X.-X. Shen

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.

A genome-scale Opisthokonta tree of life: toward phylogenomic resolution of ancient divergences

The paper reconstructs a taxon-rich Opisthokonta tree of life using genome-scale data, suggesting a Mesoproterozoic origin and unresolved deep divergences within Holozoa.

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.

OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

OrthoSNAP identifies single-copy orthologs from gene family trees, increasing the number of markers for molecular evolution studies by splitting and pruning gene families.

Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum

The paper examines gene loss in the DNA mismatch repair pathway across fungal species, finding extensive MMR gene loss in powdery mildew lineages associated with increased mutation rates.

PhyKIT: a UNIX shell toolkit for processing and analyzing phylogenomic data

PhyKIT provides a UNIX shell toolkit for processing and analyzing phylogenomic data, offering functions to evaluate sequence alignments, trees, and evolutionary relationships.

Rooting the animal tree of life

This paper investigates the root placement in the animal tree of life by analyzing 15 phylogenomic studies and finding that Ctenophora-sister is supported under constrained site-heterogeneous models.

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.

Feature Frequency Profile-based phylogenies are inaccurate

This paper evaluates the accuracy of FFP-based phylogenies and finds they perform poorly compared to standard methods like concatenation and coalescence.

ClipKIT: a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

ClipKIT trims multiple sequence alignments to retain phylogenetically-informative sites, improving phylogenomic inference accuracy and efficiency.

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.

Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices

The paper identifies four factors causing outlier genes in phylogenomic matrices and shows how excluding them can mislead evolutionary inferences.

Recurrent loss of abaA, a master regulator of asexual development in filamentous fungi, correlates with changes in genomic and morphological traits

The paper investigates the loss of abaA, a master regulator of asexual development in fungi, and shows its correlation with morphological changes in asexual fruiting bodies across multiple fungal lineages.

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.

The impact of natural selection on the evolution and function of placentally expressed galectins

This study examines the molecular evolution of placental galectins across mammals and humans, identifying signatures of natural selection and structural differences in a common haplotype.

A robust phylogenomic timetree for biotechnologically and medically important fungi in the genera Aspergillus and Penicillium

The paper constructs a robust phylogenomic timetree for Aspergillus and Penicillium fungi using multiple genome datasets and phylogenetic methods to identify incongruent branches and estimate divergence times.

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.

Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata

This study investigates the genomic features and evolution of a conditionally dispensable chromosome (CDC) in the tangerine pathotype of Alternaria alternata, revealing its role in pathogenicity and horizontal gene transfer.

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.