Reptile & Amphibian Forums

I see this forum is not as lively as it use to be. At any rate, I will pose a problem similar to what I addressed here 2- 3 years ago.

I recently came across the following quote. "Subspecies are defunct in modern systematic theory and have no place in current classification! "

Below, I describe the most recent findings regarding the Rubber Boa (Charina bottae) and then pose a question dealing with taxonomy.

1) A dwarf form of the Rubber Boa (Charina bottae) has been discovered to occur throughout parts of S. Calif. from the southern tip of the main Sierra Nevada Mts. south about 100 miles to the southern most limits of the species range in the San Jacinto Mts. southeast of Riverside, Calif..

North of the extreme southern part of the Sierra Nevada Mts., all other live and preserved Rubber Boa populations that have been examined in California and elsewhere in the species distribution in North America represent the large morph of the species.

2) Dwarf morph females and males reach maximum lengths of about 22 inches and 19 1/2 inches respectively. All dwarf populations exhibit relatively low mean ventral and maximum dorsal scale row counts.

Large morph females and males examined from preserved material attain lengths of at least 25 and 21 inches respectively. Keep in mind that considerable shrinkage occurs with preservation. From live samples, females of 27 - 30 inches and males of 22 - 24 inches have been recorded. Mean ventral and maximum dorsal scale row counts of the large morph are measurably higher than the dwarf form.

3) According to the mtDNA study by Javier Rodriguez-Robles, Glenn Stewart, and Ted Papenfuss, the Rubber Boa is represent by a southern clade and a northern clade which were estimated to have been isolated from one another for 4 - 7 million years. The paper urged the recognition of two species, the Northern Rubber Boa (Charina bottae) and the Southern Rubber Boa (Charina umbratica) representing the two clades.

4) The southern clade is composed of just two populations of the dwarf morph that occur in the San Jacinto and San Bernardino Mts. All other populations of the dwarf morph (with both size and scalation features similar to the San Jacinto and San Bernardino populations), along with all populations of the large morph, were assigned to the northern clade.

It would appear that a conflict exists between the mtDNA evidence and nuclear DNA (morphological traits) evidence. With or without using subspecific designations, is there anyone that is willing to pose a plausible taxonomic explanation / solution to the situation described above?

Richard F. Hoyer (Corvallis, Oregon)

P.S. I can post a somewhat more detailed version if anyone believes that might help.

First a disclaimer- I am not a taxonomist, and I am not particularly familiar with rosy boas. I'm just throwing out some ideas here.

You draw a connection here between size and relatedness, but this is not necessarily the case. I can see a few scenarios that would result in the conflict between MtDNA and morphological data.

1). The adult size of these snakes is non-genetic. The 'dwarf forms' simply live in a habitat that causes them to remain small. A number of factors could lead to this: prey is scarce or of poor quality; seasonal activity is limited; larger individuals are selectively preyed upon; individuals breed at small size or early age, diverting nutrients from growth; etc. Thus the two lineages are affected by the same factors in the southern mountains. Perhaps if the southern lineage reached farther north, it would also show regional variation in size.

2). The adult size of these snakes is genetic, but small size has evolved in parallel in the southern lineage and in southern populations of the northern lineage. Similar selective factors have resulted in similar phenotypes.

3). The converse of (2)- The adult size of these snakes is genetic, but small size is the ancestral state. Some populations of the northern lineage have evolved to larger size.

4.) The adult size of these snakes is genetic, and represents a primary division between a dwarf lineage and a large lineage. This is in actual conflict with the MtDNA data and could result in different taxonomic conclusions. Perhaps the MtDNA was skewed by incomplete sorting of mitochondrial lineages due to a recent divergence between these two lineages, or represents an earlier incomplete divergence between two lineages, followed by subsequent partial reintegration and redivergence.

5.) The converse of (4)- the southern and small northern snakes are evidence of an older incomplete divergence.

Taxonomy really has no way to deal with (4) and (5); only one split is important, the most recent one. So the following taxonomic schemes would be suitable:

Scenario 1:

Charina "Northern"
Charina "Southern"

Scenario 2:

Charina "Northern"
-----"Northern Large"
-----"Northern Small"
Charina "Southern"

Scenario 3:

same as 2

Scenario 4:

Charina "Large"
Charina "Small"

Scenario 5:

Charina "Northern"
Charina "Southern"

batrachos,
Thanks for your response. And by the way, the species involved is the Rubber Boa and not the Rosy Boa.

I have posed this same question elsewhere. So far, no one has even attempted a response let alone pose a solution either with or without the use of subspecific designations. So you stand alone in providing some input and that is appreciated.

At times, I have found myself agreeing with Ron Nussbaum who in a 1974 paper on the species, discarded the then 3 recognized subspecies and simply lumped all Rubber Boas into a single species. Yet that arrangement overlooks the present situation (unknown at that time) where there are two discernable groupings of the species. On the one hand, there is the large morph populations characterized by large size, relatively high ventral and dorsal scale row count. In contrast, there are the dwarf morph populations all characterized by small size and with relatively lower ventral and dorsal scale row counts.

In addition, these two groupings are clustered geographically. Had such information been available in bygone years, the two groups would either have been designated as subspecies or species. However, the present mtDNA results throws a monkey wrench into that scenario. At the present, I can think of two explanation that might tend to be consistent with the mtDNA results.

1) One might argue for retention of the two species, the Southern Rubber Boa and Northern Rubber Boa with the latter being composed of two subspecies as follows: All large morph populations would comprise a northern subspecies and all other dwarf populations (expect those in the San Bernardino and San Jacinto Mts.) would constitute a southwestern subspecies of the Northern Rubber Boa.

2) A second scenario would be to have three subspecies. All large morph populations would belong to the northern subspecies, the dwarf populations in the San Bernardino and San Jacinto Mts. would belong to a southeastern subspecies, and all other dwarf population in S. Calif. would belong to a southwestern subspecies.

Of course, the problem with both scenarios is that they disregard the current vogue of discarding all subspecific designations. I am not knowledgeable enough about how to interpret mtDNA results but the data presented in Javier's paper might suggest additional scenarios as well.

I did not post the longer explanation which indicates all Rubber Boas populations occupy the identical ecological niche regardless of geography. They are all nest robbers mostly preying on small mammal nestlings (shrews, moles, mice, gophers, voles, rats, etc.) Secondly, I have already completed some crosses between dwarf and large morph specimens and size is definitely under genetic control. In addition, maintaining juvenile and subadult specimens of both size morphs under identical laboratory conditions substantiates that size is genetically controlled and not a function of differing environmental conditions.

Re your forum name, are you fondly 'attached' to slender salamanders? Thanks again for your input.

Richard F. Hoyer

Haha, my mistake with the rubber/rosy mix-up. I should really proofread my posts.

Like I said, I am not a taxonomist or a geneticist; I just read a few herp taxonomy papers now and again. I am not convinced that MtDNA analysis alone is an adequate taxonomic tool, especially for relatively recently diverged species, but I don't know enough about the statistics and assumptions involved to really dispute the practice. I know a lot of people use it who are much more clever than I am, but it still seems like too little evidence to make strong conclusions from.

I think subspecies are a good way to recognize diversity below the species level. But the new breed of taxonomists are much more interested in the patterns connecting species than in the species themselves. There are a lot of things about cladistic and phylogenetic approaches to taxonomy that just seem to me to be missing out on some of the important things that taxonomy is good for, and also seem to be ignoring some of the realities of organisms. Species are not nodes. But what can you do?

I can see your taxonomic quandary. The vogueish thing to do, I guess, would be to separate the rubber boa into three full species in place of the three subspecies you describe below. If you can sample along the area where the large and small Sierra Nevada populations come together and find a fairly narrow intergrade zone, or an abrupt change from one body type to another, that would be sufficient evidence for separate species status for most splitters. Since the southern populations are allopatric anyways, totally eliminating any possible intergrade zone, that leaves you with three species of rubber boas.

The situation is somewhat similar to the Elaphe obsoleta complex; the morphological and MtDNA data don't line up. In that case, Burbrink et al. interpreted this to mean that the various ratsnake lineages had developed northern dark and southern light populations in parallel. They chose to give no taxonomic recognition to the various color phases within each lineage. Of course, every situation is different, and this might not be the appropriate interpretation for rubber boas.

I hope you can find a more qualified person to bounce ideas off of. It's worth a shot to send emails about the situation to some prominent snake taxonomists, not just ones who have worked with rubber boas.

RE: my user name, "batrachos" is just the Greek word for frog. I studied Greek in college, and I like frogs, so it seemed natural enough. I believe "Batrachoseps" comes from "batrachos" "ceps" (="head". I'm a Tennessean and have little experience with the slender sallies or other western fauna.

Good luck!

Batrachos,
Your analysis regarding mtDNA testing ,etc. mirrors my own views. Thanks again for your responses.

Richard F. Hoyer

>>batrachos,
>>Thanks for your response. And by the way, the species involved is the Rubber Boa and not the Rosy Boa.
>>
>>I have posed this same question elsewhere. So far, no one has even attempted a response let alone pose a solution either with or without the use of subspecific designations. So you stand alone in providing some input and that is appreciated.
>>
>>At times, I have found myself agreeing with Ron Nussbaum who in a 1974 paper on the species, discarded the then 3 recognized subspecies and simply lumped all Rubber Boas into a single species. Yet that arrangement overlooks the present situation (unknown at that time) where there are two discernable groupings of the species. On the one hand, there is the large morph populations characterized by large size, relatively high ventral and dorsal scale row count. In contrast, there are the dwarf morph populations all characterized by small size and with relatively lower ventral and dorsal scale row counts.
>>
>>In addition, these two groupings are clustered geographically. Had such information been available in bygone years, the two groups would either have been designated as subspecies or species. However, the present mtDNA results throws a monkey wrench into that scenario. At the present, I can think of two explanation that might tend to be consistent with the mtDNA results.
>>
>>1) One might argue for retention of the two species, the Southern Rubber Boa and Northern Rubber Boa with the latter being composed of two subspecies as follows: All large morph populations would comprise a northern subspecies and all other dwarf populations (expect those in the San Bernardino and San Jacinto Mts.) would constitute a southwestern subspecies of the Northern Rubber Boa.

That is an untenable arrangement on the basis of mtDNA data. The two populations in the north that are characterized by large size represent two different waves of migrations from the south. These two populations are not known to interbreed. Rodriguez-Robles et al. pointed this out in their paper:

"...the Sierra Nevada and the Northwestern subclades...have completely allopatric distributions, with a break that occurs somewhere in the vicinity of Lassen Volcanic National Park in northeastern California (between the localities of C. b. bottae samples 6 and 14, which lie about 120 (airline) km apart; Fig. 1)."

Because of allopatry, there is the possibility (albeit remote) that these two distinct lineages may not even be able to interbreed with each other. In that case they could be considered distinct species. Their large body sizes may have evolved convergently (because of similar environmental conditions) or through parallel evolution (because of the independent expression of the same gene that is inherited from their common ancestor). Hence this particular similarity alone cannot be used to group them as a single species or even subspecies until further study. If it is parallelism which is responsible for their large body sizes, then they can be considered the same subspecies or species provided that they can interbreed.

>>2) A second scenario would be to have three subspecies. All large morph populations would belong to the northern subspecies, the dwarf populations in the San Bernardino and San Jacinto Mts. would belong to a southeastern subspecies, and all other dwarf population in S. Calif. would belong to a southwestern subspecies.

This arrangement is also not tenable. Personally, I would group the dwarf boas in Kern County with the umbratica subspecies to the south, and divide the two northern lineages as separate subspecies for the time being. I am assuming that dwarfism is an ancestral condition (which seems very likely) and that the Kern County animals have retained this ancestral condition. If dwarfism is indeed ancestral, then the two allopatric populations to the north almost certainly evolved their large body sizes independently of each other and therefore they should not be lumped together as a single subspecies because of morphological similarities that are likely convergent.

>>Of course, the problem with both scenarios is that they disregard the current vogue of discarding all subspecific designations. I am not knowledgeable enough about how to interpret mtDNA results but the data presented in Javier's paper might suggest additional scenarios as well.

We can safely disregard the philosophical aversion to the subspecies category exhibited by many cladists. The cladists embrace a classification philosophy that is unique to themselves and their philosophy has contributed much to the chaos we see today in taxonomy.

>>I did not post the longer explanation which indicates all Rubber Boas populations occupy the identical ecological niche regardless of geography. They are all nest robbers mostly preying on small mammal nestlings (shrews, moles, mice, gophers, voles, rats, etc.) Secondly, I have already completed some crosses between dwarf and large morph specimens and size is definitely under genetic control. In addition, maintaining juvenile and subadult specimens of both size morphs under identical laboratory conditions substantiates that size is genetically controlled and not a function of differing environmental conditions.

If dwarfism is under genetic control, then it is all the more reason not to lump the two allopatric large morph populations to the north as a single taxon. Have you tried hybridizing the coastal boas with the large morph Sierra Nevada boas? If the hybrids are infertile or if they refuse to mate, we may well have two different species. If their large body sizes are under the control of different genes, then there is a possibility that at least some of the hybrids could exhibit the ancestral state of dwarfism. The rubber boa is a very interesting species indeed.

>>If dwarfism is indeed ancestral, then the two allopatric populations to the north almost certainly evolved their large body sizes independently of each other and therefore they should not be lumped together as a single subspecies because of morphological similarities that are likely convergent.

A similar situation exists in the species Lampropeltis getulus, the common kingsnake. There are two subspecies that are characterized by melanism, L. g. niger and L. g. nigritus. These two taxa acquired the trait of melanism independently of each other, and they are also allopatric in distribution. Taxonomists in general do not consider them the same subspecies. Similarly, the 2 large morphs of the Rubber boa most likely required the large morph phenotype independently and they are allopatric. They should therefore not be lumped.

CK,
See my message to your other post below.

Richard F. Hoyer

CK,
I returned from my trip to S. Calif. about a week ago and now have time to address some of the comments contained in your April 19th post.

You quoted a passage from the 'Discussion' section in Javier's paper as follows: "...the Sierra Nevada and the Northwestern subclades...have completely allopatric distributions, with a break that occurs somewhere in the vicinity of Lassen Volcanic National Park in northeastern California (between the localities of C. b. bottae samples 6 and 14, which lie about 120 (airline) km apart; Fig. 1)."

It is normal for a reader of published research to automatically assume that the authors were factually correct in making statements. But in this case with the issue of allopatry, they clearly didn't. Let me first mention that Glenn Stewart sent me a draft of the mtDNA paper to review. I made a number of comments one of which questioned the claim of allopatry. At the time, Glenn explained why he thought Javier had indicated that to be the case and although I totally disagreed, I did not continue to challenge that point thinking that the editor or reviewers would pick up on that issue. In hindsight, the reviewers dropped the ball as well.

As a matter of fact, there are a number of flaws in that particular section of the paper. For instance, Table #1 indicates the origin of sample # 6 is from Eagle Lake, Lassen Co., #14 from Forest Road 17, Nevada Co., and #15 from Greenhorn Creek, Plumas Co. Due east of Mt. Lassen, Plumas and Lassen Counties adjoin. Nevada County is immediately
south of Plumas Co. Then when you view Fig. 1, you will note that the arrow has Nevada County sample #14 being situated above Plumas County sample #15 whereas it should be below sample #15.

In supposed support for claiming the two subclades have an allopatric distribution, the authors then site a distance of 120 direct kilometers between samples #6 and #14. The authors overlooked the fact that specimen #15 in Plumas county is closer to sample #6. And if my memory serves me correctly, when I checked a few years ago, sample #6 and #15 are about 60 km apart.

But I ask, how does the distance between vouchers provide support for allopatry? I have no idea of how the authors arrived at the notion that citing a distance between where two voucher specimens originate is support for allopatry. It would seem to me they didn't think through that situation very well nor did the reviewers do their job by challenging that point. If one understands the (mostly) random nature of how specimens become voucher, citing distances as support for any particular conclusion about a species is quite risky.

So the major error made is the statement you quote is the authors stating the two subclades are allopatric in distribution. Again, with not having spoken to Javier in that connection, I haven't any idea where such a notion arose. You might note that they do not cite any reference in support of their claim nor is there any reference to personal observations by any of the authors. New information stated as if factual in research publications should automatically be suspect when such claims lack support or verification of any sort.

At the time of the publication, many years had passed since I had been in the vicinity of Mt. Lassen. So during subsequent trips south to S. Calif. or on the return trips, I made it a point to travel all around that region and even took time to make some searches. As had been my impression from bygone years, suitable Rubber Boa habitat is extensive in all directions and unbroken throughout and beyond the immediate Mt. Lassen region.

During my trips, I collected two specimens in eastern Shasta Co near Burney approximately 25 - 30 miles slightly northwest of Mt. Lassen. Another specimen was collected in western Lassen County just east of the Shasta Co. line and about 15 miles slightly northeast of Mt. Lassen. Two other specimens were found in extreme northeastern Tehama County slightly southeast of Mt. Lassen by about 15 miles and just 2 - 3 miles from Plumas County. A few years ago, Chris Feldman and another grad student at Utah State U. collected a number of specimens for CAS near Mt. Lassen either in Lassen and / or adjacent Plumas counties, reasonably close proximity to Mt. Lassen, and in-between localities represented by specimens #6 and #15. Coupled with the knowledge of extensive and unbroken suitable boa habitat in that region, these recent findings dispel any notion of allopatry existing between the two subclades. That members of the two subclades interbreed is highly probable.

Accepting the author's claim of allopatry, you mentioned the remote possibility that the members of the two subclade would be reproductively incompatible. In my efforts to possibly shed light on the inheritance of the size factor(s), I have made the following crosses between males of the Sierra Nevada subclade and females of the Northwestern subclade.

dwarf morph Tehachapi Mt., Kern Co. male X large morph, Blodgett. Benton Co., Oregon female
dwarf morph Tehachapi Mt., Kern Co. male X large morph Mendocino County, Calif. female
dwarf morph Tehachapi Mt., Kern Co. male X large morph Starker Pit, Benton Co., Oregon female

Below are the reciprocal crosses made between males of the Northwestern subclade and females of the Sierra Nevada subclade.

large morph Berkeley, Alameda Co., Calif. male X dwarf morph female, Breckenridge Mt., Kern Co., Calif.
large morph Berkeley, Alameda Co., Calif. male X dwarf morph female, Poso Creek , Kern Co., Calif.
large morph Chapman site, Benton Co., Oregon male X dwarf morph female, Breckenridge Mt., Kern Co., Calif.

For the most part, the above crosses resulted in full term, live neonates with a few stillbirths.

With my understanding that distribution of the species is continuous from Kern Co. to British Columbia and the likelihood that the subclades are interbreeding, I have not undertaken crosses between large morphs of the two subclades.

When I was operating under the permits held by Dr. Stewart, my initial cross in 1996 was between a Northern Clade large morph female from Oregon and a Southern Clade dwarf male from the San Bernardino Mts. That cross produced 4 full term, live neonates, two male and two females. One of the female neonates died for unknown reasons and during the second or third year, one of the males died after eating a juvenile Ensatina.

The one surviving F-1 female proved to be fertile as a few years ago, she was backcrossed to a dwarf morph male and produced a litter. The fact that a cross between the two major clades produced fertile offspring lends credence to the notion that crosses between the two subclades should also produce fertile offspring. But since it takes from 6 - 10 years before female specimens reach sexual maturity, there hasn't been enough time for any of those F-1 specimens to have reached maturity at this point.

And just to add some added information to ponder, crosses between dwarf morph males and large morph female have produced only large morph neonates. Crosses between dwarf morph females and large morph males have produced only dwarf morph neonates.

Richard F. Hoyer

Hi Richard, thank you very much for your thoughtful response. After reading the new information you have provided concerning additional specimens and localities, I must nevertheless conclude that these new specimens have not disproven Rodriguez-Robles' claim that the two large morph subclades are completely allopatric. He apparently based his claim on his mtDNA data, which shows that at any one locality, only one or the other large morph mtDNA haplotypes are present, but not both. Now, if someone, anyone, were to come up with new data which shows that both of the large morph mtDNA haplotypes are in fact present at a single locality, then the claim of complete allopatry can be falsified.

The mtDNA data suggests that the Northwestern large morph lineage migrated along the coast westward from western Kern County, and then expanded its range northward and thence eastward to occupy much of the present range of the rubber boa north of Kern County, but exclusive of the Sierra Nevada Mountain Range. And this migration apparently took place before the Sierra Nevada large morph even evolved, because the small morph Kern County boas show a closer genetic relationship to the Sierra Nevada large morph snakes than either of them does to the Northwestern large morph. In other words, the Sierra Nevada large morph and Kern County small morph boas share a more recent common ancestor with each other than either of them does with the Northwestern large morph boas. That determination comes straight from the mtDNA data of Rodriguez-Robles et al. To me that suggests the common ancestor of the Northwestern (large morph) and Kern County boas was very likely a dwarf morph snake. The 2 subsequent lineages that came from this common ancestor went their separate ways, one along the coast and became exclusively large morph, and the other along the Sierra Nevada Mountains, but remaining small morph until a large morph population evolved later in the Sierra Nevada Mountains north of Kern County. And these two large morphs apparently have never met.

As I said earlier, there is no mtDNA data to demonstrate that the Northwestern large morph has ever met the Sierra Nevada large morph. I understand your objection to this claim because you believe that the area between the supposed gap in distribution is suitable habitat for boas and some boas have been found within this gap. Unfortunately, there is no mtDNA data from these specimens to show which population they originated from, and more importantly, there is no data to show that both types occur in the same locality. Until that data becomes available, Rodriguez-Robles claim of complete allopatry remains the best supported theory. Like all scientific theories, however, it can be falsified by additional data.

It is unfortunate that no crosses have been attempted between Northwestern large morph and Sierra Nevada large morph boas. Of course there is every reason to believe that they are probably reproductively compatible, because they are morphologically similar, which suggests that neither has evolved into a different species. But then again, reproductive compatibility cannot be assumed. It must be demonstrated. Of course it is equally untenable to assume that they cannot interbreed. Hence I do not support splitting the Northwestern and Sierra Nevada large morph snakes into different species because of allopatry. The best solution would be to treat them as different subspecies, as least for the time being. Lumping them on the basis of their similarity as large morph snakes is unacceptable because they apparently evolved their large morph phenotypes independently of each other. As I said in another post, lumping the 2 large morphs would be similar to lumping Lampropeltis getulus niger and L. g. nigritus as a single species because they both show a propensity for melanism.

Finally, your crosses between small morph and large morph snakes seem very interesting, as size seems to be linked with sex somehow. Are these crosses between Northwestern large morph and small morph snakes or are these crosses between Sierra Nevada large morph and the small morph snakes?

>>Finally, your crosses between small morph and large morph snakes seem very interesting, as size seems to be linked with sex somehow. Are these crosses between Northwestern large morph and small morph snakes or are these crosses between Sierra Nevada large morph and the small morph snakes?>>

Okay that was a dumb question. You gave locality data for your crosses and they were between small morph and Northwestern large morph snakes. It would be very interesting to see if crosses between Northwestern and Sierra Nevada large morphs snakes will be fertile, and if the offsprings will be large morph, small morph or a mix of both.

For now, I believe a 3 subspecies arrangement is better than either a single species without subspecies designation, 2 subspecies or 2 or even 3 species arrangement. The 3 subspecies should be divided geographically into Northwestern, Sierra Nevada and umbratica races. The small morph Kern County snakes should be included in umbratica, as their small body size suggest that they haven't changed since they became isolated geographically from boas living in Southern California. Umbratica would then be a paraphyletic subspecies. I am not bothered by paraphyletic taxa, but the cladists would definitely be. The alternative of recognizing a Sierra Nevada Kern County boas as a single subspecies would result in a heterogeneous mix of ancestral small morph morphotype and Sierra Nevada large morph morphotypes, which is confusing and not very useful.

CK,
Conjecture and other forms of speculation are commonly included in the 'Discussion' sections of published accounts. However, in this particular instance where different forms of a species potentially meet in a zone of intergradation, it would be important that large sample size and geographical representation is needed in order to make assertions that would engender a reasonable degree of confidence. From my perspective, not finding overlap of mtDNA on the basis of two random samples at a stated distance of 120 km apart is not the type of evidence upon which to arrive at a conclusion of allopatry and produce any degree of confidence.

Without having adequate geographical representation, assumptions should instead be based on existing evidence coupled with applying basic biological principles. Thus, with continuous suitable Rubber Boa habitat occurring in all directions in the greater Mt. Lassen region, with no evidence of existing barriers, with no known potential barriers in recent history perhaps as far back as the last ice age, and no documented break in distribution of the species in that region, early on I considered it to be a given that members of both subclades overlap in distribution, a conclusion that is just the opposite of that mentioned in the mtDNA paper.

And as mentioned, since the paper was published, I went back to verify one way or the other, my understanding of habitat plus make some searches for the species. You are correct in that the finding of additional specimens in the zone between where the two nearest but different subclade specimens were identified does not disprove Javier's claim of allopatry. But not finding and break in suitable habitat and finding the new specimen provides evidence that the distribution of the species in very likely to be continuous which in turn leads to the likely scenario that there is a zone of intergradation between the two subclades (vs. allopatry).

The finding of 5 specimens by myself and then other specimens found later by Chris Feldman weakens, and virtually discounts the notion contained in the following quote: "These two subclades have completely allopatric distributions, with a break that occurs somewhere in the vicinity of Lassen Volcanic National Park in northeastern California (between the localities of C .b. bottae samples 6 and 14 which lie about 120 (airline) km apart; Fig. 1)."

But without Javier having considered all evidence, I maintain that the claim of allopatry itself was not warranted in the first place. Another way of looking at the situation would be as follows: If the nearest two specimens of different subclades had been 400 km apart, would that be sufficient evidence upon which to make a claim of allopatry? Or, if the two specimens had been 1 km apart, would that evidence support a claim of allopatry? To my way of thinking, the distance between ONLY two samples is meaningless in arriving at a conclusion of allopatry. Just by chance alone, as the distance between specimens increases, the chance of overlap diminishes. By the same token, the claim that a break exists between the two subclades based on only two samples that are 120 km apart is equally flawed. As mentioned, I don't believe the authors gave enough thought to this area of their discussion.

To his credit, on page 233, Javier states, "It is unclear what barriers, if any, presently separate the Sierra Nevada and Northwestern subclades of C. bottae." It is too bad the authors did not check this out as Berkeley (where Javier did this study) is only a couple hundred miles from the Mt. Lassen region. From earlier treatment in the text, one assumes he is referring to barriers of a physical nature. But other barriers might exists. Despite that I consider overlap between the two subclades as being a foregone conclusion, a certain level of 'allopatry' with only marginal overlap could exit if there occurs some type of selection against the survival of hybrids between the two subclades.

I am reminded of just how easy it is to be critical ---- as if I had not made some similar errors in the past (which I have). But having done so, I tend to be more cautious. I suspect that semantics are a bit of a problem as my interpretation may not be what Javier was trying to convey. I agree when you mention, "He apparently based his claim on his mtDNA data, which shows that at any one locality, only one or the other large morph mtDNA haplotypes are present, but not both."

You go on to mention, "Now, if someone, anyone, were to come up with new data which shows that both of the large morph mtDNA haplotypes are in fact present at a single locality, then the claim of complete allopatry can be falsified." At the present time, another mtDNA study is in progress which in addition to rerunning the same samples in the first study, expands the geographical representation of the species and overall sample size. Included are about 10 to 12 new samples where specimens came from nearby or between where samples #6 and #15 were found. Also, there are two samples from the Ruby Mts. in Elko County, Nevada. I am curious as to which subclade will be represented by those two specimens.

I expect that the results will be the same or at least similar to what Javier's paper describes but with perhaps a few different wrinkles. However, without having numerous samples from the Mt. Lassen region, I don't have any great expectations that any new information will emerge.

Richard F. Hoyer

>>CK,
>>Conjecture and other forms of speculation are commonly included in the 'Discussion' sections of published accounts.>>

I agree with that absolutely.

>>However, in this particular instance where different forms of a species potentially meet in a zone of intergradation, it would be important that large sample size and geographical representation is needed in order to make assertions that would engender a reasonable degree of confidence.>>

Sample size will always be a source of disagreement. Of course a larger sample size is better. Keep in mind, however, that Rodriguez-Robles' mtDNA data represented the first investigation of this kind on the rubber boa. They do not have the foresight of available data to guide them as to where they should sample and how large a sample they should have. Overall I think they did a very good job of picking their samples. In a similar case, it was shown, using human x chromosome markers, that the first wave of human migration out of Africa went straight to Australia. However, there is no genetic evidence in the first investigations to show that the Australian lineage left its traces in Asia, which is located between Africa and Australia. Despite the lack of evidence, Spencer Wells, a Stanford geneticist, went to south India and obtained DNA samples from a remote village where it is thought that genetic evidence may be preserved without being swamped by later waves of human migration from the Middle East. And he succeeded. He found genetic evidence of the Australian lineage in this small Indian village. Similarly, it is possible, with additional sampling, to show that the allopatry conclusion may be false. But it will take genetic evidence to refute Rodriguez-Robles' claim of allopatry, the same sort of evidence that Spencer Wells took pains to gather.

>>From my perspective, not finding overlap of mtDNA on the basis of two random samples at a stated distance of 120 km apart is not the type of evidence upon which to arrive at a conclusion of allopatry and produce any degree of confidence.>>

I understand your objection to Rodriguez-Robles' conclusion, and I agree that the sample size may not have been large enough to justify his conclusion. Nevertheless, his conclusion is based on the available data, and it is a logical conclusion. It will take more than reasoned arguments to falsify his conclusion. It will take contradictory mtDNA data. It will take a herpetological equivalent of Spencer Wells to gather the data to either prove or disprove Rodriguez-Robles.

>>Without having adequate geographical representation, assumptions should instead be based on existing evidence coupled with applying basic biological principles. Thus, with continuous suitable Rubber Boa habitat occurring in all directions in the greater Mt. Lassen region, with no evidence of existing barriers, with no known potential barriers in recent history perhaps as far back as the last ice age, and no documented break in distribution of the species in that region, early on I considered it to be a given that members of both subclades overlap in distribution, a conclusion that is just the opposite of that mentioned in the mtDNA paper. >>

If you draw a range map using the available mtDNA data, the two subclades are in fact allopatric. You may believe that the mtDNA data is inadequate, but Rodriguez-Robles did base their conclusion on the data they have on hand. Of course better data may well overturn their conclusion, but then again it may not.

>>And as mentioned, since the paper was published, I went back to verify one way or the other, my understanding of habitat plus make some searches for the species. You are correct in that the finding of additional specimens in the zone between where the two nearest but different subclade specimens were identified does not disprove Javier's claim of allopatry. But not finding and break in suitable habitat and finding the new specimen provides evidence that the distribution of the species in very likely to be continuous which in turn leads to the likely scenario that there is a zone of intergradation between the two subclades (vs. allopatry). >>

Yes, I agree that the zone of intergradation is possible, and perhaps even probable. But the difficulty in accepting it as real is the lack of supporting mtDNA data.

>>The finding of 5 specimens by myself and then other specimens found later by Chris Feldman weakens, and virtually discounts the notion contained in the following quote: "These two subclades have completely allopatric distributions, with a break that occurs somewhere in the vicinity of Lassen Volcanic National Park in northeastern California (between the localities of C .b. bottae samples 6 and 14 which lie about 120 (airline) km apart; Fig. 1)." >>

It would be great if we can determine the mtDNA haplotypes of these new speciments. That would help in settling the controversy perhaps.

>>But without Javier having considered all evidence, I maintain that the claim of allopatry itself was not warranted in the first place. >>

I have to disagree with you here. Rodriguez-Robles' conclusion is solidly grounded on the available evidence to them. New evidence may have surfaced since their conclusion which may or may not falsify their conclusion. But so far I have not seen any evidence that could falsify the allopatry theory.

>>Another way of looking at the situation would be as follows: If the nearest two specimens of different subclades had been 400 km apart, would that be sufficient evidence upon which to make a claim of allopatry? Or, if the two specimens had been 1 km apart, would that evidence support a claim of allopatry? To my way of thinking, the distance between ONLY two samples is meaningless in arriving at a conclusion of allopatry. Just by chance alone, as the distance between specimens increases, the chance of overlap diminishes. By the same token, the claim that a break exists between the two subclades based on only two samples that are 120 km apart is equally flawed. As mentioned, I don't believe the authors gave enough thought to this area of their discussion.>>

You are correct that Rodriguez-Robles may have erred in their conclusion, and they may in fact have not thought about the possibility that the two subclades may in fact have met. However, anyone who disagrees with their conclusion is free to falsify it with mtDNA data. There is a similar controversy as to whether the Mt. Hamilton specimen of Lampropeltis zonata is an intergrade between L. z. multifasciata and L. z. zonata. Guess what? mtDNA evidence shows that it is instead a member of L. z. multicincta. So, the availability of mtDNA data can often help settle endless arguments.

>>To his credit, on page 233, Javier states, "It is unclear what barriers, if any, presently separate the Sierra Nevada and Northwestern subclades of C. bottae." It is too bad the authors did not check this out as Berkeley (where Javier did this study) is only a couple hundred miles from the Mt. Lassen region. From earlier treatment in the text, one assumes he is referring to barriers of a physical nature. But other barriers might exists. Despite that I consider overlap between the two subclades as being a foregone conclusion, a certain level of 'allopatry' with only marginal overlap could exit if there occurs some type of selection against the survival of hybrids between the two subclades. >>

I know you feel strongly that the claimed allopatry is not real. And in fact you may well be correct. However, science relies on evidence, so it must take evidence, in the form of mtDNA data, to show that your theory is correct.

>>I am reminded of just how easy it is to be critical ---- as if I had not made some similar errors in the past (which I have). But having done so, I tend to be more cautious. I suspect that semantics are a bit of a problem as my interpretation may not be what Javier was trying to convey. I agree when you mention, "He apparently based his claim on his mtDNA data, which shows that at any one locality, only one or the other large morph mtDNA haplotypes are present, but not both."
>>
>>You go on to mention, "Now, if someone, anyone, were to come up with new data which shows that both of the large morph mtDNA haplotypes are in fact present at a single locality, then the claim of complete allopatry can be falsified." At the present time, another mtDNA study is in progress which in addition to rerunning the same samples in the first study, expands the geographical representation of the species and overall sample size. Included are about 10 to 12 new samples where specimens came from nearby or between where samples #6 and #15 were found. Also, there are two samples from the Ruby Mts. in Elko County, Nevada. I am curious as to which subclade will be represented by those two specimens.>>

Wonderful news! The new data hopefully will resolve the controversy. Based on the old data, the Nevada specimens are almost certainly going to belong to the Northwestern subclade, i.e. more closely related to boas from Berkeley than to boas from the geographically closer Sierra Nevada Mountain Range.

>>I expect that the results will be the same or at least similar to what Javier's paper describes but with perhaps a few different wrinkles. However, without having numerous samples from the Mt. Lassen region, I don't have any great expectations that any new information will emerge.
>>
>>Richard F. Hoyer

Perhaps you can give the investigators some input as to your concerns. Hopefully they can include more samples near the area of supposed allopatry. If a snake with the mtDNA haplotype of the Northwestern subclade is found within the known range of the Sierra Nevada subclade or vice versa, then allopatry is disproven. For the time being, the available evidence is consistent with the theory of complete allopatry.

Regards.

CK,
Concerning your next to last paragraph and the results of crosses that have been made thus far, I suggest ignoring the point about large and dwarf morphs. In other words, both reciprocal crosses (3 each) were made between boas of the Sierra Nevada and Northwestern subcades. All such crosses proved to be viable in that full term neonates were produced. Since these crosses occurred in recent years, insufficient time has elapsed in order to determine if the F-1 offspring are fertile.

However with respect to reproductive compatibility, it should be noted that the original cross in 1996 was between a Southern Clade male and Northern Clade female which produced 4 full term neonates. Of the two surviving male and female F-1 progeny, the F-1 female has been determined to be fertile. That a cross between specimens that have been isolated from between 4.4 to 12.3 million years (according to Javier's paper) can reproduce, produce full term neonates, and produce progeny that are themselves fertile does not lend support to any assumption that matings between members of the two subclades would result in infertile progeny.

Secondly, F-1 results between crosses of the two large morph populations would not likely shed any light on the factor(s) that produce the large morph condition. That is because regardless of the male parent, large morph females of the Northwestern subclade have produced only large morph progeny. Nothing of certainty can be mentioned about what large morph females of the Sierra Nevada subclade would produce but odds are that they too would produce only large morph progeny if mated to males the Northwestern subclade or males of the Southern Clade. One would have to take such crosses to either backcross or F-2 generations to potentially reveal differences that may occur.

Richard F. Hoyer

>>CK,
>>Concerning your next to last paragraph and the results of crosses that have been made thus far, I suggest ignoring the point about large and dwarf morphs. In other words, both reciprocal crosses (3 each) were made between boas of the Sierra Nevada and Northwestern subcades. All such crosses proved to be viable in that full term neonates were produced. Since these crosses occurred in recent years, insufficient time has elapsed in order to determine if the F-1 offspring are fertile.>>

Are these offsprings small or large morphs? You did not say. It is important to keep such phenotypic data because it can help a geneticist in figuring out how the different morphs are controlled genetically.

>>However with respect to reproductive compatibility, it should be noted that the original cross in 1996 was between a Southern Clade male and Northern Clade female which produced 4 full term neonates. Of the two surviving male and female F-1 progeny, the F-1 female has been determined to be fertile. That a cross between specimens that have been isolated from between 4.4 to 12.3 million years (according to Javier's paper) can reproduce, produce full term neonates, and produce progeny that are themselves fertile does not lend support to any assumption that matings between members of the two subclades would result in infertile progeny. >>

Time really has very little (if anything) to do with reproductive compatibility. As Ernst Mayr points out, there are some plants that have been isolated on opposite sides of an ocean for millions of years and yet they remain reproductively compatible. OTOH, polyploidy can result in instantaneous speciation, within a single generation since the hybrids in general have low viability. Unfortunately, such knowledge has not prevented some taxonomists from using genetic distance to draw species boundaries. If they found that two populations have been isolated from one another for a few million years, then they assume that these two populations are different species. Speciation is not a function of time, but a function of adaptations to niches. Rapid speciation can occur if there are many unfilled niches and intense intraspecific competition within the old niche. The often cited Cichlid fishes of the African lakes are classic examples of rapid speciation. Conversely, two populations that have been isolated for over 10 million years may still be conspecific because neither had changed or adapted to a new niche.

>>Secondly, F-1 results between crosses of the two large morph populations would not likely shed any light on the factor(s) that produce the large morph condition.>>

You may be correct. But reproductive compatibility cannot be assumed. Of course, the best sort of data would be evidence from nature. If intergrades between the Northwestern and Sierra Nevada subclades are found in nature, then the question is answered.

>>That is because regardless of the male parent, large morph females of the Northwestern subclade have produced only large morph progeny.>>

That is a very interesting fact. However, you also stated in an earlier post that "Crosses between dwarf morph females and large morph males have produced only dwarf morph neonates."

That would suggest to me some sort of sex linkage in the inheritance of the large and small morph phenotypes.

>>Nothing of certainty can be mentioned about what large morph females of the Sierra Nevada subclade would produce but odds are that they too would produce only large morph progeny if mated to males the Northwestern subclade or males of the Southern Clade.>>

That is a reasonable hypothesis but it cannot be assumed. It has to be tested.

>>One would have to take such crosses to either backcross or F-2 generations to potentially reveal differences that may occur.
>>
>>Richard F. Hoyer

Hopefully someone would take the time and effort to perform these captive breeding experiments, and then report the results to the scientific community. It would be of interest to evolutionary biologists how the large morphs evolved from the small morph snakes that seem to represent the ancestral condition in the rubber boa. What environmental conditions and/or historical events in the past favored the evolution of the large morphs, for example, would be of interest to evolutionary biologists, even though these questions may not be of interest to the taxonomists.

Hi, Richard, I just noticed that I haven't paid close enough attention to the mtDNA cladograms of Rodriguez-Robles. Up to now, I have treated the Sierra Nevada snakes as presumptively large morph and that they form a single lineage. It turns out there are two sublineages within the Sierra Nevada subclade. Specifically, genetic data shows that the specimens from loc. #15, #17, #18, #19 and #26 (Tulare Co.) represent an older lineage than the sublineage which consists of Kern County dwarf boas plus the remaining Sierra Nevada snakes, including loc. #16. Based on genetic data, there is a chance that snakes from #15, #17, #18, and #19 and #26 (Tulare Co.) may be dwarf morph snakes. It may be worthwhile to have a look at these voucher specimens to verify their morphology. If they turn out to be small morph, then we may have both small morph and large morph boas living in the Sierra Nevada range. This sublineage (#15, #17, #18, #19 and #26) appears to have migrated northward along the Sierra Nevada at a slightly earlier time period than the boas from other localities that are large morph.

If boas from loc. #15, #17, #18, #19 and #26 turn out to be large morph snakes, then one possible explanation is that despite their earlier arrival in the northern part of the range, their small morph phenotype was later swamped by the large morph phenotype that arrived later. The phenotype of the small morph early arrivals died out, leaving only the mtDNA of their small morph ancestors. However, based on your captive breeding data, a female dwarf morph would only produce offsprings with the dwarf morph phenotype, even when mated with a large morph male, therefore it is difficult to see how her mtDNA will get passed on to a large morph snake, since all her offsprings will be small morph and mtDNA is matrilineal in descent. If a dwarf morph phenotype F1 individual can produce large morph offsprings when back crossed to a large morph male, however, that could result in large morph snakes with the ancient small morph mtDNA haplotype.

A second explanation (if this early sublineage is large morph)is that the males from this sublineage dominated mating of later arriving snakes which may be small morph. Subsequently, natural selection favored the large morph individuals, and the small morphs snakes died out, leaving only the large morph snakes we see today. This explanation is less likely by the way than the first one.

To solve this mini-mystery, it is important that morphological data be obtained from both the voucher specimens at loc. #15, #17, #18, #19 and #26 to ascertain whether they are large or small morph. Morphological data from the captive crosses between small and large morph boas are also needed. For now, C. bottae taxonomy is even more complicated than I had previously imagined.

CK,
Besides the dwarf form occurring in Riverside, San Bernardino and Kern Counties, I have evidence the dwarf morph also occurs adjacent to Kern County in Ventura County in the Mt. Pinos, Frazier Mt., and Alamo Mt. region just west of I-5 and the grapevine. And the dwarf morph also occurs in southern in Tulare County in the south-central and southeastern parts of the Southern Kern Plateau. No specimens have been collected in the southwestern part of the S. Kern Plateau so it is not known if the dwarf form occurs in that region. Also, no information is at hand to indicate how far north the dwarf form occurs on the Kern Plateau before it intergrades with the large morph.

With respect to Fig. 1 in the mtDNA paper, although the connections between groups and the relative length of arms provide a reasoned sense of relatedness, without knowing precisely the meaning of the numbers attached to the arms at the left, I am not able to make a complete assessment of the results as shown.

As for your last post of May 15th, when I reviewed Javier's paper, I also noted the disjunct nature of that part of the tree in Fig. 1B that includes specimens #26, 15, 17, 18, and 19. And there are other seemingly anomalous situations that are not explained in the text.

There is no defining characters by which dwarf and large morph specimens can be readily discerned one from another on an individual basis. The manner in which I have identified populations as being of the large morph was by finding adult specimens that exceeded the currently known maximums for the dwarf morph.

The known approximate maximum lengths of the dwarf morph are about 22 to 22 1/4 inches (558 - 565 mm) for females and 19 1/2 - 19 3/4 inches (494 - 500 mm) for males. So when I find specimens that exceed those lengths, then I have assigned such populations as belonging to the large morph. That dwarf morph specimens may be 'lurking' within large morph population is a possibility but they cannot be detected. Juvenile, subadults and small adults of the large morph for the most part are indistinguishable from members of the dwarf morph of similar size.

I have examined sufficient samples from the regions in which specimens 15. 17, 18, 19 and 26 originate to consider all such populations to be of the large morph. I have examined each of those specimens and all but #18 are essentially larger than the largest dwarf morphs. Number 18 from Yuba county has a preserved length of 226 mm and give a 10% adjustment for shrinkage, would be about 291 mm alive. Since large morph specimens occur from the same area, I consider that specimen simply to be a small subadult of the large morph.

You mention, "For now, C. bottae taxonomy is even more complicated than I had previously imagined." Just last night I received an email form the individual doing the new mtDNA study. Up until then, despite a much larger sample size and greater geographical representation, I was concerned that nothing new would result from his efforts and that the study would turn out only repeating what Javier had already determined.

That now seems to have changed by the extraordinary results that have been obtained. I am not at liberty to mention just what new information has turned up but if it holds up, the complexity will be even greater than what was revealed in Javier's paper.

Richard F. Hoyer

>>CK,
>>Besides the dwarf form occurring in Riverside, San Bernardino and Kern Counties, I have evidence the dwarf morph also occurs adjacent to Kern County in Ventura County in the Mt. Pinos, Frazier Mt., and Alamo Mt. region just west of I-5 and the grapevine. And the dwarf morph also occurs in southern in Tulare County in the south-central and southeastern parts of the Southern Kern Plateau. No specimens have been collected in the southwestern part of the S. Kern Plateau so it is not known if the dwarf form occurs in that region. Also, no information is at hand to indicate how far north the dwarf form occurs on the Kern Plateau before it intergrades with the large morph.>>

Hi, Richard. Thanks for the reply. I have noticed that L. z. multifasciata is replaced by L. z. multicincta in the Sierra Nevada near Tulare County and the same seems to apply to the small morph/large morph rubber boas in the same area.

>>With respect to Fig. 1 in the mtDNA paper, although the connections between groups and the relative length of arms provide a reasoned sense of relatedness, without knowing precisely the meaning of the numbers attached to the arms at the left, I am not able to make a complete assessment of the results as shown.>>

Those numbers given are statistical support for the particular node in the diagram, in percentages. A number of 100 means it is well supported. 50 means that it is as reliable as flipping a coin.

>>As for your last post of May 15th, when I reviewed Javier's paper, I also noted the disjunct nature of that part of the tree in Fig. 1B that includes specimens #26, 15, 17, 18, and 19. And there are other seemingly anomalous situations that are not explained in the text.>>

It was not explained because to Rodriguez-Robles et al., that part of the cladogram is not anomalous, because they did not know of the existence of small and large morph snakes at the time they published their paper, according to you. It looks anomalous to me because these large morph snakes appeared to have migrated to the north before other populations of large morph Sierra Nevada snakes had split from the Kern County small morph snakes. That to me suggests a possibility that the large morph may have evolved as many as 3 different times in the history of the rubber boa, once in the Northwestern subclade and twice in the Sierra Nevada subclade. This is of course possible, but seemingly less likely than if the large morph snakes of the Sierra Nevada had only evolved from a small morph ancestor only once.

>>There is no defining characters by which dwarf and large morph specimens can be readily discerned one from another on an individual basis. The manner in which I have identified populations as being of the large morph was by finding adult specimens that exceeded the currently known maximums for the dwarf morph.
>>
>>The known approximate maximum lengths of the dwarf morph are about 22 to 22 1/4 inches (558 - 565 mm) for females and 19 1/2 - 19 3/4 inches (494 - 500 mm) for males. So when I find specimens that exceed those lengths, then I have assigned such populations as belonging to the large morph. That dwarf morph specimens may be 'lurking' within large morph population is a possibility but they cannot be detected. Juvenile, subadults and small adults of the large morph for the most part are indistinguishable from members of the dwarf morph of similar size.
>>
>>I have examined sufficient samples from the regions in which specimens 15. 17, 18, 19 and 26 originate to consider all such populations to be of the large morph. I have examined each of those specimens and all but #18 are essentially larger than the largest dwarf morphs. Number 18 from Yuba county has a preserved length of 226 mm and give a 10% adjustment for shrinkage, would be about 291 mm alive. Since large morph specimens occur from the same area, I consider that specimen simply to be a small subadult of the large morph.>>

Thank you for the information. Would loc. #26 be in the range of L. z. multicincta? If so, there is a virtually identical correspondence between the transition from L. z. multifasciata to L. z. multicincta and the transition from small morph to large morph C. bottae in the Sierra Nevada Mountains. Here we may see L. z. multifasciata and small morph C. bottae south of an invisible boundary and we then see L. z. multicincta and large morph C. bottae occuring north of this boundary. Perhaps the same set of environmental conditions may be responsible for producing darker L. zonata individuals and larger rubber boas.

>>You mention, "For now, C. bottae taxonomy is even more complicated than I had previously imagined." Just last night I received an email form the individual doing the new mtDNA study. Up until then, despite a much larger sample size and greater geographical representation, I was concerned that nothing new would result from his efforts and that the study would turn out only repeating what Javier had already determined.
>>
>>That now seems to have changed by the extraordinary results that have been obtained. I am not at liberty to mention just what new information has turned up but if it holds up, the complexity will be even greater than what was revealed in Javier's paper.
>>
>>Richard F. Hoyer

Thanks for the info. I understand the sensitive nature of the data and will await its publication. Hopefully it will answer the question of whether the Northwestern and Sierra Nevada subclades are allopatric or not. But if not, then perhaps future studies can address that question more specifically.

Regards.

CK,
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.

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.

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.

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.

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.

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.

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

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.

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.

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!

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

>>CK,
>>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.

CK,
Concerning C. bottae distribution, immediately below is part of a message I sent yesterday to my son in Utah who also has been involved with the species. (See his www.rubberboas.com web site.) In relation to the unique mtDNA results that recently came to light, I mentioned the following:
------------------------------------------------------------
"And once again, all of this relates to the overall distribution of the species as well as the dwarf form. When William Flaxington sent me the male boa found at 7300 ft. on Benton Crossing Road east of Lake Crowley along Hwy. 395 (north of Bishop), it renewed my gut feeling that the species is quite likely to occur 20 to 25 miles northeast into western Nevada. In checking the elevation in that region, you find that just south and north of Mono Lake, there appears to be unbroken elevation at and above 7000 ft. into Nevada and continuing south into the White Mts. of Nevada and Calif. If I weren't so darn old, a trip into the various sections of W. Nevada would be in the works."
--------------------------------------------------------------

Richard F. Hoyer

>>CK,
>>Concerning C. bottae distribution, immediately below is part of a message I sent yesterday to my son in Utah who also has been involved with the species. (See his www.rubberboas.com web site.) In relation to the unique mtDNA results that recently came to light, I mentioned the following:
>>------------------------------------------------------------
>> "And once again, all of this relates to the overall distribution of the species as well as the dwarf form. When William Flaxington sent me the male boa found at 7300 ft. on Benton Crossing Road east of Lake Crowley along Hwy. 395 (north of Bishop), it renewed my gut feeling that the species is quite likely to occur 20 to 25 miles northeast into western Nevada. In checking the elevation in that region, you find that just south and north of Mono Lake, there appears to be unbroken elevation at and above 7000 ft. into Nevada and continuing south into the White Mts. of Nevada and Calif. If I weren't so darn old, a trip into the various sections of W. Nevada would be in the works."
>>--------------------------------------------------------------
>>
>>Richard F. Hoyer

Indeed, I just located Benton Crossing Road in Yahoo maps, and this road is found on the slopes of a mountain that runs continuously all the way past Benton into Mineral County, Nevada.
So, it is quite possible that the rubber boa went around the eastern slopes of the Sierrae Nevada and into westen Nevada. If so, this population could be a different lineage than the large morph Sierra Nevada lineage but will still be part of the Sierra Nevada subclade. Things are indeed getting more complicated and more interesting. Thanks for the info. You can click on the link below to see the map.

Benton Crossing Road and vicinity

CK,
Actually, I have some fragmentary evidence of where the dwarf and large morphs may intergrade in the Greenhorn Mts. of southern Tulare county. I recorded data from about 17 specimens in that region. The data suggest a mixture of the two morphs and thus I have tentatively considered that region to be where the two morphs intergrade. The crosses I have initiated have been designed to try and determine just what genetic mechanism might account for the two morphs being able to retain their separate identities in face of the prospect they must come in contact and hybridize.

I have tentatively assigned the boa population in the southern Greenhorn Mts. south of Alta Sierra and hwy. 155 as being the dwarf morph as the few specimens from that region suggest they are dwarf. Voucher specimens from the vicinity of Sequoia Nat. Park indicate the large morph occurs in that part of Tulare Co. And thus those 17 specimens found in-between are of particular interest. And here is where future nuclear DNA research would be indicated. If one or more markers could be found that identify the dwarf from the large morph, then testing those 17 specimens could potentially provide some insight.

As mentioned, totally unknown is just how far the dwarf from occurs on the Kern Plateau before it most assuredly comes in contact with the large morph. And as mentioned,
another unknown is if the dwarf form occurs all the way to the extreme southwest region of the Kern Plateau just east of Kernville. If I were younger, that would be one of the areas in which I would conduct searches for the species.

Richad F. Hoyer

>>CK,
>>Actually, I have some fragmentary evidence of where the dwarf and large morphs may intergrade in the Greenhorn Mts. of southern Tulare county.>>

If I remember correctly, the Greenhorn Mts. is approximately the northern limit of L. z. multifasciata. North of this area L. z. multicincta predominates. That is why I said there seems to be an invisible line in Tulare County, north of which lies the large morph rubber boas and L. z. multicincta and south of which can be found small morph rubber boas and L. z. multifasciata.

>>I recorded data from about 17 specimens in that region. The data suggest a mixture of the two morphs and thus I have tentatively considered that region to be where the two morphs intergrade.>>

It is possible that this is the zone of intergradation. However, small and large morph Sierra Nevada subclade snakes have similar mtDNA haplotypes.

>>The crosses I have initiated have been designed to try and determine just what genetic mechanism might account for the two morphs being able to retain their separate identities in face of the prospect they must come in contact and hybridize. >>

Some of the data you gave suggest that size is somehow sex linked. So if they intergrade, the different size morphs can remain distinct since there is no blending inheritance.

>>I have tentatively assigned the boa population in the southern Greenhorn Mts. south of Alta Sierra and hwy. 155 as being the dwarf morph as the few specimens from that region suggest they are dwarf. Voucher specimens from the vicinity of Sequoia Nat. Park indicate the large morph occurs in that part of Tulare Co. And thus those 17 specimens found in-between are of particular interest. And here is where future nuclear DNA research would be indicated. If one or more markers could be found that identify the dwarf from the large morph, then testing those 17 specimens could potentially provide some insight.>>

That would take an awful lot of work of mapping the entire genome and then finding the particular gene responsible. I am not sure there would be funding to do that and I am not sure if anyone would spend that much time and effort to identify the genetic basis for that one trait.

>>As mentioned, totally unknown is just how far the dwarf from occurs on the Kern Plateau before it most assuredly comes in contact with the large morph. And as mentioned,
>>another unknown is if the dwarf form occurs all the way to the extreme southwest region of the Kern Plateau just east of Kernville. If I were younger, that would be one of the areas in which I would conduct searches for the species.
>>
>>Richad F. Hoyer

It appears from what you have told me so far, that all the boas found within Kern County should be the dwarf form. This is the most likely scenario: the dwarf form is ancestral, and one large morph evolved from the small morph ancestor, as the Northwestern subclade, and migrated north along the coast into northern and central California, Oregon, Idaho and Utah. The dwarf morph in the south remained largely unchanged morphologically until one population reached the area north of the Greenhorn Mountains, where it evolved into the large morph and then migrated north to the area just south of the Mt. Lassen area, but could go no further. Perhaps the small morph also took a separate route and migrated northeast, around the eastern slopes of the Sierra Nevada and into western Nevada. Or perhaps the Northwestern subclade went around the Sierra Nevada and into the state of Nevada before expanding its range south and back into southeastern California. mtDNA data would probably provide an answer to these questions because mtDNA is an excellent set of markers for tracing ancestor-descendant relationships.

CK,
As for the issue of allopatry of the subclades, here is something else to consider. Because Javier's closest samples between the two subclades occurred in close proximity to Mt. Lassen, he addressed allopatry in a manner that appears to pertained to that specific region. The authors failed to consider (perhaps were not aware) that the species occurs well east of the Mt. Lassen region into far eastern California continuing across the border into western, and northern Nevada (and beyond). Thus, no explanation exists that would
advance the notion of allopatry between the two subclades where they occur far beyond Mt. Lassen. (Hind sight becomes ever so sharp after the fact.)

For instance, I have examined all voucher specimens from Nevada as contained in the U. of Nevada-Reno collection. There are a half dozen specimens from Washoe county which runs from near Reno north to the Oregon border and adjacent to Calif. Wonder to which subclade or subclades those specimens belong? What explanation might be advanced to suggest allopatry of the boas in that region? Or would it be more reasonable to suggest that the two subclades are likely to come in contact somewhere in that region?

I understand the position that until evidence is at hand, one needs to remain open to all possibilities. Thus, without overlap of specimen of each subclade having been
documented, one cannot assert that either parapatry or sympatry occurs between the subclades. On the other hand, two random samples 120 km (or 64 km) apart does not constitute verification of anything. (Persistent aren't I?)

Another way of viewing the situation is that exiting evidence gives the appearance or perception of allopatry. From my undergraduate training in wildlife science and experience since, if there is one dictum in science to which I adhere is that since perceptions are frequently in error, they should not be taken (nor stated) as if factual. A year ago March, I published a 'Viewpoint' in the Journal of Kansas Herpetology that deals with that very topic. The title was "The Fallacy of Perceptions" and I gave examples where perceptions by professionals and by state wildlife agencies have been grossly in error.

One of the best papers in herpetology that deals with 'perceptions' was published by Whit. Gibbons and titled, "Perceptions of Species Abundance, Distribution, and Diversity: Lessons from Four Decades of Sampling on a Government- Managed Reserve". He describes how one particular species was originally considered to be scarce or rare but over time, was found to be far more common and widespread than originally perceived.

I can't state for certain that Javier's assertion of allopatry is in error but the application of biological concepts suggest that the odds would indicated his position is likely to be incorrect. As a matter of fact, I don't have problems with conjecture if stated as being an option to consider. My main objection is when such speculation is stated in a manner as if it were factual.

Richard F. Hoyer

>>CK,
>>As for the issue of allopatry of the subclades, here is something else to consider. Because Javier's closest samples between the two subclades occurred in close proximity to Mt. Lassen, he addressed allopatry in a manner that appears to pertained to that specific region. The authors failed to consider (perhaps were not aware) that the species occurs well east of the Mt. Lassen region into far eastern California continuing across the border into western, and northern Nevada (and beyond). Thus, no explanation exists that would
>>advance the notion of allopatry between the two subclades where they occur far beyond Mt. Lassen. (Hind sight becomes ever so sharp after the fact.)>>

Their data shows that the Sierra Nevada subclade is confined largely to the western slopes of the Sierra Nevada mountains, and the general direction of the expansion of the range (gleaned from the mtDNA data) of this subclade is from south to north. In hindsight, you are correct, they did not consider the possibility that the Sierra Nevada subclade may have expanded its range eastward into Nevada to possibly meet the Northwestern subclade in western and central Nevada. Their mtDNA sample did not address this possibility.

>>For instance, I have examined all voucher specimens from Nevada as contained in the U. of Nevada-Reno collection. There are a half dozen specimens from Washoe county which runs from near Reno north to the Oregon border and adjacent to Calif. Wonder to which subclade or subclades those specimens belong?>>

mtDNA data on these specimens would answer that question, because the 2 subclades have different mtDNA haplotypes.

>> What explanation might be advanced to suggest allopatry of the boas in that region? Or would it be more reasonable to suggest that the two subclades are likely to come in contact somewhere in that region?>>

One possible explanation is that the Northwestern subclade has, for some unknown reason, never been able to gain a foothold in the Sierra Nevada mountains, despite having moved north into Oregon as long ago as a couple million years ago. Perhaps volcanic activity prevented it from entering the norther Sierra Nevada and the arid Central Valley prevented it from reaching the Central Sierra Nevada. The absence of the Northwestern subclade from the Sierra Nevada mountains is well supported by mtDNA data; not one single specimen of the boas of the Sierra Nevada has the mtDNA haplotype of the Northwestern subclade. If the Sierra Nevada subclade is in turn unable to inhabit the arid lower slopes of the eastern Sierra Nevada, then these two subclades would be separated by unsuitable habitat for both subclades.

>>I understand the position that until evidence is at hand, one needs to remain open to all possibilities. Thus, without overlap of specimen of each subclade having been documented, one cannot assert that either parapatry or sympatry occurs between the subclades. On the other hand, two random samples 120 km (or 64 km) apart does not constitute verification of anything. (Persistent aren't I?)>>

You may well be correct that allopatry is an artifact of observation. Sometimes we do forget what Robert Inger once said, and I paraphrase him here: the distribution map of the rubber boa is more likely to be a distribution map of human collectors.

>>Another way of viewing the situation is that exiting evidence gives the appearance or perception of allopatry. From my undergraduate training in wildlife science and experience since, if there is one dictum in science to which I adhere is that since perceptions are frequently in error, they should not be taken (nor stated) as if factual. A year ago March, I published a 'Viewpoint' in the Journal of Kansas Herpetology that deals with that very topic. The title was "The Fallacy of Perceptions" and I gave examples where perceptions by professionals and by state wildlife agencies have been grossly in error.
>>
>>One of the best papers in herpetology that deals with 'perceptions' was published by Whit. Gibbons and titled, "Perceptions of Species Abundance, Distribution, and Diversity: Lessons from Four Decades of Sampling on a Government- Managed Reserve". He describes how one particular species was originally considered to be scarce or rare but over time, was found to be far more common and widespread than originally perceived. >>

Of course, I agree with that. Many species that were once thought to be rare are in fact quite common. It is just that we humans do not know them well enough to know where to look.

>>I can't state for certain that Javier's assertion of allopatry is in error but the application of biological concepts suggest that the odds would indicated his position is likely to be incorrect. As a matter of fact, I don't have problems with conjecture if stated as being an option to consider. My main objection is when such speculation is stated in a manner as if it were factual.
>>
>>Richard F. Hoyer

His theory of allopatry may well be proven wrong with additional data. This is normal practice in science. Nearly nothing is considered unchallengeable objective truth. Even something that seems as solidly supported as Newtons' laws of motion turn out to be in need of revision by the discovery of quantum mechanics. If it makes you feel better, Rodriguez-Robles' allopatry theory ought not be taken as unchallengeable objective truth, but nevertheless it is indeed the best theory supported by the currently available data. Can new data falsify the allopatry theory? Absolutely!

CK,
>>Their data shows that the Sierra Nevada subclade is confined largely to the western slopes of the Sierra Nevada mountains, and the general direction of the expansion of the range (gleaned from the mtDNA data) of this subclade is from south to north. In hindsight, you are correct, they did not consider the possibility that the Sierra Nevada subclade may have expanded its range eastward into Nevada to possibly meet the Northwestern subclade in western and central Nevada. Their mtDNA sample did not address this possibility>You may well be correct that allopatry is an artifact of observation. Sometimes we do forget what Robert Inger once said, and I paraphrase him here: the distribution map of the rubber boa is more likely to be a distribution map of human collectors.

CK,
Don't know what happened to my prior post.

The reason that Javier's data shows the majority of the Sierra Nevada subclade specimens occurring on the western slopes of the Sierra Nevada Mts. is more likely due to the nature of how specimens are collected than being representative of the true distribution of that subclade. A number of variables are involved with how specimens end up as vouchers and invariably such collecting does not represent an accurate picture either of relative abundance or geographical representation. Thus, there is considerable risk at trying to arrive at meaningful conclusions simply based on the origin of vouchers.

As for both subclades not occurring in each other's region, I suspect that this situation is similar to what occurs with many recognized subspecies where they retain their individual identities beyond where intergradation occurs, sometimes in very narrow zones.

I am not familiar with Robert Inger. Long ago I recognized the exact same thing not only for the boa but for other secretive species. That is why I cited the paper by W. Gibbons in that his results match my own experience and my analysis vouchers in institutional collections, that is, the history of specimens being vouchered over time. As you may have noted in many publications, they will mention this or than species has a spotty distribution. Well, where suitable habitat is spotty, such characterization are probably correct. But in some instances, the spotty distribution is really a reflection of the spotty nature of finding and vouchering specimens.

If you review the older field guides by Stebbins, you will note he refers to the boa as having a spotty distribution. Before his latest revision of 2003, he contacted me asking me to comment on his treatment of the Rubber Boa and Sharp-tailed Snake. I mentioned the same thing about spotty collecting giving an erroneous perception and mentioned that suitable boa habitat is continuous from northern Kern County all the way to B. C. sop how could the species have a spotty distribution? Since he too understands and accepts habitat association as valid, you will note in the latest edition he dropped the 'spotty distribution' for he species as a whole but retained it for the southern part of the species range where it is indeed spotty.

Richard F. Hoyer

>>CK,
>>Don't know what happened to my prior post.
>>
>>The reason that Javier's data shows the majority of the Sierra Nevada subclade specimens occurring on the western slopes of the Sierra Nevada Mts. is more likely due to the nature of how specimens are collected than being representative of the true distribution of that subclade. A number of variables are involved with how specimens end up as vouchers and invariably such collecting does not represent an accurate picture either of relative abundance or geographical representation. Thus, there is considerable risk at trying to arrive at meaningful conclusions simply based on the origin of vouchers.>>

Certainly. Let's not forget also that animal ranges are not static. It is changing all the time as new habitats are created and old habitats are lost, even in the absence of human intervention. The rubber boa migrated north millions of years before modern human beings even evolved and before there were human beings in the Western Hemisphere. Something interesting happened in the past, and rubber boas are now absent from the San Gabriel Mountains.

>>As for both subclades not occurring in each other's region, I suspect that this situation is similar to what occurs with many recognized subspecies where they retain their individual identities beyond where intergradation occurs, sometimes in very narrow zones.>>

One good thing about mtDNA data is that it can often reveal evidence of lineage mixing. For example, R. G. Zweifel claims that there is a large zone of intergradation in L. zonata in the northern part of its range between L. z. zonata and L. z. multicincta. Most of the snakes in the intergrade zone have the mtDNA haplotype of the relatively young lineage of multicincta, including those within the range of Zweifel's L. z. zonata. However, there is one interesting specimen from Oregon (loc. #31 AF136216; MVZ 225920; US: Oregon, Jackson Co., northeast of Ashland) which has a mtDNA haplotype that is much older than any of the multicincta specimens, and which is closer to the older multifasciata mtDNA haplotype. In fact, #31 is closely related to multifasciata from Kern, Santa Barbara, Monterey and Santa Cruz Counties. So, the supposed zone of intergradation between zonata and multicincta appears to be a zone of intergradation between an ancient lineage of L. z. multifasciata and a newer lineage of L. z. multicincta instead. L. z. zonata may actually be either L. z. multifasciata or L. z. multifasciata x L. z. multicincta! I think in that case, L. z. multifasciata would be an invalid name, and it would be synonymized with L. zonata. L. z. multicincta appears to be much more successful and swamped the L. z. multifasciata mtDNA haplotype in northwestern California. It was perhaps fortuitous that the loc. #31 was sampled or this fact would not have come to light. So, if there is intergradation between the Northwestern subclade and the Sierra Nevada subclade, mtDNA data has the potential of revealing it.

>>I am not familiar with Robert Inger. Long ago I recognized the exact same thing not only for the boa but for other secretive species. That is why I cited the paper by W. Gibbons in that his results match my own experience and my analysis vouchers in institutional collections, that is, the history of specimens being vouchered over time. As you may have noted in many publications, they will mention this or than species has a spotty distribution. Well, where suitable habitat is spotty, such characterization are probably correct. But in some instances, the spotty distribution is really a reflection of the spotty nature of finding and vouchering specimens.>>

Certainly. But mtDNA evidence again may provide valuable insights into whether distributional gaps are real or not. MtDNA is often used for determining lineage divergence date, so it is often possible to figure out how recently a species may have occupied a particular part of its range. The relatively young lineage age of the various populations of the southern rubber boa shows that they have only occupied their present range recently. This is probably the result of these boas having undergone a severe population decline in the recent past and then recovering subsequently to rapidly expand their range. Additionally, using mtDNA data, we can figure out how a species has expanded its range. In the case of the rubber boa, mtDNA tells us that the Northwestern subclade originated somewhere in Kern County, then it migrated west towards the coast and then expanded its range northward to Monterey, Santa Cruz, and Marin Counties, and then continuing north to northwestern California, Oregon and Washington. From there it went east, but there is no evidence of it going into the western slopes of the Sierra Nevada Mountains, at least not yet. This subclade may well have invaded the eastern slopes of Sierra Nevada but we just don't know because of a lack of data. The Sierra Nevada lineage is a bit younger than the Northwestern subclade, so it has had less time to expand its range. So, it is quite possible that Sierra Nevada subclade may not have had the time to stray too far from the Sierra Nevada mountains. It certainly had less time than the Northwestern subclade to colonize new areas. It may not have had enough time to expand northward to Mt. Lassen or to western Nevada. We just don't know until the mtDNA data of snakes from these areas have been determined.

>>If you review the older field guides by Stebbins, you will note he refers to the boa as having a spotty distribution. Before his latest revision of 2003, he contacted me asking me to comment on his treatment of the Rubber Boa and Sharp-tailed Snake. I mentioned the same thing about spotty collecting giving an erroneous perception and mentioned that suitable boa habitat is continuous from northern Kern County all the way to B. C. sop how could the species have a spotty distribution? Since he too understands and accepts habitat association as valid, you will note in the latest edition he dropped the 'spotty distribution' for he species as a whole but retained it for the southern part of the species range where it is indeed spotty.
>>
>>Richard F. Hoyer

The southern rubber boa has a spotty distribution probably because of some relatively recent catastrophic event. The lineage itself is old, but the various branches of this lineage diverged relatively recently from each other, probably from a small, restricted population that had an even more restricted distribution than it is "enjoying" today. Many of the older branches of this lineage may have died out during the catastrophe, leaving but a single lineage to later expand into its present range. Since most of the current range of the rubber boa probably is uninhabitable during the last ice ages because of glaciation at high elevations, these boas were probably forced into lower elevations during the ice ages. While they are there, they may have to compete against the closely related rosy boa, albeit quite unsuccessfully. The rosy boa, being larger and better adapted to arid conditions, may have had the upper hand in the interspecific competition between the small morph southern rubber boa. Without competition from the Rosy boa, it is certainly possible, even probable, that the rubber boa's range in the north is much more continuous than thought.

CK,
Still have many boas to survey and return to the field so just taking a short break this evening.

As I believe I mentioned before, I was fearful that the current mtDNA study on C. bottae would merely repeat the information in the prior mtDNA study of the species. As of about a week or 10 days ago, the individual conducting the new study has revealed some of the key results. He requested that I not reveal any specifics at this time as some of the results are preliminary.

But I can say with reasonable assurance that one block buster discovery will change the way C. bottae taxonomy is viewed. It's a bit difficult not to 'spill the beans' as it was the last few samples I suggested be tested, and then sent last summer, that produced the startling results. But I quickly add that the reason I suggested those samples be tested was to cover all bases from a geographical standpoint with respect to the two morphs. I had no inkling that those specimens would have the effect of what I believe will require a revision of C. bottae taxonomy. Actually there is one more sample that I have urged be tested but unfortunately, the lab facilities that were being used are no longer available. So that one last piece of the puzzle apparently will have to wait.

And just the past two days, he has relayed information dealing with the two subclades. Ta da! Without mentioning specifics, preliminary results indicate there occurs some
overlap in the distributions of the two subclades.

Richard F. Hoyer

>>CK,
>>Still have many boas to survey and return to the field so just taking a short break this evening.
>>
>>As I believe I mentioned before, I was fearful that the current mtDNA study on C. bottae would merely repeat the information in the prior mtDNA study of the species. As of about a week or 10 days ago, the individual conducting the new study has revealed some of the key results. He requested that I not reveal any specifics at this time as some of the results are preliminary.
>>
>>But I can say with reasonable assurance that one block buster discovery will change the way C. bottae taxonomy is viewed. It's a bit difficult not to 'spill the beans' as it was the last few samples I suggested be tested, and then sent last summer, that produced the startling results. But I quickly add that the reason I suggested those samples be tested was to cover all bases from a geographical standpoint with respect to the two morphs. I had no inkling that those specimens would have the effect of what I believe will require a revision of C. bottae taxonomy. Actually there is one more sample that I have urged be tested but unfortunately, the lab facilities that were being used are no longer available. So that one last piece of the puzzle apparently will have to wait.
>>
>>And just the past two days, he has relayed information dealing with the two subclades. Ta da! Without mentioning specifics, preliminary results indicate there occurs some
>>overlap in the distributions of the two subclades.
>>
>>Richard F. Hoyer

Without knowing the specifics, it is difficult to analyze the results. Based on what you have said, there is some overlap of the two subclades. That would indeed be different from the findings of Rodriguez-Robles et al. As I pointed out before, there are striking similarities in the migration and distribution of Lampropeltis zonata and Charina bottae and also notable differences. One notable similarity is the coastal migration route from Kern County to Oregon and Washington. Both L. zonata and C. bottae took separate coastal and Sierra Nevada migratory routes north. The coastal populations of both species also apparently failed to invade the Sierra Nevada Mountains despite having made the migration earlier than the Sierra Nevada subclades. In the case of L. zonata, the Sierra Nevada subclade did meet with the coastal subclade by invading the territory of the coastal subclade. So, my prediction is that the Sierra Nevada subclade of the rubber boa would be the more likely candidate to have invaded the territory of the Northwestern subclade. I will await the results and see if my prediction is correct or not.

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.

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.

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

>>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.

>>At times, I have found myself agreeing with Ron Nussbaum who in a 1974 paper on the species, discarded the then 3 recognized subspecies and simply lumped all Rubber Boas into a single species. Yet that arrangement overlooks the present situation (unknown at that time) where there are two discernable groupings of the species. On the one hand, there is the large morph populations characterized by large size, relatively high ventral and dorsal scale row count. In contrast, there are the dwarf morph populations all characterized by small size and with relatively lower ventral and dorsal scale row counts.>>

Phenotypically, there appear to be two groups based on your findings. A small morph and a large morph. The subspecies Nussbaum invalidated were ostensibly not based on these same phenotypes.

>>In addition, these two groupings are clustered geographically. Had such information been available in bygone years, the two groups would either have been designated as subspecies or species. However, the present mtDNA results throws a monkey wrench into that scenario. At the present, I can think of two explanation that might tend to be consistent with the mtDNA results.>>

There is something to keep in mind. Molecular evolution is independent of organismal evolution. This is a conclusion that has been nearly universally accepted after years of research pioneered by the late Allan Wilson and his students at UC Berkeley. Chance mutations at the molecular level occur at a more or less constant rate, provided that they are neutral substitutions. These rather regular changes at the molecular level is what enables the molecular clock hypothesis. The molecular clock is how Rodriguez-Robles et al. came up with their estimate of lineage divergence time of several million years among the populations of boas they studied.

Organismal evolution, such as the evolution of the large morph phenotype, is not governed by mtDNA. In other words, a change in the mtDNA is almost certainly NOT going to result in the appearance of the large morph. We must therefore look elsewhere for clues as to when and how the large morph phenotype evolved.

We do know from the mtDNA data that the boas of Kern County are geographically isolated from those in Southern California for a long period of time since they have developed different mtDNA markers. That is all that the mtDNA data can tell us: how long ago they last shared a common ancestor. mtDNA cannot tell us whether the Kern County and Southern California boas are different subspecies or different species. This is one reason Rodriguez-Robles et al. attempted to use morphological characters (instead of mtDNA) to define the Southern California populations as one species and the rest of the boas as a different species. Of course, you have in the past claimed that these characters cannot be used since they do not define these two populations. Further, you now suggest the authors were unaware of the fact that the Kern County boas are dwarf populations, just like those to the south.

Hence there really is no "conflict" between mtDNA data and "nuclear DNA" or organismal data, since they are independent of each other and they inform us of different events in the evolutionary history of the rubber boa. A synthesis of both types of data would suggest that despite the long periods of geographic isolation between Kern County and Southern California boas, there have not been any changes in either population phenotypically (while the mtDNA of both populations continue to accumulate changes through time). IOW, both populations appeared to have retained their ancestral condition of dwarfism. They have therefore undergo stasis. We can therefore safely lump these two populations into not only a single species, but a single subspecies. It is safe because your captive experiments suggest that there is no reproductive isolation between these two populations.

The southern boas therefore should not be given species status. Both the Kern County and the Southern California boas should instead be classified as C. b. umbratica.

>>1) One might argue for retention of the two species, the Southern Rubber Boa and Northern Rubber Boa with the latter being composed of two subspecies as follows: All large morph populations would comprise a northern subspecies and all other dwarf populations (expect those in the San Bernardino and San Jacinto Mts.) would constitute a southwestern subspecies of the Northern Rubber Boa.>>

As I have said above, the two species hypothesis is untenable because the Southern California subspecies and the Kern County subspecies have a common ancestor and both have changed little. Why classify a population as a different species because there have not been any evolutionary change? That would seem illogical.

>>2) A second scenario would be to have three subspecies. All large morph populations would belong to the northern subspecies, the dwarf populations in the San Bernardino and San Jacinto Mts. would belong to a southeastern subspecies, and all other dwarf population in S. Calif. would belong to a southwestern subspecies. >>

This arrangement is untenable as well. If you are familiar with the common kingsnake, Lampropeltis getulus, you would know that there are two subspecies characterized by dark coloration, namely L. g. niger and L. g. nigritus. They evolved their melanism independently of each other and they are allopatric. Hence no scientist would lump them as a single subspecies despite their similarities.

The coastal large morph boas almost certainly evolved from a small morph population that lived in western Kern County (which may have since become extinct), whereas the Sierra Nevada large morph boas probably evolved from the eastern Kern County small morph boas located directly to its south in the Sierra Nevada Mountains. The mtDNA data shows that none of the living small morph Kern County boas are genetically close to the coastal large morph population, which would suggest that the coastal population evolved its large morph phenotype first (from a small morph snake that has since become extinct, ostensibly in the area now devoid of rubber boas along the coast), and that the Sierra Nevada large morph evolved its phenotype much later from a small morph population in the southern Sierra Nevada.

>>Of course, the problem with both scenarios is that they disregard the current vogue of discarding all subspecific designations. I am not knowledgeable enough about how to interpret mtDNA results but the data presented in Javier's paper might suggest additional scenarios as well.>>

That is not the real problem. The subspecies category is useful and most biologists who are not straightjacketed by cladistic dogma will continue to use the subspecies category. The real problem with your particular 3 subspecies arrangement is that you drew the line at the incorrect places. The Southern California and Kern County dwarf boas should not be divided into two subspecies since neither of them have changed from their common ancestor, despite the long periods of geographical isolation that is evidenced from the mtDNA data. OTOH, the mtDNA data clearly shows that the coastal large morph population evolved the large phenotype before the Sierra Nevada large morph. The two populations do not meet in the southern parts of their ranges, being separated from each other by the Kern County dwarf boas, and they also do not meet in the northern Sierra Nevada, as Rodriguez-Robles et al. pointed out in their paper.

The only 3 subspecies arrangement that makes sense is a southern California-Kern County subspecies, a coastal large morph subspecies, and a Sierra Nevada large morph subspecies. Such an arrangement is in accord with the mtDNA data as well as accepted taxonomic practice of not recognizing convergently similar populations as a single subspecies.

>>Richard F. Hoyer>>

Regards, and have a good trip.

>>First a disclaimer- I am not a taxonomist, and I am not particularly familiar with rosy boas. I'm just throwing out some ideas here.
>>
>>You draw a connection here between size and relatedness, but this is not necessarily the case. I can see a few scenarios that would result in the conflict between MtDNA and morphological data.
>>
>>1). The adult size of these snakes is non-genetic. The 'dwarf forms' simply live in a habitat that causes them to remain small. A number of factors could lead to this: prey is scarce or of poor quality; seasonal activity is limited; larger individuals are selectively preyed upon; individuals breed at small size or early age, diverting nutrients from growth; etc. Thus the two lineages are affected by the same factors in the southern mountains. Perhaps if the southern lineage reached farther north, it would also show regional variation in size.

Environmental conditions may well be partially responsible, as the southern boas are found in mountain habitats that have cold, icy winters.

>>2). The adult size of these snakes is genetic, but small size has evolved in parallel in the southern lineage and in southern populations of the northern lineage. Similar selective factors have resulted in similar phenotypes.

That is a possibility that cannot be ruled out. The mtDNA data suggests that the species originated in the south but migrated to the north.

>>3). The converse of (2)- The adult size of these snakes is genetic, but small size is the ancestral state. Some populations of the northern lineage have evolved to larger size.

That is probably most likely. In fact, there are two allopatric northern lineages which took different routes to the north. One apparently migrated west along the mountains of Kern County and thence north along the coast ranges of coastal California, and then east across Oregon and Washington to Idaho and Utah. The other northern lineage took the Sierra Nevada route northward.

>>4.) The adult size of these snakes is genetic, and represents a primary division between a dwarf lineage and a large lineage. This is in actual conflict with the MtDNA data and could result in different taxonomic conclusions. Perhaps the MtDNA was skewed by incomplete sorting of mitochondrial lineages due to a recent divergence between these two lineages, or represents an earlier incomplete divergence between two lineages, followed by subsequent partial reintegration and redivergence.

Little chance of that because the two northern lineages almost certainly evolved their large body size independently, since they are allopatric and since they have different migration routes. South of both lineages of large morphs are the small morph snakes.

>>5.) The converse of (4)- the southern and small northern snakes are evidence of an older incomplete divergence.
>>
>>Taxonomy really has no way to deal with (4) and (5); only one split is important, the most recent one. So the following taxonomic schemes would be suitable:
>>
>>Scenario 1:
>>
>>Charina "Northern"
>>Charina "Southern"
>>
>>Scenario 2:
>>
>>Charina "Northern"
>>-----"Northern Large"
>>-----"Northern Small"
>>Charina "Southern"
>>
>>Scenario 3:
>>
>>same as 2
>>
>>Scenario 4:
>>
>>Charina "Large"
>>Charina "Small"
>>
>>Scenario 5:
>>
>>Charina "Northern"
>>Charina "Southern"

The mtDNA data suggests to me the following scenario:

Southern small,
Northern Coastal large
Northern Sierra Nevada large

Pending evidence that the two allopatric large morphs are unable to interbreed, I am assuming that they can interbreed on the basis of their morphological similarities and the lack of evidence of major obstacles to interbreeding (such as different numbers of chromosomes and polyploidy). To me then, the Rubber boas should be classified as three subspecies, not two distinct species. The three subspecies arrangement calls attention to the fact that the two northern lineages evolved independently, and also invites further study to determine whether they have become reproductively isolated or not.

>>I see this forum is not as lively as it use to be. At any rate, I will pose a problem similar to what I addressed here 2- 3 years ago.
>>
>>I recently came across the following quote. "Subspecies are defunct in modern systematic theory and have no place in current classification! "

That is not so at all. Subspecies are very much in general use. The comment above came obviously from a cladist espousing cladistic dogma. Cladists (taxonomists who adhere to classification convention advocated by Hennig) deal with taxonomic characters. To the cladists, a difference of a single character is evidence of "speciation." Since there is no such thing as a fraction of a character, there is no way for a cladist to recognize subspecies, since the smallest taxnomic unit in their system is the species.

>> Below, I describe the most recent findings regarding the Rubber Boa (Charina bottae) and then pose a question dealing with taxonomy.
>>
>>1) A dwarf form of the Rubber Boa (Charina bottae) has been discovered to occur throughout parts of S. Calif. from the southern tip of the main Sierra Nevada Mts. south about 100 miles to the southern most limits of the species range in the San Jacinto Mts. southeast of Riverside, Calif..
>>
>>North of the extreme southern part of the Sierra Nevada Mts., all other live and preserved Rubber Boa populations that have been examined in California and elsewhere in the species distribution in North America represent the large morph of the species.
>>
>>2) Dwarf morph females and males reach maximum lengths of about 22 inches and 19 1/2 inches respectively. All dwarf populations exhibit relatively low mean ventral and maximum dorsal scale row counts.
>>
>>Large morph females and males examined from preserved material attain lengths of at least 25 and 21 inches respectively. Keep in mind that considerable shrinkage occurs with preservation. From live samples, females of 27 - 30 inches and males of 22 - 24 inches have been recorded. Mean ventral and maximum dorsal scale row counts of the large morph are measurably higher than the dwarf form.
>>
>>3) According to the mtDNA study by Javier Rodriguez-Robles, Glenn Stewart, and Ted Papenfuss, the Rubber Boa is represent by a southern clade and a northern clade which were estimated to have been isolated from one another for 4 - 7 million years. The paper urged the recognition of two species, the Northern Rubber Boa (Charina bottae) and the Southern Rubber Boa (Charina umbratica) representing the two clades.
>>
>>4) The southern clade is composed of just two populations of the dwarf morph that occur in the San Jacinto and San Bernardino Mts. All other populations of the dwarf morph (with both size and scalation features similar to the San Jacinto and San Bernardino populations), along with all populations of the large morph, were assigned to the northern clade.
>>
>>It would appear that a conflict exists between the mtDNA evidence and nuclear DNA (morphological traits) evidence. With or without using subspecific designations, is there anyone that is willing to pose a plausible taxonomic explanation / solution to the situation described above?
>>
>>Richard F. Hoyer (Corvallis, Oregon)
>>
>>P.S. I can post a somewhat more detailed version if anyone believes that might help.

I am familiar with the paper to which you are referring. That paper is a very interesting one, and it shows that the rubber boa probably originated in Southern California, but these southern populations underwent a recent catastrophic event. The few isolated extant populations appear to be derived from a common ancestor quite recently, as the southern populations partially recovered from the catastrophic event of the recent past which must have decimated them.

The northern populations appeared to have migrated out of the south in two separate waves. One of them apparently took the coastal route and went north all the way to Oregon, Washington and also dispersed itself into Utah and other western states. The other wave of migration occurred through the Sierra Nevada Mountains. If I remember the paper correctly, there is no evidence that the coastal migrants ever met the Sierra Nevada migrants. These facts can be gleaned from the mtDNA evidence.

What cannot be determined from the mtDNA evidence is whether the southern boa is a separate species from the northern populations. The authors of the paper you mentioned attempted to use morphological traits to divide the rubber boa into two species, but these traits represent unconvincing evidence of species status. To me, it is best to recognize the southern populations as a subspecies, not a full species. These boas are all derived from a single common ancestor. The two "clades" recognized by Rodriguez-Robles et al. can just as easily be called subclades. Besides, a clade is not a species. In fact, one can call all species of snakes a clade, since a clade is merely defined as a group that includes all of the descendants of a single common ancestor and the common ancestor itself. Hence to synonymize the term species and the term clade is simply untenable.

KC,
Thanks for the input.

At the time, the senior author was not aware that the dwarf morph occurred throughout S. Calif. and not solely in the San Bernardino and perhaps San Jacinto Mts.

The authors thought there was a sweet of characters that with reasonable confidence, one could readily distinguish between Southern and Northern Rubber Boas. That turns out not to be true if one is comparing the boas of the southern clade from the San Bernardino Mts. (and presumably from the San Jacinto Mts. which have never been studied) with members of dwarf populations from elsewhere in S. Calif. This is especially the case for the boas from the Mt. Pinos region which are extremely close in all respects to the boas in the San Bernardino Mts. except that the mtDNA results indicates the Mt. Pinos populations belongs to the northern clade.

Although the paper stated that the Northwestern and Sierra subclades were allopatric with the break occurring in the Mt. Lassen area, that is incorrect as there is no break whatsoever in the distribution of the species from northern Kern County all the way to British Columbia and east to Montana, Wyoming ,etc.

Richard F. Hoyer

>>KC,
>>Thanks for the input.
>>
>>At the time, the senior author was not aware that the dwarf morph occurred throughout S. Calif. and not solely in the San Bernardino and perhaps San Jacinto Mts.

That explains a lot about their taxonomic proposal. Thanks for the information.

>>The authors thought there was a sweet of characters that with reasonable confidence, one could readily distinguish between Southern and Northern Rubber Boas. That turns out not to be true if one is comparing the boas of the southern clade from the San Bernardino Mts. (and presumably from the San Jacinto Mts. which have never been studied) with members of dwarf populations from elsewhere in S. Calif. This is especially the case for the boas from the Mt. Pinos region which are extremely close in all respects to the boas in the San Bernardino Mts. except that the mtDNA results indicates the Mt. Pinos populations belongs to the northern clade.

mtDNA data is merely distance data, which means it is a measure of how long ago two populations last shared a common ancestor. As biologists (including Charles Darwin) have known for a long time, some species and some populations evolve much more slowly than others. For example, we all know of such species as the coelacanth, which has changed very little over hundreds of millions of years. The fact that the Kern County boas are part of the "northern clade" may simply mean that these animals have become isolated from their southern populations geographically for a long period of time. Their similar morphologies would appear to me as the result of "stasis" or no change from the ancestral condition. Should we then classify a population as a different species or subspecies, despite the lack of change, simply because it has become geographically isolated from the ancestral population? The answer is no to a vast majority of biologists. Evoluton means change. Changes in the mtDNA is not evolution, since these changes are the result of random mutations which do not affect the fitness or survival of the species.

>>Although the paper stated that the Northwestern and Sierra subclades were allopatric with the break occurring in the Mt. Lassen area, that is incorrect as there is no break whatsoever in the distribution of the species from northern Kern County all the way to British Columbia and east to Montana, Wyoming ,etc.
>>
>>Richard F. Hoyer

I assume you have unpublished data to show that the boas occur within the break. If so, it is very interesting and it should be published. The mtDNA data of these animals should be obtained to see if they belong to the coastal lineage or the Sierra Nevada lineage or both. If both types are present, it does not mean that they are interbreeding because mtDNA is passed on only from mother to daughter. Other types of data are needed to determine if they are both present and whether they interbreed. This data could help us solve the problem of Rubber Boa taxonomy. Regards.

CK,
I am in the process of preparing to leave for S. Calif. on the 25th and am short of time to respond.

I have made a number of crosses that indicate that boas for the different clades and subclades that are paired carry on courtship behavior, coupling, and can produce viable offspring. If you wish details, I can provide them after I return. I can be reached at charinabottae@earthlink.net if you wish.

Richard F. Hoyer

>>CK,
>>I am in the process of preparing to leave for S. Calif. on the 25th and am short of time to respond.
>>
>>I have made a number of crosses that indicate that boas for the different clades and subclades that are paired carry on courtship behavior, coupling, and can produce viable offspring. If you wish details, I can provide them after I return. I can be reached at charinabottae@earthlink.net if you wish.
>>
>>Richard F. Hoyer

Have a good trip. That means there is a lack of evidence that the 2 northern large morph populations are different species, because if they either refuse to mate or if they produce infertile offspring in the laboratory then that would mean that they may have evolved into different species.

However, there is a disturbing lack of evidence that they are found in the same locality in nature. You claim that the distribution of boas is continuous and therefore the two northern populations are not allopatric, contra to what Rodriguez-Robles et al. are claiming, but that would require data in the form of museum specimens or published information to verify.

If they do meet and interbreed freely in nature, then they are unquestionably conspecific. Nevertheless, the 2 large morph populations should not be considered a single subspecies unless it can be demonstrated that they evolved their phenotypes in parallel rather than convergently. If the mechanism is parallelism, the same gene is responsible for their large size. If it is convergence, then different genes may be responsible for the 2 large morph phenotypes, and it may be possible to obtain dwarf boas when snakes from the 2 different large morph populations are crossed in the laboratory. So, whether the 2 northern large morph populations are considered the same subspecies would be contingent upon whether they intergrade and on the nature of the genetic control of the large morph phenotype.