Indeed. And the evolutionary conclusions that could be drawn from the transposable elements were limited.A high-proportion of the HERV-K insertions occurred after hominoid chimp divergence, making them useless for interspecific comparisons. Some of the comparisons of subtypes of HERV-K were useful, but the transpositions themselves appear to occur largely on timescales that are fast compared with species divergence. There appears to be little diversity among humans in the HERV-K insertions, but that may be a result of our species' genetic homogeneity.
Comparison of SINEs between human and chimp genomes may be similarly disappointing. Humans have three times the number of lineage specific SINEs. And quoting the initial chimp genome paper "In any case, the presence of such anomalies suggests that caution is warranted in the use of single-repeat elements as homoplasy-free phylogenetic markers." The chimp genome paper discusses other classes of transposable elements, and some of them look more phylogenetically promising, but to claim they are likely to replace genes in comparative genomics is grossly optimistic and unwarranted.
I disagree and this has all ready taken place to a large extent. Fundamental to this is that it turns out that the repeat elements are such a major component of genomes and this wasn't known until the full genomes were sequenced.
The Science article I linked to article addresses this to some degree in relating how looking only at genes there is very little difference between chimp and human and the reasosn for our differences are in no way apparent. Gene relationships have been extensively examined over decades (hence my comment to you the other day that you have reached the 1980's) and the very high degree of homology doesn't seem to be able to explain the differences in species.
A clue that transposable element activity of some sort did appear in the 1980's and 90's with the sequencing of a number of G-Protein coupled receptor genes. It was found that many of these genes surprisingly were intronless. This was indicative of class I transposition having been involved in the evolution of this large and important class of genes. Other intronless genes have been found as well.
Breakage and recombination that can be mediated by transposons and repeats elements provide a mechanisms for chromosomal rearrangements (as McClintock was the first to discover) which fits well with an mechanisms for mutations over the course of evolution. This is combined with the epigentic understanding of gene regulation and eu/heterochromatin strucure/function associated with high repeat regions provides a basis for not only the structural chromosomal changes which define species and reflect evolution but a genetic regulatory mechanisms whereby regulation of genes which are essentially interchangable between species can provide for the vast differences in phenotype not reflected in the genotypes (ie the genes are pretty much the same so how do they specify human vs chimp).
As I pointed out, the most recent authoritaive genome study from the sequencing consortium just published in nature and analyzed these sort of questions.
"In any case, the presence of such anomalies suggests that caution is warranted in the use of single-repeat elements as homoplasy-free phylogenetic markers."
is that what I am talking about is not their uitilty as homoplsy-free markers, but their distribution (and discovery via analysis) throughout geneomes at regions of divergence.
Treating them as if they are genes with sequences that can be used to compare phylogeny based on homology would require probably more than caution, it just wouldn't be the thing to do.
Much of the focus in this area is to actually identify repeats. Using the first known characterized repeats or elements as if they are genes is not what is being addressed. So, yes, I agree with you about the approach you outline. But that is not what I am talking about.