By Jason Stajich, on December 26th, 2008
A recent paper in MBE presents evidence that the Taphrinomycota (containing S. pombe and Pneumocystis) are in fact a monophyletic group. This is considered an early branch in the Ascomycota with the Pezizomycotina (filamentous ascomycete fungi like Neurospora and Aspergillus) and Saccharomycotina (fungi mainly with yeast forms including Candida and Saccharomyces). The monophyly of Taphrinomyoctina fungi is something that has been fairly accepted but there are a few publications reporting conflicting evidence in some sets gene trees. This conflict is most likely due to Long Branch Attraction (LBA) and the Philippe lab has long worked on this problem of LBA working to develop tools like PhyloBayes that attempt to correct for LBA with a parameter rich model and using lots of data (like whole [...]
By Jason Stajich, on April 22nd, 2008
A link to the story about Matteo Garbelotto’s work on Phytophthora ramorum and showing that the source in California is likely from ornamentals from a nursery. The work is to appear soon in Molecular Ecology but alas is not available yet.
A recent paper on updated Phytophthora phylogeny from Jamie Blair and co-authors is also out in FGB. [...]
By Jason Stajich, on March 11th, 2008
Estimating divergence times is notorious difficult and the field can be downright rancorous with some being accused of reading tea leaves and chicken entrails – interesting reading for personalities as much as the different scientific approaches. There are several different approaches to trying to estimate a divergence time among species, using [...]
By Jason Stajich, on February 8th, 2008
A review in Plant Cell from Darren Soanes and colleagues summarizes some of the major findings about evolution of phytopathogenic fungi gleaned from genome sequencing highlighting 12 fungi and 2 oomycetes. By mapping evolution of genes identified as virulence factors as well as genes that appear to have similar patterns of diversification, we can hope to derive some principals about how phytopathogenic fungi have evolved from saprophyte [...]
By Jason Stajich, on November 19th, 2007
Fungi, like most organisms, take an active role in finding food for survival. When thinking about hostile takeovers by fungi, one probably thinks about mycelia growing towards nutrients, rotting plant matter, the ability to extract nutrients from a living host, or perhaps producing toxins or secondary metabolites that can affect the host. However, [...]
By Jason Stajich, on July 30th, 2007
Back from ISMB/ECCB and a mountain of things left undone that somehow still need doing … including a quick entry about what was interesting at the [...]
By sharpton, on March 30th, 2007
Perhaps not a surprise to anyone that has dabbled in evolutionary analysis of proteins, Kawahara and Imanishi (BMC Evolutionary Biology 2007) confirm that not every protein evolves via a molecular clock in Saccharomyces
sensu scricto. Using everyone’s favorite evolutionary tool, PAML, the authors identify protein lineages via a whole genome scan that evolve relatively slow [...]
By Jason Stajich, on March 18th, 2007
The Candida clade of Hemiascomycete fungi have received much attention from funding bodies so that many genomic and experimental resources are available address questions of pathogenecity and industrial applications of these species.
The Candida genus
Traditionally, species of yeasts that were thought to be asexual were given the genus name Candida. This has lead to Candida being a sort of taxonomic rubbish [...]