Taken together, Yusim et al. [ 12] concluded that the apparent clustering of CTL epitopes in epitope maps was a signature of a large-scale adaptation of HIV-1 to the human population.
Such regulation could facilitate large scale adaptations in response to changes in growth conditions [ 13], for example when the bacterium associates with or dissociates from a host organism.
The lack of any large-scale adaptation of HIV-1 to reduce its number of CTL epitopes -as reported by this study- is not necessarily in contradiction with the possible fixation of certain CTL epitope escape mutations at the population level [41], [44], especially if these occur in combination with compensatory mutations [72].
In all three cases there was no sign of any large-scale adaptation of HIV-1 clade B to its human host over the last 30 years: the number of epitope precursors, MHC-binding peptides and CTL epitopes per HIV-1 sequence remained constant over time.
Finally, bacteria living in environments of distinct salinity (halophiles versus halotolerants) and temperature (mesophiles versus psychrophiles and thermophiles) were compared, to assess any large-scale adaptation of their metabolic network to these environments.
We have previously reported that HIV-1 did not show any large-scale adaptation to the cellular immune response over the last three decades [ 11], using HIV-1 population sequence data sets and CTL epitope predictors.
In order to support such software adaptation, a large scale of data should be continuously monitored and supervised.
Therefore we conclude that the visually apparent clustering of CTL epitopes in epitope maps should not be interpreted as a signature of a past large-scale adaptation of HIV-1 to the human cellular immune response.
Therefore, the visually apparent clustering of CTL epitopes in epitope maps should not be interpreted as a signature of a past large-scale adaptation of HIV-1 to the human cellular immune response.
Furthermore, this species has a wide distribution range in Eurasia, which allows testing for local adaptation at a large scale [34].
Despite high guppy abundances in the oil-polluted sites, as well as evidence of some parallel habitat-associated morphological divergence, reciprocal transplant experiments failed to show local adaptation in fitness components (survival and growth) on a small scale and showed only weak and inconsistent adaptation on a large scale.
