# Analysing fungal ITS data - questions about the pipeline - phylogenetic analysis

**URL:** https://forum.qiime2.org/t/analysing-fungal-its-data-questions-about-the-pipeline-phylogenetic-analysis/18981
**Category:** General Discussion
**Created:** [March 25, 2021, 3:06pm UTC](https://forum.qiime2.org/t/analysing-fungal-its-data-questions-about-the-pipeline-phylogenetic-analysis/18981 "2021-03-25T15:06:29Z")
**Posts on this page:** 1
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### Author: ![Nicholas\_Bokulich](https://forum.qiime2.org/user_avatar/forum.qiime2.org/nicholas_bokulich/32/19937_2.png) [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [March 27, 2021, 6:22am UTC](https://forum.qiime2.org/t/analysing-fungal-its-data-questions-about-the-pipeline-phylogenetic-analysis/18981/2 "2021-03-27T06:22:33Z")

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Hi @Cat ,

> [@Cat](#):
>
> whilst not often seen, the ITS1 region does produce a reasonable tree and is used frequently in published analyses including gold standard taxonomy papers from eg CBS.

This is sort of true — ITS alignments are sometimes used for examining phylogeny of _closely related_ fungal species. Thus, fungal taxonomy papers (which are generally concerned with parsing closely related species/groups) will sometimes use this for comparison of isolated strains.

> [@Cat](#):
>
> I would argue that a taxonomy paper is a far cry from a mycobiome study

Indeed it is. In a mycobiome study you are almost inevitably comparing fungi from highly divergent groups. ITS will not generate a reliable alignment/phylogeny for such divergent groups.

As a non-coding region, it is highly variable, which is a two-edged sword: on the one hand, this means that it can be used to differentiate even many closely related species (taxonomically and phylogenetically) but on the other hand the mutation rate is so high that it loses the "molecular clock" aspects of conserved genes (such as rRNA genes) that are used for molecular phylogeny of highly divergent groups.

This looks like a relevant paper on the topic:

> **[The effects of increasing genetic distance on alignment of, and tree...](https://www.sciencedirect.com/science/article/abs/pii/S1055790302003664?via%3Dihub)**
>
> We examined how alignment of internal transcribed spacers of rDNA in fungi and plants changes with increasing genetic distance by successive removal o…

I hope that helps!

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