Loss of resolution in cladograms

A cladogram
is a graphic image (a diagram) typically generated from software, and typically based on a list of taxa and a list of characters, each one scored for each taxon. The cladogram is supposed to model actual evolutionary relationships among organisms. Ideally every cladogram will be fully resolved with every taxon sufficiently different from its sisters to merit its own node or branch. This is the basis for lumping and splitting. In practice loss of resolution occurs when sisters are not sufficiently different from one another. This can happen due to one or more of several problems:

  1. Three taxa are in reality too closely related. As an example, you may have input several specimens of the same genus and species, like “Tyrannosaurus rex,” without having characters in your characters list that could taxonomically separate them. Two identical taxa nest together, no problem. Three identical taxa produce loss of resolution. We saw something like this earlier in pterosaurs were two Rhamphorhynchus specimens had the same score and were deemed to be an adult and juvenile of the same species – but the third sister taxon (of the same putative species!) did not have the same score.
  2. Two sister taxa share no characters in common despite being closely related. This occurs most often when a skull-only taxon nests as a sister to a skull-less taxon, but it could also occur with other combinations of missing parts.
  3. One taxon is in a ‘by default’ nesting. It should not be in your taxon list because in reality it is not closely related to any other taxon in your taxon list. For instance, when one attempts to nest the pterosaurs “Pteranodon” or “Dimorphodon” with generic and specific members of the Archosauria or Archosauriformes, or when one attempts to nest “Homo sapiens” with generic and specific members of the Ichthyosauria. No telling what can happen in those instances, but anyone is able to try.
  4. Too few characters #1. If you have only 5 or 50 characters, there may not be a large enough list of traits to split your taxa apart. Statistically the list becomes large enough for 98% certainty at around 150 characters and becomes incrementally better with every character added thereafter. The large reptile tree uses 228 characters, many with more than two options, and has complete resolution (except for skull-less and skull-only taxa nesting as sisters (#2 above) with 546 taxa. Thus in practice there is no 3:1 character:taxon ratio as you may have learned about in theory.
  5. Too few characters #2. If your sister specimens are only represented by a few bones or parts of bones then two sister taxa may not resolve.
  6. Too few characters #3. Legless burrowing tetrapods appear to converge in their remaining traits so you better have a sufficient number of traits to lump and split the various clades. Otherwise the legless clades tend to be attracted to one another.
  7. Too few taxa. This goes back to #3 above because by throwing in one ‘by default’ taxon, like “Vancleavea” into an unrelated clade, like “Archosauriformes,” without also including the verified sisters of “Vancleavea,” like “Helveticosaurus” and “Askeptosaurus,” might produce loss of resolution because “Vancleavea” shares so few traits with any archosauriforms and the addition of the other thalattosaurs will clarify relationships. You may not have loss of resolution, but by adding taxa you’ll eliminate these ‘by default’ taxa.
  8. Using suprageneric taxa. If you can pick traits from one partial specimen AND another partial specimen to get enough traits to fill a suprageneric character list for a single taxon, then you’ve created a chimaera that can only lead to trouble. Even if your two taxa are incomplete, that’s better than creating a single cherry-picked chimaera taxon.
  9. Mistakes in scoring. Since humans are scoring all characters, mistakes can happen and they can affect nestings. Mistakes are often due to: 1) trying to maintain a paradigm or tradition; 2) too much leeway or opinion possible in a choice of possible scoring options; 3) inadvertent transpositions of data; 4) typos; 5) relying on the veracity of prior scorings, etc. Double and triple check your work and the work of others when you find loss of resolution. Errors are easy to make.
  10. Loss of resolution can occur at several levels: 1) in a simple heuristic search you need only one character score to lump and split sister taxa from your list of several dozen to several hundred traits; 2) in a bootstrap/jacknife search you need at least three character scores to lump and split taxa to raise your bootstrap score over 50%.

In my manuscripts,
when I report that my trees are fully resolved, that never seems to impress the referees (or they don’t believe it). Perhaps that is so because so many accepted manuscripts have loss of resolution at several nodes for many of the above reasons. That is not acceptable in most cases (exception: skull-only taxa will continue to occasionally nest with skull-less taxa).

We know better now.
We now have a large gamut “umbrella” study that continues to recover relationships within the Reptilia as it continues to increase in size. This large study provides a basis for smaller, more focused studies. When the old unverified traditions and paradigms have been replaced with verified models and relationships, then we’ll all have more confidence in recovered trees.

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