New synthetic tree for barnacles collection?

[Christine Ewers]

Hi!

I have been working on the barnacles collection in Open Tree of Live, and would like to get a new synthesis tree for this collection. Could you generate one for me and my group?

Thank you,

Christine Ewers-Saucedo

[Karen Cranston]

There is a new synthesis in the clade workshop repository:

https://github.com/OpenTreeOfLife/clade-workshops/tree/master/synthesis_trees

Let us know if you have any questions!

Cheers,

Karen

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[Christine Ewers]

Thank you!

Christine

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[Christine Ewers]

Hi Karen and team!

I have been analyzing the new synthetic barnacle tree, and realized something odd: In a taxa I know a lot about (the genus Chelonibia), I am missing species and resolution which I know are in the input trees. Specifically, Hayashi et al. 2013 reconstructed a phylogeny including Chelonibia patula, C. testudinaria, C. manati, and C. caretta. The tree is uploaded, OTUs are mapped and the tree is in the "barnacles" collection. However, in the synthetic tree, only Chelonibia caretta is supported by phylogenetic data. In fact, the synthetic barnacle tree looks exactly like the open tree of life at this node. I have not checked other nodes. How could this have happened? Any way to fix this?

All the best,

Christine

[Christine Ewers]

Quick update: In the genera Chthamalus and Megabalanus, the open tree of life and the synthetic barnacle tree look different. But within Megabalanus, I found another species missing from the synthetic tree: Megabalanus tintinnabulum. 

Christine

[Christine Ewers]

Alright, update number two. I was mistaken: The synthetic tree is accurate. What I realized is that if a species has subspecies, only the subspecies occur as a tip in the synthetic tree. Example: Chelonibia patula has a subspecies, Chelonibia patula dentata. In the synthetic tree, the only tip is Chelonibia patula dentata. Is there any thought of including the species as a tip as well?

Christine

[Jonathan A Rees]

The species is present as the parent of the subspecies. It would not be correct to put the species as sister to one of its subspecies. If this presents a problem for your analysis, maybe you could prune off anything below species before processing? If you are using the API, the API calls will tell you the rank, or you can just look at the lexical form of the label - species usually have binomials.

"Tip" is not a biologically or nomenclaturally meaningful distinction in the synthetic tree. Some tips are genera, some are varieties, and so on.

[Mark Holder]

Hi Christine,
I suspect that you are not the only user who would want to see the
tree cut off at the species level. So I've submitted a couple of issue
to support that in the future:
one for the front end: https://github.com/OpenTreeOfLife/opentree/issues/948
and one for the server side:
https://github.com/OpenTreeOfLife/treemachine/issues/218

Jonathan, do we have tips that are above the species level? It seems
like we would want to avoid that. It would be good to see if that is
coming in at the taxonomy pruning stage of the synthesis or in the
production of the taxonomy.

all the best,
Mark

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[Jonathan A Rees]

Tips that are known, because of their rank, to be above the species level are flagged 'barren' and are suppressed for synthesis purposes.

There are parts of the tree, especially in microbes, where ranks are not designated or not known to us. To be on the safe side, tips without rank information that are not known to be below species level are not marked 'barren'. It is conceivable that a speciesless family, or a subspecies not known to belong to a species, say, would come in without a designated rank, in which case it could end up in the synthetic tree. No semantics is given to the form of the name since that is not a reliable indicator (in general).

[Christine Ewers]

Thank you, Mark!

I came across this issue when I was comparing the full synthetic tree (of barnacles in my case) with the synthetic tree that only has tips supported by phylogenetic studies (“phylo only tree”). In the phylo only tree, species level names were at the tips, while in the synthetic tree, subspecies were at the tips. So it seemed as if the tips of the phylo only tree were not in the synthetic tree. Now I am thinking about how to make these tip labels the same (which they are), without loosing information or renaming tips that I should not..

While probably not correct, at least some taxonomies list both subspecies and corresponding species as valid. In my favorite example: Both Chelonibia patula and Chelonibia patula dentata are supposedly valid. Thus I asked whether both could remain in the synthetic tree.

Thanks to everybody!
Christine

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[Yan Wong]

I have a perl script that cuts off all the subspecies from the draftversion newick file, based on taxonomy.tsv. Would that be useful to anyone? I guess it should work for subtrees too.

Yan

[Yan Wong]

p.s. I've observed a good number of tips above the species level on the online version of the tree. E.g. https://tree.opentreeoflife.org/opentree/opentree4.0@854320/Charites

or is that not what you meant?

[Jonathan A Rees]

Thanks for the Charites case, I was not aware of it.  It is a bug somewhere in the system.

https://github.com/OpenTreeOfLife/reference-taxonomy/issues/194

[Tony Rees]

FYI IRMNG has/had a number of fossil genus names acquired from sources where they were not flagged as such (it's a work in progress to detect these and flag them, some still to be done). Charites was one such name, appearing in the 2006 Catalogue of Life as apparently extant, but was manually flagged as fossil in IRMNG subsequently and appears as fossil there at this time. Maybe it would be not too hard for you to run a check of names flagged as fossil in the copy of IRMNG that you have but as extant in opentree and generate a list of discrepancies? (I don't mind eyeballing the list if it is not too large). It could offer an alternative route to the parent-inheritance method mentioned above and pick up a few more things requiring fixing.

Regards - Tony

Tony Rees, New South Wales, Australia

https://about.me/TonyRees

On 6 April 2016 at 03:34, Jonathan A Rees <re...@mumble.net> wrote:

Thanks for the Charites case, I was not aware of it.  It is a bug somewhere in the system.

https://github.com/OpenTreeOfLife/reference-taxonomy/issues/194

[Yan Wong]

On Tuesday, 5 April 2016 18:34:46 UTC+1, Jonathan Rees wrote:

Thanks for the Charites case, I was not aware of it. 

Here's another taxon above the species level that I just stumbled across:

https://tree.opentreeoflife.org/opentree/argus/ottol@678209/Nanoarchaeota

But it's not extinct, so not the same as the Charites case. I don't know if above-species taxa are expected on the tree in general. 

[Yan Wong]

On 13 Apr 2016, at 09:26, Yan Wong <y...@pixie.org.uk> wrote:

> Here's another taxon above the species level that I just stumbled across:
>
> https://tree.opentreeoflife.org/opentree/argus/ottol@678209/Nanoarchaeota

In fact, it seems that there is only one species recognised in this group, /Nanoarchaeum equitans/, so I’m somewhat surprised that this species is present in the taxonomy but not placed underneath
Nanoarchaeota on the tree:

https://tree.opentreeoflife.org/opentree/argus/ottol@395935/Nanoarchaeum-equitans

Yan

[Mark Holder]

Hi,
Thanks for pointing this out. I started an issue
https://github.com/OpenTreeOfLife/reference-taxonomy/issues/199

I think that the genus in Nanoarchaeota should not be flagged as
"incertae sedis" Currently it is, so that taxon is suppressed from the
synthetic tree.

all the best,
Mark