A cladogram issue illustrated
This post is dedicated to
reader Neil B. who suggested I review the reference below (Bapst 2013). It is a paper on the limits of resolution using theoretical cladograms. Frankly, it is over my head. Apologies, Neil. I stand by my large reptile tree cladogram as an reflection of actual evolutionary events. The tree is a practical application, not a theoretical one. However, let me offer some theory below (It probably duplicates something that has been published before that I am unaware of. If so, don’t turn me in!)
Some workers,
perhaps most current workers, follow the paradigm that you need at least 3x as many characters in order to attempt to resolve a list of taxa in phylogenetic analyses. In counterpoint, the large reptile tree currently employs only 228 characters versus a current total of 640 taxa with full resolution.
So what’s going on?
‘In practice’ does not seem to be following ‘in theory.’ Of course, all the theoretical problems go away when you employ subsets of the large reptile tree, using only 12 to 50 taxa instead of the whole list. These subsets also employ 228 characters (most of them, I hope, parsimony informative), and that raises the ratio of those analyses above 3x. But that’s not even necessary.
Here’s a simplified solution that seems to help explain this issue.
You might think 1 character dichotomy should split 2 taxa, and it does. But one character dichotomy also lumps two taxa on each sides of that split. Ratio: 1 character/4 taxa.
Figure 1. Characters vs. taxa in analyses. Note one character lumps and splits 4 taxa. Two characters lumps and splits 8 taxa. Three characters lumps and splits 12 taxa given the present list of traits.
I’ve only extended this example
to three character dichotomies splitting and lumping 12 taxa with complete resolution using a 1:4 character:taxon ratio.
Now imagine
having a trait trichotomy (like fins, feet AND flippers) or four trait options (add limbless to this list) and you can see the possibilities for nesting more taxa with complete resolution increase greatly with relatively few characters. Of course, we’ll never completely fill in the large grids. It gets complicated fast with missing taxa and incomplete taxa and evolution going the way it wants to go without regard for the order of the matrix.
This then
is how the large reptile tree is able to keep adding taxa without adding characters. I don’t think I’ve even come close to hitting the limit for taxa yet. The 3x rule does not appear to hold true here. Rather the maximum number of taxa looks to be several multiples of the number of characters in theory, a smaller number in practice.
If one can define a new species
by a set of traits that no other species has, one should be able to split that taxon apart from all other taxa in phylogenetic analysis. Right? That’s all we’re trying to do here. So far, the large reptile tree is succeeding — and it does better (more robust bootstrap scores) as mistakes are corrected. If anyone has an old matrix, they should ask for for the latest update here.
References
Bapst DW 2013. When Can Clades Be Potentially Resolved with Morphology?
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062312
Source: https://pterosaurheresies.wordpress.com/2016/01/29/a-cladogram-issue-illustrated/
