[Taxacom] Clade age (was: Taxacom Digest)
lynn at afriherp.org
Fri Nov 11 03:36:37 CST 2011
Now for my own fairy story <G>.
As I see it, the original founder taxon had a long but narrow range subsequently divided by the rapid incision of river valleys which divided the original taxon into several isolated populations. I say rapid because the geology across the original range was uniform and relatively soft (shales) and isolated because the river valleys are inhospitable to the species concerned. This same pattern turns up in various taxa that would have shared the habitat before it became divided, these include vertebrates, invertebrates and plants. What is obvious is that all of these share the common characteristics of very specific habitat requirements and low vagility (ability to disperse). More habitat tolerant and more mobile species were not affected. I imagine that the original species population would have had various character state mutations in the process of incorporation. These would have had points of origin along the length of the range and while some might not have dispersed very far others on the other extreme might have spread across the whole range. Subsequent retention or loss of these mutations in the isolates coupled with any new independent mutations might provide a very confused dataset for cladistic analysis. There would be a number of shared derived characters but they would not resolve into clades in any consistent way. It is possible that polytomies may be fairly frequent but over time become invisible due to the extinction of all but one or two of the descendent lines. I can see how it could arise due to rising or lowering sea levels (depending on whether they are marine or terrestrial species). I recall an interesting paper by Voris on sea snakes that looked at sea level changes in SE Asia.
I am not a biochemist or molecular biologist so have no idea what gene is involved although I guess I could find out quickly enough.
I find the idea of using cladistic type analyses to determine species rather curious as species are usually defined by their unique characters and not their relationships to other species.
On 11 Nov 2011, at 00:14, Jason Mate wrote:
I apologize for dropping out for a while but I had to undergo minor surgery after my trip and as everybody has moved on there is little point in pursuing the previous topic. Live and let live! In regards to Ann´s questions it boils down to mutation rates. There are several oft quoted numbers (averages) in the literature. Something in the range of 0.7-4/site per 10(power of 9) years are the general ballpark figures (although for Drosophila I have seen as high as 14?). These are only general average figures. You have to consider the inherent biases (compositional biases, positional biases, structural, etc), so your mutation rates are only a rough approximation for a particular bp.
If your gene of choice fails to recover any differences in a group of species I suggest trying another commonly used gene. Trial and error is the only way to find out which gene shows promising variation (and it could still be the wrong sort!). I recall a presentation on Curculio phylogeny which encountered a similar problem with certain species pairs, even when the rest of the group showed "normal" variation. The article is to be found in this link http://www.ncbi.nlm.nih.gov/pubmed/15223041, and I imagine that they discuss it.
In regards to the second topic, it is a problem that affects systematics in general and not just cladistics (although I accept Richard´s comment that some hard core cladists would have problems accepting this scenario). Speciation is hardly clean but if you assume, for the sake of argument, that a range was "instantly" divided into separte ranges that then evolved into separate species then you would most likely end with a hard polytomy or at best a poorly supported cladogram that may not even represent the biogeography of the group (still a polytomy). But, as there is no pattern of biogeographical subdivision to uncover anyway, who cares?! However, if the range was broken "gradually" (from the perspective of mutation rates) then it is likely that some of the splits will be recoverable. Of course the resulting phylogeny may still be rubbish. My only questions in this regard are if the gene that Lynn mentions shows no variation at all or is the variation just "noise" (I don´t like to call it noise as if is information after all, just the wrong kind for your question).
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