Ordway site with 572 species, 556 species can be initially matched on Opentree (synthetic tree); Still 16 species miss match:

Among them,

Note from Open tree:This taxon is in our taxonomy but not in our tree synthesis database. This can happen for a variety of reasons, but the most probable is that is has a taxon flag (e.g. incertae sedis) that causes it to be pruned from the synthetic tree. See the taxonomy browser for more information about this taxon.

Ceanothus microphyllus 877139

Dactyloctenium aegyptium 752144

Heterotheca subaxillaris 206813

Imperata cylindrica 740074

Sacciolepis striata 3956672

Serenoa repens 71637

Dolichandra unguis-cati 1001573

Erigeron foliosus var. foliosus as (Erigeron foliosus) 696078

Gnaphalium antillanum 569718 (Gamochaeta antillana)

Zanthoxylum clava-herculis 3942437

Sideroxylon reclinatum subsp. rufotomentosum as (Sideroxylon reclinatum) 1077723

Quercus laevis x hemisphaerica #hybrid delete/ or as Quercus laevis

Quercus laevis x incana #hybrid delete/ or as Quercus laevis

Heliopsis buphthalmoides #not found in opentree, but accepted names in other database TPL, Tropics

Pluchea baccharis #not found in opentree, but accepted names in other database TPL, Tropics

Verbesina heterophylla #query from Opentree API, best match is "Berberis heterophylla" (totally different family, maybe unreliable)

some of those issues appeared frequently, based on different species list I have tried. It would be great to fix them on OTL side:

• 1. if there is a "-" in species names (e.g., Dolichandra unguis-cati, Zanthoxylum clava-herculis), the script ("get_ottids_for_taxa.py") will fail to grap ottids, so will not present in the result tree.

  Those two example names can be found in the Open tree, ottid1001573, and ottid3942437.

• 2. how to add those species in two categories below to the subtree:

  • Cat1: species do have ottid, but not present in the synthetic tree (those two add back in scripts not working on my side)

  • Cat2: species not found in opentree, but accepted names in other database TPL, and Tropics.

• 3. what approach do you recommend to convert the ottids to species names, phyx or "convert_ottids_names_tre.py"? The results obtained from both are required manual fixing or modification.
  • A. phyx can only replace ottid (old.name) on the tips labels to species name (new.name), but those internal-node (mrcaott...) will be still left in the tree, right? So for the internal-labels either manually rename or remove.
  • B. "convert_ottids_names_tre.py" will rename every ottid with names, but usually the tree format (newick) is not valid in the resultant tree file (either "(", or ";" missing ).