Rob Sansom gave a talk about this subject in last years SVPCA meeting, and we mentioned it in the BKK meeting afterwards. It was then ongoing, this is the results:
Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees
Robert S. Sansom & Matthew A. Wills
Fossils are vital for calibrating rates of molecular and morphological change through geological time, and are the only direct source of data documenting macroevolutionary transitions. Many evolutionary studies therefore require the robust phylogenetic placement of extinct organisms. Here, we demonstrate that the inevitable bias of the fossil record to preserve just hard, skeletal morphology systemically distorts phylogeny. Removal of soft part characters from 78 modern vertebrate and invertebrate morphological datasets resulted in significant changes to phylogenetic signal; it caused individual taxa to drift from their original position, predominately downward toward the root of their respective trees. This last bias could systematically inflate evolutionary rates inferred from molecular data because first fossil occurrences will not be recognised as such. Stem-ward slippage, whereby fundamental taphonomic biases cause fossils to be interpreted as erroneously primitive, is therefore a ubiquitous problem for all biologists attempting to infer macroevolutionary rates or sequences.
Scientific Reports 3, 2545 doi:10.1038/srep02545