Re: [opentreeoflife] Choosing specific ("best") backbone phylogeny?

[Emily Jane McTavish]

Hi Christine,

Congrats on the new barnacle classification!

There are a few options for incorporating it into OpenTree.
A long term approach is to include this taxonomy in the OpenTree unified taxonomy. Karen Cranston could better speak to what is required for that. But if it is already in WoRMS, I think it will get automatically included in the next taxonomy revision. That will take a while though.

A great short term/immediate option (which I have been trying out in birds) is to upload the taxonomy and treat it as a poorly resolved phylogeny, and include it as the lowest ranked barnacle tree. That way it will provide structure without overruling any phylogenetic estimates, but it will overrule the current OpenTree taxonomic relationships.

https://tree.opentreeoflife.org/curator/collection/view/kcranston/barnacles
I'm not sure how up to date this barnacles collection is, but you could add the taxonomy here as the lowest ranked tree, as well as another trees you want included.
(upload and curation instructions at https://github.com/OpenTreeOfLife/opentree/wiki/Submitting-phylogenies-to-Open-Tree-of-Life)

Adding the new taxonomy as a 'tree' does require mapping the names used there to the taxon concepts included in the OpenTree taxonomy. This can result in mapping names to older or non-preferred versions of names or synonyms, which can be a bit frustrating - but the OpenTree algorithm is agnostic as to preferred names, as long as the synonyms refer to the same biological entity.
This approach does let you add taxa that are in the new taxonomy but missing from the OpenTree taxonomy using the "taxon addition" function in the tree upload app.

This taxonomy can be included in the next whole synthesis run - but to immediately see the effects, you can run custom synthesis (a new function, in beta testing version) to generate a tree for just the barnacles using the barnacles collection. The API is described here:
https://github.com/OpenTreeOfLife/ws_wrapper/blob/synth-on-demand/synth-on-demand.md

I'm happy to provide more detail on any of these steps, although I'm a little slow on email at the moment as I'm on maternity leave.

Hope that helps!
Emily Jane

On 6/7/21 12:58 AM, Christine Ewers wrote:

Dear all,

my colleagues and I just published an updated classification for barnacles, which reflects phylogenetic results much better than previous taxonomies. Our new taxonomy is now the valid barnacle taxonomy of WoRMS. I would like to get the barnacle tree of life with only this classification as taxonomic backbone, as it should cause very few taxonomic breaks. Is this possible? How would I go about it? 

Here the updated classification:

https://academic.oup.com/zoolinnean/advance-article/doi/10.1093/zoolinnean/zlaa160/6149353

Thank you,

Christine

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Emily Jane McTavish
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School of Natural Sciences
University of California, Merced
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