To understand how species evolve, they must be studied both at the genomic and ecological level. New sequencing technologies are used to study population differentiation at the level of the whole genome. Linking genetic divergence with adaptive process remains difficult though, as organisms live in complex environments. Parasites allow circumventing this problem because their reproductive success depends on their ability to use their hosts; in particular viruses replicate in the host cells. It can be expected that some portions of the genomes of parasites are under strong adaptive pressures, particularly in response to host defenses or during host swtching. We study the genomic diversity of two models that parasitize moths: baculoviruses and parasitoids wasps of the genus Cotesia.
The diversity of viruses allows understanding issues of genome evolution through many angles. Indeed virus, replicating in the cells of their hosts, are forced to adapt to the relatively small niches, which facilitates the definition of ecological niche. There is also the replicative constraints on genome size, which impose a trade-off between genome content and fitness. Here, we are in the context of free (exogenous) viruses, whose cycle includes a virion stage containing the genetic information necessary for horizontal transmission and replication of the virus in a host. There are also so-called endogenous viruses, whose genome is integrated into the host genome. These viruses replicated along with the host genome are passed vertically between host generations. In the long term these endogenous viral sequences are doomed to extinction unless they provide an adaptive benefit to their host. This is referred to as domestication of viral sequences, and in the case where the host uses viral particles, as symbiotic virus. Our work focuses on the genome evolution of exogenous virus, of domesticated viruses and of their hosts.