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RE: C. bottae taxonomy

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Posted by: CKing at Sun Nov 30 13:16:09 2008  [ Report Abuse ] [ Email Message ] [ Show All Posts by CKing ]  
   

>>CK,
>> But of course, I may not be interpreting those figures in the manner you indicate.
>>
>>But if I am, then it would appear that the Calabar and/or Rosy Boa are the ancestral types to the Rubber Boa.
>>

I would like to elaborate a little bit on this point. The Calabar and Rosy Boas are chosen by Rodriguez-Robles et al. as the outgroup for the rubber boa, ostensibly because they relied on Kluge's morphological analysis, which has since been proven to be inaccurate. That means these two species were thought to be close relatives or possible ancestors, but not descendants, of the Rubber Boa, but they may not. The choice of outgroup is important because it can potentially mean success or failure of the analysis. An outgroup is chosen to "anchor the tree." There are of course phylogenetic studies in which the tree is not anchored. These trees are called "unrooted." It is difficult to tell from an unrooted tree which particular species or population is the most basal. Hence most researchers choose to root their trees with a carefully chosen outgroup.

An outgroup serves more than anchoring a tree. They provide a set of characters (either molecular or morphological) that are likely to be ancestral within the group being analyzed. For example, an analysis of the relationships among terrestrial vertebrates would often utilize a fish of some sort as an outgroup. An analysis of relationships among reptiles may utilize an amphibian as an outgroup. Characters that are shared between the outgroup and the ingroup would most likely be ancestral characters. For example, the vertebral column is shared between fish, amphibian and reptile, hence this character is regarded as an ancestral character. If an amphibian or reptile have evolved without a vertebral column, then most likely this is a new character state (although it must be pointed out that this hypothetical situation has not evolved).

Fish do not have fingers and toes, but most terrestrial vertebrates do. This means fingers and toes can be used to identify the basal most group of tetrapods. Some, more derived groups such as the caecilians also lack fingers and toes, but since they share other features with tetrapods, their lack of fingers and toes identify them as a more derived group than the basal tetrapods. If, however, the caecilians were chosen erroneously as the "outgroup" in an analysis of the tetrapods, then one may mistake other features found in the caecilians as basal to all tetrapods. For example, the features the caecilians share with salamanders, frogs and toads may result in the Lissamphibians being classified as among the most basal tetrapods, whereas the earliest known amphibians would be misclassified as much more derived. Hence it is very important not to choose a member of the ingroup as the outgroup.

When molecular characters are used to analyze relationships, it is often difficult to tell whether a particular nucleotide substitution is ancestral or not, unlike well studied morphological characters like the vertebral column. If a particular molecular character is shared by both the outgroup and most (but not necessarily all) of the members of the ingroup, then systematists can be reasonably sure that this character is an ancestral one. When the ancestral characters have been identified, systematists (or their computer programs) will start looking for more recently evolved characters that can identify the next branching points.

For example, if character a (analogous to fingers and toes in the example above) is not found in the outgroup but is shared by almost all members of the ingroup, then this character most likely evolved after the ingroup has become isolated from the outgroup. Fingers and toes are examples of the so called "synapomorphs" or shared derived characters.

If another character, b, for example, is shared by all boas north of the San Bernardino mountains, but not found in either the outgroup or umbratica, then this character probably evolved in the last common ancestor of the northern subclade (Northwestern Sierra Nevada). The search continues to identify characters that are shared by a progressively less inclusive groups. That is how systematists are able to identify branching points and subgroups within the tree. Of course, convergence can occur and sometimes a section of a gene can be lost due to mutation. So it is never as easy as one may imagine and the outcome may not be as perfectly reliable as a textbook perfect example may be. Of course if the outgroup is chosen incorrectly, the tree can be downright anomalous.

If the Rosy Boa is in fact a descendant of the Rubber Boa, as a recent mtDNA study of the Rosy Boas suggests to ME personally, then its choice as an outgroup in Rodriguez-Robles et al.'s analysis of the rubber boa may have caused some of the result to be anomalous. I said "may" because the Rosy Boa may have been sufficiently far removed phylogenetically from most members of the Northern subclades to have misled the analysis.

Nevertheless, I think it wise to exclude the Rosy Boa when the next researcher analyzes rubber boa taxonomy. A more suitable choice as outgroup, which is suggested by some recent independent mtDNA analyses, is Exiliboa, the Mexican dwarf Boa. Studies have shown that this species is probably ancestral to both the Rubber and Rosy Boas. Hence there is little chance that Exiliboa may have descended from Charina bottae. If Exiliboa is used as the outgroup for a combined analysis of Charina bottae and Lichanura trivirgata with a large number of samples of each species, then perhaps there is clear evidence of how the Rubber and Rosy Boas are related to each other.


   

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