My only problem with DNA being the last word on the subject is the evolutionary plasticity cichlids posses. It is known that cichlids evolve faster that most other groups of fish and other animals for that matter.
While I mostly agree with you on the genetic plasticity of cichlids, I have also noticed in this forum that sometimes molecular studies have been “frowned upon” basically on the (sound) argument that inferring the whole evolutionary history of a determined taxon based on only one or two (out of millions of) genetic loci may be (and most certainly is) misleading.
However, let us not forget that Systematics is in essence the Science of identifying, naming and most important, establishing evolutionary relationships amongst different taxa. This last activity or discipline is called Phylogenetics.
Phylogenetics on the other hand is in essence the Science of discerning synapomorphies and uncovering through those the evolutionary paths of taxa…... In other words, it is about identifying characteristics which are homologous (shared by all members of a particular taxon e.g. presence of a dorsal fin in the Cichlidae) and which ideally show some degree of variation or states (e.g. in the number of spines and soft rays present) which may reflect e.g. genetic mutations that happened somewhere along the parental line of descent, and which may allow us to draw conclusions as to the evolutive relations of taxa within a taxon (e.g. Thoricthys, Vieja and Herichthys within Cichlidae). As a general rule of thumb, the more of these homologous-variant-characters or attributes (also called character-states) are found and taken into account, the more likely the true evolutionary paths of a particular taxon and its relation to others may by discerned.
The fundamental problem becomes distinguishing which characteristics may be homologous, that is have been inherited along the line of descent from a common ancestor that “first developed it”, and which characters are analogous, that is, are the product of convergent evolution.
In some cases this may be a rather straight forward task……. For example: while dolphins and cichlids both have dorsal fins, it becomes obvious that such structure is analogous and not homologous. The trait was not inherited down the line from a common ancestor, but is the product of convergent evolution consequence of mammals returning to the sea. Therefore, it cannot be deduced that cichlids and dolphins are related based on the possession of a dorsal fin, as it is obvious that dolphins are not cichlids.
In other cases discerning whether a single “characteristic” on itself –be it colour, shape, number of spines, patterns of behaviour, or a sequence of bases that conform a gene- is homologous or analogous becomes extremely difficult…… For example: The breeding dress of Amphilophus macracanthus and the Herichthys cyanoguttatus complex. Is its “apparent state” consequence of a common ancestor inheriting such trait down the line, or an adaptation acquired through a convergent evolutionary process?
The diagnosis of Cichlasoma scitulum for example is based on a series of character-states which, to mention one C. scitulum differs from C. fecetum in having 8-9 anal-fin spines vs. 6-7. In this case, both species are identical in so many “relevant” characters that it can be demonstrated that both species are indeed very close, and that the meristic differences are probably the product of a set of states (6-7 and 8-9 spines) within a homologous structure (anal fin) that appeared in an ancestor –probably due to mutation- which inherited them down its line of descent diverging into a separate lineage (species).
From the above it may be concluded that any attribute –including a gene locus- may be a “good” or a “bad” phylogenetic character depending upon whether its “existence” is the product of convergence, or of it being inherited in a particular new form (state) down the line of descent.
As you well state, the apparent genetic plasticity of cichlids does not help in this matter. However, it is my opinion that the value of molecular characters is as good a character as any other meristhic, morphometric or qualitative character, as long as it represents a synapomorphy, and may be qualitatively expressed in terms of clear-cut and preferably discontinuous states......... But that is another story.
Mauricio De La Maza