Freshwater Ichthyosporeans 1 & 2, and Marine Ichthyosporeans 1 have no descendants

[hyanwong]

These are from SILVA, but seem to have no subtaxa, and may simply be RNA sequence clusters. Not sure if anything need to be done about this or not, to if it is symptomatic of a general SILVA issue

Metadata	Do not edit below this line
Author	Yan Wong
Upvotes	0
URL	tree.opentreeoflife.org/opentree/argus/opentree5.0@ott5251365/Freshwater-Ichthyosporeans-1
Target node label	Freshwater Ichthyosporeans 1
Synthetic tree id	opentree5.0
Synthetic tree node id	ott5251365
Source tree id(s)
Open Tree Taxonomy id
Supporting reference	N/A

[jar398]

Hmm, if we got rid of this we'd have to get rid of most of SILVA... This one does seem odd, since it's annotated as an 18S ribosomal RNA gene, but the SILVA tree we use is based on 16S; but the annotations are often wrong.

In the OTT 2.10 draft this cluster is not flagged 'unclassified' any more, so it will be available as an OTU and will show up in the synthetic tree. The earlier 'unclassified' flag was a mistake.

I think I'm going to mark this 'wontfix'. This is respecting Laura Katz's request from a few years back that the synthetic tree expose as much microbial diversity as possible. (There are another 300,000 clusters like this one waiting in the wings.) But is there more that you know about this group to suggest that SILVA's taxonomic placement and/or description is wrong? E.g. is there reason to think freshwater ichthyosporeans don't exist? The SILVA taxonomy curator (probably Pelin Yilmaz) had enough faith in this cluster to invent a name for a group that would contain it.

[hyanwong]

I think the problem is partially with the name. These are clearly temporary made-up clade names. I doubt they have much taxonomic authority behind them (but I could be wrong). It's odd that they contain no species in the synthetic tree: I suspect that either a number of ichthyosporeans identified by other studies belong in these groups. But it's not my area. I can ask an expert who I know (Iñaki Ruiz-Trillo)

[jar398]

This group does have a member, as you can see in the SILVA taxonomy browser. NCBI gives it a name with the word 'uncultured' in it. Uncultured taxa from NCBI only are filtered out as 'unclassified,' but since SILVA classifies them they occur unflagged in the taxonomy - not in 2.9, which has a bug, but it will appear in 2.10.

For 'microbes' we use the taxonomy from SILVA (on the advice of Laura Katz), which, as I say, is the work of one or a small number of people. SILVA made a big phylogenetic tree based on 16S sequences organized into clusters, and then, partly based on known groups, gave names to internal nodes that were well supported. But there were a lot of groups left over for which there was phylogenetic signal but no name. So they just made up names, as you say. Since Open Tree is about phylogenetic relationships and nomenclature is not a primary concern, SILVA seems a good match to the project.

I suppose that if the SILVA team cared a lot about proper description they would research each group to figure out its biology so that it could be described and given a 'respectable' name. That sounds really really hard to me. The phylogeny is way ahead of taxonomy and I doubt they are funded to do anything other than sequence-based taxonomy.

I can't say anything about the quality of the phylogeny, but I think they are being conservative; many nodes in the taxonomy are big polytomies, which to me says they're being conservative in saying which nodes are well enough supported to deserve names.

[mtholder]

the empty groups will be fixed with https://github.com/OpenTreeOfLife/edOTTs/commit/eaf0da51bd01dcc30327c2a8036c76a4aff01cb3 Freshwater Ichthyosporeans 1 was left because it has descendants.