New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Annelida #382

Open
opentreeapi opened this Issue Apr 9, 2018 · 5 comments

Comments

Projects
None yet
3 participants
@opentreeapi

opentreeapi commented Apr 9, 2018

I notice on the.synthetic tree annelids are not on there and when I.look for them on the database it thinks they are extinct

================================================
Metadata | Do not edit below this line
:------------|:----------
Author | Danielle Wilson
Upvotes | 0
URL | /contact
Target node label |
Synthetic tree id |
Synthetic tree node id |
Source tree id(s) |
Open Tree Taxonomy id |
Supporting reference | opentree.org

@opentreeapi

This comment has been minimized.

opentreeapi commented Apr 9, 2018

I tried to link to opentree.org because a website was required and it showed an error message

================================================
Metadata | Do not edit below this line
:------------|:----------
Author | Danielle Wilson
Upvotes | 0

@opentreeapi

This comment has been minimized.

opentreeapi commented Apr 9, 2018

Here is the link I was trying to get to

https://tree.opentreeoflife.org/opentree/opentree9.1@ott155737/Lophotrochozoa

================================================
Metadata | Do not edit below this line
:------------|:----------
Author | Danielle Wilson
Upvotes | 0

@mtholder

This comment has been minimized.

Member

mtholder commented Apr 10, 2018

Hi Danielle,
thanks for reporting the issue. Annelids are not flagged as extinct in our taxonomy. The taxonomy page for them is https://tree.opentreeoflife.org/taxonomy/browse?name=Annelida (I do realize that the "e.g. extinct" text at the top of the page may make it look like they are flagged that way, but that is intended as explanatory note to show what the flags look like.

I think you can find most of them from navigating around: https://tree.opentreeoflife.org/opentree/opentree9.1@mrcaott24ott102965/Myzostomida--Clitellata

I think that they don't show up in the tree because the current tree does not put Myzostomida with the rest of the Annelids. Taxonomies vary on what goes inside Annelida. If you are curious about the details, there are a couple of Open Tree GitHub issues where this is discussed: OpenTreeOfLife/germinator#112 and OpenTreeOfLife/reference-taxonomy#238

The longer term solution is for the browser to show you the relevant part of the tree when a taxon is not monophyletic. This has been a long standing issue (see OpenTreeOfLife/germinator#85 ). The good news is that we are pretty close to having a new tool for serving up the synthetic tree that would fix this. Unfortunately, it still needs a bit more testing before being deployed.

@opentreeapi

This comment has been minimized.

opentreeapi commented Apr 13, 2018

Thank you. I didn't know Annelida wasn't monophyletic. Thank you for teaching me. I think a Tree of Life should consist of monophyletic lineages and try and stay away from paraphyletic and polyphyletic lineages. I am not a professional taxonomist I just like to research this kind of thing. It's interesting to me.

================================================
Metadata | Do not edit below this line
:------------|:----------
Author | Danielle Wilson
Upvotes | 0

@jar398

This comment has been minimized.

Member

jar398 commented Apr 13, 2018

Myzostomida is a genetic outlier and gets put in different places by different studies. I think Annelida could only be seen as nonmonophyletic if you believed both that Myzostomida is outside of it taxonomically (as NCBI says) and that Myzostomida is deep enough inside of it phylogenetically. Both of these claims are pretty weak, so don't call it quits yet.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment