Skip to content
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

all "BIEN_taxonomy_*()" queries list class as "Equisetopsida" #25

Open
gabehassler opened this issue Jan 27, 2021 · 3 comments
Open

all "BIEN_taxonomy_*()" queries list class as "Equisetopsida" #25

gabehassler opened this issue Jan 27, 2021 · 3 comments

Comments

@gabehassler
Copy link

I was trying to get taxonomic information about a large number (>3,000) of species across the entire phylogeny, and I noticed that no matter which species I entered into BIEN_taxonomy_species(<species>), the resulting dataframe listed the class as Equisetopsida.
All other information appears to be correct.

Here's an example:

> x <- BIEN_taxonomy_species(c("Arabidopsis thaliana", "Ginkgo biloba", "Sequoiadendron giganteum"))
> x$class
[1] "Equisetopsida" "Equisetopsida" "Equisetopsida" "Equisetopsida"

This is a great resource btw. Thanks so much for developing and maintaining it!

@bmaitner
Copy link
Owner

Thanks for the note! This issue is related to taxonomic lags. The higher classification used by Tropicos (and the TNRS, hence BIEN) at the time of our last update followed Reveal and Chase 2009 in applying the Equisetopsida to all land plants, not just horsetails. Horsetails are now known to be nested in the ferns. @ojalaquellueva will this issue be addressed in the forthcoming update to BIEN?

@ojalaquellueva
Copy link

ojalaquellueva commented Jan 27, 2021

@bmaitner correct. The TNRS classification is taken straight from Tropicos, which follows APG III (Reveal and Chase 2009) in placing all land plants in class Equisetopsida. It will take some fiddling to change that as Tropicos still hasn't changed their higher taxonomic backbone. Most likely I'll make the World Flora Online (WFO) backbone the default higher classification and keep Tropicos as an alternative.

@ojalaquellueva
Copy link

@bmaitner I suggest closing this issue as there is no problem here. It is just the classification used, which is fine. I may switch to a different higher classification with the next rebuild and we can revisit this discussion then.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants