Download 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
• Highest overlap with other genes (AFToL)
• Alignment issues across a broad
phylogenetic spectrum can be dealt with
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)
> 95%
> 95%
1500
Species
1000
500
0
0
1000
2000
3000
Isolates
4000
5000
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)
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)
•Most endophytes &
endolichenic fungi are
Ascomycota.
•Beyond this level,
specificity is an open
question.
Parasitism vs. mutualism?
Horizontal vs. vertical
transmission?
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)
ARC
Miadlikowska et al., Mycologia, 2003