I haven’t had a lot of time for reading lately, so I am still in the process of reading the paper. I am just now at the critique of the molecular evidence for a chimp/human clade. Here is a longish quote:
Morphological data are not immune to the possibility of homoplasy, but neither are molecular data. In fact, the lack of a comprehensive theory of homology in molecular systematics is its main weakness. As with demonstrated morphological similarity, similarity between DNA sequences can be due to primitive retention, reversal, homoplasy or simply to being non-homologous (e.g. convergent). The only bases for claiming demonstration of molecular homology are the limited data set of four nucleotides and their positions relative to each other (sequence order). DNA sequences are further inherently ambiguous because a substitution event leaves no evidence of replacement, which would seem to be a critical element towards hypothesizing whether matching base pairs represent primitive retention, convergence, or unique derivation.
In addition, in order to compare supposedly homologous DNA sequences one must align sequences of different lengths, which is a procedure that requires assumptions about deletions or additions that underlie the observed disparity in nucleotide sequence order and length. In the end, there is no objective way to assess the relative phylogenetic value for the number of gaps and substitutions that are assumed in order to align sequences of different lengths (Marks, 2003). Thus, statements of sequence homology are not generated from individual comparative outgroup character analysis as they are in morphological analyses. Rather, the claim of sequence homology is the result of an overall best fit between an artificially reconstructed sequence and subsequent measures of phenetic
similarity (Giribet et al., 2002; De Laet, 2005; Redelings & Suchard, 2005; Phillips, 2006; Kjer et al., 2007).
Discuss amongst yourselves…