If a molecular systematist were to presume that a genus or species group is a clade, then he/she really has blind faith concerning the soundness of prior morphological anlayses, the very analyses that he/she is testing/challenging using molecular techniques! Isn't it ironic?



Yes, molecules can be adaptive or neutral. Usually neutral characters evolve much more quickly than adaptive ones. It is often not difficult to tell whether a molecule is neutral or adaptive. For example, there is no reason to believe that SINE characters or microsatellites are adaptive. These characters have been used very successfully to study phylogenetic history. SINE characters, for example, are practically free of homoplasy. In molecular systematics, as it is in morphological analysis, character goodness and character choice are very important determinants of success or failure. The goodness of morphological characters, on the other hand, are often much more difficult to evaluate. For example, if a species of aquatic newt has smaller eyes than 3 closely related but more terrestrial species, is it possible to know whether the large eyes of the terrestrial species are the result of a single speciation event or 2 or three independent speciation events? In other words, is the large eyes of the terrestrial species a homology or a homoplasy? Sometimes it is almost impossible to tell without molecular data.



There is little doubt that the future of phylogenetic analysis will be based primarily on molecules. However, in the field of paleontology, in which molecular data is extremely difficult to obtain, morphological characters would still need to be used. Luckily, even though molecular evidence may be lacking, fossil data, specifically stratigraphic data, is not. These can be used to corroborate morphological analyses.
SINE characters

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