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Posted by WW on October 18, 2001 at 06:09:24:
In Reply to: Re: New Taxonomy of the Elaphe obsoleta complex posted by Frank Burbrink on October 18, 2001 at 00:00:19:
: If you are going to comment on my paper, then you should read it correctly. I only threw out subspecific intermediates in the subspecific analyses...not in the grand analyses.
Fair point - my apologies for the misinterpretation.
In any case, I agree entirely that you showed convincingly that the conventional ssp. are best forgotten. I also don't have a problem with any of the phylogeographic analysis.
I am less sure about considering the three obsoleta lineages to be species. First of all, the supposed barriers (Mississippi, Apalachicola) appear to be pretty leaky, as shown in the "asterisked" specimens in your tree. By the time you focus on populations near the contact zones, these asterisked specimens actually make up a reasonable proportion of the specimens from those zones. While I am no fan of the BSC, I would nevertheless argue that if two lineages represent independently evolving entities, i.e., evolutionary species, then they need to be more or less genetically separated. Extensive gene flow makes independent evolution a doubtful proposition.
Second, the only morphological analyses that show the three clades to be morphologically clearly distinct are those where you use the clades as single OTUs for your DFAs - this is circular, as the DFA attempts to maximise separation between groups. You can't use a technique that assumes homogeneity of groups and is designed to maximise separation between them to test homogenetity of groups and separation bewteen them! On the other hand, those analyses which do not include these a priori assumptions don't support any kind of categorical distinction between the mtDNA clades. The PCA plots, and the DFAs using regional samples as OTUs in Figs. 14-15, show at best a weak, partial separation between these clades - and these are precisely the analyses which do NOT make a priori assumtpions about the nature of your mtDNA clades. If anything, the fact that it is precisely Florida specimens of your eastern clade which fall outside the range of variation of the Central clade suggests clinal variation, if anything. I have run more than my fair share of DFAs and PCAs over the years, so I think I have a pretty good idea of what the results look like when you do have separate species present - see link below.
The fact that the morphology shows some agreement with the mtDNA clades does suggest that these represent historical lineages, but does not exclude the possibility that other factors, including extensive genetic exchange between the clades, may be at work.
: Also, you should pay attention to a paper coming out in Sys. Bio. next year by Wiens and Penkrot that provide rules for naming mtDNA clades.
Will look out for it - thanks for the pointer. See also the paper by Puorto et al., downloadable at the link below.
: Because mtDNA is inherited maternally, it evolves at 4 times the rate of nuclear genes. This makes mtDNA genes very useful in determining lineages of newly split organisms.
By the same token, it also means that an mtDNA phylogeny often gives very little information about patterns of gene flow - in fact, you can have a strong mtDNA phylogeographic pattern embedded inside an organism in which gene flow runs perpendicularly to mtDNA clade contact zones - see, for instance:
Thorpe, Roger S. and Richard, Murielle. Evidence that ultraviolet markings are associated with patterns of molecular gene flow. Proceedings of the National Academy of Sciences of the United States of America 98 (7): 3929-3934. March 27, 2001.
Abstract
Recent studies have shown UV vision and markings to be important in vertebrates, particularly birds, where behavioral experiments have demonstrated its potential importance in sexual selection. However, there has been no genetic evidence that UV markings determine patterns of evolution among natural populations. Here we report molecular evidence that UV markings are associated with the pattern of gene flow in the Tenerife lizard (Gallotia galloti). This species has vicariance-induced, approximate east-west lineages in Tenerife closely congruent with the primary lineages of the sympatric gecko species. Against expectations, these molecular phylogeographic lineages (representing geological history) and isolation-by-distance do not appear to influence gene flow. Sexually mature males from populations either side of a latitudinal ecotone have different UV markings and gene flow appears to be linked to this difference in UV markings. It may be that these groups with different UV sexual markings mate assortatively, restricting the gene flow between them. This has implications for debate on the relative importance of vicariance and biotopes in influencing biodiversity, with this evidence supporting the latter.
Don't get me wrong, yours is a great study - I just happen to thik that some of the conclusions are not fully supported by the evidence as currently published.
Cheers,
Wolfgang
