1. Lichens and Ascomycota broadly Alternative markers to COI ITS

2. Why? Easy to amplify and sequence Mixture of highly conserved (5.8S) and variable sites (ITS 1 and 2) Most broadly used marker for systematic and ecological studies of fungi at the species level Highest overlap with other genes (AFToL) Alignment issues across a broad phylogenetic spectrum can be dealt with

3. Most broadly used marker for taxonomic and ecological studies of fungi at the species level Highest number of reference sequences = highest identification accuracy Detection of fungal contaminants in DNA isolates (endolichenic fungi closely related to lichen mycobionts) Essential to detect and characterize the hyperdiverse unknown Ascomycota species (70,000-1.5 m)

4. > 95%

6. Most broadly used marker for taxonomic and ecological studies of fungi at the species level Highest number of reference sequences = highest identification accuracy Detection of fungal contaminants in DNA isolates (endolichenic fungi closely related to lichen mycobionts) Essential to detect and characterize the hyperdiverse unknown Ascomycota species (70,000-1.5 m)

7. Highest overlap with other genes (AFToL) What are the putative ecological/physiological roles? What are the most closely related taxa? = phylogenies ≠ similarity Reconstruction of trait evolution on comprehensive phylogenies Branch lengths are important and trees not significantly worse than the optimal tree are needed = Bayesian MCMC searches More genes needed (nucSSU, nucLSU, RPB1, RPB2)

8. Most endophytes & endolichenic fungi are Ascomycota. Beyond this level, specificity is an open question. Parasitism vs. mutualism? Horizontal vs. vertical transmission?

11. Alignment issues across a broad phylogenetic spectrum can be dealt with Decouple tree searches from phylogenetic placement of unknowns Phylogenies need to be based on multigene datasets Use ITS only to search phylogenetic placement of unknown on a backbone constraint tree 5.8S can be aligned across the fungi (life), and ITS 1 and 2 can be coded to provide new sets of characters (arc)

12. ARC Miadlikowska et al., Mycologia, 2003