• Publications
  • Influence
Contentious relationships in phylogenomic studies can be driven by a handful of genes
TLDR
A maximum likelihood framework is used to quantify the distribution of phylogenetic signal among genes and sites for 17 contentious branches and 6 well-established control branches in plant, animal and fungal phylogenomic data matrices, finding that resolution in some of these 17 branches rests on a single gene or a few sites. Expand
Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
TLDR
It is argued that reductive evolution is a major mode of evolutionary diversification and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. Expand
A versatile and highly efficient toolkit including 102 nuclear markers for vertebrate phylogenomics, tested by resolving the higher level relationships of the caudata.
TLDR
Experimental tests and a demonstration for a particular case show that the NPCL toolkit is a highly reliable, fast, and cost-effective approach for vertebrate phylogenomic studies and thus has the potential to accelerate the completion of many parts of the vertebrate tree of life. Expand
Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data
TLDR
These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. Expand
One thousand two hundred ninety nuclear genes from a genome-wide survey support lungfishes as the sister group of tetrapods.
TLDR
Phylogenetic analyses of a data set comprising 1,290 nuclear genes encoding 690,838 amino acid residues provided overwhelming evidence that the lungfishes are the closest living relatives of the land vertebrates. Expand
Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles.
TLDR
This work takes advantage of the multiple genome alignment resources from the University of California-San Cruz Genome Browser and presents a simple and straightforward bioinformatic approach to automatically screen for candidate nuclear protein-coding locus (NPCL) markers. Expand
Enlarged Multilocus Data set Provides Surprisingly Younger Time of Origin for the Plethodontidae, the Largest Family of Salamanders.
TLDR
This work argues that the classic "Out of Appalachia" hypothesis of plethodontid origins is problematic, and proposes the hypothesis that these salamanders are much younger, arising close to the K-T boundary (~66 Ma). Expand
Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts
TLDR
Phylogenetic analyses of this gene cluster suggest that pulcherrimin biosynthesis and utilization were ancestral to budding yeasts, but the biosynthesis genes and, subsequently, the utilization genes, were lost in many lineages, mirroring other microbial public goods systems that lead to the rise of cheater organisms. Expand
Eukaryotic Acquisition of a Bacterial Operon
TLDR
The horizontal operon transfer of a siderophore biosynthesis pathway from relatives of Escherichia coli into a group of budding yeast taxa is reported, showing that the co-linearly arranged secondary metabolism genes are expressed, exhibit eukaryotic transcriptional features, and enable the sequestration and uptake of iron. Expand
Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
TLDR
Hanseniaspora is an ancient lineage that has diversified and thrived, despite lacking many otherwise highly conserved cell cycle and genome integrity genes and pathways, and may represent a novel system for studying cellular life without them. Expand
...
1
2
3
4
5
...