GTDB Forum

Gross taxon splitting, eg Pseudomonas_S among Xanthomonadaceae

According to bac120_r202.tree and sp_clusters_r202.tsv, Pseudomonas_S (boreopolis, GCA_014654535) is not among the Pseudomonadaceae, but among Xanthomonadaceae. I suppose this is based on precedence from an old type specimen’s name, but are there plans to rename such gross cases, perhaps working with ICSP?
At finer levels of splitting the remaining Pseudomonas are not monophyletic but are invaded by other genera such as Azotobacter. Was it monophyletic in an earlier tree?
Likewise there is splitting of Xanthomonas. What’s the general policy on toleration of taxon-splitting in the tree?

Hello

Thanks for your request.

Regarding the first part of your question:

Yes, the name of the genus Pseudomonas_S reflects the fact that this genus [and its sole species] originally was thought to be part of the Pseudomonas sensu stricto. However, we never planned to propose new generic names for such cases as this is not our primary objective. Also the current system is rather slow to do this in the effective manner that would be aligned with our taxonomic releases. We believe that descriptions of new taxa and naming should remain a community effort and not of a single resource.

The primary objective of GTDB is to provide the taxonomic framework by incorporating existing opinions and aligning or unifying them to the same standards. In the past, however, we have done this by proposing new Latin names for higher taxa. We have stopped this practice as it was adding confusion to the system.

Regarding the second part of your questions:

Nope, genus Pseudomonas as it is known in NCBI (note: it reflects published opinions) never has been monophyletic in GTDB.

Xanthomonas has been split as intermixed with other genera, but we consider reconciliation based on the recent opinion published by Bansal et al. (2012).

The level of ‘splitting tolerance’ depends on the RED of the genus as it is originally defined, it’s local surrounding and statistical support in the tree.

We try to preserve the original [boundaries] definitions of genera as much as possible and introduce changes only where necessary. Ideally this should be align with existing published opinion.

Hope this answers your questions!

best wishes,

Masha