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RE: C. bottae taxonomy - A new wrinkle

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Posted by: CKing at Mon May 19 11:54:30 2008  [ Report Abuse ] [ Email Message ] [ Show All Posts by CKing ]  

>>If the zonata study to which you refer was by Javier, then though Rob Lovich, I contributed some tissue to that study from the zonata population in the San Bernardino Mts. >>

Fascinating that you have a personal connection to that illuminating study. Yes, Rodriguez-Robles' mtDNA study of L. zonata is the paper I am referring to. It shows, even if Rodriguez-Robles themselves may not agree, how well R. G. Zweifel was able to determine relationships within L. zonata using morphology alone. About the only mistake Zweifel made was to call the Santa Monica Mt. population L. z. pulchra, when it is actually L. z. parvirubra. And of course the Mt. Hamilton population, which he believes to be L. z. multifasciata x L. z. zonata, is actually a trans-Valley leak from the Sierra Nevada multicincta. The subspecies L. z. zonata may actually be part of the intergrade population of L. z. multicincta and L. z. multifasciata. Sorry to throw so much stuff at you, but I am excited by that paper and the valuable phylogenetic information contained therein.

>>As of the present time, I have contributed about half of the samples for the current C. bottae mtDNA study. I still am in possession of over 600 tissue samples that I hope one day someone can be of use, particularly for an in-depth nuclear DNA study. The recent new results I find particularly rewarding as those samples were not part of the initial study and only at my urging did the individual agree to have them tested. I asked about the Mt. Lassen situation but he has yet to examine those results. >>

Good for you. Often people who are doing the genetic studies may not be as knowledgeable of the organisms themselves. They are most concerned about lineages and sometimes pay little or no attention to how intraspecific variation may have arisen. Nuclear DNA studies can reveal evidence of intergradation, something the mtDNA data alone may not be able to reveal. I know there have been some taxonomic proposals made on the basis of mtDNA studies, and these have been unsatisfactory, and the opponents of these proposals often demand nuclear DNA studies as confiramtion. Of course mtDNA studies are not always reliable, but even when they are, there is often no direct link between mtDNA lineages and the morphological traits that define subspecies and species, not to mention higher taxa. Hence it is really not a good practice to do taxonomy by delimiting mtDNA clades and assigning names to these clades. Nevertheless mtDNA is a valuable tool, and it has revealed details about past evolutionary history that nuclear DNA studies will not be able to reveal.

>>However, from the table that lists the localities of tested samples in this new study, 13 new samples originate from the general region close to samples #6 (Eagle Lake) and #15 (Greenhorn Creek east of Quincy) in Javier's study. However, in checking the localities on my de Lorme atlas software map, only 6 of are located what might be considered as in-between 6 and 15. So I am not all that hopeful that new information will emerge to clarify the issue.>>

The additional samples do help. Even if the gap is not bridged, there could still be evidence of intergradation. As I pointed out, all that it takes is for a snake with Sierra Nevada mtDNA to be found within the known range of the Northwestern subclade, or vice versa, and we will have evidence that the complete allopatry theory needs revision. If the two subclades remain divided, even if the gap had shrunk, then the evidence would be consistent with complete allopatry. There is no need to despair if the two subclades has never met. It actually becomes a very interesting problem to be solved. Did they fail to meet because of volcanic activity? Or did they fail to meet because the Northwestern subclade members cannot survive in the habitats within the Sierra Nevada mountains. These are some of the questions that hopefully will interest a future investigator. But since careers are often at stake, and since research interests are often under the influence of professors, these questions may not get any answers for decades.

>>Instead of some type of barrier or break occurring in the distribution of the species in that region, those 13 new samples add support to the scenario of a continuous distribution. Even if there had never been a single boa documented in that region, the biological evidence of unbroken suitable habitat clearly indicates an unbroken distribution of the species particularly in this instance where there is zero evidence of any existing barrier or break in boa distribution in the region. As mentioned, simply by having two voucher specimens having been found 60 or 120 km apart is not evidence of a discontinuous distribution. And that is why I was perplexed that Javier would state that the two subclades are separated by some imagined break that occurs somewhere in the vicinity of Lassen Volcanic National Park. >>

One scenario that would prevent an organism from occupying seemingly suitable habitat is that the organism only recently evolved, and have not had time to disperse into these areas. Even though the rubber boa has been around for over 10 million years, it has only dispersed into the Sierra Nevada range relatively recently. The relatively young age of the Sierra Nevada subclade was hinted at by Rodriguez Robles. They said, "On the other hand, the very short branches in the ML tree within the umbratica clade and the Sierra Nevada subclade are suggestive of shallow differentiation of mtDNA haplotypes,..." They, however, appeared not to have seriously considered the possibility that the San Bernardino and San Jacinto mountain populations only recently diverged from each other, most likely because the last ice ages forced these snakes down the mountains, and only after an ice age has ended can they disperse up to the higher elevations. Similarly, the young lineage age of the Sierra Nevada subclade was due to the inability of rubber boas to spread north from the vicinity of Tulare County. I should mention that Sierra Nevada populations of L. zonata also show evidence of recent divergence. So, whatever it was that kept the rubber boas from reaching the Sierra Nevada range north of Tulare County also kept L. zonata from doing the same. If the Sierra Nevada subclade arrived too late, and the Northwestern subclade are unable to colonize the Sierra Nevada range despite their apparent close proximity, then the allopatric distribution is real and it can be explained.

>>You mention having to disprove his Theory. Theories are established on a preponderance solid evidence and not on pure speculation. Since no evidence exists for the imagined break in distribution, there is nothing to disprove. On the contrary, it should be up to researchers to present solid evidence for the existence of a barrier or a break in distribution.>>

Your claim is that absence of evidence is not evidence of absence. You are pointing out that an absence of evidence of boas in the gap is not evidence of absence of intergradation. Well, normally that is how science works. However, as Ernst Mayr pointed out, sometimes the absence of evidence can be taken as evidence of absence. For example, he pointed out that the absence of evidence that the rumored continent of Atlantis exists, after decades of exploration of most of the earth's surface, should be taken as evidence that Atlantis does not exist. Your claim is that Rodriguez et al. did not search hard enough for evidence of intergradation. That is of course a valid claim. However, it is also up to the individuals who believe in intergradation to show evidence. So far, such evidence still does not exist. I know you feel strongly that there is no reason why such evidence cannot exist, but I am sorry to say that until such evidence does turn up, Rodriguez-Robles' theory has not been disproven.

>>As for sample #26 from the southern Sierras (Tulare County) that was aligned with 4 specimens from the northern Sierras, that in itself seems a bit odd. Since Fig. 1B showed
>>those 5 specimens to be somewhat disjunct from the Sierra Nevada subclade, I looked up their collection data. I found there is an error for #26 in that the coordinates are for the center of the city of Tulare. Yesterday I informed the researcher of that error. The specimen is from the Cal Poly collection and hopefully Glenn Stewart will be able to find the correct locality information.>>

Thank you. To err is human, and mistakes are often made, even by researchers.

>>Either I have failed to adequately communicate the biological realities regarding the two subclades in the Mt. Lassen area or perhaps my understanding of the term 'allopatric' is somehow different from common usage or understanding. It has been my understanding that allopatry is where populations are isolated from one another and never meet. It they meet somewhere but essentially remain separate, the term parapatric would come into play. Where two populations meet and where there occurs some overlap in distribution, I have considered that to be a case of sympatry>>

Well, so far the available evidence shows that the Northwestern subclade and Sierra Nevada subclade has never met. They are completely allopatric. You do have evidence that boas occur within the area in which Rodrigues-Robles et al. claim none can be found. However, there is no mtDNA data yet on these additional specimens, so it is too early to say whether Rodrigues-Robles et al.'s theory has been disproven or not.

>>I will concede that the subclades could basically be parapatric and that any overlap of mtDNA types could be minimal due to some reproductive / behavior incompatibility or selection against hybrids. But without evidence of any existing barrier, the odds are essentially 100% that the two subclades meet and thus overlap even if only to a small degree. Now if my understanding of the terms 'allopatric' , 'parapatric' and 'sympatric' are incorrect, then at least you can understand where I have gone astray. >>

I know you think that it is illogical and implausible how these two subclades can be allopatric when seemingly suitable habitat exist between the two. There are plausible explanations. One of them is that the Northwestern subclade has never been able to gain a foothold in the Sierra Nevada mountains. That is well supported by data. Because the Northwestern subclade migrated north early and spread widely, to Canada in the North, and Utah to the east, and yet there is no evidence that it has ever invaded the Sierra Nevada Mountains. The Sierra Nevada Mountain boas, however, entered the Sierra Nevada range only recently from the vicinity of Tulare County. This subclade may simply not have enough time to disperse far enough north to meet with the Northwestern subclade yet. And perhaps Rodriguez-Robles was correct that volcanic activity may have prevented them from meeting. It is of course possible that the lack of evidence of intergradation is due to lack of adequate collecting in the area in question. One way to find out is to collect more intensively in the area. I know R. C. Stebbins worked hard and collected intensively in San Diego for evidence of intergradation between subspecies of Ensatina. May be it would take the same sort of hard work in the Mt. Lassen area to see if boas intergrade in the area.

>>In some respects, interpretations of results boils down to the 'art' or creativity that is inherent in scientific endeavors. I have wondered how others would have written the manuscript on C. bottae taxonomy given the same data and mtDNA results. Understanding the species as (I think) I do, I would not have even hinted that a break in distribution occurs in the Mt. Lassen area based on the results that show the two subclades as having separate distributions. And theorizing what some type of past or present barrier accounts for the
>>complete separation of the two subclades is the type of speculation I believe to be unwarranted. The problem with such speculation is that subsequently, others cite such claims
>>as if established fact. As examples, such speculation about the Sharp-tailed Snake only eating slugs and the blunt tail of the boa being a defense against predators are two cases where conjecture essentially became established fact in subsequent references of those species.>>

I understand your frustration. However, one can argue endlessly whether Rodriguez-Robles et al. was correct in their interpretation of their results. But there is nothing in their results which is inconsistent with allopatry. One may argue that their sample is inadequate, and that may be true, but their results do support allopatry, not intergradation.

>>That Javier has a creative imagination was also revealed in a previous study he did on the diet in the Rubber Boa. Based on the results he obtained, he made the claim that a shift in diet occurs in the species whereby small members of the species only consume lizards and their eggs. Larger specimens of the species then includes small mammals and birds and ceases to eat lizard eggs.
>>What he did not understand (and again, this is where the review process failed) is that the boa occurs in regions that lack any egg laying lizards. The N. Alligator Lizard, a live bearer, occurs sympatric in a reasonably large area of the boas in Oregon, Washington, and B.C. I have recorded umpteen cases in which juvenile and small subadult boas have consumed nestling small mammals just as do the adults. I believe this particular case is where Javier placed to much faith in results extracted from a relatively small sample without adequate geographical representation. And I contend that situation was another clear example where the review process failed--miserably I might add!

Great stuff! You have data to falsify Rodriguez-Robles explanation of diet. That is great! What you would need is also data if you want to disprove allopatry.

>>As for allopatry, a similar situation occurs with respect to the large and dwarf morphs. If my understanding of the term 'allopatry' is correct as indicating complete separation,
>>then up to early 2002, based on the information at hand, I considered it very likely that the two morphs had allopatric distributions with the dwarf form occurring only on the isolated mountain peaks and ranges south of the main Sierra Nevada Mts.
>>At the time I completed my study of the SRB in the San Bernardino Mts. and discovered that population was indeed a dwarf form of the species, starting in 1997 I began working my way north and west to determine if other populations of the species were also dwarf. By 2001, I determined that the Tehachapi Mt. population was dwarf and had fragmentary data suggesting the same situation for boas on Mt. Pinos and on Breckenridge Mt.
>>In 2001, with my binocs I scanned the Scodie Mts. due east of Lake Isabella. With what appeared to be coniferous trees at the upper elevations, I entertained the notion that the species might exist in that small isolated mt. range despite being surrounded by Mojave Desert. Maps indicated an elevation of 6000 ft. The boa had already been document on the Piutes due east of Breckenridge but not the Scodie Mts. At the time, I mentioned to Brad Alexander of Kernville that we should make searches there in 2002.
>>In April of 2002, I could not get down the weekend Brad chose to go to the Scodie Mts. Along with Robert Hansen and others, Brad found a single female boa (under a lone piece of
>>roofing tin) in the Scodie Mts. which by all indications was an adult of the dwarf morph. As a matter of fact, that boa produced a litter which pretty much clinched that issue. Then in late April of 2002, as the two of us were driving up to the S. Kern Plateau to conduct searches (Brad for zonata and myself for Charina), I asked if he thought the dwarf morph occurred on the Kern Plateau. I expected him to reach the same conclusion as myself but instead he indicated he felt the dwarf morph would occur there as well. And as it has turned out (and to my surprise), he was right. So much for my 'theory' of allopatric distributions of the two size morphs.
>>Discovering the dwarf form on the S. Kern Plateau and in the southern Greenhorn Mts. changed by view 180 degrees. Yes, still allopatric in their broad scale distribution but certain no longer allopatric on a finer scale as there simply has to be zones in the Greenhorn Mts. and on the Kern Plateau where the two morphs came in contact. Constructing an imaginary geographical barrier that would keep the two morph separated would be just as implausible as theorizing imaginary geographical barriers in the Mt. Lassen region.
>>Richard F. Hoyer

Again great stuff. This is how scientific discovery often come to pass. Dedicated individuals who work tirelessly to find out the truth. I congratulate you on your insight and efforts. However, your new claim that the dwarf morph is not allopatric with the Sierra Nevada large morph is based on finding small morph snakes in the Kern and Tulare county area. Are large morph snakes also found in the same area? As far as I know from our communication, only small morph snakes are found in the south and only large morph snakes are found in the north of some invisible line somewhere in Tulare County.


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