It's more complicated than thought.
Three possible scenarios have been put forward to explain the 'excess' of segmental duplications within the human−ape lineage when compared to other genomes22, 23: frequent de novo duplication, a slow culling of duplications by deletion, and/or extensive gene conversion of ancient duplications11, 24, 25. Cross-species comparison of the chimpanzee-only duplications among humans and the great apes revealed that the majority (11 out of 17) of the duplications were restricted to the chimpanzee (multiple hybridization signals were not observed in human, gorilla or orang-utan; Supplementary Table S12). These probably emerged as a consequence of de novo segmental duplication after speciation. Six out of seventeen of the chimpanzee-only duplications, however, were also duplicated in the gorilla (and in one case orang-utan). We propose that these apparent duplications arose before the divergence of humans and great apes and have been subsequently deleted within the human lineage, although a small fraction of these (approx30%) are expected to be due to lineage-specific sorting in the ancestral chimpanzee−gorilla population26.
From Nature 437, 88-93 (1 September 2005) | doi: 10.1038/nature04000 A genome-wide comparison of recent chimpanzee and human segmental duplications
Ze Cheng1, Mario Ventura2, Xinwei She1, Philipp Khaitovich3, Tina Graves4, Kazutoyo Osoegawa5, Deanna Church6, Pieter DeJong5, Richard K. Wilson4, Svante Pääbo3, Mariano Rocchi2 and Evan E. Eichler1
You see, there are events wherein shared elements seem to be deleted. Not seeing something in all common ancestors excpet one would not discount common descent.
Also note the finding of elements specific to chimp in gorilla and orangutan.
Sorry for the "internal duplciate".
It seems the authors are trying to explain the appearance of gene duplications within the genomes of great apes. In comparing humans and chimps, they find the majority of duplicated DNA segments are shared and found in other great apes. OK great.
Next they examine the duplicated sequences that are either in humans only or chimps only. From this section in the paper you provided there are 17 sequences where they do cross species comparison (with gorillas and orangutans).
11 out of the 17 are found only in chimp, and not in either humans or in the other great apes. The authors conclude these are newer mutations which occurred after the chimps split off from everyone else. Logical enough.
Next, they observe the other 6 are found in chimps, gorillas and orangutans, yet not in humans. Here they conclude that in the human lineage these duplications once existed but were deleted out over time (after the split from chimps). That also sounds reasonable.
Now note however that in neither of these situations do we see multiple events occurring in the different lineages (they either occur in the chimp alone or in humans alone). So I am unsure how this supports your “multiple independent events” hypothesis (unless you are trying to say these duplications all occurred independently in chimps, gorillas and orangutans which are not what the authors are implying in the least.)
Perhaps you thought the fact that humans apparently deleted these segments was somehow relevant to our previous discussion on L-GLO. Not at all. The Nature paper looks at large stretches of DNA that are duplicated repeatedly throughout the human and chimp genomes. This is not uncommon (especially in regions of DNA which are not “used” by the organism). Nor is it strange that repeated segments of DNA in tandem will eventually be removed from the genome over generations. The authors even explain this in the next several paragraphs:
This effect…suggests that loci near clusters of segmental duplication may be more susceptible to duplication/deletion due to an increased frequency of non-allelic homologous recombination.
This is easy to understand with some basic knowledge of molecular genetics. Remember we are talking about relatively large DNA sequences here that are repeated. You have a sequence: -A- -B- -C- -C- -C- -C- -C- -F- where the letters represent these large segments, you can see how the matching of the ‘C’ sequence can slip during DNA replication.The L-GLO deletion on the other hand is a single nucleotide deletion! There is no way that this example represents some kind of deletion hotspot that you perhaps were implying (again I am unsure if that actually was your intent).
It is like saying there is a general increase in lighting storms over the Northeastern US. In this context, the phenomenon of L-GLO would be like lightining striking exactly page 137 (and ONLY page 137) of “The Count of Monte Cristo” in the main library of Boston, New York and Philadephia simulatenously.