I find this difficult to believe, and even more difficult to verify:
http://jrs.sagepub.com/content/97/12/560.long
"...
Retrovirus-related elements massively repeated in the human genome include LTRs and the long and short interspersed repeats known as LINES and SINES.8 The fact that humans have twice as many LINES as chimpanzees suggests that large numbers have been acquired since the human line split from the presumptive common ancestor. Varieties of SINE, known as Alu elements, are restricted to primates. Consisting of roughly 300 base pairs, these 'pseudogenes' have massively replicated themselves in our ancestral genome and now number more than a million copies. Indeed, they continue to form new copies at the mean rate of one every 200 births.
..."
In my searching I am not able to find good examples of a LINE, SINE or endogenous retrovirus that is present in the human genome but not in chimpanzee (and/or gorilla). If humans really have 2-fold more of these elements it seems to me that aligning a large region of a human chromosome to the equivalent region from chimpanzee would show deletions in chimpanzee (insertions in human). But I have not had luck with that method.
For one example, human chromosome 7 has dozens of repeats annotated:
LOCUS AC008071 129938 bp DNA linear PRI 08-OCT-2003
DEFINITION Homo sapiens BAC clone RP11-388L11 from 7, complete sequence.
ACCESSION AC008071
...
repeat_region 4903..4928
/rpt_family="(CA)n"
repeat_region 5237..5768
/rpt_family="L1"
repeat_region 5769..6255
/rpt_family="L1"
repeat_region 6745..6799
/rpt_family="L2"
repeat_region 6843..7063
/rpt_family="L1"
repeat_region 7064..7365
/rpt_family="Alu"
repeat_region 7366..8260
/rpt_family="L1"
repeat_region 8261..8573
/rpt_family="Alu"
repeat_region 8574..8879
/rpt_family="L1"
repeat_region 8880..9177
/rpt_family="Alu"
repeat_region 9178..9795
/rpt_family="L1"
repeat_region 9796..11659
/rpt_family="MER1_type"
...
But that region is 100% colinear with chimpanzee, even though the repeats are not annotated in the chimpanzee entry.
LOCUS AC192996 174131 bp DNA linear PRI 31-JAN-2007
DEFINITION Pan troglodytes BAC clone CH251-170I4 from chromosome 7, complete
sequence.
ACCESSION AC192996
I know of one or two endogenous retroviruses that are new in the human/chimp/gorilla line vs other primates, but I am finding it difficult to confirm for myself that the human genome is riddled with changes like this, not found in the chimpanzee genome.
See also:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1424692/pdf/AJHGv78p671.pdf
Recently Mobilized Transposons in the Human and Chimpanzee Genomes
The American Journal of Human Genetics Volume 78 April 2006
pages 671 - 679
https://biosci-batzerlab.biology.lsu.edu/publications.html
Mark Batzer has a LOT of very good work on this.
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