So for example, you are positing that a deletion at the same exact position in the human, chimp and gorilla L-GLO genes occurred independently of each other?
I'm not sure what you are referring to by L-GLO, but the answer is no.
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.