This study investigates the evolutionary dynamics of eukaryotic LTR retroelements beyond traditional phylogenetic trees, revealing a complex network of relationships. Using 268 non-redundant LTR retroelements, the researchers analyzed phylogenetic patterns and network structures to trace the history of these elements. The results show that LTR retroelements form a time-evolving network influenced by phylogenetic patterns, epigenetic host factors, and phenotypic plasticity. The Ty1/Copia and Ty3/Gypsy families represent the oldest patterns in this network, which mimic eukaryotic macroevolution. The emergence of the Bel/Pao, Retroviridae, and Caulimoviridae families is linked to distinct inflations of the Ty3/Gypsy family at different evolutionary times. This suggests that Ty3/Gypsy ancestors diversified more than their Ty1/Copia counterparts. The study also highlights that connectivities among phenotypic markers follow a power-law distribution, indicating an inflationary mode of evolution. The network includes multiple reticulate events, such as gene recruitment, genome rearrangement, recombination, and horizontal transfer. The research provides evidence that LTR retroelements have evolved through a combination of vertical and horizontal processes, leading to the emergence of diverse lineages. The study also identifies eight reticulate evolution markers to construct phenotypic network models. The findings suggest that the evolutionary history of LTR retroelements can be traced as a network that reflects the complexity of eukaryotic evolution, with distinct families emerging at different geological eras. The study emphasizes the importance of considering network biology in understanding the evolution of complex systems.This study investigates the evolutionary dynamics of eukaryotic LTR retroelements beyond traditional phylogenetic trees, revealing a complex network of relationships. Using 268 non-redundant LTR retroelements, the researchers analyzed phylogenetic patterns and network structures to trace the history of these elements. The results show that LTR retroelements form a time-evolving network influenced by phylogenetic patterns, epigenetic host factors, and phenotypic plasticity. The Ty1/Copia and Ty3/Gypsy families represent the oldest patterns in this network, which mimic eukaryotic macroevolution. The emergence of the Bel/Pao, Retroviridae, and Caulimoviridae families is linked to distinct inflations of the Ty3/Gypsy family at different evolutionary times. This suggests that Ty3/Gypsy ancestors diversified more than their Ty1/Copia counterparts. The study also highlights that connectivities among phenotypic markers follow a power-law distribution, indicating an inflationary mode of evolution. The network includes multiple reticulate events, such as gene recruitment, genome rearrangement, recombination, and horizontal transfer. The research provides evidence that LTR retroelements have evolved through a combination of vertical and horizontal processes, leading to the emergence of diverse lineages. The study also identifies eight reticulate evolution markers to construct phenotypic network models. The findings suggest that the evolutionary history of LTR retroelements can be traced as a network that reflects the complexity of eukaryotic evolution, with distinct families emerging at different geological eras. The study emphasizes the importance of considering network biology in understanding the evolution of complex systems.