Goals:

OpenTree of the Fabaceae

What is OpenTree?

OpenTree is a synthetic supertree of all life.  It is composed or individual phylogenies combined with a taxonomic backbone that connects all life in a single phylogentic tree. It currently contains over 2.3 million tips.  It uses published and curated phylogenies. For more on OpenTree click here.

The goal of this project to to aggregate all phylogenetic knowledge of the Fabaceae into OpenTree to generate a single synthetic supertree of the legumes.  The current version of OpenTree contains 23,410 terminal taxa in the Fabaceae; however, most of the data is from the taxonomy and there are not enough phylogenies to do justice to our work.

Therefore we need to get more Fabaceae trees into OpenTree. I have been uploading and curating my Fabaceae trees and am happy to do this for other people. Please feel free to join in by uploading and curating your own trees or other legume trees.  Please email if you have any questions.

How we can use a OpenTree of the Fabaceae

  • A visualization of the Fabaceae phylogeny (see PhyloLink)

  • Link GBIF spatial distributions to the tree

  • Integrate trait data to the phylogeny

  • Overlay phylogeny on environmental data layers

  • Use subtrees in other analyses

  • Speak quantitatively about the Fabaceae

How to improve the OpenTree of the Fabaceae

Input phylogenies for OpenTree need to be published studies.  It is quite easy to submit a tree to OpenTree, especially if it is already deposited in TreeBase.

I am happy to curate the phylogenies for the community. The curator:

  • Imports the tree

  • Checks the rooting

  • Maps OTUs to the OpenTree taxonomy

  • Updates the metadata, such as phylogeny methods

  • Adds publication information

If you want to learn how to curate phylogenies in OpenTree see the  OpenTree curation instructions.

  • Please send me the following information

    • A pdf of the paper so I can check the data to the paper​

    • The tree file for the paper

      • TreeBase number is best or​

      • the Nexus tree file, preferably from another database

    • If the study has more than one tree figure, which one(s) is best for OpenTree

  • I may have questions, such as issues with names in the OTU mapping​

  • I'll try to send the uploaded information to you so that you can follow along

Please send information on any Fabaceae phylogeny that should be included. I am keeping a list. 

All images from the Australian Plant Image Index

© 2018 by Joe Miller.