Although I am currently using DNA to recognize mollusk species, I agree that it is only one tool. I am especially doubtful of the claim that DNA work will speed up the task of identifying all organisms. Adding an expensive and complicated step to the process of describing organisms does not speed it up. However, DNA is a very useful tool, and encouraging taxonomists to include DNA data, when possible, is good. Excluding fossils or otherwise unsequenceable taxa from consideration in systematics, however, is unwise.
>How does one use DNA sequencing to determine that the variation one is seeing in the DNA is in the correct genes and to a sufficient extent to prevent two animals from producing viable offspring...is that not the definition of a species?<
That is a definition of a species. Most definitions are based on a concept similar to that, although the degree of separation varies. For example, a phylogenetic species concept defines species as distinct evolutionary lineages. These lineages might interbreed to a limited extent (especially at first), but not enough to prevent them from heading their separate ways, evolutionarily.
Interbreeding within a species should produce a mixing of genes, and thus DNA variation within a species is expected to be more or less continuous, perhaps with slight barriers corresponding to subspecies. Different species, on the other hand, should show consistent differences. However, unless you sequence a lot of individuals, representing the geographic and morphological range of the taxa, you have limited confidence about the difference between a few points within continuous variation (i.e., one variable species) and separate taxa.
For example, I am trying to sort out ecophenotypic variation versus taxonomic differences in an endangered group of freshwater mussels. Based on morphology, no one knows how many species there were and how many are still alive. From work on other unionids, we have identified some genes that generally show significant differences between species. Sequencing them for my taxa indicates that there is considerable diversity, suggesting multiple species, not just individual variation. However, many of these are so rare that they have already been listed as extinct in some references, so large samples are not feasible. Instead, I am comparing DNA and morphological differences. If both differ appreciably, I have no problem identifying them as species. If the differences are lower, then they may be subspecies. If one shows large differences and the other does not, then I would suspect that there are taxonomically significant differences that were missed by the other approach.
Not only are different DNA sequences variable in how much they differ between organisms, they also vary as to how variable they are. For example, vertebrates (and most other animals) show almost no variation in mitochondrial gene order, yet bivalves have some variation within families and drastic variation within the class. Thus, you cannot simply say that species, subspecies, etc. have a certain percentage DNA difference, or even that they have a certain percentage difference in a particular gene.
Morphological data provide an important check on DNA studies. For example, a recent paper on bivalve DNA was misled because they got bacterial sequences from two unrelated bivalves. Those two grouped together quite strongly, because the bacterial sequences were much more similar to each other than to anything else in the study. Many similar pitfalls are possible in molecular studies. I have extracted DNA from small mollusks only to discover that I actually had DNA from a sipunculid worm living in the shell, not the original inhabitant.
Dr. David Campbell
Old Seashells
University of Alabama
Biodiversity & Systematics
Dept. Biological Sciences
Box 870345
Tuscaloosa, AL 35487-0345 USA
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That is Uncle Joe, taken in the masonic regalia of a Grand Exalted Periwinkle of the Mystic Order of Whelks-P.G. Wodehouse, Romance at Droitgate Spa
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