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Endogenous retroviruses (ERVs) arise from the ancient integration of retroviruses into the germ cells of hosts, leading to their vertical transmission over generations. These elements can multiply and form families of repeated sequences that occupy a significant proportion of genomes and play an active role in their structuring and evolution. While in most species the exogenous retroviruses at the origin of ERVs have disappeared, in small ruminants a family of ERVs still coexists with its exogenous counterparts. This makes them a unique model for exploring the dynamics of endogenization, duplication processes and host-virus coevolution. The first part of this thesis provided an exhaustive inventory of ERVs in the goat and sheep reference genomes, revealing several waves of endogenization over the last 40 million years. Two families stand out for their abundance in the goat genome. One has intact elements close to exogenous retroviruses still in circulation, suggesting recent duplications or ongoing endogenization, while the other is composed of incomplete elements, implying the presence of several different duplication mechanisms. The second part focused on the analysis of ERV insertion polymorphism in more than 1,000 small ruminant genomes. The results show a high degree of variability, with specific insertion profiles depending on the species, breed or geographical location. These data confirm the recent activity of certain families of ERVs. Finally, the third part looked at the coexistence of endogenous and exogenous forms. A comparison of endogenous and exogenous retroviruses has enabled us to gain a better understanding of their insertion dynamics and to identify regions that discriminate between particularly close endogenous and exogenous sequences, which are essential for infection diagnosis. This thesis provides the basis for reconstructing the past and present evolutionary history of endogenous retroviruses in small ruminants. This project provides new fundamental knowledge on the evolutionary dynamics of retroviruses and their implications for the biology of livestock species.