Wulf wrote:
"The point I wanted to come to was if experiense has shown that phylogenetic analysis based on molecular data are more reliable than based on morphometric analysis. I do not want to say that the "old fashoned" workers were all wrong, but some papers that are based on molecular data support evidence for a different phylogeny of species than the ones created by using morphological data."
Me:
Actually the great systematists of the past, who could not rely on molecular characters even if they wanted to, are not only not “all wrong,” but they are more likely to be correct than many modern day systematists who call themselves cladists. That is because these past greats often relied on detailed comparative anatomy, unlike many cladists who often rely uncritically on superficial similarities. The reason morphological characters are often unreliable is because they are often adaptive. If one reads Darwin’s book “Origin,” one can see how he and his colleagues often distrust adaptive characters and show more confidence in degenerate or “rudimentary organs.” If an organ is not needed by an organism’s way of life, Darwin reasons, then two organisms possessing the same rudimentary organ would be good evidence that they share a common ancestor. Darwin, in chapter 13 of “Origin”, also discusses at length the importance of embryology and ontogeny in phylogenetic analysis. Since embryological features such as gill slits are obviously not adaptive in mammalian embryos, their presence is thus strong evidence that mammals have an ancestor that possessed gill slits and hence gills. Mammals therefore once had an ancestor that breathed with gills. In contrast, most modern day cladists simply ignore phylogenetic clues that may be found in developmental biology, physiology or biogeography.
The reason molecular characters are often more reliable is because there are many parts of the genome of an organism that are more or less selectively neutral. The third nucleotide in each codon of a protein encoding DNA sequence, for example, can undergo mutation without affecting the amino acid being coded. Such mutations are therefore due entirely to chance. Two organisms with nearly identical nucleotide sequences, including the third nucleotides of all the codons, would almost certainly be closely related, since it would be unlikely that chance alone would produce identical random mutations in two different lineages evolving independently of each other. There are also molecules, such as serum albumin, which have no apparent function. These molecules are therefore selectively neutral and they are the analog of Darwin’s rudimentary organs. They too are often more informative of phylogenetic relationships than, say, ventral scale count, which is an adaptive character that can often evolve independently in two distantly related species.
Further, because morphology is more often adaptive, a species which has entered a new adaptive zone may undergo so much evolutionary change that its morphology may not resemble its closest relative. A classic example is that of the whales. They have no limbs and no hair and they are more fish like in their morphology than mammal like. Hence it was, until very recently, a mystery as to which group of mammal is ancestral to the whales. Despite the morphological disparity, the molecules of whales clearly show an affinity to the artiodactyls (camels, pigs, deers, cattle, hippos and relatives). Since most of the whales' molecules are not involved in the adaptation to the whales’ aquatic habitat, they retain their similarities to the whales' closest relatives, whereas almost every part of the morphology of whales have changed due to adaptation and nearly all morphological clues of the whales' ancestry have disappeared.
Morphological analyses therefore often fail to include divergent outgroups; such analyses result in the recognition of paraphyletic groups that the systematist may think, albeit falsely, are holophyletic. Phylogenies that are constructed on the basis of superficial, convergent similarities would result in unnatural polyphyletic groups. The morphological systematists who analyze their characters carefully often find themselves recognizing what turn out to be paraphyletic groups. The morphological systematists who think that they are "objective" by refusing to analyze the goodness of their characters would most likely find themselves recognizing polyphyletic groups.
Next time you read a morphological phylogenetic analysis, see if you can find any discussions at all of character goodness. If you cannot find any, then chances are that the results are not very reliable. Garbage in, garbage out applies equally to molecular systematics and morphological systematics.
roblems and Solutions, Syst. Biol. 50(5):689–699