Evolutionary rate shifts suggest species-specific adaptation events in HIV-1 and SIV

Maoz Gelbart; Adi Stern

Further research will be required to understand if and how this has affected the adaptation of 240 the virus to the human host. 241 . CC-BY-NC-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi. org/10.1101/190769 doi: bioRxiv preprint Limitations. This study has several limitations. First, the availability of full coverage of SIVcpz 242 and the SIVgor genomes is still low, reducing the statistical power of the analysis. Indeed, we 243 noted that increasing the sample size of group M sequences that are much more available, led 244 to detection of more rate shifting sites (Supplementary File 1) . We expect that the availability of 245 additional SIVgor sequences will increase the number of rate shift events that are unique in that 246 clade, possibly revealing more important sites for this lineage. Second, the method that we 247 utilized to identify rate shifts is calibrated to identify dramatic changes in the evolutionary rate 248 along a lineage. Accordingly, it cannot detect sites where a "content shift" occurred, i.e. the 249 amino acid changed and remained conserved in two complementary lineages, since this entails 250 only a minor change in evolutionary rate. This is partially demonstrated in Gag30, where the rate 251 of evolution changed mildly, while the content of this site changed between chimpanzee and 252 human viruses. 253