Lineage concept vs cladistics in continental biostratigraphy

The white hair of my chief Ph.D. supervisor is to some degree explained by his livelong efforts to get a grip on Carboniferous to Permian continental biostratigraphy - trying out different groups such as cockcroaches, conchostracans, freshwater sharks, and amphibians.

One of the underlying concepts which I suppose I will always find hard to believe is the idea of searching for and finding so-called lineages, i.e. series of species occurring subsequently in the stratigraphic record which show stepwisely distinct anatomies because each species has descended from the respective next-oldest species.

Of course every species has an ancestor and many have descendants but how can I define them from the fossil record? Is there not the typical problem of epistemic vagueness of the ancestor in any kind of phylogeny (e.g. discussed by Wolf-Ernst Reif in some of his many theoretical papers on cladistics in paleontology)?

Searching for lineages leads to a fallacy?

The idea that whithin a continental sedimentary succession a certain species occurring deeper than a related species should be regarded as the ancestor of the latter - unless disproven - always reminded of a type of logical fallacy called post hoc ergo procter hoc: "B occurred later than A, therefore A must be the reason for B." In terms of imposing the lineage concept: "Species B occurred subsequent to species A, therefore A must be the ancestor of B."

If a multiple- and irregularly branched bush is a good analogon to how evolution works I daresay the idea of a biostratigrapher to pick up the isolated fragements of branches (i.e. fossils) and glue them together in a few long continuous branches results in a bad model of the bush.

The problems occur after I have established a biostratigraphic zonation concept on the basis of what I think is a lineage: Someone working on the same material puts the species of my 'lineage' into a cladistic analysis and finds that there is almost no concordance between the appearance date of a species and its likely phylogenetic position.

If I do agree that similarities/ dissimilarities in morphology, histology, behavior, etc. should form the basis of a classification and consider the data basis of the phylogenetic analysis as sufficient I will have to admit that my scheme has been proven wrong. Or else if I suppose that the data are not sufficient and I myself cannot add more then I will have to concede that my scheme is at least no more valid than the alternative.

Proving microevolution depends on the sufficiency of "population" samples?

Im not saying that it is impossible to find arguments in favor of an ancestor-descendant relationship: Imagine I have large enough sample of specimens of the supposedly related species A, B, and C from three successive horizons. For A, B, C the empiric distributions of morphological parameters can be compared:
If the mean value & variance for A is not signficantly distinct from the mean and variance of B and
if the mean value & variance for B is not signficantly distinct from the mean and variance of C
but given a significant difference in the mean values/ variances of A and C,
I could infer that from A to C microevolution took place...
...but do we have such samples, let's say for tetrapods?

An example: Amphibian Biostratigraphy

These problems have been discussed for the amphibian biostratigraphy of the European Permocarboniferous as developed by Werneburg and Schneider and applied for various amphibian occurrences, see for example:

R. Werneburg & J.W. Schneider, 2006, Amphibian biostratigraphy of the European Permo-Carboniferous. In: S.G. Lucas, G. Cassinis and J.W. Schneider, Editors, Non-Marine Permian Biostratigraphy and Biochronology: Geological Society of London, Special Publications 265 (2006), pp. 201–215. [Link]

R. Werneburg, A. Ronchi, and J.W. Schneider, 2007, The Early Permian Branchiosaurids (Amphibia) of Sardinia (Italy): Systematic Palaeontology, Palaeoecology, Biostratigraphy and Palaeobiogeographic Problems. Palaeogeography, Palaeoclimatology, Palaeoecology, Volume 252, Issues 3-4, 3 September 2007, Pages 383-404 [Link]

The zonation scheme and proposed lineages have been criticized by Steyer (2004) as being a stratophenetic rather than a true phylogenetic approach considering the criteria how the authors relate different species:

J. S. Steyer, 2004, Phylogenetic or stratophenetic systematics? - Comment of R. Werneburg: The branchiosaurid amphibians from the Lower Permian of Buxières-les-Mines, Bourbon l’Archambault Basin (Allier, France) and their biostratigraphic significance. Bull. Soc. géol. France, 2004, 175 (4), 423-425
[Link]

Another particular problem is that amphibians are known to be abundantly subject to heterochronous evolution - evolutionary shifts in the ontogenesis, in particular, neoteny, is a common phenomen and can obscure characteristic features.

A recent analysis by Schoch & Milner (2008) on branchiosaurids, a group of neotenic small dissorophoid temnospondylians which is often considered for biostratigraphy, features a cladistic approach and proposes a scenario, related to which nodes of the tree neoteny/ life style changes occurred:

R.R. Schoch & A.R. Milner, 2008, The intrarelationships and evolutionary history of the temnospondyl family Branchiosauridae. Journal of Systematic Palaeontology (2008), 6 : 409-431 [link]

While the relationship of Branchiosaurus forming the outgroup of major clades (Melanerpeton-clade, Apateon-clade) is correspondent to the order of occurrences in the stratigraphic record, certain long ghost lineages occur - in particular the interpretation of Apateon gracilis/Melanerpeton gracile shows a mismatch between the cladistic approach of Schoch & Milner and the scheme of Werneburg & Schneider. This divergence is also the consequence of conflicting interpretations of the gracil(e/is) material, however, it demonstrates the potential for stratigraphic misinterpretation:

If I believe that a species forms the end member of a lineage because it is the youngest in certain sedimentary sequences I may underestimate the species' stratigraphic range - unlike the cladistic analysis which (if well-founded) would imply a deep divergence suggesting that some of the earlier record of the species is missing.

Decoupling (continental) biostratigraphic zonation from the lineage concept

Assuming that evolution works rather bush-like than lineage-like, I dont' see why we can't keep a biostratigraphic zonation even in the case of sparse continental records. I still can associate a series of morphologically defined taxa with a certain stratigraphic range and spatial distribution - until the concept has been shown not to be adequate (or not outside a more narrowly defined spatiotemporal window).

Whether it is a lineage-like relationship of species or another factor (related to geography, climate, ecology or else) that makes biostratigraphy work is a question which might be solved only in some cases.