plants, challenging the assumption that these yeasts are only contaminants.

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.

Mitochondria-encoded genes contribute to the evolution of heat and cold tolerance among Saccharomyces species

The paper identifies mitochondrial DNA contributions to thermal tolerance differences between Saccharomyces species through genetic screening and recombinant analysis.

sppIDer: a species identification tool to investigate hybrid genomes with high-throughput sequencing

sppIDer identifies species and interspecies hybrids using high-throughput sequencing data by mapping reads to a combined reference genome and analyzing ploidy and genomic contribution.

Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

This study evaluates four maximum likelihood phylogenetic programs on empirical data sets, finding that exhaustive methods outperform faster ones for single-gene trees and IQ-TREE excels in concatenation-based species tree inference.

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.