It's not a false assertion and I actually demonstrated in your own example that the one article in that ToC on comparative genomics used transposable element distribution.
I'm beginning to think you don't quite grasp what a genome actually is.
How do you suggest this be resolved. You want to argue over the number of papers published that have done genomic comparisons using different methods.
OK. Rather a side issue, but it can be addressed by finding every article that has compared genomes and seeing what types of analyses were done. I would agree that number of genes, homology between gene sets, rRNA homologies were done. Transposable element analysis is much harder to do which is why it is a current focus.
I will initially refer you to the Chimp genome papers in Nature. Two were published One, the basic initial report:
Nature 437, 69-87 (1 September 2005) | Initial sequence of the chimpanzee genome and comparison with the human genome
including a section on genome evolution wherien nucleotide substitutions were examined, as well as insertions and deletions. Insertion of transposable elements were speficially looked at and catalogued.
The secomd sister article, Nature. 2005 Sep 1;437(7055):88-93. A genome-wide comparison of recent chimpanzee and human segmental duplications.
This touches exactly on the issue of transposable elements on genomic evolution. In the last pre-discussion paragraph the author's state the importance of transposons to genomic structure and evolution:
We propose that most of the asymmetrical increase of duplicated DNA in the chimpanzee lineage has emerged as a mechanistic consequence of changes in chromosome structure and not selection. The subterminal caps are an idiosyncratic structural aspect of African great ape chromosomes28, which are generally regarded as heterochromatic. Similar to human pericentromeric DNA, the regions have served as sinks for duplicative transposition and expansion of particular euchromatic segments. This process has led to an overall increase in chimpanzee genome size of at least 16 Mb since human and chimpanzee separated. It is interesting that the same region that represents the site of chromosome 2 fusion29 in the human lineage has undergone a segmental duplication hyperexpansion within the subterminal region of chimpanzee chromosomes. This may suggest an inherent instability of this segment of DNA, further extending the association of segmental duplication and chromosomal rearrangement without a direct cause and effect relationship
Science also did an article about the findings associated with the chimp genome and wrote:
But as suggested by earlier work on portions of the chimp genome, other kinds of genomic variation turn out to be at least as important as single nucleotide base changes. Insertions and deletions have dramatically changed the landscape of the human and chimp lineages since they diverged. Duplications of sequence "contribute more genetic difference between the two species--70 megabases of material--than do single base pair substitutions," notes Evan Eichler, also of UW, Seattle, who led a team analyzing the duplications. "It was a shocker, even to us."
From Chimp Genome Catalogs Differences With Humans, Elizabeth Culotta, 9-2-05 Science
The centrality of transposable elements to evolution is becoming more clear with every passing day.
The analysis consists pretty much only of breakpoints. Coincidntally to our discussion, this chromosome contains FRA3B.
Breakpoints were compared with other primates to look at evolutionary questions.
One excerpt here:
Further comparative FISH analysis revealed that a large-scale pericentric inversion occurred in the ancestor of the African apes and is present in modern human chromosome 3 as well as the chimpanzee and gorilla orthologues, but not in orang-utan or Old World monkeys14. Two scaffolds from the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) rhesus macaque Mmul_0.1 assembly were found to span both breakpoints of the human inversion (Fig. 2; see Supplementary Table 4 for breakpoint details). The macaque 5' breakpoint is characterized by a short homologous GTGG track (Fig. 2b) and by a mammalian interspersed repeat (MIR) that was split by a segmental duplication before the inversion resulting in one part, designated MIR A, present in boundary I and a second part, designated MIR B, present in boundary III (see Fig. 2a). The MIR at the 3' end of boundary III was present in the segmental duplication and may have been involved in the insertion event. A number of simple repeats and low complexity regions were found within 1 kb of the breakpoint (see Supplementary Table 5). Each of these elements, including retrotransposons15, short homologous sequence and alternating purine-pyrimidine tracks16 have been reported for many other breakpoints.
My bold. Break point analysis, as Stultis brought up is extremely important to understanding evolutionary relationshsips and mechanisms and transposon and similar elements are associated with these breakage points.