Genome-scale data and the development of novel statistical phylogenetic approaches have
greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its …

Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically
diverse as plants or animals. To understand budding yeast evolution, we analyzed the …

Phylogenomic studies have resolved countless branches of the tree of life, but remain strongly
contradictory on certain, contentious relationships. Here, we use a maximum likelihood …

Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous
inference of homology and saturation of substitutions, are thought to negatively impact …

Phylogenomic studies using genome-scale amounts of data have greatly improved
understanding of the tree of life. Despite the diversity, ecological significance, and biomedical and …

Horizontal gene transfer (HGT) is an important evolutionary force shaping prokaryotic and
eukaryotic genomes. HGT-acquired genes have been sporadically reported in insects, a …

Understanding the phylogenetic relationships among the yeasts of the subphylum
Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and …

Plant-pathogenic fungi form intimate interactions with their associated bacterial microbiota
during their entire life cycle. However, little is known about the structure, functions and …

The sizes of the data matrices assembled to resolve branches of the tree of life have increased
dramatically, motivating the development of programs for fast, yet accurate, inference. For …

Identifying our most distant animal relatives has emerged as one of the most challenging
problems in phylogenetics. This debate has major implications for our understanding of the …