>>CK,
>>There are three 'trees' in Javier's paper. If I am following your process correctly, in Fig. 3A, specimen #26 would be the ancestral type for all boas in the Sierra Nevada subclade. In Fig. 3B, specimen #26 would be the ancestral type for all Sierra Nevada and Northwestern subclade boas. In Fig. 4, it would appear that specimens #15, 17, 18, and 19 are the ancestral types for all Sierra Nevada and Northwestern subclade boas. But of course, I may not be interpreting those figures in the manner you indicate.>>

Yes you are correct. There are 3 trees. I was basing my conclusion on Fig. 3A. Fig. 3B is based on the assumption that the third position of the 3 nucluotide genetic code is more likely to undergo mutation since a change in this position does not change the amino acid that is coded in most cases. In many adaptive molecules, this would be a tenable hypothesis, but in the case of mtDNA, this is a rather dubious assumption since mtDNA has been shown to be a rather neutral molecule (at least the part of the genes used for genetic studies). Fig. 4 is the maximum likelihood tree and it shows the southern rubber boa being ancestral to both the Northwestern and Sierra Nevada subclades. It does show #15, 17, 18, and 19 being slightly more basal to the Sierra Nevada subclade than #26.

>>But if I am, then it would appear that the Calabar and/or Rosy Boa are the ancestral types to the Rubber Boa. >>

Not quite. The Calabar and Rosy Boa are chosen by Rodriguez-Robles et al. as the outgroups. This part is rather arbitrary and it is based on Kluge's hypothesis that the Calabar and Rosy boas are the closest relatives of the rubber boa. Since then, some studies have shown that the Exiliboa is actually the closest relative of the rubber boa and that the Rosy Boa may have descended from an isolated population of the rubber boa in northern Baja california. I have seen studies in which a member of the in group has been chosen as the outgroup. For example, there was one European researcher who picked Lampropeltis, a descendant of a species of Elaphe which migrated from the Old World to the New World, as an outgroup to the genus Elaphe. That researcher was implying that Lampropeltis is ancestral to Elaphe, which is of course absurd.

>>Just because #26 branched off earlier and thus is older than the other specimens, I do not understand just why her lineage and not some other ancestral type, now extinct or still in existence but just haven't been found and tested, may have given rise to the other lineages in the tree.>>

Of course it is certainly possible that some unknown lineage is the true sister group to the Sierra Nevada subclade. Most scientists point out that our closest relative is the chimpanzee, but of course there are a number of extinct hominids, such as Australopithecus and of course Homo erectus, which are actually more closely related to us than the chimpanzee.

>>A good number of years ago, I was surprised at the lack of representation in mtDNA studies. When I questioned that point, I was told that such representation was not necessary as new samples from the same region did not materially add to results. I am now of the opinion that I was correct all along, that inadequate representation can often lead to erroneous interpretations of the results obtained from such studies.>>

More extensive sampling is of course always better. However, no matter how extensive the sampling is, inadequate sampling can always be invoked. In many cases, most mtDNA haplotypes in any one locality tend to become extinct due to chance, so often a single sample from any one locality is good enough. However, in case of recent mixing of two or more populations in one area, a larger sample can be more informative.

>>Interpretations are made on the basis that the samples tested are seemingly the last word and thus finite. Rick's study has demonstrate that is not the case and I venture to say that the current study also lacks adequate representation in a number of regions. Seemingly not taken into account is that there may be a good number of closely related or identical haplotypes of specimens #26 that may occur north, south, east, and west of where #26 originated near Camp Nelson. Without having much larger sample size and geographical representation, to interpret that this or that population migrated in any direction is premature to my way of thinking.>>

One must realize that scientists must base their conclusions on the available facts. No study is the final word. Any new fact that comes into light may and often can falsify an existing theory. One needs to look no further than the case of Lord Kelvin, who miscalculated the age of the earth because he did not know anything about radioactivity.

>>Concerning the distribution of the two size morphs, my sample size from the Tehachapi Mts. and Breckenridge Mt. are large enough to assert that like the San Bernardino boa population, those two populations are also of the dwarf morph. But besides having an adequate sample size, there are other clues that indicate whether the boas from any particular region belong to the dwarf or large morph phenotype. >>

Thanks for the info. It appears then that the most likely explanation for the fact that #26 is a large morph is the intergradation hypothesis.

>>The maximum and mean lengths of neonates of litters produced is one clue. The lengths of mature individuals is another. The lengths at which males and females attain maturity is another. And the rate of growth over time is another. For the populations in which I lack an adequate sample, some of the above clues indicate that the population of boas in the Mt. Pinos area, in the Scodie Mts., in the Greenhorn Mts. south of Alta Sierra all in Kern County, and on the Southern Kern Plateau in Tulare County are all of the dwarf form. Then by geographical proximity, one would expect the dwarf form to occur in the Piute Mts., Alamo Mt., Frazier Mt., Sawmill Mt. and Mt. Abel where the species has been documented in Kern County and the San Jacinto Mts. of Riverside County.>>

If they are all small morph, then it would be interesting to see whether some of their mtDNA haplotypes are closer to those of the San Bernardino/San Jacinto Mt. areas. Presently, the mtDNA data suggests a contraction of the rubber boa range in the Kern and Tulare County area, with rubber boas being absent from Kern County. Subsequently and more recently, dwarf morph boas from Tulare Co. recolonized Kern County. At about the same time, the large morph evolved in Tulare County and migrated north into the Sierra Nevada Mountain, which had previously been closed to both L. zonata and C. bottae from both the north and the south.

>>Until some nuclear markers are found, I believe it is not plausible to determine with any certainty just where a mixture of dwarf and large morph genotypes exists.
>>
>>Richard F. Hoyer

There is no need to resort to nuclear markers, although they would be helpful. Morphology can tell us which morph a boa may belong to and mtDNA can tell us about ancestry. There is a recent paper on Taricha, which shows that the Sierra newt and the Southern California newt intergrade to a limited extent in the Tulare County area. This is quite unexpected because it had been thought that the Southern California newts were restricted to the coast. So, apparently, there is some exchange between the fauna of the southern Sierra Nevada and coastal Southern California.

I think the next researcher to investigate rubber boa phylogenetics should sample the Kern and Tulare County areas much more extensively than before as this area seems to offer the most clues as to how, when and where the migration of the Northwestern and Sierra Nevada subclades may have begun. Rodriguez-Robles et al. did not have the wisdom of hindsight or prior studies to guide their initial sampling, but they did a wonderful job nevertheless picking their samples. Future researches can certainly build on the findings of Rodriguez-Robles et al.

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