"One of the big weaknesses of the cladistic system is it's disregard of the sequence of fossils in the stratigraphic record. This is based on the fact that cladists seem to assume it is enough simply to know all the characteristics of the representative members of a group in order to work out their precise phylogentic relationships. If the resulting cladogram agrees with the fossil record for the group, the "basal" (= primitive) taxa appearing first, the most "derived" (=advanced) taxa last, well and good. If it doesn't the fossil sequence is rejected. The reasoning seems to be that since the fossil record is so incomplete in any case the missing taxa simply weren't preserved, but lived elsewhere. The result is a series of hidden or "ghost" lineages that are based on absolutely no evidence other than assumptions drawn from (possibly unreliable) cladograms.
A good illustration of the vagaries of (either one or both) the cladistic method and the fossil record is shown in the diagrams below, from Philippe Janvier's book Early Vertebrates. At the top are cladograms of two families of closely related early Devonian Ostracoderms (armoured jawless fish - in this case Osteostraci), the Kiaeraspididae (A) and the the Boreaspididae (B). Both groups of organisms are found in the same locality (the Wood Bay Formation of Spitzberg) and the animals when alive presumably lived in a very similiar environment and had similiar habits (lagoonal bottom-dwelling filter-feeders). At the bottom is shown the stratigraphic range of each of these taxa. These creatures were geographically localised (endemic) and lived in conditions that favoured preservation. In addition their hard exoskeletons (head shields) were easily preserved. So we have pretty optimal conditions here.
Now, here is something interesting. The Kiaeraspidid (A1) cladistic analysis matches their stratigraphic occurances (A2). The most basal or primitive species (a) also appears earliest (at the bottom of the stratigraphic chart). And the most advanced or specialised ("derived") species (g) and (h) occur last (top of time range diagram).
But the exact same cladistic analysis applied to the Boreaspidids (B1) does not match their stratigraphic occurances (B2). Although the basal taxon (i) is also among the earliest, some of the most advanced types (r) are equally ancient.
illustration from Philippe Janvier Early Vertebrates
(Clarendon Press, Oxford, 1996), p.286
So we have a situation where apparent "ancestors" (well, the grand-uncles rather than the grand-fathers, because cladistics is all about the descendents of the common ancestor, never the common ancestor at the base of the node) appear after their "descendents"
The cladistic assumption is simply that the fossil record is incomplete. These creatures evolved elsewhere, or if they evolved in that locality they were not preserved. However, it is possible to reconstruct the "ghost lineages" - e.g. the dotted line in the Sigurdfjellet formation leading to the j/k/l/m cluster that appears on the next formation up (more recent).
I would offer an alternative and I believe much simpler (though obviously equally one-sided) explanation. The cladistic analysis of the Boreaspidids may simply not be as accurate as the Kiaeraspidid analysis. The j/k/l/m cluster, rather than being a basal group, may actually be an advanced one, like the s/t grouping, and it only appears primitive (perhaps through degeneration or loss of characteristics).
It is of course impossible to tell which of these two alternatives is the correct one. Lacking a functioning time machine, one cannot travel back and actually observe these creatures evolving, making stopover observations at, say, 50,000 year intervals, while hopefully avoiding the grandfather paradox! ;-) In that way phylogenetics is not and cannot be a hard science in the way chemistry, physics, or even neontological (study of extant species) biology is. Between science and metaphysics there is not such a gap after all, a sobering realisation that nevertheless gives a perceptive insight into the way our understanding of the world works."
I WILL ANALYZE THIS IN THE NEXT POST.