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Lichens and Ascomycota broadly

Lichens and Ascomycota broadly. Alternative markers to COI. ITS. 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

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Lichens and Ascomycota broadly

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  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% > 95%

  5. 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)

  6. 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)

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

  8. 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)

  9. ARC Miadlikowska et al., Mycologia, 2003

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