Root of bacterial tree?

Bacterial Taxonomy
1

Hello,

What is considered to be the root of the bacterial tree for GTDB release 202?

Thanks,

Kate Shulgina

2

Hi. The GTDB reference tree should be treated as unrooted. If your question is in regards to calculating RED, we use an operational definition which uses the median RED value over a set of plausible rootings (see https://www.nature.com/articles/nbt.4229 for details).

3

Hi. Sorry to reactivate an old post. But in case of using the bacterial or archaea trees from GTDB to infer Duplication, Transfer and Loss events in a gene tree, we need a rooted species tree. Would you recommend something in particular for rooting those trees?

Best regards,
Lucas

4

Hi Lucas,

I don’t have a strong opinion and the GTDB reference trees should be treated as effectively unrooted. You might find the following manuscripts useful:

Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution
https://academic.oup.com/ismej/article/18/1/wrae129/7713227

A rooted phylogeny resolves early bacterial evolution
https://www.science.org/doi/10.1126/science.abe0511

Cheers,
Donovan