Convergent evolution in macaques

Simlar sequences between humans and other apes are often cited as strong evidence of common descent.
The following paper (unfortunately I only have the abstract) details how six macaques developed similar mutations in independent lines.The env gene of three simian immunodeficiency virus (SIV) variants developed convergent mutations during disease progression in six rhesus macaques. The monkeys had been inoculated with supercoiled plasmids encoding infectious proviruses of SIVmac239 (a pathogenic, wild-type strain), SIVdelta3 (the live attenuated vaccine strain derived from SIVmac239), or SIVdelta3+ (a pathogenic progeny virus that had evolved from SIVdelta3). All six monkeys developed immunodeficiency and progressed to fatal disease. Although many divergent mutations arose in env among the different hosts, three regions consistently mutated in all monkeys studied; these similar mutations developed independently even though the animals had received only a single infectious molecular clone rather than standard viral inocula that contain viral quasispecies. Together, these data indicate that the env genes of SIVmac239, SIVdelta3, and SIVdelta3+, in the context of different proviral backbones, evolve similarly in different hosts during disease progression. http://www.ncbi.nlm.nih.gov...
{Shortened display form of URL, to restore page width to normal - Adminnemooseus}If we observe similar mutations arising independently then how do we know when they arise independently and when the arise due to inheritance?Thanks[This message has been edited by judge, 10-27-2003][This message has been edited by Adminnemooseus, 10-27-2003]

Thanks for all the replies (particularly to Taz for the links).
I am just an amatuer so I may have to ask a couple of dumb questions here..(And it is so difficult to find creationist discussions of this stuff, which is why I am trying to lok at papers themselves).The similar mutations happen in independent lines of the gene in the virus and yet these mutations are selected for during the life of the macaque?
If I understand this correctly ..how long does it take for these muations to be selected for?Have i understood? (I'm not sure I have)[This message has been edited by judge, 10-28-2003]