>>CK,
>>Although there were about 13 new samples tested in the greater Mt. Lassen region, there still exists considerable distances between samples. The distance between members of the two subclades in now down to about 45 km from Javier's stated 120 km. However as mentioned, he overlooked Sierra subclade sample #15 near Quincy in Plumas county which is about 65 - 70 km from the Northwestern subclade sample #6 at Eagle Lake.
>>
>>But actually, the deepest occurrence of one subclade into the 'territory' of the other subclade came from two specimen that are not in either of those two counties and extend about 32 to 35 km into the area considered to be occupied by the other subclade. But it remains to be seen if these preliminary results are real.
>>
>>Should the new result become firm, one could still argue that the subclades are allopatric by simply gerrymandering the manner in which one draws an imaginary line or 'break' to separate members of the two subclades. Until one finds two boas of the two subclades under the same rock, there can always be the claim that theoretically, allopatry has not been disproved.
>>

Hi, Richard, thanks for the additional details. Certainly it is possible to draw the ranges to show allopatry. But if the result you cite is real, then there is at least evidence that allopatry is very likely the result of incomplete sampling. Allopatry may not be disproven, but it is much less well supported than before.

>>Mentioned earlier is that Javier's study shows specimen #26 from Tulare county closely aligned with boas from Butte, Yuma, and Plumas counties, sample 17, 18, 19, and 15.
>>And in his Fig. 3B, those four boas are apart from the Sierra Nevada subclade with no explanation in the text. What are your thoughts on that issue.>>

Yes I did mention earlier that the Plumas Co. specimens appear to be more closely allied to Tulare Co. loc. #26 than to the Sierra Nevada boas to the immediate south. The many unresolved polytomies in this part of the tree show that snakes from the many localities of the Sierra Nevada dispersed rapidly north from Tulare County. It looks like some sort of barrier (physical or climatic or a combination of both) had kept the rubber boa from entering the Sierra Nevada Mountains from the south, and once that barrier is removed, the rubber boa found favorable habitat and the population exploded. Simultaneously, there was no other barrier to dispersal within this mountain range, so the rubber boa dispersed rapidly, driven by intense interspecific competition and the presence of vast unoccupied expanses of favorable habitat. It is as though the rubber boa found paradise within the Sierra Nevada Mountains.

>>The current study incorporated Javier's 38 samples and the raw data extracted from those samples. Once again, instead of Tulare Co. sample #26 aligning with boas in nearby counties, it again aligns with boas from more northern counties. But with the increased sample size, there is another Tulare Co. specimens that accompanies #26 in aligning with boas from Butte, Yuma, Nevada, Sierra, and Plumas counties. What are the possible explanations for such results?
>>
>>Richard F. Hoyer

If the new study again ally the Plumas County boas with the Tulare County boas, then it may be evidence that there were 2 separate waves of migration north from Tulare County. Rodrigues-Robles et al.'s data does show two sublineages of the Sierra Nevada subclade, one consisting of the Plumas Co. boas, and the other consisting of a mixture of small morph Kern Co. and large morph Sierra Nevada boas south of Plumas Co. Fig. 4 of Rodrigues-Robles et al. shows that the Plumas County speciments represent an older lineage than the other Sierra Nevada boas. This older lineage may have migrated north at a much earlier date than the other Sierra Nevada boas. Of course, it is also possible that the Plumas County specimens may have represented a trans-Valley leak from the Northwestern subclade. Arguing against a trans-Valley leak is the fact that the boas closest to the route for such a leak are all aligned more closely with the small morph Kern County boas. Nevertheless it is also possible that the descendants of the trans-Valley leak may have been genetically swamped by later arrivals from the Southern Sierra Nevada, at least in the localities south of Plumas County.

Without actually seeing the entire new tree, it is difficult to make meaningful interpretations. Based on Rodriguez-Robles' data, it is clear that the Plumas Co. boas represent an older lineage. How these boas migrated to Plumas Co. (i.e. via the trans-Valley corridor or via an earlier migration north along the Sierra Nevada mountains) remains an unanswered question. If it was a trans-Valley leak, then perhaps the Sierra Nevada subclade may need to be redefined to exclude the Plumas County specimens.

Anyhow, the Sierra Nevada subclade now include two different morphs, the small and large morphs. Despite their close genetic relationship with each other, I believe the small morph Kern County boas within the Sierra Nevada subclade should be assigned to the umbratica subspecies, since they appear to retain the ancestral condition of small morph and since their distribution is intermediate between umbratica to the south and large morph snakes of the Sierra Nevada and Northwestern subclades to the north. The Kern County small morph situation is analogous to the human-chimp-gorilla one. Human and chimp share a closer genetic relationship with each other than either one does with the gorilla, just as the small morph Kern Co. boas share a closer genetic relationshp with the Sierra Nevada large morph boas than they do with umbratica. But morphologically, chimp and gorilla are closer and represent retention of an ancestral morphology. The Kern County small morph boas are morphologicallly closer to umbratica, and they also appear to have retained the ancestral morphology of the umbratica subclade.

Most traditional taxonomists would classify chimp and gorilla in the same taxon (Pongidae) and separate human from the chimp and gorilla in another taxon (Hominidae). Similarly, the small morph Kern Co. boas should be classified with the southern rubber boa in C. b. umbratica and the large morph Sierra Nevada boas should be classified as a different subspecies than the small morph Kern Co. boas.

Cladists, however, would do things differently. They dislike paraphyletic groups like Pongidae and they also dislike the subspecies concept. So, a cladist may simply lump all rubber boas into the same species without recognizing any subspecies. Similarly, many cladists have proposed lumping human, chimp and gorilla into the same family Hominidae in order to eliminate paraphyly. Hominidae is the older name, but calling chimps and gorilla "hominids" would be a travesty. Nevertheless it would not bother the cladists one bit. If Pongidae is the older name, then it would not have bothered them to call human beings pongids, or apes either. But since evolution is defined as descent with modification, taxonomists should indeed take into account the amount of modification when classifying organisms. Classifying the rubber boas as 3 different subspecies would be consistent with the amount of modifications revealed by mtDNA and morphologocal studies made by you and others like Rodrigues-Robles et al. Thanks to your work, there is a much clearer understanding of the relationships within the rubber boa. Classifying the rubber boas as a single species without subspecies distinction would obscure the information of the amount of modification that have evolved within this species.

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