I’m constantly adding taxa to the large reptile tree (LRT, 1147 taxa) and that every addition affects and is affected by every other taxa as the software seeks to find the most parsimonious combination of scores that ultimately should reflect evolutionary events in nature. I’m also constantly making corrections as I see them (sort of like Fig. 1) a YouTube video you can click to view. (This was considered the entertainment in the 1960s, shortly after the wide adoption of color TV).
Recently I fell behind
and did not realize the tree had lost resolution. That happens because I only test relevant parts (like birds) when I add in a new taxon. The problem is, when you take the relevant subsets down to examine the issues, you might get, as I did, your resolution back. The taxa are bing affected from afar.
It came to my attention
that the LRT, as a whole unit, had some issues. Only a few bad scores in a cladogram of this size can rapidly and algorithmically multiply the number of MPTs (most parsimonious trees). They’re easy to find. I only need to know to look for them.
Most of the issues were centered around
basal mammals and their pre-mammal analogs.
Now everything is back in order.
All the plates are spinning again. The tree is fully resolved, as I just tested it in whole, not in part.
Admit your errors. Fix them. Keep moving forward. Watch out for more errors creeping in.