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.
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.
Retract your false assertions and apologize. You breezed on this thread with a direct insult to me, and have continued throughout. I ignored your first few insults; then I asked you to stop; and when you refused, I decided that if you can't act like a civilzed human being, you don't deserve to be treated like one.