you are perhaps missing the fact that ‘distance’ is an arbitrary measure when discussing DNA sequences. since the function of much of DNA is unknown, there are many assumptions involved in such a measurement that are to say the least unlikely to be true.

Furthered by the old problem that regardless of what DNA sequences may say, diversity seems to be packaged in more or less discrete packages. there are discontinuities in nature that would not be captured by the single axis of ‘genetic distance’ or even more complicated measures. In short, one would have to construct an arbitrary threshold for delimitation (this threshold has been used in delimitation issues see ‘Nei’s Genetic Distance’ and plethodontid salamanders).

there are even more problems here musing. hybridization between differentiated forms (under other circumstances, forms delimited as disparate taxa) or contact between differentiated lineages of similar forms (including cryptic speciation which is genetic divergence unaccompanied by morphological or phenotypic divergence, a phenomenon which is being reported more frequently since the advent of the molecular revolution) cause severe problems for the construction of phylogenetic trees that would be the raw data for the delimitation procedures you suggest as an alternative.

one last problem is the issue of incomplete lineage sorting. Populations separated from ancestral areas by vicariant events may have differential genetic frequencies and private alleles not shared between the separated groups. These alleles could result from mutation/selection after the vicariance, or they could represent the structure of the ancestral population pre-vicariance. there is no known method that can distinguish between these two alternatives, so weak inference from other sources of data is the only possible method.

all of these issues demand as a solution the adoption of some arbitrary (arbitrary because such delimitations will necessarily be determined as a function of the taxa and history involved and not from first principles) standard for delimitation. This is the typological fallacy that is no different from standard morphological or biological species concepts.

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I guess I am puzzled by the following statement:

“this does not escape the typological fallacy that remains a major obstacle to an evolutionary understanding of speciation process and species delimitation.”

I believe my suggestion that the DNA should be used to establish taxonimes means that we would abandon the concept of species altogether and rather use DNA mapping to establish that one organism is closer to or farther from another.

If we combine DNA mapping with chromosomal data, then at least for natually evolved entities, would we not have established a “species free” taxonomy?

What am I missing?

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this does not escape the typological fallacy that remains a major obstacle to an evolutionary understanding of speciation process and species delimitation.

the success of a pluralism of concepts and the failure of any one concept to work for all taxa is a strong argument against the existence of a species category. i tend to take the position that a species is whatever a taxonomist calls it. and that varies with a lot of things.

good friend says that species names and concepts are the last vestiges of creationism in biology. the move to a rank free classification does not seem to resolve these issues, as far as i can see. things need names for communication and that will never stop being an issue.

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not neccessarily. We could perhaps reduce the number of species, but that does not mean that diverse variants would not need to be considered (al la the interesting article in National Geographic on blind cave fish: http://news.nationalgeographic.com/news/2008/01/080108-cave-fish.html ).

What does seem to be breaking down is our rigid taxonomic structures which may make indexing harder.

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and this would be bad why?

We can already say comfortably that rigidly separating most of the big cats into different species does not appear to be rigorously correct. And of course bacteria defy classical speciation arguments with their exchange of DNA material with relative abandonment. Plants of course hybridize. Polar Bears and Grizzilies cross breed. And so on.

It would appear that our classical “tree of life models” with clean delineation of branches is perhaps confounding us here. At the branch points it would appear that it is more a cloud than a distinct crisp branching.

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it would seem that the DNA matching would be the gold standard for establishing taxonomies.

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If they get well and truly stumped they ship parts of a specimen off to a lab equipped for DNA analysis. They lack the resources, and my wife lacks the interest in biochemistry and genetics, to do it themselves. She’s more of a behaviour and wanting to handle it and cut it up kind of person. Me, were I a biologist, I’d go straight for the DNA.

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