It has made even more progress in the decade since 1995 when the authors made that statement.
This article lists 35 different categories of assumption/problems relevant to molecular phylogenic studies. The plethora of assumptions involved make such studies anything but simple, easy, and clear. Uncounted Assumptions
There are many assumptions having to do with regularity and sample error significantly affecting the reliability of phylogenetic analysis, even purportedly Bayesian in nature, that are commonly ignored or incorrectly passed off as trivial in the speculative literature. The tree itself is a branching series of nested sets (e.g. the set of all taxa exhibiting certain state changes). A set may appear to be more definite a concept than a sample, yet it cannot be any better than the samples included in it, and a set is itself a sample.[snip]...Below is a list of presuppositions (variously discussed in general by, among others, Avise, 1994; Felsenstein, 2004; Huelsenbeck et al., 1994; Jenner, 2004; Kolaczkowski & Thornton, 2004; Lipscomb et al., 2003; Lyons-Weiler & Milinkovitch, 1997; Maddison, 1996; Naylor & Adams, 2003; Philippe et al., 1996; Pickett & Randle, 2005; Rokas et al., 2003; Ronquist, 2004; Ruedas et al., 2000; Sites et al., 1996; Templeton, 1986; Wendel & Doyle, 1998; Wilcox, et al., 2002). These can be important but are commonly not factored in, and this is especially true in the older literature. Some are obvious and major problems, and some are cryptic to the non-adept, or merely minor, or inapplicable to particular loci.
Please refer to this and THOUSANDS of other studies done since 1995 that use this graceful, easy, clear and simple method ...
Here's a link to a working proof of the study you cited that I found for free: Alu insertion loci and platyrrhine primate phylogeny
"...Short INterspersed Elements (SINEs) make very useful phylogenetic markers because the integration of a particular element at a location in the genome is irreversible and of known polarity. These attributes make analysis of SINEs as phylogenetic characters an essentially homoplasy-free affair."
And what happens when data happens to contradict the evolutionary prediction, i.e., the "known primitive derived polarity"? If elements are periodically inserted during the course of primate evolution, generating a unique new family of interspersed repeats that create markers suitable for phylogenetic analyses, then why the need for so many ad hoc rationalizations to explain away the legions of inserted element that do not comform to nested hierarchies? How is that pseudogene studies are ballyhooed when they accomodate evolutionary predictions, but are somehow never a threat to evolutionary theory when they contradict evolutionary predictions?
Contrary to the evolutionary assumption of the study you cited above that Alu insertions are irreversible, precise deletions of Alu units can occur. In the study below, a gorilla-human shared Alu was absent at the orthologous chimp locus, and an extra 12 bp right Alu-flanking repeat, added to an empty-site sequence, marked the missing-Alu spot:
Connie M. Westhoff1 and Dwane E. Wylie1(1) School of Biological Sciences, University of Nebraska, 325 Manter Hall, 68588 Lincoln, NE, USA
Received: 8 September 1905 Accepted: 12 January 1996
Abstract The human Rh blood-group system is encoded by two homologous genes,RhD andRhCE. TheRH genes in gorillas and chimpanzees were investigated to delineate the phylogeny of the humanRH genes. Southern blot analysis with an exon 7-specific probe suggested that gorillas have more than twoRH genes, as has recently been reported for chimpanzees. Exon 7 was well conserved between humans, gorillas, and chimpanzees, although the exon 7 nucleotide sequences from gorillas were more similar to the humanD gene, whereas the nucleotide sequences of this exon in chimpanzees were more similar to the humanCE gene. The intron between exon 4 and exon 5 is polymorphic and can be used to distinguish the humanD gene from theCE gene. Nucleotide sequencing revealed that the basis for the intron polymorphism is anAlu element inCE which is not present in theD gene. Examination of gorilla and chimpanzee genomic DNA for this intron polymorphism demonstrated that theD intron was present in all the chimpanzees and in all but one gorilla. TheCE intron was found in three of six gorillas, but in none of the seven chimpanzees. Sequence data suggested that theAlu element might have previously been present in the chimpanzeeRH genes but was eliminated by excision or recombination. Conservation of theRhD gene was also apparent from the complete identity between the 3'-noncoding region of the human D cDNA and a gorilla genomic clone, including anAlu element which is present in both species. The data suggest that at least twoRH genes were present in a common ancestor of humans, chimpanzees, and gorillas, and that additionalRH gene duplication has taken place in gorillas and chimpanzees. TheRhCE gene appears to have diverged more thanRhD among primates. In addition, theRhD gene deletion associated with the Rh-negative phenotype in humans seems to have occurred after speciation."
Cordially,
Interesting exceptions to the overwhelming genetic similarity shared between humans and chimps such as an ALU element shared by gorillas and humans but not chimps are exactly that, interesting exceptions. The overwhelming majority of such neutral genetic changes such as ERV insertions and psuedogenes ARE shared in common to a greater degree in humans and chimps than between humans and gorillas. Anecdotes of a particular element do nothing substantial to change this overwhelming mathematical alignment that conforms to the assumption of natural selection and common ancestry.