Hi, Richard, if you are still visiting this forum, here is something that I just thought of. Rodriguez-Robles et al.'s mtDNA data looks to be in good shape, however there is one anomaly in their tree (actually more than one). That anomaly is the relationship between the rubber and rosy boas. In their tree, the rosy boa is shown to share a more recent common ancestor with the Calabar boa than with the rubber boa. Biogeographically, such a tree makes no sense.

The rosy and rubber boas are obviously close relatives morphologically, and it is very likely that the rosy boa directly descended from the rubber boa. The disjunct distribution of the small morph rubber boa can be explained by a change in the climate and habitat of what is now the Mojave Desert. The rubber boa's distribution was once continuous between the San Bernardino Mt. and Kern County localities, but when the Mojave Desert formed, the Kern County population became isolated from the Southern California populations because of extinction of the rubber boa in this area. Apparently not all of the boas became extinct. Some of them evolved into a new species, namely the Rosy boa, which is better adapted to arid conditions than the small morph rubber boa. The Rosy boa was then able to disperse into arid environments in Arizona and southern California. It is the Rosy boa which is apparently responsible for the spotty distribution of the small morph rubber boa (i.e. umbratica) in Southern California. If someone were to analyze the mtDNA of both the rubber boa and rosy boa, then it may well be shown that the rosy boa is in fact a descendant of the rubber boa.

This anomaly may be responsible for the relatively poor statistical support for the Sierra Nevada subclade (the node with the number 72 next to it). If the rosy boa is in fact a descendant of the rubber boa, then Rodriguez-Robles erred in choosing the rosy boa as an outgroup in constructing their tree. The choice of outgroup is important in phylogenetic analysis and it often meant the difference between a successful one and an unsuccessful one. If a member of the ingroup is chosen as the outgroup, then the tree can be anomalous. That is because similarities are used to construct a tree. A similarity that is due to recent common ancestry but which is mistaken as an shared ancestral character can result in an anomalous tree. You may want to raise that possibility with Rodriguez-Robles or with the scientists who are analyzing mtDNA of the rubber boa.

Regards.

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