(For non-biologists, homoplasy is convergent similarity and homology is similarity due to common descent.)
I think we are in basic agreement that function (broadly defined to include developmental constraints, etc.), common descent, design, and convergence can all lead to similarities among organisms. I would emphasize that the presence of a common function does not rule out a role for common descent; perhaps the ancestor already encountered the functional constraints and adapted to them, or the developmental constraints are inherited from a common ancestor.
Of course, in this situation the signal of common descent is muddied by the other factors, but it is nonetheless present. The presence of some ambiguity makes it important to examine multiple lines of evidence, but if they all point in similar directions it seems reasonable to accept this.
>PR: Have you ever seen anyone (let alone a textbook) consider the problem of independence between genes and morphological features, which is a requirement for the reliability of similar phylogenetic trees confirming each other?<
I do not have many textbooks handy to check, but many workers assert independence, at any rate. It seems reasonable to assume that genetic features that closely approximate a neutral evolution model are independent of morphology. Genes with a function unrelated to the morphology seem like safe choices as well, although lack of relationship is difficult to absolutely prove. For example, the physiological effects of spending long intervals underwater and holding the breath could account for many of the similarities between whale and hippo proteins. On the other hand, I have thought a little about my 18S ribosomal sequences for assorted bivalves and cannot think of any reason why two clams would need significantly different protein assembly mechanisms. Likewise, the morphological features with obvious functional aspects (e.g., adaptation for deep burrowing) seem convergent from several other lines of evidence (various molecules as well as other morphology). Other morpholo!
gical features that have either no obvious selective merit or else have multiple options seem to be better phylogenetic indicators, as shown by consistency among features.
Dr. David Campbell
Saint Mary's College of Maryland
18952 E. Fisher Road
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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 Droigate Spa
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