>>CK,

>>But unless the raw mtDNA data somehow can ascertain the relative ages of populations, then I have to concede that perhaps my original views were in error and there exists the possibility that the dwarf morph evolved from the large morph.
>>
>>I know so little about mtDNA research but I can envision one potential piece of evidence that may indicate the relative age of populations. You can give me your thoughts about the following: If a large number of mtDNA haplotypes exist in a relatively small geographical region, wouldn't that indicate that over time, a large number of mutational events had occurred? In contrast, if there are much fewer mtDNA haplotypes in a geographical region, would that possibly indicate a much younger age?>>

Hi, Richard, I gave a pretty long winded and convoluted answer in my original answer to your post. So I will try to be more coherent, if not more concise, this time. Since life began some 3.5 billion years or so ago, it has evolved into the present bewildering variety. Since all life can be traced back to a single ancestor, all organisms have the same absolute age. When we talk about the age of a population, we are really talking about how long ago a population has diverged from a common ancestor, either with another population of the same species or a different species. To measure how long ago two organisms last shared a common ancestor, biologists turn to something called genetic distance. Genetic distances are best measured using molecules because the rates of morphological evolution vary greatly. Some organisms change very little morphologically over hundreds of millions of years, and living individuals look almost identical to fossils that are hundreds of millions of years old. The coelacanth is a good example. Some organisms can change drastically over a short period of time. So it is not possible to know how long since two organisms last shared a common ancestor by measuring morphological disparity.

Molecules, however, evolve more or less in a clock like manner, because chance mutations occur randomly and the probability of a mutation during DNA/RNA replication is quite similar for a vast majority of organisms. Of course many molecules change very little over the eons because changes can make them non-functional. The chlorophyll molecule is a very good example of an adaptive and slowly evolving molecule that resists changes. Other molecules are less vital and they can change more rapidly. The late Allan Wilson of UC Berkeley, a pioneer in molecular systematics, realized this. He and his students contributed a great deal to the understanding of the relationships and relative ages of divergence among different living organism by measuring molecular distance using more or less neutral molecules. To do this, he searched for molecules that are not vital to an organism's survival. One of those molecules he found was serum albumin, a protein with no known function, and which can mutate rather freely. Another molecule he found is mtDNA.

By measuring or estimating the genetic distance (i.e. the number of differences in their nucleotide sequences) using mtDNA or other molecules, the amount of time that has elapsed since two organisms last shared a common ancestor can be estimated. The theory is that when two organisms share the same parent, their mtDNA molecules are identical. As these organisms become separated geographically and evolved, the number of nucleotide differences would increase through time. Of course, the molecular clock must be calibrated using fossils, so there are disagreements among biologists as to how fast a molecule may have evolved over time, if their calibrations are different.

The genetic distance between umbratica and the northern subclades (Northwestern plus Sierra Nevada subclades) is the greatest within C. bottae. The distance between the Northwestern subclade and the Sierra Nevada subclade is much smaller. And of course the genetic distance between any two populations within the Sierra Nevada subclade is among the smallest seen within this species. The distances between any 2 population of umbratica is also very short, suggesting a relatively recent common ancestor.

The last common ancestor of umbratica and the 2 northern subclades is the ancestor to all of the C. bottae populations existing today. Was this common ancestor found in southern California or the southern Sierra Nevada? We may never know the answer to that question because we cannot observe history but we can only infer it. Chances are, however, that this ancestor lived in southern California because the likely ancestor of both C. bottae and Lichanura trivirgata is the Mexican dwarf boa. Therefore it is a simpler (but not necessarily correct) and more likely explanation is that Exiliboa gave rise to C. bottae in Southern California before retreating south into Mexico due to climatic and geological changes occurring in the area of northwestern Mexico.

If umbratica is ancestral to the 2 northern subclades, then the ancestral form of C. bottae is more likely to be the dwarf form. Again, this would be the simpler (but again not necessarily correct) and more likely explanation, since Exiliboa is a small snake that thrives in mesic environments. If the large morph is ancestral, then we would need Exiliboa to give rise to a large morph snake that is perhaps better adapted to xeric environments (like those boas found in eastern Oregon for example), and from this large morph animal, a small morph snake adapted to a more mesic environment re-evolved. Evolutionary biologists call this an evolutionary reversal. Reversals are of course possible and in some instances they are even probable. In most other cases, they are less likely because for biological organisms, it is often not possible to "go home again." For an organism like a whale, an evolutionary reversal back to life on land is probably not possible because whales have become so well adapted to living in the sea and because they have lost almost all traces of their hindlimbs.

Therefore, on the basis of genetic distance, biogeography and the fact that reversal is less likely, I believe that the dwarf morph is the ancestral form of C. bottae.

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