Species boundaries in fungi - Percentage of identity between two isolates from the same species. (Dec/20/2010 )

When you compare two homologs genes (e.g. ITS, or Beta-tubulin) from two different isolates of related organisms, how similar enough (percentage of nucleotide identity) do they have to be to make them isolates of the same species? And what is the percentage you can expect among different species, but belonging to the same genus?
Does anybody know a review that explain how to infer the relatedeness of different organisms, based on sequences of housekeeping genes? And the identity thresholds that make them belonging to the same species, or same genus, etc... Thanks.

Most people would use tree-building software to do some sort of parsimony analysis. It won't tell you whether they are the same species though, just how similar the sequences are. The definition of separate species is rather fluid, and I suspect would depend entirely on the organism you are looking at.

It is a very difficult question you are asking, that cannot be answered generally.

The establishment of new species is often very subjective and depends on the "school" that dominates research on your fungi. Some groups create millions of s.sp./f.sp. and others make new species out of every different strain.
If you want to use DNA data, the story does not get easier. There are genera where only one nucleotide difference in the ITS is enough to qualify for a new species whereas in other genera you need more than 2% of difference. The same is true for other genes as well. Usually there is consent today that you need to find a clear, reproducible physiological/morphological difference between two isolates to qualify for separate species.
Good taxonomic works can be found in the "Studies in Mycocolgy" series, especially the issues entitled "Celebrating xy years of biodiversity" might contain some helpful works.

Edit: bad spelling

thanks for your guys response!