>>In his PhD. thesis, B.N. Campbell (1997) examined the molecular phylogenetics of Boidae using the mitochondiral cytochrome b gene. He examined 47 blood samples as well as 143 tissue samples representing 44 species. As a result, Campbell concluded that data from cytochrome b gene were unable to resolve the phylogeny of the Pythonidae in most aspects.

Noone says moleuclar markers are infalible. For a start, as in all cases, you need the right tool for the right job, and you need to be lucky enough to be studying an organism where there is a story

Disclaimer: I have not seen Campbell's thesis. However, if, as I suspect, the different Pythonine lineages are very old, then a fairly fast-evolving gene like cytb may not be the best choice of marker due to heavy saturation. Second, it is also possible that the Pythonines are the result of a rapid adaptive radiation, i.e., the different lineage splits happened in quick succession. In that case, this is going to be difficult to resolve in any case.

>>As pointed out by Henderson (1997) mtDNA of West Indian taxa of Corallus varies only slightly from Corallus hortulanus, but there is a notable divergence between them in morphologic characters.
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>>So, I would conclude that phylogenetic analysis only on the base of molecular analysis can lead to wrong hyptheses about the phylogeny of species.

Referring specifically to the Henderson study (and by implication to a large number of offshore island species in general), then we must not confuse different parts of the story being told by different markers and the notion that "molecular analysis can lead to wrong hyptheses about the phylogeny of species". Chances are that Henderson's mtDNA phylogeny is spot on: the differentiated island populations are recent derivatives of mainland populations, but which diverged rapidly after getting to the islands - a very common story. The mtDNA information is not misleading in any way, and neither is the morphological data - they simply tell a different part of the story. Of course, you and the others are correct in saying that having both sources of evidence at hand greatly strengthens our ability to get to the bottom of the entire story.

The question of what one does with recently diverged populations like that is a subject of debate, and really down to personal philosophy/preference. Some like to recognise them as separate phylogenetic/evolutionary species due to morphological differentiation and allopatry, others would rather sink them back into the mainland species based on phylogenetic considerations.

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>>There also seems to be still a general methodological problem in molecular systematics. The weighting of data as preferred by some taxonomists may influence phylogenetic relationships. "Subjective" weighting or rejecting of data seems to be more like a "...if they woun't fit, I'll make them fit..." thing and there are several methods to handle data sets used in phylogenetic studies.

That is a bit of an overstatement. By and large, weighting methods in molecular systematics seek to exploit our understanding of how DNA sequences evolve to compensate for artefacts like transition bias etc. Moreover, these weighting approaches have now been supplanted by more rigorous model-based approaches such as Maximum Likelihood and Bayesian methods.

Cheers,

Wolfgang
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