It would help greatly if you refer to the diagram below:

I drew this diagram as a simplified version of Rodriguez-Robles's tree presented in their paper. If you look at the bottom of the diagram, you will see an arrow with the word "Time" underneath it. Above this arrow is a diagram depicting the relationship among the 3 different lineages of rubber boas based on the mtDNA data. Most such diagrams do not show the arrow and the word "Time" because it is assumed that the reader already knows that this is meant in such a diagram. However, in a cladogram, the time dimension is not drawn proportionally. That means as we go from left to right, it is understood that events that have occurred to the far left are the most ancient and that events that are depicted on the farthest right are the most recent, usually the present. However, there is no attempt to depict time in such a way that two different lines of the same length represent the same amount of time. This is not the case, however, in Rodriguez-Robles’ fig. 4, in which there is an attempt to depict time proportionally.

Again, referring to this diagram, one sees a dot with two lines diverging from the dot. The dot represents the common ancestor of all living rubber boas at a given time. We do not know when that time might have been. The two lines branching off this first dot represents the two descendant lineages of this common ancestor. In a budding event, only one of these two lineages are different from the common ancestor. In a splitting event, both lineages are different. That means at that particular time represented by the dot, two rubber boa mtDNA lineages evolved. The lineage eventually known as umbratica evolved at that time, since the line that leads from this first dot ultimately to a group of populations known collectively as umbratica is a straight line, without further diverging lines. On the other hand, the other line (closer to the bottom than the line that led to umbratica) from this first dot further diverges into two different lineages at a later time. One is the Sierra Nevada subclade and the other is the Northwestern subclade. Since the appearance of the umbratica lineage predates the appearance of the other two lineages, systematists consider umbratica to be the first lineage to have evolved. The other two lineages of rubber boas evolved later. However, the mtDNA data tells us nothing about the morphology of any of these lineages. They only tell us that their mtDNA are different because of substitutions in their nucleotide sequences.

Without any knowledge of the rubber boas at the time the umbratica lineage evolved, since such information can only come from the incomplete fossil record, systematists can only infer the morphology of the lineages at the particular periods of time depicted in the cladogram. Since all of the populations of the umbratica lineage are dwarf forms, there is also a good chance that the dwarf form is the ancestral morphotype of the umbratica lineage. However, we still do not know whether the common ancestor of all living boas is a dwarf form or a large morph. We can infer that by examining the morphology of the other two lineages. One of these, the Northwestern subclade, is a large morph, whereas the other lineage, the Sierra Nevada subclade, is a mix of small and large forms. Therefore one of two things could have happened: 1) the common ancestor of all living rubber boas is a large morph, and dwarfism evolved in the umbratica lineage and then dwarfism evolved once again in the Sierra Nevada lineage independently or 2) the common ancestor of all living rubber boas is the dwarf form, and that the large morph evolved independently in the Sierra Nevada and Northwestern subclades. As I discussed in my previous post, I believe that possibility number 2 is more likely since dwarfism is found in the oldest lineage-umbratica and one of the descendant lineages, whereas the large morph is unknown in umbratica.

I hope I have adequately explained myself. If not, feel free to pose further questions.

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