>>CK,
>>Just to add a bit more to our 'brainstorming'.session.
>>The sample of vouchers I examined from the Santa Cruz Mts. indicates that population belongs to the large morph. So due to geographical proximity, up to now I too considered it likely that the boa population in Monterey County (and San Luis Obispo Co.) would belong to the large form as well. Yet I always try to remain open to alternative explanations.
>>
>>When I went through my folders on the vouchers I had examined from the Smithsonian, CAS, and MVZ collections, I found just the three Monterey Co. females all of which were somewhat small. Not much can be gleaned from such a small sample so here we have another region that needs to be explored.
>>
>>Seems to me that at one time, the mountainous areas of Santa Cruz and Monterey Counties were separate by intrusion of the sea into the central valley. So I wonder if that barrier may have any implication on the nature of those two populations.>>

The mountains of Monterey and Santa Cruz Counties are separated by the Salina Valley, which is probably an effective barrier to the dispersion of some species. For example, the northern and southern newts currently assigned to Taricha torosa are allopatric, separated by the Salinas Valley, with one population to the north and the other to the south, without any evidence of mixing. On the other hand, this area appears to be ineffective in isolating L. zonata populations from one another.

>>And like yourself, I originally 'assumed' that the dwarf morph was ancestral. After confirming that the San Bernardino boa population was indeed a dwarf form of the species, in about 1996, I gave considerable thought to the issue large and dwarf morphs. I devised a hypothesis to explain the likely selection factors whereby the large morph evolved from the dwarf form. At the time, I passed those thoughts on to Glenn Stewart and Dr. Robert Mason here at Oregon State U. but haven't concerned myself with that aspect since.>>
>>But unless the raw mtDNA data somehow can ascertain the relative ages of populations, then I have to concede that perhaps my original views were in error and there exists the possibility that the dwarf morph evolved from the large morph.>>

It is highly unlikely, but certainly possible, that the large morph is ancestral. MtDNA data can in fact ascertain the relative ages of populations. It is a rather neutral molecule, which means nucleotide substitution is due almost entirely to chance, much like radioactive decay. The molecular clock is of course not as accurate as the atomic clock, and of course the molecular clock must be calibrated with the fossil record, which is highly fragmentary. What we see in the rubber boa is that the umbratica lineage is the oldest. How do we know? Basically we know because we see a large number of differences in the mtDNA compared to other rubber boa populations. The greater the number of these mutations, the greater the amount of time has elapsed since two populations last shared a common ancestor. All of the populations within umbratica, OTOH, share very few differences. That means all umbratica populations share a very recent common ancestor. That is how I came to the conclusion that umbratica almost became extinct in the recent past.

Similarly, if you take two boas from, say, the Sierra Nevada subclade, you will see that they are also very similar to each other in their mtDNA, suggesting again that these populations share a relatively recent ancestor. But if you compare the mtDNA of the Sierra Nevada subclade and Northwestern subclade, you will see a greater number of differences. The greatest number of differences in mtDNA can be found if you compare the mtDNA of an umbratica with the mtDNA of a Northwestern subclade boa, or if you compare umbratica with the Sierra Nevada subclade. It shows that the umbratica lineage has been isolated from other boas forthe longest period of time. This lineage has accumulated a large number of mutations in its mtDNA that are unique to itself and not shared with any other lineage. It is this large number of nucleotide substitutions that has enabled Rodriguez-Robles to estimate the age of the rubber boa as a species. It takes time to accumulate all of these mutations. Therefore umbratica appears the oldest lineage. Other lineages, such as the Sierra Nevada subclade, are younger, because they share a number of mutations with the Northwestern subclade.

>>I know so little about mtDNA research but I can envision one potential piece of evidence that may indicate the relative age of populations. You can give me your thoughts about the following: If a large number of mtDNA haplotypes exist in a relatively small geographical region, wouldn't that indicate that over time, a large number of mutational events had occurred? In contrast, if there are much fewer mtDNA haplotypes in a geographical region, would that possibly indicate a much younger age? >>

See above for how lineage age is determined. If you see a large number of haplotypes in an area, it may simply mean that the populations within a particular area are isolated from each other, so that they are unable to mix freely. For example, there are several distinct mtDNA haplotypes within Ambystoma tigrinum californiense within its relatively limited range. That only indicates that A. t. californiense from different parts of its range has been prevented from interbreeding freely probably because of geographical barriers. To measure lineage age, one must examine the number of nucleotide substitutions that have occurred, not the number of haplotypes that may be present.

>>Should there be a large number of different mtDNA haplotypes and few identical haplotypes in the San Bernardino and San Jacinto Mts. in relation to other regions, then perhaps relative age can be inferred. Perhaps the ratio of unique to identical haplotypes per given region is such a clue. The existence of 32 identical haplotypes from N. Calif. to B.C. to Montana, Utah and Nevada may suggest such a scenario. >>

The haplotypes of the Northwestern subclade are not identical. The differences in mtDNA sequence between populations within this subclade are relatively large. If you look at fig. 4 of Rodriguez-Robles, you will see that the branch lengths between different populations are much longer within this subclade than in either the Sierra Nevada subclade or in umbratica. That means there are many more mtDNA sequence differences between a boa from Santa Cruz County and Berkeley than there are differences between a boa from El Dorado County and Madera County. All of the boas of the Northwestern subclade, however, do share a more recent common ancestor with each other they they do with either the Sierra Nevada subclade or umbratica.

>>If the frequency of different and identical haplotypes per geographical area can be interpreted as an indication of age, then here again is another argument for testing much larger samples per any geographical area.>>

Unfortunately it cannot. If you go to New York City, you will see a lot of different mtDNA haplotypes among the human beings living there. It does not mean that New York City has one of the oldest human populations in the world. If you go to Africa, however, you will see that the mtDNA differences between two Africans from different parts of Africa are often much greater than the mtDNA differences between two non Africans anywhere else in the world. That means all non-Africans in the human species share a more recent common ancestor with each other than many Africans do with each other. Normally, we would expect to see the same in umbratica. We should see lots of old lineages within umbratica, comparable to what we see among Africans. But instead we only see a single ancient umbratica lineage with lots of newly evolved branches at the top. That is indicative of a recent bottleneck, or population crash within umbratica. Without the presence of the umbratica lineage, scientists may have concluded that C. bottae is a much younger species than it really is.

>>As a side note, as I was looking up the information on the specimens I have examined from Monterey County, I ran across three more old vouchers that originated within the Mt. Lassen area. One specimen from the Smithsonian was collected along Mill Creek in northeastern Tehama County due south of Lassen Peak. Then the CAS collection has two specimens collected in 1926 and 1949 with the former coming from the Lake Almanor peninsula and the other from near Westwood. This latter specimens is just about half way between the Northwestern subclade Eagle Lake specimen and Sierra Nevada subclade Quincy specimen in Javier's study.
>>
>>It would be my guess that Javier and others entertained the notion of a break in the distribution of the species based on the distance of 120 km they thought occurred between the two subclades, the specimen from Eagle Lake in Lassen County and specimen from Nevada County. Had they realized that their specimen from near Quincy in Plumas County
>>cut that distance about in half, I don't think they would have indicated a break occurred in the distribution of the species.
>>
>>I get a sense they may have rushed the publication a bit. And it still strikes me odd that none of the reviewers caught that error. I suspect the reviewers were versed in aspects of molecular research and not in natural history.
>>
>>Richard F. Hoyer

Well, biology is a highly specialized discipline nowadays. It is often difficult for one researcher working on one species to judge the work of another researcher working on another species. Besides, professional biologists are often very busy, teaching, doing research, and so on, so reviewing papers often does not get the amount of time or attention that it deserves.

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